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Terrell JR, Taylor SJ, Schneider AL, Lu Y, Vernon TN, Xhani S, Gumpper RH, Luo M, Wilson WD, Steidl U, Poon GMK. DNA selection by the master transcription factor PU.1. Cell Rep 2023; 42:112671. [PMID: 37352101 PMCID: PMC10479921 DOI: 10.1016/j.celrep.2023.112671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 04/07/2023] [Accepted: 06/02/2023] [Indexed: 06/25/2023] Open
Abstract
The master transcriptional regulator PU.1/Spi-1 engages DNA sites with affinities spanning multiple orders of magnitude. To elucidate this remarkable plasticity, we have characterized 22 high-resolution co-crystallographic PU.1/DNA complexes across the addressable affinity range in myeloid gene transactivation. Over a purine-rich core (such as 5'-GGAA-3') flanked by variable sequences, affinity is negotiated by direct readout on the 5' flank via a critical glutamine (Q226) sidechain and by indirect readout on the 3' flank by sequence-dependent helical flexibility. Direct readout by Q226 dynamically specifies PU.1's characteristic preference for purines and explains the pathogenic mutation Q226E in Waldenström macroglobulinemia. The structures also reveal how disruption of Q226 mediates strand-specific inhibition by DNA methylation and the recognition of non-canonical sites, including the authentic binding sequence at the CD11b promoter. A re-synthesis of phylogenetic and structural data on the ETS family, considering the centrality of Q226 in PU.1, unifies the model of DNA selection by ETS proteins.
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Affiliation(s)
- J Ross Terrell
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA
| | - Samuel J Taylor
- Departments of Cell Biology, Oncology, and Medicine, Ruth L. and David S. Gottesman Institute for Stem Cell Research and Regenerative Medicine, Blood Cancer Institute, and the Montefiore Einstein Cancer Center, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Amelia L Schneider
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA
| | - Yue Lu
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA
| | - Tyler N Vernon
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA
| | - Suela Xhani
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA
| | - Ryan H Gumpper
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA
| | - Ming Luo
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA; Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303, USA
| | - W David Wilson
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA; Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303, USA
| | - Ulrich Steidl
- Departments of Cell Biology, Oncology, and Medicine, Ruth L. and David S. Gottesman Institute for Stem Cell Research and Regenerative Medicine, Blood Cancer Institute, and the Montefiore Einstein Cancer Center, Albert Einstein College of Medicine, Bronx, NY 10461, USA.
| | - Gregory M K Poon
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA; Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303, USA.
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Patrick DM, de la Visitación N, Krishnan J, Chen W, Ormseth MJ, Stein CM, Davies SS, Amarnath V, Crofford LJ, Williams JM, Zhao S, Smart CD, Dikalov S, Dikalova A, Xiao L, Van Beusecum JP, Ao M, Fogo AB, Kirabo A, Harrison DG. Isolevuglandins disrupt PU.1-mediated C1q expression and promote autoimmunity and hypertension in systemic lupus erythematosus. JCI Insight 2022; 7:e136678. [PMID: 35608913 PMCID: PMC9310530 DOI: 10.1172/jci.insight.136678] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 05/18/2022] [Indexed: 11/24/2022] Open
Abstract
We describe a mechanism responsible for systemic lupus erythematosus (SLE). In humans with SLE and in 2 SLE murine models, there was marked enrichment of isolevuglandin-adducted proteins (isoLG adducts) in monocytes and dendritic cells. We found that antibodies formed against isoLG adducts in both SLE-prone mice and humans with SLE. In addition, isoLG ligation of the transcription factor PU.1 at a critical DNA binding site markedly reduced transcription of all C1q subunits. Treatment of SLE-prone mice with the specific isoLG scavenger 2-hydroxybenzylamine (2-HOBA) ameliorated parameters of autoimmunity, including plasma cell expansion, circulating IgG levels, and anti-dsDNA antibody titers. 2-HOBA also lowered blood pressure, attenuated renal injury, and reduced inflammatory gene expression uniquely in C1q-expressing dendritic cells. Thus, isoLG adducts play an essential role in the genesis and maintenance of systemic autoimmunity and hypertension in SLE.
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Affiliation(s)
- David M. Patrick
- Department of Veterans Affairs, Nashville, Tennessee, USA
- Division of Clinical Pharmacology and
- Division of Cardiovascular Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Néstor de la Visitación
- Division of Clinical Pharmacology and
- Department of Pharmacology, University of Granada, Granada, Spain
| | | | - Wei Chen
- Division of Clinical Pharmacology and
| | - Michelle J. Ormseth
- Division of Cardiovascular Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Division of Rheumatology and Immunology, Department of Medicine, and
| | - C. Michael Stein
- Division of Clinical Pharmacology and
- Division of Rheumatology and Immunology, Department of Medicine, and
| | | | | | | | | | - Shilin Zhao
- Vanderbilt Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Charles D. Smart
- Division of Clinical Pharmacology and
- Department of Molecular Physiology and Biophysics
| | | | | | | | - Justin P. Van Beusecum
- Ralph H. Johnson VA Medical Center and
- Division of Nephrology, Department of Medicine, Medical University of South Carolina, Charleston, South Carolina, USA
| | | | - Agnes B. Fogo
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | | | - David G. Harrison
- Division of Clinical Pharmacology and
- Division of Cardiovascular Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
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6
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Le Coz C, Nguyen DN, Su C, Nolan BE, Albrecht AV, Xhani S, Sun D, Demaree B, Pillarisetti P, Khanna C, Wright F, Chen PA, Yoon S, Stiegler AL, Maurer K, Garifallou JP, Rymaszewski A, Kroft SH, Olson TS, Seif AE, Wertheim G, Grant SFA, Vo LT, Puck JM, Sullivan KE, Routes JM, Zakharova V, Shcherbina A, Mukhina A, Rudy NL, Hurst ACE, Atkinson TP, Boggon TJ, Hakonarson H, Abate AR, Hajjar J, Nicholas SK, Lupski JR, Verbsky J, Chinn IK, Gonzalez MV, Wells AD, Marson A, Poon GMK, Romberg N. Constrained chromatin accessibility in PU.1-mutated agammaglobulinemia patients. J Exp Med 2021; 218:212070. [PMID: 33951726 PMCID: PMC8105723 DOI: 10.1084/jem.20201750] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 02/09/2021] [Accepted: 03/16/2021] [Indexed: 12/19/2022] Open
Abstract
The pioneer transcription factor (TF) PU.1 controls hematopoietic cell fate by decompacting stem cell heterochromatin and allowing nonpioneer TFs to enter otherwise inaccessible genomic sites. PU.1 deficiency fatally arrests lymphopoiesis and myelopoiesis in mice, but human congenital PU.1 disorders have not previously been described. We studied six unrelated agammaglobulinemic patients, each harboring a heterozygous mutation (four de novo, two unphased) of SPI1, the gene encoding PU.1. Affected patients lacked circulating B cells and possessed few conventional dendritic cells. Introducing disease-similar SPI1 mutations into human hematopoietic stem and progenitor cells impaired early in vitro B cell and myeloid cell differentiation. Patient SPI1 mutations encoded destabilized PU.1 proteins unable to nuclear localize or bind target DNA. In PU.1-haploinsufficient pro–B cell lines, euchromatin was less accessible to nonpioneer TFs critical for B cell development, and gene expression patterns associated with the pro– to pre–B cell transition were undermined. Our findings molecularly describe a novel form of agammaglobulinemia and underscore PU.1’s critical, dose-dependent role as a hematopoietic euchromatin gatekeeper.
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Affiliation(s)
- Carole Le Coz
- Division of Immunology and Allergy, Children's Hospital of Philadelphia, Philadelphia, PA
| | - David N Nguyen
- Division of Infectious Diseases, Department of Medicine, University of California San Francisco, San Francisco, CA.,Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA.,Diabetes Center, University of California San Francisco, San Francisco, CA.,Innovative Genomics Institute, University of California Berkeley, Berkeley, CA.,Gladstone-University of California San Francisco Institute of Genomic Immunology, San Francisco, CA
| | - Chun Su
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA.,Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Brian E Nolan
- Division of Rheumatology, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL.,Department of Pediatrics, Feinberg School of Medicine, Northwestern University, Chicago, IL
| | - Amanda V Albrecht
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA
| | - Suela Xhani
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA
| | - Di Sun
- Division of Immunology and Allergy, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Benjamin Demaree
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA.,University of California Berkeley-University of California San Francisco Graduate Program in Bioengineering, University of California, San Francisco, CA
| | - Piyush Pillarisetti
- Division of Immunology and Allergy, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Caroline Khanna
- Division of Immunology and Allergy, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Francis Wright
- Division of Infectious Diseases, Department of Medicine, University of California San Francisco, San Francisco, CA.,Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA
| | - Peixin Amy Chen
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA.,Diabetes Center, University of California San Francisco, San Francisco, CA.,Innovative Genomics Institute, University of California Berkeley, Berkeley, CA.,Gladstone-University of California San Francisco Institute of Genomic Immunology, San Francisco, CA
| | - Samuel Yoon
- Division of Immunology and Allergy, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Amy L Stiegler
- Departments of Pharmacology, Yale University, New Haven, CT
| | - Kelly Maurer
- Division of Immunology and Allergy, Children's Hospital of Philadelphia, Philadelphia, PA
| | - James P Garifallou
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Amy Rymaszewski
- Division of Allergy and Immunology, Department of Pediatrics, Medical College of Wisconsin, Milwaukee, WI
| | - Steven H Kroft
- Department of Pathology, Medical College of Wisconsin, Milwaukee, WI
| | - Timothy S Olson
- Division of Oncology, Children's Hospital of Philadelphia, Philadelphia, PA.,Department of Pediatrics, Perelman School of Medicine, Philadelphia, PA
| | - Alix E Seif
- Division of Oncology, Children's Hospital of Philadelphia, Philadelphia, PA.,Department of Pediatrics, Perelman School of Medicine, Philadelphia, PA
| | - Gerald Wertheim
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA.,Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Struan F A Grant
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA.,Department of Pediatrics, Perelman School of Medicine, Philadelphia, PA.,Division of Diabetes and Endocrinology, Children's Hospital of Philadelphia, Philadelphia, PA.,Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Linda T Vo
- Diabetes Center, University of California San Francisco, San Francisco, CA.,Innovative Genomics Institute, University of California Berkeley, Berkeley, CA
| | - Jennifer M Puck
- Division of Allergy, Immunology, and Bone Marrow Transplantation, Department of Pediatrics, University of California, San Francisco, CA.,University of California San Francsico Institute for Human Genetics and Smith Cardiovascular Research Institute, University of California, San Francisco, CA.,UCSF Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA
| | - Kathleen E Sullivan
- Division of Immunology and Allergy, Children's Hospital of Philadelphia, Philadelphia, PA.,Department of Pediatrics, Perelman School of Medicine, Philadelphia, PA.,Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - John M Routes
- Division of Allergy and Immunology, Department of Pediatrics, Medical College of Wisconsin, Milwaukee, WI
| | - Viktoria Zakharova
- Laboratory of Molecular Biology, Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia
| | - Anna Shcherbina
- Department of Immunology, Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia
| | - Anna Mukhina
- Department of Immunology, Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia
| | - Natasha L Rudy
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL
| | - Anna C E Hurst
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL.,Department of Pediatrics, University of Alabama at Birmingham, Birmingham, AL
| | - T Prescott Atkinson
- Department of Pediatrics, University of Alabama at Birmingham, Birmingham, AL
| | - Titus J Boggon
- Departments of Pharmacology, Yale University, New Haven, CT.,Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT
| | - Hakon Hakonarson
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA.,Department of Pediatrics, Perelman School of Medicine, Philadelphia, PA
| | - Adam R Abate
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA.,University of California Berkeley-University of California San Francisco Graduate Program in Bioengineering, University of California, San Francisco, CA.,Chan Zuckerberg Biohub, San Francisco, CA
| | - Joud Hajjar
- William T. Shearer Center for Human Immunobiology, Texas Children's Hospital, Houston, TX.,Department of Immunology, Allergy and Rheumatology, Baylor College of Medicine, Houston, TX
| | - Sarah K Nicholas
- William T. Shearer Center for Human Immunobiology, Texas Children's Hospital, Houston, TX.,Department of Immunology, Allergy and Rheumatology, Baylor College of Medicine, Houston, TX
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX.,Texas Children's Hospital, Houston, TX.,Baylor-Hopkins Center for Mendelian Genomics, Houston, TX
| | - James Verbsky
- Division of Allergy and Immunology, Department of Pediatrics, Medical College of Wisconsin, Milwaukee, WI
| | - Ivan K Chinn
- William T. Shearer Center for Human Immunobiology, Texas Children's Hospital, Houston, TX.,Department of Immunology, Allergy and Rheumatology, Baylor College of Medicine, Houston, TX
| | - Michael V Gonzalez
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Andrew D Wells
- Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, PA.,Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA.,Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Alex Marson
- Division of Infectious Diseases, Department of Medicine, University of California San Francisco, San Francisco, CA.,Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA.,Diabetes Center, University of California San Francisco, San Francisco, CA.,Innovative Genomics Institute, University of California Berkeley, Berkeley, CA.,Gladstone-University of California San Francisco Institute of Genomic Immunology, San Francisco, CA.,Chan Zuckerberg Biohub, San Francisco, CA.,Parker Institute for Cancer Immunotherapy, San Francisco, CA
| | - Gregory M K Poon
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA
| | - Neil Romberg
- Division of Immunology and Allergy, Children's Hospital of Philadelphia, Philadelphia, PA.,Department of Pediatrics, Perelman School of Medicine, Philadelphia, PA.,Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
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