1
|
Zhu YP, Speir M, Tan Z, Lee JC, Nowell CJ, Chen AA, Amatullah H, Salinger AJ, Huang CJ, Wu G, Peng W, Askari K, Griffis E, Ghassemian M, Santini J, Gerlic M, Kiosses WB, Catz SD, Hoffman HM, Greco KF, Weller E, Thompson PR, Wong LP, Sadreyev R, Jeffrey KL, Croker BA. NET formation is a default epigenetic program controlled by PAD4 in apoptotic neutrophils. Sci Adv 2023; 9:eadj1397. [PMID: 38117877 PMCID: PMC10732518 DOI: 10.1126/sciadv.adj1397] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 12/04/2023] [Indexed: 12/22/2023]
Abstract
Neutrophil extracellular traps (NETs) not only counteract bacterial and fungal pathogens but can also promote thrombosis, autoimmunity, and sterile inflammation. The presence of citrullinated histones, generated by the peptidylarginine deiminase 4 (PAD4), is synonymous with NETosis and is considered independent of apoptosis. Mitochondrial- and death receptor-mediated apoptosis promote gasdermin E (GSDME)-dependent calcium mobilization and membrane permeabilization leading to histone H3 citrullination (H3Cit), nuclear DNA extrusion, and cytoplast formation. H3Cit is concentrated at the promoter in bone marrow neutrophils and redistributes in a coordinated process from promoter to intergenic and intronic regions during apoptosis. Loss of GSDME prevents nuclear and plasma membrane disruption of apoptotic neutrophils but prolongs early apoptosis-induced cellular changes to the chromatin and cytoplasmic granules. Apoptotic signaling engages PAD4 in neutrophils, establishing a cellular state that is primed for NETosis, but that occurs only upon membrane disruption by GSDME, thereby redefining the end of life for neutrophils.
Collapse
Affiliation(s)
- Yanfang Peipei Zhu
- Department of Pediatrics, University of California San Diego, La Jolla, CA 92093, USA
- Immunology Center of Georgia, Augusta University, Augusta, GA 30912, USA
| | - Mary Speir
- Division of Hematology/Oncology, Boston Children’s Hospital, Boston, MA 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - ZheHao Tan
- Department of Pediatrics, University of California San Diego, La Jolla, CA 92093, USA
| | - Jamie Casey Lee
- Department of Pediatrics, University of California San Diego, La Jolla, CA 92093, USA
| | - Cameron J. Nowell
- Monash Institute of Pharmaceutical Sciences, Parkville, Victoria 3052, Australia
| | - Alyce A. Chen
- Division of Hematology/Oncology, Boston Children’s Hospital, Boston, MA 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Hajera Amatullah
- Department of Medicine, Division of Gastroenterology and the Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Harvard Medical School, Boston MA 02114, USA
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Ari J. Salinger
- Program in Chemical Biology and Department of Biochemistry and Molecular Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Carolyn J. Huang
- Division of Hematology/Oncology, Boston Children’s Hospital, Boston, MA 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Gio Wu
- Department of Pediatrics, University of California San Diego, La Jolla, CA 92093, USA
| | - Weiqi Peng
- Department of Pediatrics, University of California San Diego, La Jolla, CA 92093, USA
| | - Kasra Askari
- Scripps Research Institute, La Jolla, CA 92037, USA
| | - Eric Griffis
- Nikon Imaging Center, University of California San Diego, La Jolla, CA 92093, USA
| | - Majid Ghassemian
- Biomolecular and Proteomics Mass Spectrometry Facility, University of California San Diego, La Jolla, CA 92093, USA
| | - Jennifer Santini
- UCSD School of Medicine Microscopy Core, University of California San Diego, La Jolla 92093, CA, USA
| | - Motti Gerlic
- Department of Clinical Microbiology and Immunology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | | | | | - Hal M. Hoffman
- Department of Pediatrics, University of California San Diego, La Jolla, CA 92093, USA
| | - Kimberly F. Greco
- Biostatistics and Research Design Center, Institutional Centers for Clinical and Translational Research, Boston Children’s Hospital, Boston, 02115, USA
| | - Edie Weller
- Division of Hematology/Oncology, Boston Children’s Hospital, Boston, MA 02115, USA
- Biostatistics and Research Design Center, Institutional Centers for Clinical and Translational Research, Boston Children’s Hospital, Boston, 02115, USA
| | - Paul R. Thompson
- Program in Chemical Biology and Department of Biochemistry and Molecular Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Lai Ping Wong
- Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02114, USA
| | - Ruslan Sadreyev
- Department of Genetics, Harvard Medical School, Boston, MA 02114, USA
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Kate L. Jeffrey
- Department of Medicine, Division of Gastroenterology and the Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Harvard Medical School, Boston MA 02114, USA
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Ben A. Croker
- Department of Pediatrics, University of California San Diego, La Jolla, CA 92093, USA
- Division of Hematology/Oncology, Boston Children’s Hospital, Boston, MA 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| |
Collapse
|
2
|
Rojas RA, Kutateladze AA, Plummer L, Stamou M, Keefe DL, Salnikov KB, Delaney A, Hall JE, Sadreyev R, Ji F, Fliers E, Gambosova K, Quinton R, Merino PM, Mericq V, Seminara SB, Crowley WF, Balasubramanian R. Phenotypic continuum between Waardenburg syndrome and idiopathic hypogonadotropic hypogonadism in humans with SOX10 variants. Genet Med 2023; 25:100855. [PMID: 37272927 DOI: 10.1016/j.gim.2023.100855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023] Open
Affiliation(s)
- Rebecca A Rojas
- Harvard Reproductive Sciences Center, The Reproductive Endocrine Unit and The Endocrine Unit of the Department of Medicine, Massachusetts General Hospital, Boston, MA
| | - Anna A Kutateladze
- Harvard Reproductive Sciences Center, The Reproductive Endocrine Unit and The Endocrine Unit of the Department of Medicine, Massachusetts General Hospital, Boston, MA
| | - Lacey Plummer
- Harvard Reproductive Sciences Center, The Reproductive Endocrine Unit and The Endocrine Unit of the Department of Medicine, Massachusetts General Hospital, Boston, MA
| | - Maria Stamou
- Harvard Reproductive Sciences Center, The Reproductive Endocrine Unit and The Endocrine Unit of the Department of Medicine, Massachusetts General Hospital, Boston, MA
| | - David L Keefe
- Harvard Reproductive Sciences Center, The Reproductive Endocrine Unit and The Endocrine Unit of the Department of Medicine, Massachusetts General Hospital, Boston, MA
| | - Kathryn B Salnikov
- Harvard Reproductive Sciences Center, The Reproductive Endocrine Unit and The Endocrine Unit of the Department of Medicine, Massachusetts General Hospital, Boston, MA
| | - Angela Delaney
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD
| | - Janet E Hall
- National Institute of Environmental Health Sciences, Research Triangle, NC
| | - Ruslan Sadreyev
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA
| | - Fei Ji
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA
| | - Eric Fliers
- Amsterdam University Medical Center, location AMC, Department of Endocrinology and Metabolism, Amsterdam, The Netherlands
| | - Katarina Gambosova
- Stormont-Vail Health, Cotton O'Neil Diabetes and Endocrinology, Topeka, KS
| | - Richard Quinton
- Translational and Clinical Research Institute, Newcastle University, Newcastle-upon-tyne, UK
| | - Paulina M Merino
- Institute of Maternal and Child Research, University of Chile, Santiago, Chile
| | - Veronica Mericq
- Institute of Maternal and Child Research, University of Chile, Santiago, Chile
| | - Stephanie B Seminara
- Harvard Reproductive Sciences Center, The Reproductive Endocrine Unit and The Endocrine Unit of the Department of Medicine, Massachusetts General Hospital, Boston, MA
| | - William F Crowley
- Harvard Reproductive Sciences Center, The Reproductive Endocrine Unit and The Endocrine Unit of the Department of Medicine, Massachusetts General Hospital, Boston, MA
| | - Ravikumar Balasubramanian
- Harvard Reproductive Sciences Center, The Reproductive Endocrine Unit and The Endocrine Unit of the Department of Medicine, Massachusetts General Hospital, Boston, MA
| |
Collapse
|
3
|
Gnanaguru G, Tabor SJ, Bonilla GM, Sadreyev R, Yuda K, Köhl J, Connor KM. Microglia refine developing retinal astrocytic and vascular networks through the complement C3/C3aR axis. Development 2023; 150:dev201047. [PMID: 36762625 PMCID: PMC10110418 DOI: 10.1242/dev.201047] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 01/30/2023] [Indexed: 02/11/2023]
Abstract
Microglia, a resident immune cell of the central nervous system (CNS), play a pivotal role in facilitating neurovascular development through mechanisms that are not fully understood. Previous reports indicate a role for microglia in regulating astrocyte density. This current work resolves the mechanism through which microglia facilitate astrocyte spatial patterning and superficial vascular bed formation in the neuroretina during development. Ablation of microglia increased astrocyte density and altered spatial patterning. Mechanistically, we show that microglia regulate the formation of the spatially organized astrocyte template required for subsequent vascular growth, through the complement C3/C3aR axis during neuroretinal development. Lack of C3 or C3aR hindered the developmental phagocytic removal of astrocyte bodies and resulted in increased astrocyte density. In addition, increased astrocyte density was associated with elevated proangiogenic extracellular matrix gene expression in C3- and C3aR-deficient retinas, resulting in increased vascular density. These data demonstrate that microglia regulate developmental astrocyte and vascular network spatial patterning in the neuroretina via the complement axis.
Collapse
Affiliation(s)
- Gopalan Gnanaguru
- Angiogenesis Laboratory, Department of Ophthalmology, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA 02114, USA
| | - Steven J. Tabor
- Angiogenesis Laboratory, Department of Ophthalmology, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA 02114, USA
| | - Gracia M. Bonilla
- Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Ruslan Sadreyev
- Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Kentaro Yuda
- Angiogenesis Laboratory, Department of Ophthalmology, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA 02114, USA
| | - Jörg Köhl
- Institute for Systemic Inflammation Research, University of Lübeck, Lübeck 23562, Germany
- Division of Immunobiology, Cincinnati Children's Hospital Medical Center and University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Kip M. Connor
- Angiogenesis Laboratory, Department of Ophthalmology, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA 02114, USA
| |
Collapse
|
4
|
Bilbo S, Smith C, Rendina D, Kingsbury M, Malacon K, Nguyen D, Tran J, Devlin B, Raju R, Clark M, Burgett L, Zhang J, Cetinbas M, Sadreyev R, Chen K, Iyer M. Microbial modulation prevents the effects of pervasive environmental stressors on microglia and social behavior, but not the dopamine system. Res Sq 2023:rs.3.rs-2548369. [PMID: 36798238 PMCID: PMC9934737 DOI: 10.21203/rs.3.rs-2548369/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
Environmental toxicant exposure, including air pollution, is increasing worldwide. However, toxicant exposures are not equitably distributed. Rather, low-income and minority communities bear the greatest burden, along with higher levels of psychosocial stress. Both air pollution and maternal stress during pregnancy have been linked to neurodevelopmental disorders such as autism, but biological mechanisms and targets for therapeutic intervention remain poorly understood. We demonstrate that combined prenatal exposure to air pollution (diesel exhaust particles, DEP) and maternal stress (MS) in mice induces social behavior deficits only in male offspring, in line with the male bias in autism. These behavioral deficits are accompanied by changes in microglial morphology and gene expression as well as decreased dopamine receptor expression and dopaminergic fiber input in the nucleus accumbens (NAc). Importantly, the gut-brain axis has been implicated in ASD, and both microglia and the dopamine system are sensitive to the composition of the gut microbiome. In line with this, we find that the composition of the gut microbiome and the structure of the intestinal epithelium are significantly shifted in DEP/MS-exposed males. Excitingly, both the DEP/MS-induced social deficits and microglial alterations in males are prevented by shifting the gut microbiome at birth via a cross-fostering procedure. However, while social deficits in DEP/MS males can be reversed by chemogenetic activation of dopamine neurons in the ventral tegmental area, modulation of the gut microbiome does not impact dopamine endpoints. These findings demonstrate male-specific changes in the gut-brain axis following DEP/MS and suggest that the gut microbiome is an important modulator of both social behavior and microglia.
Collapse
|
5
|
Adiliaghdam F, Amatullah H, Digumarthi S, Saunders TL, Rahman RU, Wong LP, Sadreyev R, Droit L, Paquette J, Goyette P, Rioux J, Hodin R, Mihindukulasuriya KA, Handley SA, Jeffrey KL. Human enteric viruses autonomously shape inflammatory bowel disease phenotype through divergent innate immunomodulation. Sci Immunol 2022; 7:eabn6660. [PMID: 35394816 PMCID: PMC9416881 DOI: 10.1126/sciimmunol.abn6660] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Altered enteric microorganisms in concert with host genetics shape inflammatory bowel disease (IBD) phenotypes. However, insight is limited to bacteria and fungi. We found that eukaryotic viruses and bacteriophages (collectively, the virome), enriched from non-IBD, noninflamed human colon resections, actively elicited atypical anti-inflammatory innate immune programs. Conversely, ulcerative colitis or Crohn's disease colon resection viromes provoked inflammation, which was successfully dampened by non-IBD viromes. The IBD colon tissue virome was perturbed, including an increase in the enterovirus B species of eukaryotic picornaviruses, not previously detected in fecal virome studies. Mice humanized with non-IBD colon tissue viromes were protected from intestinal inflammation, whereas IBD virome mice exhibited exacerbated inflammation in a nucleic acid sensing-dependent fashion. Furthermore, there were detrimental consequences for IBD patient-derived intestinal epithelial cells bearing loss-of-function mutations within virus sensor MDA5 when exposed to viromes. Our results demonstrate that innate recognition of IBD or non-IBD human viromes autonomously influences intestinal homeostasis and disease phenotypes. Thus, perturbations in the intestinal virome, or an altered ability to sense the virome due to genetic variation, contribute to the induction of IBD. Harnessing the virome may offer therapeutic and biomarker potential.
Collapse
Affiliation(s)
- Fatemeh Adiliaghdam
- Department of Medicine, Division of Gastroenterology and the Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Hajera Amatullah
- Department of Medicine, Division of Gastroenterology and the Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Sreehaas Digumarthi
- Department of Medicine, Division of Gastroenterology and the Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Tahnee L. Saunders
- Department of Medicine, Division of Gastroenterology and the Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Raza-Ur Rahman
- Department of Medicine, Division of Gastroenterology and the Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Lai Ping Wong
- Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA,Department of Genetics, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Ruslan Sadreyev
- Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA,Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Lindsay Droit
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
| | - Jean Paquette
- Montreal Heart Institute, Montreal Quebec Canada H1T 1C8
| | | | - John Rioux
- Montreal Heart Institute, Montreal Quebec Canada H1T 1C8,Université de Montréal, Montreal Quebec Canada H3C 3J7
| | - Richard Hodin
- Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | | | - Scott A. Handley
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
| | - Kate L. Jeffrey
- Department of Medicine, Division of Gastroenterology and the Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA,Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA,Correspondence: Requests for materials should be addressed to K.L.J. at
| |
Collapse
|
6
|
Guo N, McDermott KD, Shih YT, Zanga H, Ghosh D, Herber C, Meara WR, Coleman J, Zagouras A, Wong LP, Sadreyev R, Gonçalves JT, Sahay A. Transcriptional regulation of neural stem cell expansion in the adult hippocampus. eLife 2022; 11:72195. [PMID: 34982030 PMCID: PMC8820733 DOI: 10.7554/elife.72195] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 01/03/2022] [Indexed: 12/11/2022] Open
Abstract
Experience governs neurogenesis from radial-glial neural stem cells (RGLs) in the adult hippocampus to support memory. Transcription factors (TFs) in RGLs integrate physiological signals to dictate self-renewal division mode. Whereas asymmetric RGL divisions drive neurogenesis during favorable conditions, symmetric divisions prevent premature neurogenesis while amplifying RGLs to anticipate future neurogenic demands. The identities of TFs regulating RGL symmetric self-renewal, unlike those that regulate RGL asymmetric self-renewal, are not known. Here, we show in mice that the TF Kruppel-like factor 9 (Klf9) is elevated in quiescent RGLs and inducible, deletion of Klf9 promotes RGL activation state. Clonal analysis and longitudinal intravital two-photon imaging directly demonstrate that Klf9 functions as a brake on RGL symmetric self-renewal. In vivo translational profiling of RGLs lacking Klf9 generated a molecular blueprint for RGL symmetric self-renewal that was characterized by upregulation of genetic programs underlying Notch and mitogen signaling, cell cycle, fatty acid oxidation, and lipogenesis. Together, these observations identify Klf9 as a transcriptional regulator of neural stem cell expansion in the adult hippocampus. In humans and other mammals, a region of the brain known as the hippocampus plays important roles in memory. New experiences guide cells in the hippocampus known as radial-glial neural stem cells (RGLs) to divide to make new neurons and other types of cells involved in forming memories. Each time an RGL divides, it can choose to divide asymmetrically to maintain a copy of itself and make a new cell of another type, or divide symmetrically (a process known as symmetric self-renewal) to produce two RGLs. Symmetric self-renewal helps to restore and replenish the pool of stem cells in the hippocampus that are lost due to injury or age, allowing us to continue making new neurons. Proteins known as transcription factors are believed to control how RGLs divide. Previous studies have identified several transcription factors that regulate the RGLs splitting asymmetrically to make neurons and other cells. But the identities of the transcription factors that regulate symmetric self-renewal in the adult hippocampus have remained elusive. Here, Guo et al. searched for transcription factors that regulate symmetric self-renewal of RGLs in mice. The experiments found that RGLs that are resting and not dividing (referred to as ‘quiescent’) have higher levels of a transcription factor called Klf9 than RGLs that are actively dividing. Loss of the gene encoding Klf9 triggered quiescent RGLs to start dividing, and further experiments showed that Klf9 directly inhibited symmetric self-renewal. Guo et al. then used an approach called in vivo translational profiling to generate a blueprint that revealed new insights into the molecular processes involved in this symmetric division. These findings pave the way for researchers to develop strategies that may expand the numbers of stem cells in the hippocampus. This could eventually be used to help replenish brain circuits with neurons and improve the memory of individuals with Alzheimer’s disease or other conditions that cause memory loss.
Collapse
Affiliation(s)
- Nannan Guo
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, United States.,Harvard Stem Cell Institute, Cambridge, United States.,Department of Psychiatry, Massachusetts General Hospital, Harvard Medical School, Boston, United States.,BROAD Institute of Harvard and MIT, Cambridge, United States
| | - Kelsey D McDermott
- Ruth L. and David S. Gottesman Institute for Stem Cell Biology and Regenerative Medicine; Dominick Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, United States
| | - Yu-Tzu Shih
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, United States.,Harvard Stem Cell Institute, Cambridge, United States.,Department of Psychiatry, Massachusetts General Hospital, Harvard Medical School, Boston, United States.,BROAD Institute of Harvard and MIT, Cambridge, United States
| | - Haley Zanga
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, United States.,Harvard Stem Cell Institute, Cambridge, United States.,Department of Psychiatry, Massachusetts General Hospital, Harvard Medical School, Boston, United States.,BROAD Institute of Harvard and MIT, Cambridge, United States
| | - Debolina Ghosh
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, United States.,Harvard Stem Cell Institute, Cambridge, United States
| | - Charlotte Herber
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, United States.,Harvard Stem Cell Institute, Cambridge, United States
| | - William R Meara
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, United States.,Harvard Stem Cell Institute, Cambridge, United States
| | - James Coleman
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, United States.,Harvard Stem Cell Institute, Cambridge, United States
| | - Alexia Zagouras
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, United States.,Harvard Stem Cell Institute, Cambridge, United States
| | - Lai Ping Wong
- Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, United States
| | - Ruslan Sadreyev
- Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, United States
| | - J Tiago Gonçalves
- Ruth L. and David S. Gottesman Institute for Stem Cell Biology and Regenerative Medicine; Dominick Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, United States
| | - Amar Sahay
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, United States.,Harvard Stem Cell Institute, Cambridge, United States.,Department of Psychiatry, Massachusetts General Hospital, Harvard Medical School, Boston, United States.,BROAD Institute of Harvard and MIT, Cambridge, United States
| |
Collapse
|
7
|
Stanley TL, Fourman LT, Wong LP, Sadreyev R, Billingsley JT, Feldpausch MN, Boutin A, Lee H, Corey KE, Torriani M, Kleiner D, Chung RT, Hadigan CM, Grinspoon SK. Growth Hormone Releasing Hormone Reduces Plasma Markers of Immune Activation and Hepatic Immune Pathways in Nonalcoholic Fatty Liver Disease. J Endocr Soc 2021. [PMCID: PMC8090591 DOI: 10.1210/jendso/bvab048.1282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Introduction: The GH/IGF-1 axis affects multiple metabolic pathways, and animal models demonstrate that it also modulates immune function. Little is known, however, regarding effects of augmenting GH secretion on immune function in humans. This study used proteomics and gene set enrichment analysis to assess effects of a GH releasing hormone (GHRH) analog, tesamorelin, on circulating immune markers and immune-related gene pathways in the liver in people with HIV (PWH) and NAFLD. We hypothesized that tesamorelin would decrease circulating markers of immune activation in conjunction with previously reported reductions in visceral fat and hepatic triglyceride. Methods: 92 biomarkers associated with immune function (Olink Immuno-Oncology panel) were measured in plasma samples from 61 PWH with NAFLD who participated in a double-blind, randomized, 12-month trial of tesamorelin versus identical placebo. Proteins differentially altered by tesamorelin at a false discovery rate < 0.1 were considered significantly changed. Gene set enrichment analysis targeted to immune pathways was subsequently performed on liver tissue from serial biopsies. Results: Compared to placebo, tesamorelin decreased circulating concentrations of 13 proteins, including four chemokines (C-C Motif Chemokine Ligands 3 [CCL3, effect size -0.38 Log2 fold change], 4 [CCL4, -0.36 Log2 fold change], and 13 [CCL13 or MCP4, -0.42 Log2 fold change] and interleukin-8 [-0.50 Log2 fold change]), two cytokines (interleukin-10 [-0.32 Log2 fold change] and cytokine stimulating factor 1 [-0.22 Log2 fold change]), and four T-cell associated molecules (CD8A [-0.37 Log2 fold change], Cytotoxic And Regulatory T Cell Molecule [CRTAM, -0.47 Log2 fold change], granzyme A [-0.53 Log2 fold change], and adhesion G protein-coupled receptor G1 [ADGRG1, -0.54 Log2 fold change]), as well as arginase-1 [-0.95 Log2 fold change], galectin-9 [-0.26 Log2 fold change], and hepatocyte growth factor [-0.30 Log2 fold change]. No proteins in the panel were significantly increased by tesamorelin. Network analysis indicated close interaction among the gene pathways responsible for the reduced proteins, with imputational analyses suggesting down regulation of a closely related cluster of immune pathways. Targeted transcriptomics using tissue from liver biopsy confirmed an end-organ signal of down-regulated immune pathways, including pathways involved in antigen presentation, complement activation, toll like receptor and inflammatory signaling, and T-cell activation. Conclusions: Long-term treatment with tesamorelin decreased circulating markers of T-cell and monocyte/macrophage activity, with corresponding downregulation of immune pathways in the liver. These findings suggest that augmenting pulsatile GH may ameliorate immune activation in a population with metabolic dysregulation and systemic inflammation.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | - Hang Lee
- MASS GEN HOSP/HARVARD Medical SCHL, Boston, MA, USA
| | | | | | | | | | | | | |
Collapse
|
8
|
Stanley TL, Fourman LT, Wong LP, Sadreyev R, Billingsley JM, Feldpausch MN, Zheng I, Pan CS, Boutin A, Lee H, Corey KE, Torriani M, Kleiner DE, Chung RT, Hadigan CM, Grinspoon SK. Growth Hormone Releasing Hormone Reduces Circulating Markers of Immune Activation in Parallel with Effects on Hepatic Immune Pathways in Individuals with HIV-Infection and Nonalcoholic Fatty Liver Disease. Clin Infect Dis 2021; 73:621-630. [PMID: 33852720 DOI: 10.1093/cid/ciab019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 01/12/2021] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND The growth hormone (GH)/insulin-like growth factor-1 (IGF-1) axis modulates critical metabolic pathways; however, little is known regarding effects of augmenting pulsatile GH secretion on immune function in humans. This study used proteomics and gene set enrichment analysis to assess effects of a GH releasing hormone (GHRH) analog, tesamorelin, on circulating immune markers and liver tissue in people with HIV (PWH) and NAFLD. METHODS 92 biomarkers associated with immunity, chemotaxis, and metabolism were measured in plasma samples from 61 PWH with NAFLD who participated in a double-blind, randomized trial of tesamorelin versus placebo for 12 months. Gene set enrichment analysis was performed on serial liver biopsies targeted to immune pathways. RESULTS Tesamorelin, compared to placebo, decreased interconnected proteins related to cytotoxic T-cell and monocyte activation. Circulating concentrations of 13 proteins were significantly decreased, and no proteins increased, by tesamorelin. These included four chemokines (CCL3, CCL4, CCL13 [MCP4], IL8 [CXCL8]), two cytokines (IL-10 and CSF-1), and four T-cell associated molecules (CD8A, CRTAM, GZMA, ADGRG1), as well as ARG1, Gal-9, and HGF. Network analysis indicated close interaction among the gene pathways responsible for these proteins, with imputational analyses suggesting down regulation of a closely related cluster of immune pathways. Targeted transcriptomics using liver tissue confirmed a significant end-organ signal of down-regulated immune activation pathways. CONCLUSIONS Long-term treatment with a GHRH analog reduced markers of T-cell and monocyte/macrophage activity, suggesting that augmentation of the GH axis may ameliorate immune activation in an HIV population with metabolic dysregulation, systemic and end organ inflammation.
Collapse
Affiliation(s)
- Takara L Stanley
- Metabolism Unit, Massachusetts General Hospital (MGH) and Harvard Medical School (HMS), Boston, MA, USA
| | - Lindsay T Fourman
- Metabolism Unit, Massachusetts General Hospital (MGH) and Harvard Medical School (HMS), Boston, MA, USA
| | - Lai Ping Wong
- MGH Department of Molecular Biology and HMS, Boston, MA, USA
| | - Ruslan Sadreyev
- MGH Department of Molecular Biology and HMS, Boston, MA, USA
| | - James M Billingsley
- Harvard Chan Bioinformatics Core, Department of Biostatistics, Harvard School of Public Health, Boston, MA, USA
| | - Meghan N Feldpausch
- Metabolism Unit, Massachusetts General Hospital (MGH) and Harvard Medical School (HMS), Boston, MA, USA
| | - Isabel Zheng
- Metabolism Unit, Massachusetts General Hospital (MGH) and Harvard Medical School (HMS), Boston, MA, USA
| | - Chelsea S Pan
- Metabolism Unit, Massachusetts General Hospital (MGH) and Harvard Medical School (HMS), Boston, MA, USA
| | - Autumn Boutin
- Metabolism Unit, Massachusetts General Hospital (MGH) and Harvard Medical School (HMS), Boston, MA, USA
| | - Hang Lee
- Harvard Chan Bioinformatics Core, Department of Biostatistics, Harvard School of Public Health, Boston, MA, USA
| | | | - Martin Torriani
- Liver Center, Gastroenterology Division, MGH and HMS, Boston, MA, USA
| | | | | | - Colleen M Hadigan
- Laboratory of Pathology, National Cancer Institute, Bethesda, MD, USA
| | - Steven K Grinspoon
- Metabolism Unit, Massachusetts General Hospital (MGH) and Harvard Medical School (HMS), Boston, MA, USA.,National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| |
Collapse
|
9
|
Rojas RA, Kutateladze AA, Plummer L, Stamou M, Keefe DL, Salnikov KB, Delaney A, Hall JE, Sadreyev R, Ji F, Fliers E, Gambosova K, Quinton R, Merino PM, Mericq V, Seminara SB, Crowley WF, Balasubramanian R. Phenotypic continuum between Waardenburg syndrome and idiopathic hypogonadotropic hypogonadism in humans with SOX10 variants. Genet Med 2021; 23:629-636. [PMID: 33442024 PMCID: PMC8335791 DOI: 10.1038/s41436-020-01051-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 11/19/2020] [Accepted: 11/20/2020] [Indexed: 12/15/2022] Open
Abstract
PURPOSE SOX10 variants previously implicated in Waardenburg syndrome (WS) have now been linked to Kallmann syndrome (KS), the anosmic form of idiopathic hypogonadotropic hypogonadism (IHH). We investigated whether SOX10-associated WS and IHH represent elements of a phenotypic continuum within a unifying disorder or if they represent phenotypically distinct allelic disorders. METHODS Exome sequencing from 1,309 IHH subjects (KS: 632; normosmic idiopathic hypogonadotropic hypogonadism [nIIHH]: 677) were reviewed for SOX10 rare sequence variants (RSVs). The genotypic and phenotypic spectrum of SOX10-related IHH (this study and literature) and SOX10-related WS cases (literature) were reviewed and compared with SOX10-RSV spectrum in gnomAD population. RESULTS Thirty-seven SOX10-associated IHH cases were identified as follows: current study: 16 KS; 4 nIHH; literature: 16 KS; 1 nIHH. Twenty-three IHH cases (62%; all KS), had ≥1 known WS-associated feature(s). Moreover, five previously reported SOX10-associated WS cases showed IHH-related features. Four SOX10 missense RSVs showed allelic overlap between IHH-ascertained and WS-ascertained cases. The SOX10-HMG domain showed an enrichment of RSVs in disease states versus gnomAD. CONCLUSION SOX10 variants contribute to both anosmic (KS) and normosmic (nIHH) forms of IHH. IHH and WS represent SOX10-associated developmental defects that lie along a unifying phenotypic continuum. The SOX10-HMG domain is critical for the pathogenesis of SOX10-related human disorders.
Collapse
Affiliation(s)
- Rebecca A Rojas
- Harvard Reproductive Sciences Center, The Reproductive Endocrine Unit and The Endocrine Unit of the Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Anna A Kutateladze
- Harvard Reproductive Sciences Center, The Reproductive Endocrine Unit and The Endocrine Unit of the Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Lacey Plummer
- Harvard Reproductive Sciences Center, The Reproductive Endocrine Unit and The Endocrine Unit of the Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Maria Stamou
- Harvard Reproductive Sciences Center, The Reproductive Endocrine Unit and The Endocrine Unit of the Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - David L Keefe
- Harvard Reproductive Sciences Center, The Reproductive Endocrine Unit and The Endocrine Unit of the Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Kathyrn B Salnikov
- Harvard Reproductive Sciences Center, The Reproductive Endocrine Unit and The Endocrine Unit of the Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Angela Delaney
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Janet E Hall
- National Institute of Environmental Health Sciences, Research Triangle, NC, USA
| | - Ruslan Sadreyev
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
| | - Fei Ji
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
| | - Eric Fliers
- Amsterdam University Medical Center, location AMC, Department of Endocrinology and Metabolism, Amsterdam, The Netherlands
| | - Katarina Gambosova
- Stormont-Vail Health, Cotton O'Neil Diabetes and Endocrinology, Topeka, KS, USA
| | - Richard Quinton
- Translational and Clinical Research Institute, Newcastle University, Newcastle-upon-tyne, UK
| | - Paulina M Merino
- Institute of Maternal and Child Research, University of Chile, Santiago, Chile
| | - Veronica Mericq
- Institute of Maternal and Child Research, University of Chile, Santiago, Chile
| | - Stephanie B Seminara
- Harvard Reproductive Sciences Center, The Reproductive Endocrine Unit and The Endocrine Unit of the Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - William F Crowley
- Harvard Reproductive Sciences Center, The Reproductive Endocrine Unit and The Endocrine Unit of the Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Ravikumar Balasubramanian
- Harvard Reproductive Sciences Center, The Reproductive Endocrine Unit and The Endocrine Unit of the Department of Medicine, Massachusetts General Hospital, Boston, MA, USA.
| |
Collapse
|
10
|
deFilippi C, Toribio M, Wong LP, Sadreyev R, Grundberg I, Fitch KV, Zanni MV, Lo J, Sponseller CA, Sprecher E, Rashidi N, Thompson MA, Cagliero D, Aberg JA, Braun LR, Stanley TL, Lee H, Grinspoon SK. Differential Plasma Protein Regulation and Statin Effects in Human Immunodeficiency Virus (HIV)-Infected and Non-HIV-Infected Patients Utilizing a Proteomics Approach. J Infect Dis 2021; 222:929-939. [PMID: 32310273 DOI: 10.1093/infdis/jiaa196] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 04/16/2020] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND People with human immunodeficiency virus (PWH) demonstrate increased atherosclerotic cardiovascular disease (ASCVD). Statins are being studied to prevent ASCVD in human immunodeficiency virus (HIV), but little is known regarding the effects of statins on a broad range of inflammatory and cardiovascular proteins in this population. METHODS We used a highly specific discovery proteomic approach (Protein Extension Assay), to determine statin effects on over 350 plasma proteins in relevant ASCVD pathways among HIV and non-HIV groups. Responses to pitavastatin calcium were assessed in 89 PWH in the INTREPID trial and 46 non-HIV participants with features of central adiposity and insulin resistance. History of cardiovascular disease was exclusionary for both studies. RESULTS Among participants with HIV, PCOLCE (enzymatic cleavage of type I procollagen) significantly increased after pitavastatin therapy and PLA2G7 (systemic marker of arterial inflammation) decreased. Among participants without HIV, integrin subunit alpha M (integrin adhesive function) and defensin alpha-1 (neutrophil function) increased after pitavastatin therapy and PLA2G7 decreased. At baseline, comparing participants with and without HIV, differentially expressed proteins included proteins involved in platelet and endothelial function and immune activation. CONCLUSIONS Pitavastatin affected proteins important to platelet and endothelial function and immune activation, and effects differed to a degree within PWH and participants without HIV.
Collapse
Affiliation(s)
- Chris deFilippi
- Inova Heart and Vascular Institute, Falls Church, Virginia, USA
| | - Mabel Toribio
- Massachusetts General Hospital, Metabolism Unit and Harvard Medical School, Boston, Massachusetts, USA
| | - Lai Ping Wong
- Massachusetts General Hospital, Department of Molecular Biology and Harvard Medical School, Boston, Massachusetts, USA
| | - Ruslan Sadreyev
- Massachusetts General Hospital, Department of Molecular Biology and Harvard Medical School, Boston, Massachusetts, USA
| | | | - Kathleen V Fitch
- Massachusetts General Hospital, Metabolism Unit and Harvard Medical School, Boston, Massachusetts, USA
| | - Markella V Zanni
- Massachusetts General Hospital, Metabolism Unit and Harvard Medical School, Boston, Massachusetts, USA
| | - Janet Lo
- Massachusetts General Hospital, Metabolism Unit and Harvard Medical School, Boston, Massachusetts, USA
| | | | | | | | | | - Diana Cagliero
- Massachusetts General Hospital, Metabolism Unit and Harvard Medical School, Boston, Massachusetts, USA
| | - Judith A Aberg
- Mount Sinai Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Laurie R Braun
- Massachusetts General Hospital, Metabolism Unit and Harvard Medical School, Boston, Massachusetts, USA
| | - Takara L Stanley
- Massachusetts General Hospital, Metabolism Unit and Harvard Medical School, Boston, Massachusetts, USA
| | - Hang Lee
- Massachusetts General Hospital, Biostatistics Center and Harvard Medical School, Boston, Massachusetts, USA
| | - Steven K Grinspoon
- Massachusetts General Hospital, Metabolism Unit and Harvard Medical School, Boston, Massachusetts, USA
| |
Collapse
|
11
|
Borren NZ, Plichta D, Joshi AD, Bonilla G, Peng V, Colizzo FP, Luther J, Khalili H, Garber JJ, Janneke van der Woude C, Sadreyev R, Vlamakis H, Xavier RJ, Ananthakrishnan AN. Alterations in Fecal Microbiomes and Serum Metabolomes of Fatigued Patients With Quiescent Inflammatory Bowel Diseases. Clin Gastroenterol Hepatol 2021; 19:519-527.e5. [PMID: 32184182 DOI: 10.1016/j.cgh.2020.03.013] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 02/24/2020] [Accepted: 03/02/2020] [Indexed: 02/07/2023]
Abstract
BACKGROUND & AIMS Fatigue is frequent and disabling in patients with inflammatory bowel diseases (IBD) but its mechanisms are poorly understood. We investigated alterations in fecal microbiomes and serum metabolomes and proteomes in patients with quiescent IBD, with vs without fatigue. METHODS We performed a prospective observational study of patients (44% women; mean age, 39.8 y) with clinically and endoscopically quiescent Crohn's disease (n = 106) or ulcerative colitis (n = 60) at a tertiary hospital, from March 2016 through December 2018. Fatigue was assessed using the functional assessment of chronic illness therapy-fatigue scoring system and defined as a score of 43 or less. We performed metabolomic analysis of serum samples using liquid chromatography-mass spectrometry methods and proteomic analysis using multiplex proximity extension assay (PEA) technology. Stool samples were obtained from 50 patients and analyzed by shotgun metagenomic sequencing on Illumina HiSeq platform. RESULTS Of the 166 study participants, 91 (55%) were fatigued. Serum samples from patients with fatigue (n = 59) did not have significant increases in levels of inflammatory cytokines compared with serum samples from nonfatigued patients (n = 72). We found a statistically significant difference in a cluster of 18 serum metabolites between patients with fatigue (n = 84) vs without fatigue (n = 72) (P = .033); serum samples from patients with fatigue had significant reductions in levels of methionine (P = .020), tryptophan (P = .042), proline (P = .017), and sarcosine (P = .047). Fecal samples from patients with fatigue had a less diverse gut microbiome, with significant reductions in butyrate-producing bacteria, including Faecalibacterium prausnitzii (P = .0002, q =.007) and Roseburia hominis (P = .0079, q = 0.105). This fatigue-like microbiome was associated with fatigue scales and correlated with progressive depletion of metabolites from serum samples. CONCLUSIONS In an analysis of fecal and serum samples from 166 patients with IBD, we found alterations in serum metabolites and fecal microbes that were associated with fatigue.
Collapse
Affiliation(s)
- Nienke Z Borren
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts; Department of Gastroenterology and Hepatology, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Damian Plichta
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Amit D Joshi
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Gracia Bonilla
- Department of Molecular Biology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Vincent Peng
- Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, St Louis, Missouri
| | - Francis P Colizzo
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Jay Luther
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Hamed Khalili
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - John J Garber
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - C Janneke van der Woude
- Department of Gastroenterology and Hepatology, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Ruslan Sadreyev
- Department of Molecular Biology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Hera Vlamakis
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts; Department of Molecular Biology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Ramnik J Xavier
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts; Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts; Department of Molecular Biology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Ashwin N Ananthakrishnan
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts.
| |
Collapse
|
12
|
Lee S, Bukhari SI, Truesdell SS, Kollu S, Mortensen RD, Boukhali M, Jain E, Lee D, Mazzola M, Raheja R, Langenbucher A, Haradhwala N, Yanagiya A, Lawrence M, Gandhi R, Sadreyev R, Sweetser D, Haas W, Vasudevan S. Abstract B32: A specialized post-transcriptional program in chemoresistant, quiescent cancer cells. Mol Cancer Res 2020. [DOI: 10.1158/1557-3125.pi3k-mtor18-b32] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Quiescent (G0) cells are a clinically relevant fraction in cancers, which include dormant cancer stem cells, and resist clinical therapy. G0 cells reveal extensive changes in gene expression at the protein and translation levels. We previously identified that the translation mechanism is altered in G0 cancer cells. MicroRNAs, noncoding RNAs that target distinct mRNAs to alter gene expression, were found to associate with a key RNA-binding protein and enable specialized functions in G0, where they recruit noncanonical translation factors to regulate specific mRNA translation. We find that G0 leukemic cells show similar proteome and translatome to cells isolated post-chemotherapy. These data suggest that specialized post-transcriptional mechanisms in G0 leukemic cells regulate a distinct translatome to mediate chemoresistance. To understand the role of post-transcriptional regulation in chemoresistance, we compared global transcriptome, translatome and proteome profiling in chemoresistant G0 acute monocytic leukemic (AML) cells. We find that chemotherapy or G0 induction leads to DNA damage responsive ATM and stress signaling, which alter post-transcriptional and translational mechanisms. ATM and stress-activated p38 MAPK/MK2 increase AU-rich-element (ARE) bearing proinflammatory cytokine and immune gene mRNAs, by regulating a key ARE RNA binding protein and modifying canonical translation. AREs are present on 3'UTRs of tightly regulated oncogenes and cytokines, to post-transcriptionally control their expression. Both rate-limiting steps—mRNA cap recognition and tRNA recruitment—in canonical translation are altered. These signaling pathways lead to low mTOR activity in G0, which activates the cap complex inhibitor, eIF4EBP to impair canonical translation, leading to noncanonical translation of specific mRNAs with specialized cap binding and ribosome recruitment factors. In addition, stress and STAT1/interferon signaling are activated to reduce the canonical tRNA recruitment mechanism, enabling noncanonical translation of specific mRNAs. These changes permit translation of ARE bearing proinflammatory cytokine TNFa, and immune and cell-migration modulators that promote survival. Co-inhibiting p38 MAPK and TNFa that promote antiapoptosis—prior to or along with chemotherapy—decreases chemoresistance in AML cells, in vivo, and in patient samples without affecting normal cells. Our studies reveal a proinflammatory subpopulation in AML that mediates resistance, enabled by DNA damage- and stress-regulated post-transcriptional and translational mechanisms that are mediated by AU-rich-elements and a critical ARE RNA binding protein. Disrupting ARE regulation reduces TNFα and chemoresistance, revealing AREs, an important ARE RNA binding protein and noncanonical translation as regulators of chemoresistance. These studies reveal the significance of post-transcriptional regulation of proinflammatory and immune gene-mediated chemoresistance.
Citation Format: Sooncheol Lee, Syed I.A. Bukhari, Samuel S. Truesdell, Swapna Kollu, Richard D. Mortensen, Myriam Boukhali, Esha Jain, Dongjun Lee, Maria Mazzola, Radhika Raheja, Adam Langenbucher, Nicholas Haradhwala, Akiko Yanagiya, Michael Lawrence, Roopali Gandhi, Ruslan Sadreyev, David Sweetser, Wilhelm Haas, Shobha Vasudevan. A specialized post-transcriptional program in chemoresistant, quiescent cancer cells [abstract]. In: Proceedings of the AACR Special Conference on Targeting PI3K/mTOR Signaling; 2018 Nov 30-Dec 8; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Res 2020;18(10_Suppl):Abstract nr B32.
Collapse
|
13
|
Borren NZ, Plichta D, Joshi AD, Bonilla G, Sadreyev R, Vlamakis H, Xavier RJ, Ananthakrishnan AN. Multi-"-Omics" Profiling in Patients With Quiescent Inflammatory Bowel Disease Identifies Biomarkers Predicting Relapse. Inflamm Bowel Dis 2020; 26:1524-1532. [PMID: 32766830 PMCID: PMC7500522 DOI: 10.1093/ibd/izaa183] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Indexed: 02/06/2023]
Abstract
BACKGROUND Inflammatory bowel diseases (IBD) are characterized by intermittent relapses, and their course is heterogeneous and unpredictable. Our aim was to determine the ability of protein, metabolite, or microbial biomarkers to predict relapse in patients with quiescent disease. METHODS This prospective study enrolled patients with quiescent Crohn disease and ulcerative colitis, defined as the absence of clinical symptoms (Harvey-Bradshaw Index ≤ 4, Simple Clinical Colitis Activity Index ≤ 2) and endoscopic remission within the prior year. The primary outcome was relapse within 2 years, defined as symptomatic worsening accompanied by elevated inflammatory markers resulting in a change in therapy or IBD-related hospitalization or surgery. Biomarkers were tested in a derivation cohort, and their performance was examined in an independent validation cohort. RESULTS Our prospective cohort study included 164 patients with IBD (108 with Crohn disease, 56 with ulcerative colitis). Upon follow-up for a median of 1 year, 22 patients (13.4%) experienced a relapse. Three protein biomarkers (interleukin-10, glial cell line-derived neurotrophic factor, and T-cell surface glycoprotein CD8 alpha chain) and 4 metabolomic markers (propionyl-L-carnitine, carnitine, sarcosine, and sorbitol) were associated with relapse in multivariable models. Proteomic and metabolomic risk scores independently predicted relapse with a combined area under the curve of 0.83. A high proteomic risk score (odds ratio = 9.11; 95% confidence interval, 1.90-43.61) or metabolomic risk score (odds ratio = 5.79; 95% confidence interval, 1.24-27.11) independently predicted a higher risk of relapse over 2 years. Fecal metagenomics showed an increased abundance of Proteobacteria (P = 0.0019, q = 0.019) and Fusobacteria (P = 0.0040, q = 0.020) and at the species level Lachnospiraceae_bacterium_2_1_58FAA (P = 0.000008, q = 0.0009) among the relapses. CONCLUSIONS Proteomic, metabolomic, and microbial biomarkers identify a proinflammatory state in quiescent IBD that predisposes to clinical relapse.
Collapse
Affiliation(s)
- Nienke Z Borren
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA,Department of Gastroenterology & Hepatology, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Damian Plichta
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Amit D Joshi
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Gracia Bonilla
- Department of Molecular Biology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Ruslan Sadreyev
- Department of Molecular Biology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Hera Vlamakis
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA,Department of Molecular Biology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Ramnik J Xavier
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA,Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA,Department of Molecular Biology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Ashwin N Ananthakrishnan
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA,Address correspondence to: Ashwin N. Ananthakrishnan, MD, MPH, Massachusetts General Hospital Crohn’s and Colitis Center, 165 Cambridge Street, 9 Floor, Boston, MA 02114 ()
| |
Collapse
|
14
|
Kwak SS, Washicosky KJ, Brand E, von Maydell D, Aronson J, Kim S, Capen DE, Cetinbas M, Sadreyev R, Ning S, Bylykbashi E, Xia W, Wagner SL, Choi SH, Tanzi RE, Kim DY. Amyloid-β42/40 ratio drives tau pathology in 3D human neural cell culture models of Alzheimer's disease. Nat Commun 2020; 11:1377. [PMID: 32170138 PMCID: PMC7070004 DOI: 10.1038/s41467-020-15120-3] [Citation(s) in RCA: 79] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Accepted: 02/20/2020] [Indexed: 02/08/2023] Open
Abstract
The relationship between amyloid-β (Aβ) species and tau pathology in Alzheimer’s disease (AD) is not fully understood. Here, we provide direct evidence that Aβ42/40 ratio, not total Aβ level, plays a critical role in inducing neurofibrillary tangles (NTFs) in human neurons. Using 3D-differentiated clonal human neural progenitor cells (hNPCs) expressing varying levels of amyloid β precursor protein (APP) and presenilin 1 (PS1) with AD mutations, we show that pathogenic tau accumulation and aggregation are tightly correlated with Aβ42/40 ratio. Roles of Aβ42/40 ratio on tau pathology are also confirmed with APP transmembrane domain (TMD) mutant hNPCs, which display differential Aβ42/40 ratios without mutant PS1. Moreover, naïve hNPCs co-cultured with APP TMD I45F (high Aβ42/40) cells, not with I47F cells (low Aβ42/40), develop robust tau pathology in a 3D non-cell autonomous cell culture system. These results emphasize the importance of reducing the Aβ42/40 ratio in AD therapy. The relationship between amyloid-β species and tau pathology in Alzheimer’s disease is not fully understood. Here, the authors show that it is the increased ratio of amyloid-β42 and 40 isoforms drives tau pathology in 3D human neural cell culture models of the disease.
Collapse
Affiliation(s)
- Sang Su Kwak
- Genetics and Aging Research Unit, MassGeneral Institute for Neurodegenerative Disease, Department of Neurology, McCance Center for Brain Health, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA, 02129, USA
| | - Kevin J Washicosky
- Genetics and Aging Research Unit, MassGeneral Institute for Neurodegenerative Disease, Department of Neurology, McCance Center for Brain Health, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA, 02129, USA
| | - Emma Brand
- Genetics and Aging Research Unit, MassGeneral Institute for Neurodegenerative Disease, Department of Neurology, McCance Center for Brain Health, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA, 02129, USA
| | - Djuna von Maydell
- Genetics and Aging Research Unit, MassGeneral Institute for Neurodegenerative Disease, Department of Neurology, McCance Center for Brain Health, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA, 02129, USA
| | - Jenna Aronson
- Genetics and Aging Research Unit, MassGeneral Institute for Neurodegenerative Disease, Department of Neurology, McCance Center for Brain Health, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA, 02129, USA.,Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Susan Kim
- Genetics and Aging Research Unit, MassGeneral Institute for Neurodegenerative Disease, Department of Neurology, McCance Center for Brain Health, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA, 02129, USA
| | - Diane E Capen
- Center for Systems Biology and Program in Membrane Biology, Division of Nephrology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02114, USA
| | - Murat Cetinbas
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Ruslan Sadreyev
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Shen Ning
- Genetics and Aging Research Unit, MassGeneral Institute for Neurodegenerative Disease, Department of Neurology, McCance Center for Brain Health, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA, 02129, USA.,Graduate Program for Neuroscience, Boston University School of Medicine, Boston, MA, 02118, USA
| | - Enjana Bylykbashi
- Genetics and Aging Research Unit, MassGeneral Institute for Neurodegenerative Disease, Department of Neurology, McCance Center for Brain Health, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA, 02129, USA
| | - Weiming Xia
- Geriatric Research Education and Clinical Center, Edith Nourse Rogers Memorial Veterans Hospital, Bedford, MA, 01730, USA.,Department of Pharmacology and Experimental Therapeutics, Boston University School of Medicine, Boston, MA, 02118, USA
| | - Steven L Wagner
- Department of Neurosciences, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Se Hoon Choi
- Genetics and Aging Research Unit, MassGeneral Institute for Neurodegenerative Disease, Department of Neurology, McCance Center for Brain Health, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA, 02129, USA
| | - Rudolph E Tanzi
- Genetics and Aging Research Unit, MassGeneral Institute for Neurodegenerative Disease, Department of Neurology, McCance Center for Brain Health, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA, 02129, USA.
| | - Doo Yeon Kim
- Genetics and Aging Research Unit, MassGeneral Institute for Neurodegenerative Disease, Department of Neurology, McCance Center for Brain Health, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA, 02129, USA.
| |
Collapse
|
15
|
Lee S, Micalizzi D, Truesdell SS, Bukhari SIA, Boukhali M, Lombardi-Story J, Kato Y, Choo MK, Dey-Guha I, Ji F, Nicholson BT, Myers DT, Lee D, Mazzola MA, Raheja R, Langenbucher A, Haradhvala NJ, Lawrence MS, Gandhi R, Tiedje C, Diaz-Muñoz MD, Sweetser DA, Sadreyev R, Sykes D, Haas W, Haber DA, Maheswaran S, Vasudevan S. A post-transcriptional program of chemoresistance by AU-rich elements and TTP in quiescent leukemic cells. Genome Biol 2020; 21:33. [PMID: 32039742 PMCID: PMC7011231 DOI: 10.1186/s13059-020-1936-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Accepted: 01/15/2020] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Quiescence (G0) is a transient, cell cycle-arrested state. By entering G0, cancer cells survive unfavorable conditions such as chemotherapy and cause relapse. While G0 cells have been studied at the transcriptome level, how post-transcriptional regulation contributes to their chemoresistance remains unknown. RESULTS We induce chemoresistant and G0 leukemic cells by serum starvation or chemotherapy treatment. To study post-transcriptional regulation in G0 leukemic cells, we systematically analyzed their transcriptome, translatome, and proteome. We find that our resistant G0 cells recapitulate gene expression profiles of in vivo chemoresistant leukemic and G0 models. In G0 cells, canonical translation initiation is inhibited; yet we find that inflammatory genes are highly translated, indicating alternative post-transcriptional regulation. Importantly, AU-rich elements (AREs) are significantly enriched in the upregulated G0 translatome and transcriptome. Mechanistically, we find the stress-responsive p38 MAPK-MK2 signaling pathway stabilizes ARE mRNAs by phosphorylation and inactivation of mRNA decay factor, Tristetraprolin (TTP) in G0. This permits expression of ARE mRNAs that promote chemoresistance. Conversely, inhibition of TTP phosphorylation by p38 MAPK inhibitors and non-phosphorylatable TTP mutant decreases ARE-bearing TNFα and DUSP1 mRNAs and sensitizes leukemic cells to chemotherapy. Furthermore, co-inhibiting p38 MAPK and TNFα prior to or along with chemotherapy substantially reduces chemoresistance in primary leukemic cells ex vivo and in vivo. CONCLUSIONS These studies uncover post-transcriptional regulation underlying chemoresistance in leukemia. Our data reveal the p38 MAPK-MK2-TTP axis as a key regulator of expression of ARE-bearing mRNAs that promote chemoresistance. By disrupting this pathway, we develop an effective combination therapy against chemosurvival.
Collapse
Affiliation(s)
- Sooncheol Lee
- Massachusetts General Hospital Cancer Center, Harvard Medical School, 185 Cambridge St, CPZN4202, Boston, MA, 02114, USA.,Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, 02114, Massachusetts, USA.,Center for Regenerative Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02114, USA.,Harvard Stem Cell Institute, Harvard University, Cambridge, MA, 02138, USA
| | - Douglas Micalizzi
- Massachusetts General Hospital Cancer Center, Harvard Medical School, 185 Cambridge St, CPZN4202, Boston, MA, 02114, USA.,Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, 02114, Massachusetts, USA
| | - Samuel S Truesdell
- Massachusetts General Hospital Cancer Center, Harvard Medical School, 185 Cambridge St, CPZN4202, Boston, MA, 02114, USA.,Center for Regenerative Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02114, USA.,Harvard Stem Cell Institute, Harvard University, Cambridge, MA, 02138, USA
| | - Syed I A Bukhari
- Massachusetts General Hospital Cancer Center, Harvard Medical School, 185 Cambridge St, CPZN4202, Boston, MA, 02114, USA.,Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, 02114, Massachusetts, USA.,Center for Regenerative Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02114, USA.,Harvard Stem Cell Institute, Harvard University, Cambridge, MA, 02138, USA
| | - Myriam Boukhali
- Massachusetts General Hospital Cancer Center, Harvard Medical School, 185 Cambridge St, CPZN4202, Boston, MA, 02114, USA.,Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, 02114, Massachusetts, USA
| | - Jennifer Lombardi-Story
- Massachusetts General Hospital Cancer Center, Harvard Medical School, 185 Cambridge St, CPZN4202, Boston, MA, 02114, USA.,Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, 02114, Massachusetts, USA
| | - Yasutaka Kato
- Laboratory of Oncology, Hokuto Hospital, Obihiro, Japan
| | - Min-Kyung Choo
- Cutaneous Biology Research Center, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, 02129, USA
| | - Ipsita Dey-Guha
- Massachusetts General Hospital Cancer Center, Harvard Medical School, 185 Cambridge St, CPZN4202, Boston, MA, 02114, USA.,Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, 02114, Massachusetts, USA
| | - Fei Ji
- Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02114, USA
| | - Benjamin T Nicholson
- Massachusetts General Hospital Cancer Center, Harvard Medical School, 185 Cambridge St, CPZN4202, Boston, MA, 02114, USA
| | - David T Myers
- Massachusetts General Hospital Cancer Center, Harvard Medical School, 185 Cambridge St, CPZN4202, Boston, MA, 02114, USA
| | - Dongjun Lee
- Department of Convergence Medical Science, Pusan National University School of Medicine, Yangsan, 50612, 1257-1258, South Korea
| | - Maria A Mazzola
- Center for Neurological Diseases, Brigham & Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Radhika Raheja
- Center for Neurological Diseases, Brigham & Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Adam Langenbucher
- Massachusetts General Hospital Cancer Center, Harvard Medical School, 185 Cambridge St, CPZN4202, Boston, MA, 02114, USA.,Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA, 02129, USA
| | - Nicholas J Haradhvala
- Massachusetts General Hospital Cancer Center, Harvard Medical School, 185 Cambridge St, CPZN4202, Boston, MA, 02114, USA.,Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA, 02129, USA.,Broad Institute of Harvard & MIT, Cambridge, MA, 02142, USA
| | - Michael S Lawrence
- Massachusetts General Hospital Cancer Center, Harvard Medical School, 185 Cambridge St, CPZN4202, Boston, MA, 02114, USA.,Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA, 02129, USA.,Broad Institute of Harvard & MIT, Cambridge, MA, 02142, USA
| | - Roopali Gandhi
- Center for Neurological Diseases, Brigham & Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Christopher Tiedje
- Department of Cellular and Molecular Medicine, Center for Healthy Aging, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen, Denmark
| | - Manuel D Diaz-Muñoz
- Centre de Physiopathologie Toulouse-Purpan, INSERM UMR1043/CNRS U5282, Toulouse, France
| | - David A Sweetser
- Massachusetts General Hospital Cancer Center, Harvard Medical School, 185 Cambridge St, CPZN4202, Boston, MA, 02114, USA.,Department of Pediatrics, Divisions of Pediatric Hematology/Oncology and Medical Genetics, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02114, USA
| | - Ruslan Sadreyev
- Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02114, USA.,Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA, 02129, USA
| | - David Sykes
- Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, 02114, Massachusetts, USA.,Center for Regenerative Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02114, USA.,Harvard Stem Cell Institute, Harvard University, Cambridge, MA, 02138, USA
| | - Wilhelm Haas
- Massachusetts General Hospital Cancer Center, Harvard Medical School, 185 Cambridge St, CPZN4202, Boston, MA, 02114, USA.,Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, 02114, Massachusetts, USA
| | - Daniel A Haber
- Massachusetts General Hospital Cancer Center, Harvard Medical School, 185 Cambridge St, CPZN4202, Boston, MA, 02114, USA.,Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, 02114, Massachusetts, USA.,Howard Hughes Medical Institute, Chevy Chase, MD, 20815, USA
| | - Shyamala Maheswaran
- Massachusetts General Hospital Cancer Center, Harvard Medical School, 185 Cambridge St, CPZN4202, Boston, MA, 02114, USA.,Department of Surgery, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, 02129, USA
| | - Shobha Vasudevan
- Massachusetts General Hospital Cancer Center, Harvard Medical School, 185 Cambridge St, CPZN4202, Boston, MA, 02114, USA. .,Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, 02114, Massachusetts, USA. .,Center for Regenerative Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02114, USA. .,Harvard Stem Cell Institute, Harvard University, Cambridge, MA, 02138, USA.
| |
Collapse
|
16
|
Ciccone DN, Namiki Y, Chen C, Morshead KB, Wood AL, Johnston CM, Morris JW, Wang Y, Sadreyev R, Corcoran AE, Matthews AGW, Oettinger MA. The murine IgH locus contains a distinct DNA sequence motif for the chromatin regulatory factor CTCF. J Biol Chem 2019; 294:13580-13592. [PMID: 31285261 PMCID: PMC6746451 DOI: 10.1074/jbc.ra118.007348] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Revised: 06/13/2019] [Indexed: 01/03/2023] Open
Abstract
Antigen receptor assembly in lymphocytes involves stringently-regulated coordination of specific DNA rearrangement events across several large chromosomal domains. Previous studies indicate that transcription factors such as paired box 5 (PAX5), Yin Yang 1 (YY1), and CCCTC-binding factor (CTCF) play a role in regulating the accessibility of the antigen receptor loci to the V(D)J recombinase, which is required for these rearrangements. To gain clues about the role of CTCF binding at the murine immunoglobulin heavy chain (IgH) locus, we utilized a computational approach that identified 144 putative CTCF-binding sites within this locus. We found that these CTCF sites share a consensus motif distinct from other CTCF sites in the mouse genome. Additionally, we could divide these CTCF sites into three categories: intergenic sites remote from any coding element, upstream sites present within 8 kb of the VH-leader exon, and recombination signal sequence (RSS)-associated sites characteristically located at a fixed distance (∼18 bp) downstream of the RSS. We noted that the intergenic and upstream sites are located in the distal portion of the VH locus, whereas the RSS-associated sites are located in the DH-proximal region. Computational analysis indicated that the prevalence of CTCF-binding sites at the IgH locus is evolutionarily conserved. In all species analyzed, these sites exhibit a striking strand-orientation bias, with >98% of the murine sites being present in one orientation with respect to VH gene transcription. Electrophoretic mobility shift and enhancer-blocking assays and ChIP–chip analysis confirmed CTCF binding to these sites both in vitro and in vivo.
Collapse
Affiliation(s)
- David N Ciccone
- Department of Molecular Biology, Massachusetts General Hospital, and Department of Genetics, Harvard Medical School, Boston, Massachusetts 02114
| | - Yuka Namiki
- Department of Molecular Biology, Massachusetts General Hospital, and Department of Genetics, Harvard Medical School, Boston, Massachusetts 02114
| | - Changfeng Chen
- Department of Molecular Biology, Massachusetts General Hospital, and Department of Genetics, Harvard Medical School, Boston, Massachusetts 02114
| | - Katrina B Morshead
- Department of Molecular Biology, Massachusetts General Hospital, and Department of Genetics, Harvard Medical School, Boston, Massachusetts 02114
| | - Andrew L Wood
- Lymphocyte Signalling and Development, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, United Kingdom
| | - Colette M Johnston
- Lymphocyte Signalling and Development, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, United Kingdom
| | - John W Morris
- Department of Molecular Biology, Massachusetts General Hospital, and Department of Genetics, Harvard Medical School, Boston, Massachusetts 02114
| | - Yanqun Wang
- Department of Molecular Biology, Massachusetts General Hospital, and Department of Genetics, Harvard Medical School, Boston, Massachusetts 02114
| | - Ruslan Sadreyev
- Department of Molecular Biology, Massachusetts General Hospital, and Department of Genetics, Harvard Medical School, Boston, Massachusetts 02114
| | - Anne E Corcoran
- Lymphocyte Signalling and Development, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, United Kingdom
| | - Adam G W Matthews
- Department of Molecular Biology, Massachusetts General Hospital, and Department of Genetics, Harvard Medical School, Boston, Massachusetts 02114.,Department of Biological Sciences and Program in Biochemistry, Wellesley College, Wellesley, Massachusetts 02481
| | - Marjorie A Oettinger
- Department of Molecular Biology, Massachusetts General Hospital, and Department of Genetics, Harvard Medical School, Boston, Massachusetts 02114
| |
Collapse
|
17
|
Mao K, Ji F, Breen P, Sewell A, Han M, Sadreyev R, Ruvkun G. Mitochondrial Dysfunction in C. elegans Activates Mitochondrial Relocalization and Nuclear Hormone Receptor-Dependent Detoxification Genes. Cell Metab 2019; 29:1182-1191.e4. [PMID: 30799287 PMCID: PMC6506380 DOI: 10.1016/j.cmet.2019.01.022] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/29/2018] [Revised: 12/09/2018] [Accepted: 01/25/2019] [Indexed: 12/15/2022]
Abstract
In Caenorhabditis elegans, mitochondrial dysfunction caused by mutation or toxins activates programs of detoxification and immune response. A genetic screen for mutations that constitutively induce C. elegans mitochondrial defense revealed reduction-of-function mutations in the mitochondrial chaperone hsp-6/mtHSP70 and gain-of-function mutations in the Mediator component mdt-15/MED15. The activation of detoxification and immune responses is transcriptionally mediated by mdt-15/MED15 and nuclear hormone receptor nhr-45. Mitochondrial dysfunction triggers redistribution of intestinal mitochondria, which requires the mitochondrial Rho GTPase miro-1 and its adaptor trak-1/TRAK1, but not nhr-45-regulated responses. Disabling the mdt-15/nhr-45 pathway renders animals more susceptible to a mitochondrial toxin or pathogenic Pseudomonas aeruginosa but paradoxically improves health and extends lifespan in animals with mitochondrial dysfunction caused by a mutation. Thus, some of the health deficits in mitochondrial disorders may be caused by the ineffective activation of detoxification and immune responses, which may be inhibited to improve health.
Collapse
Affiliation(s)
- Kai Mao
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Fei Ji
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Peter Breen
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Aileen Sewell
- Howard Hughes Medical Institute and Department of MCDB, University of Colorado, Boulder, CO 80309, USA
| | - Min Han
- Howard Hughes Medical Institute and Department of MCDB, University of Colorado, Boulder, CO 80309, USA
| | - Ruslan Sadreyev
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Gary Ruvkun
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.
| |
Collapse
|
18
|
Sherill-Rofe D, Rahat D, Findlay S, Mellul A, Guberman I, Braun M, Bloch I, Lalezari A, Samiei A, Sadreyev R, Goldberg M, Orthwein A, Zick A, Tabach Y. Mapping global and local coevolution across 600 species to identify novel homologous recombination repair genes. Genome Res 2019; 29:439-448. [PMID: 30718334 PMCID: PMC6396423 DOI: 10.1101/gr.241414.118] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Accepted: 01/22/2019] [Indexed: 12/02/2022]
Abstract
The homologous recombination repair (HRR) pathway repairs DNA double-strand breaks in an error-free manner. Mutations in HRR genes can result in increased mutation rate and genomic rearrangements, and are associated with numerous genetic disorders and cancer. Despite intensive research, the HRR pathway is not yet fully mapped. Phylogenetic profiling analysis, which detects functional linkage between genes using coevolution, is a powerful approach to identify factors in many pathways. Nevertheless, phylogenetic profiling has limited predictive power when analyzing pathways with complex evolutionary dynamics such as the HRR. To map novel HRR genes systematically, we developed clade phylogenetic profiling (CladePP). CladePP detects local coevolution across hundreds of genomes and points to the evolutionary scale (e.g., mammals, vertebrates, animals, plants) at which coevolution occurred. We found that multiscale coevolution analysis is significantly more biologically relevant and sensitive to detect gene function. By using CladePP, we identified dozens of unrecognized genes that coevolved with the HRR pathway, either globally across all eukaryotes or locally in different clades. We validated eight genes in functional biological assays to have a role in DNA repair at both the cellular and organismal levels. These genes are expected to play a role in the HRR pathway and might lead to a better understanding of missing heredity in HRR-associated cancers (e.g., heredity breast and ovarian cancer). Our platform presents an innovative approach to predict gene function, identify novel factors related to different diseases and pathways, and characterize gene evolution.
Collapse
Affiliation(s)
- Dana Sherill-Rofe
- Department of Developmental Biology and Cancer Research, Institute for Medical Research-Israel-Canada, Hebrew University of Jerusalem, Jerusalem 91120, Israel
| | - Dolev Rahat
- Department of Developmental Biology and Cancer Research, Institute for Medical Research-Israel-Canada, Hebrew University of Jerusalem, Jerusalem 91120, Israel.,Sharett Institute of Oncology, Hadassah Medical Center, Ein-Kerem, Jerusalem 91120, Israel
| | - Steven Findlay
- Lady Davis Institute for Medical Research, Segal Cancer Centre, Jewish General Hospital, Montreal, Quebec H3T 1E2, Canada.,Division of Experimental Medicine, McGill University, Montreal, Quebec H4A 3J1, Canada
| | - Anna Mellul
- Department of Developmental Biology and Cancer Research, Institute for Medical Research-Israel-Canada, Hebrew University of Jerusalem, Jerusalem 91120, Israel
| | - Irene Guberman
- Department of Developmental Biology and Cancer Research, Institute for Medical Research-Israel-Canada, Hebrew University of Jerusalem, Jerusalem 91120, Israel
| | - Maya Braun
- Department of Developmental Biology and Cancer Research, Institute for Medical Research-Israel-Canada, Hebrew University of Jerusalem, Jerusalem 91120, Israel
| | - Idit Bloch
- Department of Developmental Biology and Cancer Research, Institute for Medical Research-Israel-Canada, Hebrew University of Jerusalem, Jerusalem 91120, Israel
| | - Alon Lalezari
- Department of Developmental Biology and Cancer Research, Institute for Medical Research-Israel-Canada, Hebrew University of Jerusalem, Jerusalem 91120, Israel
| | - Arash Samiei
- Lady Davis Institute for Medical Research, Segal Cancer Centre, Jewish General Hospital, Montreal, Quebec H3T 1E2, Canada.,Division of Experimental Medicine, McGill University, Montreal, Quebec H4A 3J1, Canada
| | - Ruslan Sadreyev
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, USA.,Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.,Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts 02114, USA
| | - Michal Goldberg
- Department of Genetics, Alexander Silberman Institute of Life Sciences, Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Alexandre Orthwein
- Lady Davis Institute for Medical Research, Segal Cancer Centre, Jewish General Hospital, Montreal, Quebec H3T 1E2, Canada.,Division of Experimental Medicine, McGill University, Montreal, Quebec H4A 3J1, Canada.,Department of Microbiology and Immunology, McGill University, Montreal, Quebec H3A 2B4, Canada.,Gerald Bronfman Department of Oncology, McGill University, Montreal, Quebec H4A 3T2, Canada
| | - Aviad Zick
- Sharett Institute of Oncology, Hadassah Medical Center, Ein-Kerem, Jerusalem 91120, Israel
| | - Yuval Tabach
- Department of Developmental Biology and Cancer Research, Institute for Medical Research-Israel-Canada, Hebrew University of Jerusalem, Jerusalem 91120, Israel
| |
Collapse
|
19
|
Lochhead RB, Ordoñez D, Arvikar SL, Aversa JM, Oh LS, Heyworth B, Sadreyev R, Steere AC, Strle K. Interferon-gamma production in Lyme arthritis synovial tissue promotes differentiation of fibroblast-like synoviocytes into immune effector cells. Cell Microbiol 2019; 21:e12992. [PMID: 30550623 DOI: 10.1111/cmi.12992] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Revised: 12/03/2018] [Accepted: 12/09/2018] [Indexed: 12/21/2022]
Abstract
Lyme arthritis (LA), a late disease manifestation of Borrelia burgdorferi infection, usually resolves with antibiotic therapy. However, some patients develop proliferative synovitis lasting months to several years after spirochetal killing, called postinfectious LA. In this study, we phenotyped haematopoietic and stromal cell populations in the synovial lesion ex vivo and used these findings to generate an in vitro model of LA using patient-derived fibroblast-like synoviocytes (FLS). Ex vivo analysis of synovial tissue revealed high abundance of IFNγ-producing T cells and NK cells. Similar to marked IFNγ responses in tissue, postinfectious LA synovial fluid also had high levels of IFNγ. HLA-DR-positive FLS were present throughout the synovial lesion, particularly in areas of inflammation. FLS stimulated in vitro with B. burgdorferi, which were similar to conditions during infection, expressed 68 genes associated primarily with innate immune activation and neutrophil recruitment. In contrast, FLS stimulated with IFNγ, which were similar to conditions in the postinfectious phase, expressed >2,000 genes associated with pathogen sensing, inflammation, and MHC Class II antigen presentation, similar to the expression profile in postinfectious synovial tissue. Furthermore, costimulation of FLS with B. burgdorferi and IFNγ induced greater expression of IL-6 and other innate immune response proteins and genes than with IFNγ stimulation alone. These results suggest that B. burgdorferi infection, in combination with IFNγ, initiates the differentiation of FLS into a highly inflammatory phenotype. We hypothesise that overexpression of IFNγ by lymphocytes within synovia perpetuates these responses in the postinfectious period, causing proliferative synovitis and stalling appropriate repair of damaged tissue.
Collapse
Affiliation(s)
- Robert B Lochhead
- Center for Immunology and Inflammatory Diseases, Division of Rheumatology, Allergy, and Immunology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - David Ordoñez
- Center for Immunology and Inflammatory Diseases, Division of Rheumatology, Allergy, and Immunology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Sheila L Arvikar
- Center for Immunology and Inflammatory Diseases, Division of Rheumatology, Allergy, and Immunology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - John M Aversa
- Department of Orthopedics, Yale University School of Medicine, New Haven, Connecticut
| | - Luke S Oh
- Department of Orthopedics, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Benton Heyworth
- Department of Orthopedics, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Ruslan Sadreyev
- Department of Molecular Biology and Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Allen C Steere
- Center for Immunology and Inflammatory Diseases, Division of Rheumatology, Allergy, and Immunology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Klemen Strle
- Center for Immunology and Inflammatory Diseases, Division of Rheumatology, Allergy, and Immunology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| |
Collapse
|
20
|
Savji N, Meijers WC, Bartz TM, Bhambhani V, Cushman M, Nayor M, Kizer JR, Sarma A, Blaha MJ, Gansevoort RT, Gardin JM, Hillege HL, Ji F, Kop WJ, Lau ES, Lee DS, Sadreyev R, van Gilst WH, Wang TJ, Zanni MV, Vasan RS, Allen NB, Psaty BM, van der Harst P, Levy D, Larson M, Shah SJ, de Boer RA, Gottdiener JS, Ho JE. The Association of Obesity and Cardiometabolic Traits With Incident HFpEF and HFrEF. JACC Heart Fail 2018; 6:701-709. [PMID: 30007554 PMCID: PMC6076337 DOI: 10.1016/j.jchf.2018.05.018] [Citation(s) in RCA: 214] [Impact Index Per Article: 35.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Revised: 05/15/2018] [Accepted: 05/16/2018] [Indexed: 01/09/2023]
Abstract
OBJECTIVES This study evaluated the associations of obesity and cardiometabolic traits with incident heart failure with preserved versus reduced ejection fraction (HFpEF vs. HFrEF). Given known sex differences in HF subtype, we examined men and women separately. BACKGROUND Recent studies suggest that obesity confers greater risk of HFpEF versus HFrEF. Contributions of associated metabolic traits to HFpEF are less clear. METHODS We studied 22,681 participants from 4 community-based cohorts followed for incident HFpEF versus HFrEF (ejection fraction ≥50% vs. <50%). We evaluated the association of body mass index (BMI) and cardiometabolic traits with incident HF subtype using Cox models. RESULTS The mean age was 60 ± 13 years, and 53% were women. Over a median follow-up of 12 years, 628 developed incident HFpEF and 835 HFrEF. Greater BMI portended higher risk of HFpEF compared with HFrEF (hazard ratio [HR]: 1.34 per 1-SD increase in BMI; 95% confidence interval [CI]: 1.24 to 1.45 vs. HR: 1.18; 95% CI: 1.10 to 1.27). Similarly, insulin resistance (homeostatic model assessment of insulin resistance) was associated with HFpEF (HR: 1.20 per 1-SD; 95% CI: 1.05 to 1.37), but not HFrEF (HR: 0.99; 95% CI: 0.88 to 1.11; p < 0.05 for difference HFpEF vs. HFrEF). We found that the differential association of BMI with HFpEF versus HFrEF was more pronounced among women (p for difference HFpEF vs. HFrEF = 0.01) when compared with men (p = 0.34). CONCLUSIONS Obesity and related cardiometabolic traits including insulin resistance are more strongly associated with risk of future HFpEF versus HFrEF. The differential risk of HFpEF with obesity seems particularly pronounced among women and may underlie sex differences in HF subtypes.
Collapse
Affiliation(s)
- Nazir Savji
- Division of Cardiology, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts
| | - Wouter C Meijers
- Department of Internal Medicine, University of Groningen, University Medical Centre Groningen, Groningen, the Netherlands
| | - Traci M Bartz
- Department of Biostatistics, University of Washington, Seattle, Washington
| | - Vijeta Bhambhani
- Division of Cardiology, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts; Cardiovascular Research Center, Massachusetts General Hospital, Boston, Massachusetts
| | - Mary Cushman
- University of Vermont Larner College of Medicine, Burlington, Vermont
| | - Matthew Nayor
- Division of Cardiology, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts
| | - Jorge R Kizer
- Department of Medicine and Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, New York
| | - Amy Sarma
- Division of Cardiology, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts
| | - Michael J Blaha
- Ciccarone Center for the Prevention of Heart Disease, Johns Hopkins University, Baltimore, Maryland
| | - Ron T Gansevoort
- Department of Internal Medicine, University of Groningen, University Medical Centre Groningen, Groningen, the Netherlands
| | - Julius M Gardin
- Division of Cardiology, Department of Medicine, Rutgers New Jersey Medical School, Newark, New Jersey
| | - Hans L Hillege
- Department of Internal Medicine, University of Groningen, University Medical Centre Groningen, Groningen, the Netherlands
| | - Fei Ji
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts
| | - Willem J Kop
- Center of Research on Psychology in Somatic Diseases, Department of Medical and Clinical Psychology, Tilburg University, Tilburg, the Netherlands
| | - Emily S Lau
- Division of Cardiology, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts
| | - Douglas S Lee
- Institute for Clinical Evaluative Sciences, Toronto, Canada
| | - Ruslan Sadreyev
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts
| | - Wiek H van Gilst
- Department of Internal Medicine, University of Groningen, University Medical Centre Groningen, Groningen, the Netherlands
| | - Thomas J Wang
- Division of Cardiovascular Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Markella V Zanni
- Division of Neuroendocrinology, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts
| | - Ramachandran S Vasan
- Framingham Heart Study, Framingham, Massachusetts; Cardiovascular Medicine Section, Department of Medicine and Section of Preventive Medicine and Epidemiology, Boston University School of Medicine, Boston, Massachusetts; Department of Epidemiology, Boston University School of Public Health, Boston, Massachusetts
| | - Norrina B Allen
- Department of Epidemiology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Bruce M Psaty
- Cardiovascular Health Research Unit, Departments of Medicine, Epidemiology and Health Services, University of Washington, Seattle, Washington; Kaiser Permanente Washington Health Research Institute, Seattle, Washington
| | - Pim van der Harst
- Department of Internal Medicine, University of Groningen, University Medical Centre Groningen, Groningen, the Netherlands
| | - Daniel Levy
- Framingham Heart Study, Framingham, Massachusetts; Center for Population Studies of the National Heart, Lung, and Blood Institute, Bethesda, Maryland
| | - Martin Larson
- Framingham Heart Study, Framingham, Massachusetts; Department of Mathematics and Statistics, Boston University, Boston, Massachusetts
| | - Sanjiv J Shah
- Division of Cardiology, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Rudolf A de Boer
- Department of Internal Medicine, University of Groningen, University Medical Centre Groningen, Groningen, the Netherlands
| | | | - Jennifer E Ho
- Division of Cardiology, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts; Cardiovascular Research Center, Massachusetts General Hospital, Boston, Massachusetts.
| |
Collapse
|
21
|
Senger S, Ingano L, Freire R, Anselmo A, Zhu W, Sadreyev R, Walker WA, Fasano A. Human Fetal-Derived Enterospheres Provide Insights on Intestinal Development and a Novel Model to Study Necrotizing Enterocolitis (NEC). Cell Mol Gastroenterol Hepatol 2018; 5:549-568. [PMID: 29930978 PMCID: PMC6009798 DOI: 10.1016/j.jcmgh.2018.01.014] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/05/2017] [Accepted: 01/18/2018] [Indexed: 12/29/2022]
Abstract
BACKGROUND & AIMS Untreated necrotizing enterocolitis (NEC) can lead to massive inflammation resulting in intestinal necrosis with a high mortality rate in preterm infants. Limited access to human samples and relevant experimental models have hampered progress in NEC pathogenesis. Earlier evidence has suggested that bacterial colonization of an immature and developing intestine can lead to an abnormally high inflammatory response to bacterial bioproducts. The aim of our study was to use human fetal organoids to gain insights into NEC pathogenesis. METHODS RNA sequencing analysis was performed to compare patterns of gene expression in human fetal-derived enterospheres (FEnS) and adult-derived enterospheres (AEnS). Differentially expressed genes were analyzed using computational techniques for dimensional reduction, clustering, and gene set enrichment. Unsupervised cluster analysis, Gene Ontology, and gene pathway analysis were used to predict differences between gene expression of samples. Cell monolayers derived from FEnS and AEnS were evaluated for epithelium function and responsiveness to lipopolysaccharide and commensal bacteria. RESULTS Based on gene expression patterns, FEnS clustered according to their developmental age in 2 distinct groups: early and late FEnS, with the latter more closely resembling AEnS. Genes involved in maturation, gut barrier function, and innate immunity were responsible for these differences. FEnS-derived monolayers exposed to either lipopolysaccharide or commensal Escherichia coli showed that late FEnS activated gene expression of key inflammatory cytokines, whereas early FEnS monolayers did not, owing to decreased expression of nuclear factor-κB-associated machinery. CONCLUSIONS Our results provide insights into processes underlying human intestinal development and support the use of FEnS as a relevant human preclinical model for NEC. Accession number of repository for expression data: GSE101531.
Collapse
Key Words
- AD, adult duodenal
- AEnS, adult-derived enterospheres
- CLDN, claudin
- CXCL, chemokine (C-X-C motif) ligand
- DMEM, Dulbecco's modified Eagle medium
- EGF, epidermal growth factor
- Enteroids
- FDR, false discovery rate
- FEnS, fetal-derived enterospheres
- FITC, fluorescein isothiocyanate
- Fetal Organoids
- HIO, human intestinal organoid
- HS, Escherichia coli human commensal isolate
- IFN, interferon
- IL, interleukin
- LPS, lipopolysaccharide A
- MAMP, microbe-associated molecular pattern
- NEC, necrotizing enterocolitis
- NF-κB, nuclear factor-κB
- Necrotizing Enterocolitis
- PBS, phosphate-buffered saline
- PCR, polymerase chain reaction
- PGE2, prostaglandin E2
- RPKM, reads per kilobase of transcript per million
- RT-PCR, reverse-transcription polymerase chain reaction
- TEER, transepithelial electrical resistance
- TLR, Toll-like receptor
- TNF, tumor necrosis factor
- WAE, wound-associated epithelial cells
- ΔΔCT, relative threshold cycle
Collapse
Affiliation(s)
- Stefania Senger
- Department of Pediatrics, Mucosal Immunology and Biology Research Center, Massachusetts General Hospital, Boston, Massachusetts,Harvard Medical School, Boston, Massachusetts
| | - Laura Ingano
- Department of Pediatrics, Mucosal Immunology and Biology Research Center, Massachusetts General Hospital, Boston, Massachusetts
| | - Rachel Freire
- Department of Pediatrics, Mucosal Immunology and Biology Research Center, Massachusetts General Hospital, Boston, Massachusetts
| | - Antony Anselmo
- Department of Molecular Biology, Cancer Center and Center for Regenerative Medicine, Massachusetts General Hospital, Boston, Massachusetts
| | - Weishu Zhu
- Department of Pediatrics, Mucosal Immunology and Biology Research Center, Massachusetts General Hospital, Boston, Massachusetts
| | - Ruslan Sadreyev
- Department of Molecular Biology, Cancer Center and Center for Regenerative Medicine, Massachusetts General Hospital, Boston, Massachusetts
| | - William Allan Walker
- Department of Pediatrics, Mucosal Immunology and Biology Research Center, Massachusetts General Hospital, Boston, Massachusetts,Harvard Medical School, Boston, Massachusetts
| | - Alessio Fasano
- Department of Pediatrics, Mucosal Immunology and Biology Research Center, Massachusetts General Hospital, Boston, Massachusetts,Harvard Medical School, Boston, Massachusetts,Correspondence Address correspondence to: Alessio Fasano, MD, Mucosal Immunology and Biology Research Center - MGHfC Harvard Medical School 114 16th Street (114-3501), Charlestown, Massachusetts 02129-4404. fax: (617) 724-1731.
| |
Collapse
|
22
|
Strle K, Sulka KB, Pianta A, Crowley JT, Arvikar SL, Anselmo A, Sadreyev R, Steere AC. T-Helper 17 Cell Cytokine Responses in Lyme Disease Correlate With Borrelia burgdorferi Antibodies During Early Infection and With Autoantibodies Late in the Illness in Patients With Antibiotic-Refractory Lyme Arthritis. Clin Infect Dis 2017; 64:930-938. [PMID: 28077518 DOI: 10.1093/cid/cix002] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 01/04/2017] [Indexed: 01/17/2023] Open
Abstract
Background Control of Lyme disease is attributed predominantly to innate and adaptive T-helper 1 cell (TH1) immune responses, whereas the role of T-helper 17 cell (TH17) responses is less clear. Here we characterized these inflammatory responses in patients with erythema migrans (EM) or Lyme arthritis (LA) to elucidate their role early and late in the infection. Methods Levels of 21 cytokines and chemokines, representative of innate, TH1, and TH17 immune responses, were assessed by Luminex in acute and convalescent sera from 91 EM patients, in serum and synovial fluid from 141 LA patients, and in serum from 57 healthy subjects. Antibodies to Borrelia burgdorferi or autoantigens were measured by enzyme-linked immunosorbent assay. Results Compared with healthy subjects, EM patients had significantly higher levels of innate, TH1, and TH17-associated mediators (P ≤ .05) in serum. In these patients, the levels of inflammatory mediators, particularly TH17-associated cytokines, correlated directly with B. burgdorferi immunoglobulin G antibodies (P ≤ .02), suggesting a beneficial role for these responses in control of early infection. Late in the disease, in patients with LA, innate and TH1-associated mediators were often >10-fold higher in synovial fluid than serum. In contrast, the levels of TH17-associated mediators were more variable, but correlated strongly with autoantibodies to endothelial cell growth factor, matrix metalloproteinase 10, and apolipoprotein B-100 in joints of patients with antibiotic-refractory LA, implying a shift in TH17 responses toward an autoimmune phenotype. Conclusions Patients with Lyme disease often develop pronounced TH17 immune responses that may help control early infection. However, late in the disease, excessive TH17 responses may be disadvantageous by contributing to autoimmune responses associated with antibiotic-refractory LA.
Collapse
Affiliation(s)
- Klemen Strle
- Center for Immunology and Inflammatory Diseases, Division of Rheumatology, Allergy and Immunology, and
| | - Katherine B Sulka
- Center for Immunology and Inflammatory Diseases, Division of Rheumatology, Allergy and Immunology, and
| | - Annalisa Pianta
- Center for Immunology and Inflammatory Diseases, Division of Rheumatology, Allergy and Immunology, and
| | - Jameson T Crowley
- Center for Immunology and Inflammatory Diseases, Division of Rheumatology, Allergy and Immunology, and
| | - Sheila L Arvikar
- Center for Immunology and Inflammatory Diseases, Division of Rheumatology, Allergy and Immunology, and
| | - Anthony Anselmo
- Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Ruslan Sadreyev
- Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Allen C Steere
- Center for Immunology and Inflammatory Diseases, Division of Rheumatology, Allergy and Immunology, and
| |
Collapse
|
23
|
Dai N, Ji F, Wright J, Minichiello L, Sadreyev R, Avruch J. IGF2 mRNA binding protein-2 is a tumor promoter that drives cancer proliferation through its client mRNAs IGF2 and HMGA1. eLife 2017; 6:27155. [PMID: 28753127 PMCID: PMC5576481 DOI: 10.7554/elife.27155] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Accepted: 07/23/2017] [Indexed: 01/27/2023] Open
Abstract
The gene encoding the Insulin-like Growth Factor 2 mRNA binding protein 2/IMP2 is amplified and overexpressed in many human cancers, accompanied by a poorer prognosis. Mice lacking IMP2 exhibit a longer lifespan and a reduced tumor burden at old age. Herein we show in a diverse array of human cancer cells that IMP2 overexpression stimulates and IMP2 elimination diminishes proliferation by 50–80%. In addition to its known ability to promote the abundance of Insulin-like Growth Factor 2/IGF2, we find that IMP2 strongly promotes IGF action, by binding and stabilizing the mRNA encoding the DNA binding protein HMGA1, a known oncogene. HMGA1 suppresses the abundance of IGF binding protein 2/IGFBP2 and Grb14, inhibitors of IGF action. IMP2 stabilization of HMGA1 mRNA plus IMP2 stimulated IGF2 production synergistically drive cancer cell proliferation and account for IMP2’s tumor promoting action. IMP2’s ability to promote proliferation and IGF action requires IMP2 phosphorylation by mTOR. Some types of cancers develop when genes known as oncogenes or tumor promoters become faulty, and are present at abnormally high levels or inappropriately turned on. For example, cancer cells often have extra copies of the gene IMP2 and therefore produce too much the IMP2 protein. Previous research has shown that mice that lack the IMP2 protein develop fewer cancers and live longer, while patients whose cancers make too much IMP2 have a poorer prognosis. In healthy cells, the IMP2 protein normally helps to make new gene products by stabilising certain newly produced RNA molecules – the precursors of proteins, and in some cases by promoting the translation of these RNAs into proteins. For example, IMP2 binds to the mRNA that encodes the protein IGF2, which is a protein that helps cells to grow and is commonly produced in large quantities by cancer cells. However, until now it was not clear whether IMP2 only acts by increasing the production of IGF2 or also contributes to cancer growth in other ways. Using a range of human cancer cell lines, and healthy mouse cells, Dai et al. first confirmed that without IMP2, cancer cells made less IGF2 and grew less quickly. When IGF2 was added to the cells lacking IMP2, it only partially restored their ability to grow. Further experiments revealed that cells without IMP2 had increased levels of proteins that counteract the effects of IGF2. Usually, IMP2 binds and stabilizes the mRNA that encodes the oncogenic protein HMGA1, which is known to regulate the number of ‘anti-IGF2 proteins’. However, without IMP2, the HMGA1 levels drop, which causes an increase of the anti-IGF2 proteins. This indicates that IMP2 promotes cancer cell growth both by enabling cells to produce more IGF2 and by suppressing inhibitors of IGF2 action. This suggests that cancer patients whose tumors have abnormally high levels of IMP2 may be especially sensitive to drugs that target and inhibit IGF2.
Collapse
Affiliation(s)
- Ning Dai
- Department of Molecular Biology, Massachusetts General Hospital, Boston, United States.,Diabetes unit, Medical Services, Massachusetts General Hospital, Boston, United States.,Department of Medicine, Harvard Medical School, Boston, United States
| | - Fei Ji
- Department of Molecular Biology, Massachusetts General Hospital, Boston, United States.,Department of Genetics, Harvard Medical School, Boston, United States
| | - Jason Wright
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, United States
| | | | - Ruslan Sadreyev
- Department of Molecular Biology, Massachusetts General Hospital, Boston, United States.,Department of Pathology, Harvard Medical School, Boston, United States
| | - Joseph Avruch
- Department of Molecular Biology, Massachusetts General Hospital, Boston, United States.,Diabetes unit, Medical Services, Massachusetts General Hospital, Boston, United States.,Department of Medicine, Harvard Medical School, Boston, United States
| |
Collapse
|
24
|
Chu HP, Froberg JE, Kesner B, Oh HJ, Ji F, Sadreyev R, Pinter SF, Lee JT. PAR-TERRA directs homologous sex chromosome pairing. Nat Struct Mol Biol 2017; 24:620-631. [PMID: 28692038 PMCID: PMC5553554 DOI: 10.1038/nsmb.3432] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2016] [Accepted: 06/09/2017] [Indexed: 12/25/2022]
Abstract
In mammals, homologous chromosomes rarely pair outside of meiosis. An exception is the X-chromosome, which transiently pairs during X-chromosome inactivation (XCI). How two chromosomes find each other in 3D space is not known. Here, we reveal a required interaction between the X-inactivation center (Xic) and the telomere in mouse embryonic stem cells. The sub-telomeric, pseudoautosomal region (PAR) of both sex chromosomes (X,Y) also undergoes pairing. PAR transcribes a class of telomeric RNA, dubbed “PAR-TERRA”, which accounts for a vast majority of all TERRA transcripts. PAR-TERRA binds throughout the genome, including PAR and Xic. PAR-TERRA anchors the Xic to PAR, creating a “tetrad” of pairwise homologous interactions (Xic:Xic, PAR:PAR, Xic:PAR). Xic pairing occurs within the tetrad. Depleting PAR-TERRA abrogates pairing and blocks initiation of XCI, whereas autosomal PAR-TERRA induces ectopic pairing. We proposed a Constrained Diffusion Model in which PAR-TERRA creates an interaction hub to guide Xic homology searching during XCI.
Collapse
Affiliation(s)
- Hsueh-Ping Chu
- Howard Hughes Medical Institute, Boston, Massachusetts, USA.,Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts, USA.,Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - John E Froberg
- Howard Hughes Medical Institute, Boston, Massachusetts, USA.,Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts, USA.,Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Barry Kesner
- Howard Hughes Medical Institute, Boston, Massachusetts, USA.,Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts, USA.,Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Hyun Jung Oh
- Howard Hughes Medical Institute, Boston, Massachusetts, USA.,Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts, USA.,Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Fei Ji
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts, USA.,Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Ruslan Sadreyev
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts, USA.,Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Stefan F Pinter
- Howard Hughes Medical Institute, Boston, Massachusetts, USA.,Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts, USA.,Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Jeannie T Lee
- Howard Hughes Medical Institute, Boston, Massachusetts, USA.,Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts, USA.,Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| |
Collapse
|
25
|
Bukhari SI, Truesdell SS, Lee S, Kollu S, Classon A, Boukhali M, Jain E, Mortensen RD, Yanagiya A, Sadreyev R, Haas W, Vasudevan S. Abstract 4997: Specialized microRNP and translation mechanisms in quiescent cancer cells. Cancer Res 2017. [DOI: 10.1158/1538-7445.am2017-4997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Quiescence (G0) represents an assortment of reversible, cell cycle-arrested states that are resistant to unfavorable conditions and associated with cancer persistence. G0 involves regulated gene expression with selective mRNA expression and decreased canonical translation. Low mTOR activity in G0 activates the cap complex inhibitor, eIF4EBP, and impairs canonical translation. The alternative translation mechanisms in G0 remain to be uncovered. Our data show that microRNAs, regulatory, non-coding RNAs that target distinct mRNAs to alter gene expression, can associate with alternative complexes and translation factors to regulate specific mRNA translation in G0. One subset of transcripts expressed in G0 includes specific mRNAs recruited by an FXR1a-associated microRNP (microRNA-protein complex) for translation activation in G0 mammalian cells. MicroRNPs predominantly mediate repression and downregulation; however, FXR1a-microRNP lacks conventional microRNP repressors, and instead, contains a specific RNA binding protein isoform, FXR1a. FXR1a promotes translation and is overexpressed and associated with poor prognosis in several cancers. Our data reveal that microRNA-mediated activation requires target mRNAs with unadenylated/ shortened poly(A) tails to avoid the roles of PABP in enhancing microRNA-mediated downregulation and in canonical translation that is impaired in G0. Instead of canonical translation factors that are inhibited by eIF4EBP in G0, we find alternative translation factors—a non-canonical 5’cap binding factor and an eIF4G homolog that interacts with the ribosome—are recruited by the 3’-UTR binding FXR1a-microRNP, and promote specific mRNA translation. Our data show that G0 leukemic cells are chemoresistant and their translation profile is similar to surviving leukemic cells that are isolated after clinical therapy. We find expression of critical cytokines and immune regulators in G0. Significantly, inhibiting these immune regulators in resistant G0 cancer cells reduces their survival and chemoresistance. These data reveal a specialized translation mechanism in G0 cancer cells that promotes specific mRNA translation in these conditions of reduced canonical translation, and is important for chemoresistance.
Citation Format: Syed I. Bukhari, Samuel S. Truesdell, Sooncheol Lee, Swapna Kollu, Anthony Classon, Myriam Boukhali, Esha Jain, Richard D. Mortensen, Akiko Yanagiya, Ruslan Sadreyev, Wilhelm Haas, Shobha Vasudevan. Specialized microRNP and translation mechanisms in quiescent cancer cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 4997. doi:10.1158/1538-7445.AM2017-4997
Collapse
Affiliation(s)
| | | | - Sooncheol Lee
- 1Massachusetts General Hosp. Cancer Ctr., Boston, MA
| | - Swapna Kollu
- 1Massachusetts General Hosp. Cancer Ctr., Boston, MA
| | | | | | - Esha Jain
- 2Massachusetts General Hosp., Boston, MA
| | | | | | | | - Wilhelm Haas
- 1Massachusetts General Hosp. Cancer Ctr., Boston, MA
| | | |
Collapse
|
26
|
Pym E, Sasidharan N, Thompson-Peer KL, Simon DJ, Anselmo A, Sadreyev R, Hall Q, Nurrish S, Kaplan JM. Shank is a dose-dependent regulator of Ca v1 calcium current and CREB target expression. eLife 2017; 6. [PMID: 28477407 PMCID: PMC5432211 DOI: 10.7554/elife.18931] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2016] [Accepted: 04/18/2017] [Indexed: 12/26/2022] Open
Abstract
Shank is a post-synaptic scaffolding protein that has many binding partners. Shank mutations and copy number variations (CNVs) are linked to several psychiatric disorders, and to synaptic and behavioral defects in mice. It is not known which Shank binding partners are responsible for these defects. Here we show that the C. elegans SHN-1/Shank binds L-type calcium channels and that increased and decreased shn-1 gene dosage alter L-channel current and activity-induced expression of a CRH-1/CREB transcriptional target (gem-4 Copine), which parallels the effects of human Shank copy number variations (CNVs) on Autism spectrum disorders and schizophrenia. These results suggest that an important function of Shank proteins is to regulate L-channel current and activity induced gene expression. DOI:http://dx.doi.org/10.7554/eLife.18931.001
Collapse
Affiliation(s)
- Edward Pym
- Department of Molecular Biology, Massachusetts General Hospital, Boston, United States.,Department of Neurobiology, Harvard Medical School, Boston, United States
| | - Nikhil Sasidharan
- Department of Molecular Biology, Massachusetts General Hospital, Boston, United States.,Department of Neurobiology, Harvard Medical School, Boston, United States
| | - Katherine L Thompson-Peer
- Department of Molecular Biology, Massachusetts General Hospital, Boston, United States.,Department of Neurobiology, Harvard Medical School, Boston, United States
| | - David J Simon
- Department of Molecular Biology, Massachusetts General Hospital, Boston, United States.,Department of Neurobiology, Harvard Medical School, Boston, United States.,Program in Neuroscience, Harvard Medical School, Boston, United States
| | - Anthony Anselmo
- Department of Molecular Biology, Massachusetts General Hospital, Boston, United States
| | - Ruslan Sadreyev
- Department of Molecular Biology, Massachusetts General Hospital, Boston, United States
| | - Qi Hall
- Department of Molecular Biology, Massachusetts General Hospital, Boston, United States.,Department of Neurobiology, Harvard Medical School, Boston, United States
| | - Stephen Nurrish
- Department of Molecular Biology, Massachusetts General Hospital, Boston, United States.,Department of Neurobiology, Harvard Medical School, Boston, United States
| | - Joshua M Kaplan
- Department of Molecular Biology, Massachusetts General Hospital, Boston, United States.,Department of Neurobiology, Harvard Medical School, Boston, United States.,Program in Neuroscience, Harvard Medical School, Boston, United States
| |
Collapse
|
27
|
Mueller B, Mieczkowski J, Kundu S, Wang P, Sadreyev R, Tolstorukov MY, Kingston RE. Widespread changes in nucleosome accessibility without changes in nucleosome occupancy during a rapid transcriptional induction. Genes Dev 2017; 31:451-462. [PMID: 28356342 PMCID: PMC5393060 DOI: 10.1101/gad.293118.116] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Accepted: 02/27/2017] [Indexed: 12/20/2022]
Abstract
Activation of transcription requires alteration of chromatin by complexes that increase the accessibility of nucleosomal DNA. Removing nucleosomes from regulatory sequences has been proposed to play a significant role in activation. We tested whether changes in nucleosome occupancy occurred on the set of genes that is activated by the unfolded protein response (UPR). We observed no decrease in occupancy on most promoters, gene bodies, and enhancers. Instead, there was an increase in the accessibility of nucleosomes, as measured by micrococcal nuclease (MNase) digestion and ATAC-seq (assay for transposase-accessible chromatin [ATAC] using sequencing), that did not result from removal of the nucleosome. Thus, changes in nucleosome accessibility predominate over changes in nucleosome occupancy during rapid transcriptional induction during the UPR.
Collapse
Affiliation(s)
- Britta Mueller
- Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, USA
| | - Jakub Mieczkowski
- Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, USA
| | - Sharmistha Kundu
- Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, USA
| | - Peggy Wang
- Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, USA
| | - Ruslan Sadreyev
- Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, USA.,Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, USA
| | - Michael Y Tolstorukov
- Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, USA
| | - Robert E Kingston
- Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, USA
| |
Collapse
|
28
|
Mehta S, Cronkite DA, Basavappa M, Saunders TL, Adiliaghdam F, Amatullah H, Morrison SA, Pagan JD, Anthony RM, Tonnerre P, Lauer GM, Lee JC, Digumarthi S, Pantano L, Ho Sui SJ, Ji F, Sadreyev R, Zhou C, Mullen AC, Kumar V, Li Y, Wijmenga C, Xavier RJ, Means TK, Jeffrey KL. Maintenance of macrophage transcriptional programs and intestinal homeostasis by epigenetic reader SP140. Sci Immunol 2017; 2:eaag3160. [PMID: 28783698 PMCID: PMC5549562 DOI: 10.1126/sciimmunol.aag3160] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Accepted: 02/08/2017] [Indexed: 12/29/2022]
Abstract
Epigenetic "readers" that recognize defined posttranslational modifications on histones have become desirable therapeutic targets for cancer and inflammation. SP140 is one such bromodomain- and plant homeodomain (PHD)-containing reader with immune-restricted expression, and single-nucleotide polymorphisms (SNPs) within SP140 associate with Crohn's disease (CD). However, the function of SP140 and the consequences of disease-associated SP140 SNPs have remained unclear. We show that SP140 is critical for transcriptional programs that uphold the macrophage state. SP140 preferentially occupies promoters of silenced, lineage-inappropriate genes bearing the histone modification H3K27me3, such as the HOXA cluster in human macrophages, and ensures their repression. Depletion of SP140 in mouse or human macrophages resulted in severely compromised microbe-induced activation. We reveal that peripheral blood mononuclear cells (PBMCs) or B cells from individuals carrying CD-associated SNPs within SP140 have defective SP140 messenger RNA splicing and diminished SP140 protein levels. Moreover, CD patients carrying SP140 SNPs displayed suppressed innate immune gene signatures in a mixed population of PBMCs that stratified them from other CD patients. Hematopoietic-specific knockdown of Sp140 in mice resulted in exacerbated dextran sulfate sodium (DSS)-induced colitis, and low SP140 levels in human CD intestinal biopsies correlated with relatively lower intestinal innate cytokine levels and improved response to anti-tumor necrosis factor (TNF) therapy. Thus, the epigenetic reader SP140 is a key regulator of macrophage transcriptional programs for cellular state, and a loss of SP140 due to genetic variation contributes to a molecularly defined subset of CD characterized by ineffective innate immunity, normally critical for intestinal homeostasis.
Collapse
Affiliation(s)
- Stuti Mehta
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - D Alexander Cronkite
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Megha Basavappa
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Tahnee L Saunders
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Fatemeh Adiliaghdam
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Hajera Amatullah
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Sara A Morrison
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Jose D Pagan
- Center for Immunology and Inflammatory Diseases, Division of Rheumatology, Allergy and Immunology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA
| | - Robert M Anthony
- Center for Immunology and Inflammatory Diseases, Division of Rheumatology, Allergy and Immunology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA
| | - Pierre Tonnerre
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Georg M Lauer
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - James C Lee
- Department of Medicine, University of Cambridge School of Clinical Medicine, Addenbrooke's Hospital, Cambridge, U.K
| | - Sreehaas Digumarthi
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Lorena Pantano
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Shannan J Ho Sui
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Fei Ji
- Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Ruslan Sadreyev
- Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Chan Zhou
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Alan C Mullen
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Vinod Kumar
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Yang Li
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Cisca Wijmenga
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Ramnik J Xavier
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Terry K Means
- Center for Immunology and Inflammatory Diseases, Division of Rheumatology, Allergy and Immunology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA
| | - Kate L Jeffrey
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.
| |
Collapse
|
29
|
Fusco DN, Pratt H, Kandilas S, Cheon SSY, Lin W, Cronkite DA, Basavappa M, Jeffrey KL, Anselmo A, Sadreyev R, Yapp C, Shi X, O'Sullivan JF, Gerszten RE, Tomaru T, Yoshino S, Satoh T, Chung RT. HELZ2 Is an IFN Effector Mediating Suppression of Dengue Virus. Front Microbiol 2017; 8:240. [PMID: 28265266 PMCID: PMC5316548 DOI: 10.3389/fmicb.2017.00240] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Accepted: 02/03/2017] [Indexed: 01/07/2023] Open
Abstract
Flaviviral infections including dengue virus are an increasing clinical problem worldwide. Dengue infection triggers host production of the type 1 IFN, IFN alpha, one of the strongest and broadest acting antivirals known. However, dengue virus subverts host IFN signaling at early steps of IFN signal transduction. This subversion allows unbridled viral replication which subsequently triggers ongoing production of IFN which, again, is subverted. Identification of downstream IFN antiviral effectors will provide targets which could be activated to restore broad acting antiviral activity, stopping the signal to produce endogenous IFN at toxic levels. To this end, we performed a targeted functional genomic screen for IFN antiviral effector genes (IEGs), identifying 56 IEGs required for antiviral effects of IFN against fully infectious dengue virus. Dengue IEGs were enriched for genes encoding nuclear receptor interacting proteins, including HELZ2, MAP2K4, SLC27A2, HSP90AA1, and HSP90AB1. We focused on HELZ2 (Helicase With Zinc Finger 2), an IFN stimulated gene and IEG which encodes a promiscuous nuclear factor coactivator that exists in two isoforms. The two unique HELZ2 isoforms are both IFN responsive, contain ISRE elements, and gene products increase in the nucleus upon IFN stimulation. Chromatin immunoprecipitation-sequencing revealed that the HELZ2 complex interacts with triglyceride-regulator LMF1. Mass spectrometry revealed that HELZ2 knockdown cells are depleted of triglyceride subsets. We thus sought to determine whether HELZ2 interacts with a nuclear receptor known to regulate immune response and lipid metabolism, AHR, and identified HELZ2:AHR interactions via co-immunoprecipitation, found that AHR is a dengue IEG, and that an AHR ligand, FICZ, exhibits anti-dengue activity. Primary bone marrow derived macrophages from HELZ2 knockout mice, compared to wild type controls, exhibit enhanced dengue infectivity. Overall, these findings reveal that IFN antiviral response is mediated by HELZ2 transcriptional upregulation, enrichment of HELZ2 protein levels in the nucleus, and activation of a transcriptional program that appears to modulate intracellular lipid state. IEGs identified in this study may serve as both (1) potential targets for host directed antiviral design, downstream of the common flaviviral subversion point, as well as (2) possible biomarkers, whose variation, natural, or iatrogenic, could affect host response to viral infections.
Collapse
Affiliation(s)
- Dahlene N Fusco
- Gastrointestinal Division, Department of Medicine, Massachusetts General HospitalBoston, MA, USA; Division of Infectious Diseases, Vaccine and Immunotherapy Center, Department of Medicine, Massachusetts General HospitalBoston, MA, USA; Laboratory for Systems Pharmacology, Harvard Medical SchoolBoston, MA, USA
| | - Henry Pratt
- Gastrointestinal Division, Department of Medicine, Massachusetts General Hospital Boston, MA, USA
| | - Stephen Kandilas
- Division of Infectious Diseases, Vaccine and Immunotherapy Center, Department of Medicine, Massachusetts General HospitalBoston, MA, USA; Department of Medicine, Athens University Medical SchoolAthens, Greece
| | | | - Wenyu Lin
- Gastrointestinal Division, Department of Medicine, Massachusetts General Hospital Boston, MA, USA
| | - D Alex Cronkite
- Gastrointestinal Division, Department of Medicine, Massachusetts General Hospital Boston, MA, USA
| | - Megha Basavappa
- Gastrointestinal Division, Department of Medicine, Massachusetts General Hospital Boston, MA, USA
| | - Kate L Jeffrey
- Gastrointestinal Division, Department of Medicine, Massachusetts General Hospital Boston, MA, USA
| | - Anthony Anselmo
- Department of Molecular Biology, Massachusetts General Hospital Boston, MA, USA
| | - Ruslan Sadreyev
- Department of Molecular Biology, Massachusetts General Hospital Boston, MA, USA
| | - Clarence Yapp
- Laboratory for Systems Pharmacology, Harvard Medical School Boston, MA, USA
| | - Xu Shi
- Division of Cardiology, Department of Medicine, Beth Israel Deaconess Medical Center Boston, MA, USA
| | - John F O'Sullivan
- Division of Cardiology, Department of Medicine, Massachusetts General Hospital Boston, MA, USA
| | - Robert E Gerszten
- Division of Cardiology, Department of Medicine, Beth Israel Deaconess Medical CenterBoston, MA, USA; Division of Cardiology, Department of Medicine, Massachusetts General HospitalBoston, MA, USA
| | - Takuya Tomaru
- Department of Medicine and Molecular Science, Gunma University Graduate School of Medicine Maebashi, Japan
| | - Satoshi Yoshino
- Department of Medicine and Molecular Science, Gunma University Graduate School of Medicine Maebashi, Japan
| | - Tetsurou Satoh
- Department of Medicine and Molecular Science, Gunma University Graduate School of Medicine Maebashi, Japan
| | - Raymond T Chung
- Gastrointestinal Division, Department of Medicine, Massachusetts General Hospital Boston, MA, USA
| |
Collapse
|
30
|
Lehrbach NJ, Ji F, Sadreyev R. Next-Generation Sequencing for Identification of EMS-Induced Mutations in Caenorhabditis elegans. ACTA ACUST UNITED AC 2017; 117:7.29.1-7.29.12. [PMID: 28060408 DOI: 10.1002/cpmb.27] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Forward genetic analysis using chemical mutagenesis in model organisms is a powerful tool for investigation of molecular mechanisms in biological systems. In the nematode, Caenorhabditis elegans, mutagenesis screens using ethyl methanesulfonate (EMS) have led to important insights into genetic control of animal development and physiology. A major bottleneck to this approach is identification of the causative mutation underlying a phenotype of interest. In the past, this has required time-consuming genetic mapping experiments. More recently, next-generation sequencing technologies have allowed development of new methods for rapid mapping and identification of EMS-induced lesions. In this unit we describe a protocol to map and identify EMS-induced mutations in C. elegans. © 2017 by John Wiley & Sons, Inc.
Collapse
Affiliation(s)
- Nicolas J Lehrbach
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts.,Department of Genetics, Harvard Medical School, Boston, Massachusetts
| | - Fei Ji
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts.,Department of Genetics, Harvard Medical School, Boston, Massachusetts
| | - Ruslan Sadreyev
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts.,Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| |
Collapse
|
31
|
McEwan DL, Feinbaum RL, Stroustrup N, Haas W, Conery AL, Anselmo A, Sadreyev R, Ausubel FM. Tribbles ortholog NIPI-3 and bZIP transcription factor CEBP-1 regulate a Caenorhabditis elegans intestinal immune surveillance pathway. BMC Biol 2016; 14:105. [PMID: 27927200 PMCID: PMC5143455 DOI: 10.1186/s12915-016-0334-6] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Accepted: 11/15/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Many pathogens secrete toxins that target key host processes resulting in the activation of immune pathways. The secreted Pseudomonas aeruginosa toxin Exotoxin A (ToxA) disrupts intestinal protein synthesis, which triggers the induction of a subset of P. aeruginosa-response genes in the nematode Caenorhabditis elegans. RESULTS We show here that one ToxA-induced C. elegans gene, the Tribbles pseudokinase ortholog nipi-3, is essential for host survival following exposure to P. aeruginosa or ToxA. We find that NIPI-3 mediates the post-developmental expression of intestinal immune genes and proteins and primarily functions in parallel to known immune pathways, including p38 MAPK signaling. Through mutagenesis screening, we identify mutants of the bZIP C/EBP transcription factor cebp-1 that suppress the hypersusceptibility defects of nipi-3 mutants. CONCLUSIONS NIPI-3 is a negative regulator of CEBP-1, which in turn negatively regulates protective immune mechanisms. This pathway represents a previously unknown innate immune signaling pathway in intestinal epithelial cells that is involved in the surveillance of cellular homeostasis. Because NIPI-3 and CEBP-1 are also essential for C. elegans development, NIPI-3 is analogous to other key innate immune signaling molecules such as the Toll receptors in Drosophila that have an independent role during development.
Collapse
Affiliation(s)
- Deborah L. McEwan
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA USA
- Department of Genetics, Harvard Medical School, Boston, MA USA
| | - Rhonda L. Feinbaum
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA USA
- Department of Genetics, Harvard Medical School, Boston, MA USA
| | | | - Wilhelm Haas
- Center for Cancer Research, Massachusetts General Hospital, Boston, MA USA
| | - Annie L. Conery
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA USA
- Department of Genetics, Harvard Medical School, Boston, MA USA
- Present Address: Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA USA
| | - Anthony Anselmo
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA USA
- Department of Genetics, Harvard Medical School, Boston, MA USA
| | - Ruslan Sadreyev
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA USA
- Department of Genetics, Harvard Medical School, Boston, MA USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA USA
| | - Frederick M. Ausubel
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA USA
- Department of Genetics, Harvard Medical School, Boston, MA USA
| |
Collapse
|
32
|
Wein MN, Liang Y, Goransson O, Sundberg TB, Wang J, Williams EA, O'Meara MJ, Govea N, Beqo B, Nishimori S, Nagano K, Brooks DJ, Martins JS, Corbin B, Anselmo A, Sadreyev R, Wu JY, Sakamoto K, Foretz M, Xavier RJ, Baron R, Bouxsein ML, Gardella TJ, Divieti-Pajevic P, Gray NS, Kronenberg HM. SIKs control osteocyte responses to parathyroid hormone. Nat Commun 2016; 7:13176. [PMID: 27759007 PMCID: PMC5075806 DOI: 10.1038/ncomms13176] [Citation(s) in RCA: 101] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Accepted: 09/09/2016] [Indexed: 12/20/2022] Open
Abstract
Parathyroid hormone (PTH) activates receptors on osteocytes to orchestrate bone formation and resorption. Here we show that PTH inhibition of SOST (sclerostin), a WNT antagonist, requires HDAC4 and HDAC5, whereas PTH stimulation of RANKL, a stimulator of bone resorption, requires CRTC2. Salt inducible kinases (SIKs) control subcellular localization of HDAC4/5 and CRTC2. PTH regulates both HDAC4/5 and CRTC2 localization via phosphorylation and inhibition of SIK2. Like PTH, new small molecule SIK inhibitors cause decreased phosphorylation and increased nuclear translocation of HDAC4/5 and CRTC2. SIK inhibition mimics many of the effects of PTH in osteocytes as assessed by RNA-seq in cultured osteocytes and following in vivo administration. Once daily treatment with the small molecule SIK inhibitor YKL-05-099 increases bone formation and bone mass. Therefore, a major arm of PTH signalling in osteocytes involves SIK inhibition, and small molecule SIK inhibitors may be applied therapeutically to mimic skeletal effects of PTH. Parathyroid hormone (PTH) is an endogenous hormone and osteoporosis therapeutic that suppresses sclerostin activity. Here the authors develop SIK inhibitors as potential therapeutic tools and use them to show that PTH-cAMP signalling in osteocytes inhibits SIK2 from driving Hdac4/5 nuclear shuttling to suppress sclerostin.
Collapse
Affiliation(s)
- Marc N Wein
- Endocrine Unit, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, 50 Blossom Street, Boston, Massachusetts 02114, USA
| | - Yanke Liang
- Dana Farber Cancer Institute, Department of Biologic Chemistry and Molecular Pharmacology, Harvard Medical School, 450 Brookline Avenue, Boston, Massachusetts 02215, USA
| | - Olga Goransson
- Department of Experimental Medical Sciences, Lund University, Box 188, SE-221 00 Lund, Sweden
| | - Thomas B Sundberg
- Center for the Development of Therapeutics, Broad Institute, 415 Main Street, Cambridge, Massachusetts 02142, USA
| | - Jinhua Wang
- Dana Farber Cancer Institute, Department of Biologic Chemistry and Molecular Pharmacology, Harvard Medical School, 450 Brookline Avenue, Boston, Massachusetts 02215, USA
| | - Elizabeth A Williams
- Endocrine Unit, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, 50 Blossom Street, Boston, Massachusetts 02114, USA
| | - Maureen J O'Meara
- Endocrine Unit, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, 50 Blossom Street, Boston, Massachusetts 02114, USA
| | - Nicolas Govea
- Endocrine Unit, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, 50 Blossom Street, Boston, Massachusetts 02114, USA
| | - Belinda Beqo
- Endocrine Unit, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, 50 Blossom Street, Boston, Massachusetts 02114, USA
| | - Shigeki Nishimori
- Endocrine Unit, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, 50 Blossom Street, Boston, Massachusetts 02114, USA
| | - Kenichi Nagano
- Harvard School of Dental Medicine, Department of Oral Medicine, Infection, and Immunity, 188 Longwood Avenue, Boston, Massachusetts 02115, US
| | - Daniel J Brooks
- Endocrine Unit, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, 50 Blossom Street, Boston, Massachusetts 02114, USA.,Center for Advanced Orthopaedic Studies, Department of Orthopedic Surgery, Beth Israel Deaconess Medical Center, 330 Brookline Avenue, Boston, Massachusetts 02215, USA
| | - Janaina S Martins
- Endocrine Unit, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, 50 Blossom Street, Boston, Massachusetts 02114, USA
| | - Braden Corbin
- Endocrine Unit, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, 50 Blossom Street, Boston, Massachusetts 02114, USA
| | - Anthony Anselmo
- Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, 185 Cambridge Street, Boston, Massachusetts 02114, USA
| | - Ruslan Sadreyev
- Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, 185 Cambridge Street, Boston, Massachusetts 02114, USA
| | - Joy Y Wu
- Division of Endocrinology, Department of Medicine, Stanford University School of Medicine, 300 Pasteur Dr a175, Stanford, California 94305, USA
| | - Kei Sakamoto
- MRC Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, UK
| | - Marc Foretz
- INSERM U1016, Institut Cochin, CNRS UMR8104, Universite Paris Descartes Sorbonne Pairs Cite, Paris 75013, France
| | - Ramnik J Xavier
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Department of Medicine, Massachusetts General Hospital, 55 Fruit Street, Boston, Massachusetts 02114, USA.,Center for Computational and Integrative Biology, Massachusetts General Hospital, Harvard Medical School, 55 Fruit Street, Boston, Massachusetts 02114, USA.,Program in Medical and Population Genetics, Broad Institute, 415 Main Street, Cambridge, Massachusetts 02142, USA
| | - Roland Baron
- Endocrine Unit, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, 50 Blossom Street, Boston, Massachusetts 02114, USA.,Harvard School of Dental Medicine, Department of Oral Medicine, Infection, and Immunity, 188 Longwood Avenue, Boston, Massachusetts 02115, US
| | - Mary L Bouxsein
- Endocrine Unit, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, 50 Blossom Street, Boston, Massachusetts 02114, USA.,Center for Advanced Orthopaedic Studies, Department of Orthopedic Surgery, Beth Israel Deaconess Medical Center, 330 Brookline Avenue, Boston, Massachusetts 02215, USA
| | - Thomas J Gardella
- Endocrine Unit, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, 50 Blossom Street, Boston, Massachusetts 02114, USA
| | - Paola Divieti-Pajevic
- Henry M. Goldman School of Dental Medicine, Boston University, 100 E Newton Street, Boston, Massachusetts 02118, USA
| | - Nathanael S Gray
- Dana Farber Cancer Institute, Department of Biologic Chemistry and Molecular Pharmacology, Harvard Medical School, 450 Brookline Avenue, Boston, Massachusetts 02215, USA
| | - Henry M Kronenberg
- Endocrine Unit, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, 50 Blossom Street, Boston, Massachusetts 02114, USA
| |
Collapse
|
33
|
Sarkar A, Huebner AJ, Sulahian R, Anselmo A, Xu X, Flattery K, Desai N, Sebastian C, Yram MA, Arnold K, Rivera M, Mostoslavsky R, Bronson R, Bass AJ, Sadreyev R, Shivdasani RA, Hochedlinger K. Sox2 Suppresses Gastric Tumorigenesis in Mice. Cell Rep 2016; 16:1929-41. [PMID: 27498859 DOI: 10.1016/j.celrep.2016.07.034] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Revised: 03/22/2016] [Accepted: 07/14/2016] [Indexed: 01/10/2023] Open
Abstract
Sox2 expression marks gastric stem and progenitor cells, raising important questions regarding the genes regulated by Sox2 and the role of Sox2 itself during stomach homeostasis and disease. By using ChIP-seq analysis, we have found that the majority of Sox2 targets in gastric epithelial cells are tissue specific and related to functions such as endoderm development, Wnt signaling, and gastric cancer. Unexpectedly, we found that Sox2 itself is dispensable for gastric stem cell and epithelial self-renewal, yet Sox2(+) cells are highly susceptible to tumorigenesis in an Apc/Wnt-driven mouse model. Moreover, Sox2 loss enhances, rather than impairs, tumor formation in Apc-deficient gastric cells in vivo and in vitro by inducing Tcf/Lef-dependent transcription and upregulating intestinal metaplasia-associated genes, providing a mechanistic basis for the observed phenotype. Together, these data identify Sox2 as a context-dependent tumor suppressor protein that is dispensable for normal tissue regeneration but restrains stomach adenoma formation through modulation of Wnt-responsive and intestinal genes.
Collapse
Affiliation(s)
- Abby Sarkar
- Cancer Center and Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA; Howard Hughes Medical Institute and Department of Stem Cell and Regenerative Biology, 7 Divinity Avenue, Harvard University, Cambridge, MA 02138, USA
| | - Aaron J Huebner
- Cancer Center and Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA; Howard Hughes Medical Institute and Department of Stem Cell and Regenerative Biology, 7 Divinity Avenue, Harvard University, Cambridge, MA 02138, USA
| | - Rita Sulahian
- Harvard Stem Cell Institute, Cambridge, MA 02138, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Anthony Anselmo
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Xinsen Xu
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Kyle Flattery
- Cancer Center and Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA; Howard Hughes Medical Institute and Department of Stem Cell and Regenerative Biology, 7 Divinity Avenue, Harvard University, Cambridge, MA 02138, USA
| | - Niyati Desai
- Division of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Carlos Sebastian
- Cancer Center and Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Mary Anna Yram
- Cancer Center and Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA; Howard Hughes Medical Institute and Department of Stem Cell and Regenerative Biology, 7 Divinity Avenue, Harvard University, Cambridge, MA 02138, USA
| | - Katrin Arnold
- Cancer Center and Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA; Howard Hughes Medical Institute and Department of Stem Cell and Regenerative Biology, 7 Divinity Avenue, Harvard University, Cambridge, MA 02138, USA
| | - Miguel Rivera
- Division of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Raul Mostoslavsky
- Cancer Center and Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Roderick Bronson
- Department of Pathology, Harvard Medical School, Boston, MA 02115, USA
| | - Adam J Bass
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Ruslan Sadreyev
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Ramesh A Shivdasani
- Harvard Stem Cell Institute, Cambridge, MA 02138, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Konrad Hochedlinger
- Cancer Center and Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA; Howard Hughes Medical Institute and Department of Stem Cell and Regenerative Biology, 7 Divinity Avenue, Harvard University, Cambridge, MA 02138, USA.
| |
Collapse
|
34
|
Moore JC, Tang Q, Torres Yordan N, Mulligan T, Moore FE, Lobbardi R, Ramakrishnan A, Anselmo A, Sadreyev R, Berman J, Liwski R, Weinstein B, Rawls J, Langenau DM. Abstract 4177: Dynamic visualization of cancer cell engraftment into immune compromised zebrafish. Cancer Res 2016. [DOI: 10.1158/1538-7445.am2016-4177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Cell transplantation into immune compromised mice has transformed our understanding of cancer and is now the gold standard for assessing therapeutic responses in vivo. However, mouse models are expensive and engraftment is often difficult to visualize directly. To overcome these challenges, we have developed immune compromised zebrafish (ICZ) in the transparent casper background using genome editing techniques. We have successfully targeted genes required for immune cell function and are well known to cause immune deficiency in human and mice. To date, we have developed homozygous viable mutants for recombination-activating gene 2 (rag2), DNA-dependent protein kinase (prkdc), janus kinase 3 (jak3), interleukin 2 receptor gamma (Il2rg), zeta-chain (TCR) associated protein kinase 70 (zap70), and forkhead box N1 (foxn1/nude). Gene expression analysis of marrow cells using RNAseq has identified novel transcript changes correlated with loss of specific cell types, and in conjunction with large-scale single cell transcriptional profiling, has identified specific cellular defects associated with T, B, and NK cell loss. For example, homozygous prkdc (SCID) mutant fish lack mature T and B cells, but have intact NK cell signaling. By contrast, il2rg-deficient zebrafish lack T and NK cells. Importantly, these ICZ models accurately recapitulate known human severe combined immune deficiencies and established mouse models that are commonly used for cell transplantation. Thus, it is not unexpected that a subset of zebrafish mutants have reduced immune cell function, permitting engraftment of normal hematopoietic and muscle satellite cells from allogeneic donors. Additionally, we have demonstrated robust and persistent engraftment of fluorescently labeled leukemia, rhabdomyosarcoma, neuroblastoma, and melanoma from a wide range of zebrafish strains. Because mutations have been created in optically-clear, casper-strain zebrafish and cancers are fluorescently labeled, we now have unprecedented access to directly visualize tumor cells at single cell resolution in live animals. To date, we have optimized our models to visualize neovascularization, intratumoral cell heterogeneity, clonal evolution and metastisis. The ability to transplant non-immune matched cell types will likely revolutionize the types and scale of cell transplantation experiments performed in the zebrafish and will likely permit engraftment of mouse and human cells into compound mutant ICZ models in the near future.
Citation Format: John C. Moore, Qin Tang, Nora Torres Yordan, Timothy Mulligan, Finola E. Moore, Riadh Lobbardi, Ashwin Ramakrishnan, Anthony Anselmo, Ruslan Sadreyev, Jason Berman, Robert Liwski, Brant Weinstein, John Rawls, David M. Langenau. Dynamic visualization of cancer cell engraftment into immune compromised zebrafish. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 4177.
Collapse
Affiliation(s)
| | - Qin Tang
- 1Massachusetts General Hospital, Boston, MA
| | | | | | | | | | | | | | | | - Jason Berman
- 4Dalhousie University, Halifax, Nova Scotia, Canada
| | | | | | | | | |
Collapse
|
35
|
Lobbardi R, Pinder J, Martinez-Pastor B, Blackburn J, Abraham BJ, Mansour M, Abdelfattah NS, Molodtsov A, Alexe G, Toiber D, de Waard M, Jain E, Bhere D, Shah K, Gutierrez A, Stegmaier K, Silverman LB, Sadreyev R, Asara J, Look AT, Young RA, Mostoslavsky R, Dellaire G, Langenau DM. Abstract 3583: Thymocyte selection-associated HMG box protein (TOX) induces genomic instability in T-cell acute lymphoblastic leukemia. Cancer Res 2016. [DOI: 10.1158/1538-7445.am2016-3583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
MYC and NOTCH are major oncogenic drivers in T-cell Acute Lymphoblastic Leukemia (T-ALL), yet additional collaborating genetic lesions collaborate to induce frank malignancy. To identify these factors, a large-scale transgenic screen was completed where 28 amplified and over-expressed genes found in human T-ALL were assessed for accelerating leukemia onset in the zebrafish transgenic model. From this analysis, Thymocyte selection-associated HMG protein (TOX) synergized with both MYC and NOTCH to induce T-ALL. Here, we show that TOX is highly expressed in 95% of human primary and relapse T-ALL when compared with both normal T cells and B-ALL. TOX is highly and specifically expressed in human T-ALL due to both genomic amplification and transcriptional regulation by the master transcription factors MYB/LMO2. Characterization of zebrafish T-ALLs revealed that TOX promoted genomic instability as assessed by changes in DNA content and Whole Genome Sequencing. Effects on genomic instability were confirmed by metaphase spread following TOX expression in MEF cells, confirming roles for TOX in regulating genomic instability and elevated DNA translocation potential in a wider range of cell types. To identify TOX binding partners, Tandem Mass Spectrometry was performed in human T-ALL cells. TOX was found to interact with KU70/KU80 but not other DNA repair enzymes, a result verified by co-immunoprecipitation studies. Given that TOX elevated genomic instability in the zebrafish model, that Ku70 or Ku80 loss lead to genomic instability and T cell lymphoma in mice, and that TOX bound specifically to KU70/KU80 - the initiating factors required for Non-Homologous End Joining (NHEJ) repair - we hypothesized that TOX is a negative regulator of double-strand break repair. Fluorescent repair assays were completed in 3T3 fibroblasts and confirmed that TOX inhibits NHEJ. Dynamic real-time imaging studies showed that TOX suppresses recruitment of fluorescent-tagged KU80 to DNA breaks. Importantly, TOX loss of function increased NHEJ in human T-ALL cells and reduced time to DNA repair as assessed by fluorescent Traffic Light Reporter assays and quantitative assessment of 53BP1 and γH2A.X foci resolution following irradiation. Our results show that TOX is aberrantly re-activated in 95% of human T-ALL, thereby suppressing KU70/KU80 function to promote genomic instability and ultimately elevating rates at which acquired mutations and rearrangements are amassed in developing pre-malignant T cells. Our work shows that TOX is the major oncogenic driver of genomic instability human T-ALL and locks cells in a constant state of dampened repair.
Citation Format: Riadh Lobbardi, Jordan Pinder, Barbara Martinez-Pastor, Jessica Blackburn, Brian J. Abraham, Marc Mansour, Nouran S. Abdelfattah, Aleksey Molodtsov, Gabriela Alexe, Debra Toiber, Manon de Waard, Esha Jain, Deepak Bhere, Khalid Shah, Alejandro Gutierrez, Kimberly Stegmaier, Lewis B. Silverman, Ruslan Sadreyev, John Asara, A Thomas Look, Richard A. Young, Raul Mostoslavsky, Graham Dellaire, David M. Langenau. Thymocyte selection-associated HMG box protein (TOX) induces genomic instability in T-cell acute lymphoblastic leukemia. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 3583.
Collapse
Affiliation(s)
| | - Jordan Pinder
- 2Departments of Pathology and Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | | | | | | | - Marc Mansour
- 5Department of Haematology, UCL Cancer Institute, University College London, London, United Kingdom
| | | | | | - Gabriela Alexe
- 6Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Debra Toiber
- 7Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | | | - Esha Jain
- 9Centre of Regenerative Medicine, Massachusetts General Hospital, Boston, MA
| | - Deepak Bhere
- 10Molecular Neurotherapy and Imaging Laboratory, Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston, MA
| | - Khalid Shah
- 10Molecular Neurotherapy and Imaging Laboratory, Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston, MA
| | | | - Kimberly Stegmaier
- 6Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Lewis B. Silverman
- 6Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Ruslan Sadreyev
- 12Department of Molecular Biology, Massachusetts General Hospital, Boston, MA
| | - John Asara
- 13Division of Signal Transduction, Beth Israel Deaconess Medical Center and Department of Medicine, Harvard Medical School, Boston, MA
| | - A Thomas Look
- 14Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
| | | | - Raul Mostoslavsky
- 3Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA
| | - Graham Dellaire
- 15Departments of Pathology and Biochemistry and Molecular Biology; Dalhousie University, Halifax, Nova Scotia, Canada
| | | |
Collapse
|
36
|
Ray MK, Wiskow O, King MJ, Ismail N, Ergun A, Wang Y, Plys AJ, Davis CP, Kathrein K, Sadreyev R, Borowsky ML, Eggan K, Zon L, Galloway JL, Kingston RE. CAT7 and cat7l Long Non-coding RNAs Tune Polycomb Repressive Complex 1 Function during Human and Zebrafish Development. J Biol Chem 2016; 291:19558-72. [PMID: 27405765 DOI: 10.1074/jbc.m116.730853] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2016] [Indexed: 11/06/2022] Open
Abstract
The essential functions of polycomb repressive complex 1 (PRC1) in development and gene silencing are thought to involve long non-coding RNAs (lncRNAs), but few specific lncRNAs that guide PRC1 activity are known. We screened for lncRNAs, which co-precipitate with PRC1 from chromatin and found candidates that impact polycomb group protein (PcG)-regulated gene expression in vivo A novel lncRNA from this screen, CAT7, regulates expression and polycomb group binding at the MNX1 locus during early neuronal differentiation. CAT7 contains a unique tandem repeat domain that shares high sequence similarity to a non-syntenic zebrafish analog, cat7l Defects caused by interference of cat7l RNA during zebrafish embryogenesis were rescued by human CAT7 RNA, enhanced by interference of a PRC1 component, and suppressed by interference of a known PRC1 target gene, demonstrating cat7l genetically interacts with a PRC1. We propose a model whereby PRC1 acts in concert with specific lncRNAs and that CAT7/cat7l represents convergent lncRNAs that independently evolved to tune PRC1 repression at individual loci.
Collapse
Affiliation(s)
- Mridula K Ray
- From the Department of Molecular Biology, Massachusetts General Hospital, and Department of Genetics, Harvard Medical School, Boston, Massachusetts 02114
| | - Ole Wiskow
- Harvard Stem Cell Institute, Department of Stem Cell and Regenerative Biology, Harvard University and the Stanley Center for Psychiatric Research, Broad Institute, Cambridge, Massachusetts 02138
| | - Matthew J King
- Center for Regenerative Medicine, Department of Orthopaedic Surgery, Massachusetts General Hospital, Harvard Stem Cell Institute, Harvard Medical School, Boston, Massachusetts 02114
| | - Nidha Ismail
- Center for Regenerative Medicine, Department of Orthopaedic Surgery, Massachusetts General Hospital, Harvard Stem Cell Institute, Harvard Medical School, Boston, Massachusetts 02114
| | - Ayla Ergun
- Department of Molecular Biology, Massachusetts General Hospital, and Department of Pathology, Harvard Medical School, Boston, Massachusetts 02114
| | - Yanqun Wang
- From the Department of Molecular Biology, Massachusetts General Hospital, and Department of Genetics, Harvard Medical School, Boston, Massachusetts 02114
| | - Aaron J Plys
- From the Department of Molecular Biology, Massachusetts General Hospital, and Department of Genetics, Harvard Medical School, Boston, Massachusetts 02114
| | - Christopher P Davis
- From the Department of Molecular Biology, Massachusetts General Hospital, and Department of Genetics, Harvard Medical School, Boston, Massachusetts 02114
| | - Katie Kathrein
- Division of Hematology/Oncology, Boston Children's Hospital, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Boston, Massachusetts, 02115, and
| | - Ruslan Sadreyev
- Department of Molecular Biology, Massachusetts General Hospital, and Department of Pathology, Harvard Medical School, Boston, Massachusetts 02114
| | - Mark L Borowsky
- From the Department of Molecular Biology, Massachusetts General Hospital, and Department of Genetics, Harvard Medical School, Boston, Massachusetts 02114
| | - Kevin Eggan
- Harvard Stem Cell Institute, Department of Stem Cell and Regenerative Biology, Harvard University and the Stanley Center for Psychiatric Research, Broad Institute, Cambridge, Massachusetts 02138, The Howard Hughes Medical Institute, Cambridge, MA 02138
| | - Leonard Zon
- Division of Hematology/Oncology, Boston Children's Hospital, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Boston, Massachusetts, 02115, and
| | - Jenna L Galloway
- Center for Regenerative Medicine, Department of Orthopaedic Surgery, Massachusetts General Hospital, Harvard Stem Cell Institute, Harvard Medical School, Boston, Massachusetts 02114,
| | - Robert E Kingston
- From the Department of Molecular Biology, Massachusetts General Hospital, and Department of Genetics, Harvard Medical School, Boston, Massachusetts 02114,
| |
Collapse
|
37
|
Lee J, Sarma K, Cifuentes‐Rojas C, Ergun A, Rosario A, Jeon Y, White F, Sadreyev R. ATRX Promotes Binding of PRC2 to Xist RNA and Polycomb Targets. FASEB J 2015. [DOI: 10.1096/fasebj.29.1_supplement.361.3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Jeannie Lee
- Howard Hughes Medical InstituteUnited States
- ‐ Department of Molecular BiologyMassachusetts General Hospital & Department of MolecularBiologyUnited States
| | - Kavitha Sarma
- Howard Hughes Medical InstituteUnited States
- ‐ Department of Molecular BiologyMassachusetts General Hospital & Department of MolecularBiologyUnited States
| | - Catherine Cifuentes‐Rojas
- Howard Hughes Medical InstituteUnited States
- ‐ Department of Molecular BiologyMassachusetts General Hospital & Department of MolecularBiologyUnited States
| | - Ayla Ergun
- ‐ Department of Molecular BiologyMassachusetts General Hospital & Department of MolecularBiologyUnited States
| | - Amanda Rosario
- ‐ Department of BioengineeringMassachusetts Institute of Technology & Koch Institute for Integrative Cancer ResearchMassachusetts Institute of TechnologyUnited States
| | - Yesu Jeon
- Howard Hughes Medical InstituteUnited States
- ‐ Department of Molecular BiologyMassachusetts General Hospital & Department of MolecularBiologyUnited States
| | - Forest White
- ‐ Department of BioengineeringMassachusetts Institute of Technology & Koch Institute for Integrative Cancer ResearchMassachusetts Institute of TechnologyUnited States
| | - Ruslan Sadreyev
- ‐ Department of Molecular BiologyMassachusetts General Hospital & Department of MolecularBiologyUnited States
- Department of PathologyMassachusetts General Hospital & Harvard Medical SchoolUnited States
| |
Collapse
|
38
|
Sarma K, Cifuentes-Rojas C, Ergun A, Del Rosario A, Jeon Y, White F, Sadreyev R, Lee JT. ATRX directs binding of PRC2 to Xist RNA and Polycomb targets. Cell 2015; 159:869-83. [PMID: 25417162 DOI: 10.1016/j.cell.2014.10.019] [Citation(s) in RCA: 155] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Revised: 07/22/2014] [Accepted: 10/08/2014] [Indexed: 12/20/2022]
Abstract
X chromosome inactivation (XCI) depends on the long noncoding RNA Xist and its recruitment of Polycomb Repressive Complex 2 (PRC2). PRC2 is also targeted to other sites throughout the genome to effect transcriptional repression. Using XCI as a model, we apply an unbiased proteomics approach to isolate Xist and PRC2 regulators and identified ATRX. ATRX unexpectedly functions as a high-affinity RNA-binding protein that directly interacts with RepA/Xist RNA to promote loading of PRC2 in vivo. Without ATRX, PRC2 cannot load onto Xist RNA nor spread in cis along the X chromosome. Moreover, epigenomic profiling reveals that genome-wide targeting of PRC2 depends on ATRX, as loss of ATRX leads to spatial redistribution of PRC2 and derepression of Polycomb responsive genes. Thus, ATRX is a required specificity determinant for PRC2 targeting and function.
Collapse
Affiliation(s)
- Kavitha Sarma
- Howard Hughes Medical Institute; Department of Molecular Biology, Massachusetts General Hospital, Boston, MA USA; Department of Genetics, Harvard Medical School, Boston, MA USA
| | - Catherine Cifuentes-Rojas
- Howard Hughes Medical Institute; Department of Molecular Biology, Massachusetts General Hospital, Boston, MA USA; Department of Genetics, Harvard Medical School, Boston, MA USA
| | - Ayla Ergun
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA USA; Department of Genetics, Harvard Medical School, Boston, MA USA
| | - Amanda Del Rosario
- Department of Bioengineering, Massachusetts Institute of Technology, Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA USA
| | - Yesu Jeon
- Howard Hughes Medical Institute; Department of Molecular Biology, Massachusetts General Hospital, Boston, MA USA; Department of Genetics, Harvard Medical School, Boston, MA USA
| | - Forest White
- Department of Bioengineering, Massachusetts Institute of Technology, Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA USA
| | - Ruslan Sadreyev
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA USA; Department of Genetics, Harvard Medical School, Boston, MA USA; Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA USA
| | - Jeannie T Lee
- Howard Hughes Medical Institute; Department of Molecular Biology, Massachusetts General Hospital, Boston, MA USA; Department of Genetics, Harvard Medical School, Boston, MA USA; Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA USA.
| |
Collapse
|
39
|
|
40
|
Anguera MC, Sadreyev R, Zhang Z, Szanto A, Payer B, Sheridan SD, Kwok S, Haggarty SJ, Sur M, Alvarez J, Gimelbrant A, Mitalipova M, Kirby JE, Lee JT. Molecular signatures of human induced pluripotent stem cells highlight sex differences and cancer genes. Cell Stem Cell 2012; 11:75-90. [PMID: 22770242 DOI: 10.1016/j.stem.2012.03.008] [Citation(s) in RCA: 114] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2011] [Revised: 12/10/2011] [Accepted: 03/08/2012] [Indexed: 11/25/2022]
Abstract
Although human induced pluripotent stem cells (hiPSCs) have enormous potential in regenerative medicine, their epigenetic variability suggests that some lines may not be suitable for human therapy. There are currently few benchmarks for assessing quality. Here we show that X-inactivation markers can be used to separate hiPSC lines into distinct epigenetic classes and that the classes are phenotypically distinct. Loss of XIST expression is strongly correlated with upregulation of X-linked oncogenes, accelerated growth rate in vitro, and poorer differentiation in vivo. Whereas differences in X-inactivation potential result in epigenetic variability of female hiPSC lines, male hiPSC lines generally resemble each other and do not overexpress the oncogenes. Neither physiological oxygen levels nor HDAC inhibitors offer advantages to culturing female hiPSC lines. We conclude that female hiPSCs may be epigenetically less stable in culture and caution that loss of XIST may result in qualitatively less desirable stem cell lines.
Collapse
Affiliation(s)
- Montserrat C Anguera
- Howard Hughes Medical Institute, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
41
|
Sun S, Fukue Y, Nolen L, Sadreyev R, Lee JT. Characterization of Xpr (Xpct) reveals instability but no effects on X-chromosome pairing or Xist expression. Transcription 2012; 1:46-56. [PMID: 21327163 DOI: 10.4161/trns.1.1.12401] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2010] [Revised: 05/18/2010] [Accepted: 05/19/2010] [Indexed: 11/19/2022] Open
Abstract
X-chromosome inactivation balances X-chromosome dosages in male and female mammals by transcriptionally repressing one X in the female sex. Proper counting and the mutually exclusive choice of active X and inactive X have been hypothesized to involve X-chromosome crosstalk via homologous chromosome pairing. Transient pairing of two female Xs requires noncoding Tsix and Xite. A recent study suggested a new pairing element (Xpr), located ~200 kb upstream of Xist, in the Xpct region. Xpr is proposed to induce pairing and activate Xist expression. Here, we further characterize Xpr and find that the Xpr sequence is unstable when introduced as transgenes into male ES cells. Xpr transgenes show an unusual tendency to disperse throughout the nucleus. However, we observe neither pairing between Xpr alleles nor ectopic Xist expression. In the absence of Tsix, Xpr does not induce inter-allelic Xic interactions. Female ES cells carrying Xpr transgenes are more stable. Nonetheless, pairing also does not seem to occur in female cells. We conclude that, while Xpr contains unusual properties, it most likely does not serve as a pairing or counting element. Differences in statistical methods and controls may explain some of the discrepancies.
Collapse
Affiliation(s)
- Sha Sun
- HHMI, MGH, Harvard University, USA
| | | | | | | | | |
Collapse
|
42
|
Raman S, Vernon R, Thompson J, Tyka M, Sadreyev R, Pei J, Kim D, Kellogg E, DiMaio F, Lange O, Kinch L, Sheffler W, Kim BH, Das R, Grishin NV, Baker D. Structure prediction for CASP8 with all-atom refinement using Rosetta. Proteins 2010; 77 Suppl 9:89-99. [PMID: 19701941 DOI: 10.1002/prot.22540] [Citation(s) in RCA: 363] [Impact Index Per Article: 25.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
We describe predictions made using the Rosetta structure prediction methodology for the Eighth Critical Assessment of Techniques for Protein Structure Prediction. Aggressive sampling and all-atom refinement were carried out for nearly all targets. A combination of alignment methodologies was used to generate starting models from a range of templates, and the models were then subjected to Rosetta all atom refinement. For the 64 domains with readily identified templates, the best submitted model was better than the best alignment to the best template in the Protein Data Bank for 24 cases, and improved over the best starting model for 43 cases. For 13 targets where only very distant sequence relationships to proteins of known structure were detected, models were generated using the Rosetta de novo structure prediction methodology followed by all-atom refinement; in several cases the submitted models were better than those based on the available templates. Of the 12 refinement challenges, the best submitted model improved on the starting model in seven cases. These improvements over the starting template-based models and refinement tests demonstrate the power of Rosetta structure refinement in improving model accuracy.
Collapse
Affiliation(s)
- Srivatsan Raman
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
43
|
Abstract
Only a minority of currently known protein families is characterized structurally. This makes homology-based structure modeling an essential instrument that can be viewed as the first approximation to experimental determination of protein structure. Using sequence similarity searches, we detected a distant similarity between a family of uncharacterized hypothetical proteins, COG4849, and the family of tRNA nucleotidyltransferases. The suggested remote homology between the N-terminal domain of COG4849 and the catalytic domain of tRNA nucleotidyltransferase was further supported by comparison of sequence profiles, methods for fold recognition and structure modeling. The combined multiple alignment of the two families reveals shared conservation of functionally important motifs and suggests the similarity in catalytic mechanisms of the performed reactions. Our results suggest that (i) the N-terminal domain of proteins from COG4849 shares structural similarity with the catalytic domain of tRNA nucleotidyltransferase, and (ii) this domain catalyzes the nucleotidyl transfer reaction involving two metal ions.
Collapse
Affiliation(s)
- Bong-Hyun Kim
- Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390-9038, USA
| | | | | |
Collapse
|
44
|
Abstract
MOTIVATION The development of powerful automatic methods for the comparison of protein sequences has become increasingly important. Profile-to-profile comparisons allow for the use of broader information about protein families, resulting in more sensitive and accurate comparisons of distantly related sequences. A key part in the comparison of two profiles is the method for the calculation of scores for the position matches. A number of methods based on various theoretical considerations have been proposed. We implemented several previously reported scoring functions as well as our own functions, and compared them on the basis of their ability to produce accurate short ungapped alignments of a given length. RESULTS Our results suggest that the family of the probabilistic methods (log-odds based methods and prof_sim) may be the more appropriate choice for the generation of initial 'seeds' as the first step to produce local profile-profile alignments. The most effective scoring systems were the closely related modifications of functions previously implemented in the COMPASS and Picasso methods.
Collapse
Affiliation(s)
- David Mittelman
- Howard Hughes Medical Institute Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390-9050, USA
| | | | | |
Collapse
|
45
|
Abstract
UNLABELLED PCMA (profile consistency multiple sequence alignment) is a progressive multiple sequence alignment program that combines two different alignment strategies. Highly similar sequences are aligned in a fast way as in ClustalW, forming pre-aligned groups. The T-Coffee strategy is applied to align the relatively divergent groups based on profile-profile comparison and consistency. The scoring function for local alignments of pre-aligned groups is based on a novel profile-profile comparison method that is a generalization of the PSI-BLAST approach to profile-sequence comparison. PCMA balances speed and accuracy in a flexible way and is suitable for aligning large numbers of sequences. AVAILABILITY PCMA is freely available for non-commercial use. Pre-compiled versions for several platforms can be downloaded from ftp://iole.swmed.edu/pub/PCMA/.
Collapse
Affiliation(s)
- Jimin Pei
- Howard Hughes Medical Institute, and Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390-9050, USA.
| | | | | |
Collapse
|
46
|
Abstract
We present a novel method for the comparison of multiple protein alignments with assessment of statistical significance (COMPASS). The method derives numerical profiles from alignments, constructs optimal local profile-profile alignments and analytically estimates E-values for the detected similarities. The scoring system and E-value calculation are based on a generalization of the PSI-BLAST approach to profile-sequence comparison, which is adapted for the profile-profile case. Tested along with existing methods for profile-sequence (PSI-BLAST) and profile-profile (prof_sim) comparison, COMPASS shows increased abilities for sensitive and selective detection of remote sequence similarities, as well as improved quality of local alignments. The method allows prediction of relationships between protein families in the PFAM database beyond the range of conventional methods. Two predicted relations with high significance are similarities between various Rossmann-type folds and between various helix-turn-helix-containing families. The potential value of COMPASS for structure/function predictions is illustrated by the detection of an intricate homology between the DNA-binding domain of the CTF/NFI family and the MH1 domain of the Smad family.
Collapse
Affiliation(s)
- Ruslan Sadreyev
- Howard Hughes Medical Institute, and Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390-9050, USA
| | | |
Collapse
|