1
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Yammine KM, Abularach SM, Kim SY, Bikovtseva AA, Lilianty J, Butty VL, Schiavoni RP, Bateman JF, Lamandé SR, Shoulders MD. ER procollagen storage defect without coupled unfolded protein response drives precocious arthritis. bioRxiv 2024:2023.10.19.562780. [PMID: 37905055 PMCID: PMC10614947 DOI: 10.1101/2023.10.19.562780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
Collagenopathies are a group of clinically diverse disorders caused by defects in collagen folding and secretion. For example, mutations in the gene encoding collagen type-II, the primary collagen in cartilage, can lead to diverse chondrodysplasias. One example is the Gly1170Ser substitution in procollagen-II, which causes precocious osteoarthritis. Here, we biochemically and mechanistically characterize an induced pluripotent stem cell-based cartilage model of this disease, including both hetero- and homozygous genotypes. We show that Gly1170Ser procollagen-II is notably slow to fold and secrete. Instead, procollagen-II accumulates intracellularly, consistent with an endoplasmic reticulum (ER) storage disorder. Owing to unique features of the collagen triple helix, this accumulation is not recognized by the unfolded protein response. Gly1170Ser procollagen-II interacts to a greater extent than wild-type with specific proteostasis network components, consistent with its slow folding. These findings provide mechanistic elucidation into the etiology of this disease. Moreover, the cartilage model will enable rapid testing of therapeutic strategies to restore proteostasis in the collagenopathies.
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2
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Whisler J, Shahreza S, Schlegelmilch K, Ege N, Javanmardi Y, Malandrino A, Agrawal A, Fantin A, Serwinski B, Azizgolshani H, Park C, Shone V, Demuren OO, Del Rosario A, Butty VL, Holroyd N, Domart MC, Hooper S, Szita N, Boyer LA, Walker-Samuel S, Djordjevic B, Sheridan GK, Collinson L, Calvo F, Ruhrberg C, Sahai E, Kamm R, Moeendarbary E. Emergent mechanical control of vascular morphogenesis. Sci Adv 2023; 9:eadg9781. [PMID: 37566656 PMCID: PMC10421067 DOI: 10.1126/sciadv.adg9781] [Citation(s) in RCA: 0] [Impact Index Per Article: 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: 02/02/2023] [Accepted: 07/13/2023] [Indexed: 08/13/2023]
Abstract
Vascularization is driven by morphogen signals and mechanical cues that coordinately regulate cellular force generation, migration, and shape change to sculpt the developing vascular network. However, it remains unclear whether developing vasculature actively regulates its own mechanical properties to achieve effective vascularization. We engineered tissue constructs containing endothelial cells and fibroblasts to investigate the mechanics of vascularization. Tissue stiffness increases during vascular morphogenesis resulting from emergent interactions between endothelial cells, fibroblasts, and ECM and correlates with enhanced vascular function. Contractile cellular forces are key to emergent tissue stiffening and synergize with ECM mechanical properties to modulate the mechanics of vascularization. Emergent tissue stiffening and vascular function rely on mechanotransduction signaling within fibroblasts, mediated by YAP1. Mouse embryos lacking YAP1 in fibroblasts exhibit both reduced tissue stiffness and develop lethal vascular defects. Translating our findings through biology-inspired vascular tissue engineering approaches will have substantial implications in regenerative medicine.
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Affiliation(s)
- Jordan Whisler
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Somayeh Shahreza
- Department of Mechanical Engineering, University College London, London, UK
| | | | - Nil Ege
- Tumour Cell Biology Laboratory, Francis Crick Institute, London, UK
- Mnemo Therapeutics, 101 Boulevard Murat, 75016 Paris, France
| | - Yousef Javanmardi
- Department of Mechanical Engineering, University College London, London, UK
| | - Andrea Malandrino
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Biomaterials, Biomechanics and Tissue Engineering Group, Department of Materials Science and Engineering and Research Center for Biomedical Engineering, Universitat Politècnica de Catalunya (UPC), Av. Eduard Maristany, 10-14 08019 Barcelona, Spain
| | - Ayushi Agrawal
- Department of Mechanical Engineering, University College London, London, UK
| | - Alessandro Fantin
- UCL Institute of Ophthalmology, University College London, London, UK
- Department of Biosciences, University of Milan, Via G. Celoria 26, 20133 Milan, Italy
| | - Bianca Serwinski
- Department of Mechanical Engineering, University College London, London, UK
- 199 Biotechnologies Ltd., Gloucester Road, London W2 6LD, UK
- Northeastern University London, London, E1W 1LP, UK
| | - Hesham Azizgolshani
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Clara Park
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Victoria Shone
- Experimental Histopathology Laboratory, Francis Crick Institute, London, UK
| | - Olukunle O. Demuren
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Amanda Del Rosario
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Vincent L. Butty
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Natalie Holroyd
- UCL Centre for Advanced Biomedical Imaging, Paul O'Gorman Building, 72 Huntley Street, London, UK
| | | | - Steven Hooper
- Tumour Cell Biology Laboratory, Francis Crick Institute, London, UK
| | - Nicolas Szita
- Department of Biochemical Engineering, University College London, London, UK
| | - Laurie A. Boyer
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Simon Walker-Samuel
- UCL Centre for Advanced Biomedical Imaging, Paul O'Gorman Building, 72 Huntley Street, London, UK
| | - Boris Djordjevic
- Department of Mechanical Engineering, University College London, London, UK
- 199 Biotechnologies Ltd., Gloucester Road, London W2 6LD, UK
| | - Graham K. Sheridan
- School of Life Sciences, Queen’s Medical Centre, University of Nottingham, Nottingham, UK
| | - Lucy Collinson
- Electron Microscopy Laboratory, Francis Crick Institute, London, UK
| | - Fernando Calvo
- Instituto de Biomedicina y Biotecnología de Cantabria (Consejo Superior de Investigaciones Científicas, Universidad de Cantabria), Santander, Spain
| | | | - Erik Sahai
- Tumour Cell Biology Laboratory, Francis Crick Institute, London, UK
| | - Roger Kamm
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Emad Moeendarbary
- Department of Mechanical Engineering, University College London, London, UK
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- 199 Biotechnologies Ltd., Gloucester Road, London W2 6LD, UK
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3
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Mengiste AA, Wilson RH, Weissman RF, Papa Iii LJ, Hendel SJ, Moore CL, Butty VL, Shoulders MD. Expanded MutaT7 toolkit efficiently and simultaneously accesses all possible transition mutations in bacteria. Nucleic Acids Res 2023; 51:e31. [PMID: 36715334 PMCID: PMC10085711 DOI: 10.1093/nar/gkad003] [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] [Received: 01/20/2022] [Revised: 11/16/2022] [Accepted: 01/03/2023] [Indexed: 01/31/2023] Open
Abstract
Targeted mutagenesis mediated by nucleotide base deaminase-T7 RNA polymerase fusions has recently emerged as a novel and broadly useful strategy to power genetic diversification in the context of in vivo directed evolution campaigns. Here, we expand the utility of this approach by introducing a highly active adenosine deaminase-T7 RNA polymerase fusion protein (eMutaT7A→G), resulting in higher mutation frequencies to enable more rapid directed evolution. We also assess the benefits and potential downsides of using this more active mutator. We go on to show in Escherichia coli that adenosine deaminase-bearing mutators (MutaT7A→G or eMutaT7A→G) can be employed in tandem with a cytidine deaminase-bearing mutator (MutaT7C→T) to introduce all possible transition mutations simultaneously. We illustrate the efficacy of this in vivo mutagenesis approach by exploring mutational routes to antibacterial drug resistance. This work sets the stage for general application of optimized MutaT7 tools able to induce all types of transition mutations during in vivo directed evolution campaigns across diverse organisms.
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Affiliation(s)
- Amanuella A Mengiste
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Robert H Wilson
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Rachel F Weissman
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Louis J Papa Iii
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Samuel J Hendel
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Christopher L Moore
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Vincent L Butty
- BioMicroCenter, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Matthew D Shoulders
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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4
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Mancio-Silva L, Gural N, Real E, Wadsworth MH, Butty VL, March S, Nerurkar N, Hughes TK, Roobsoong W, Fleming HE, Whittaker CA, Levine SS, Sattabongkot J, Shalek AK, Bhatia SN. A single-cell liver atlas of Plasmodium vivax infection. Cell Host Microbe 2022; 30:1048-1060.e5. [PMID: 35443155 DOI: 10.1016/j.chom.2022.03.034] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [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: 07/30/2021] [Revised: 01/31/2022] [Accepted: 03/25/2022] [Indexed: 12/15/2022]
Abstract
Malaria-causing Plasmodium vivax parasites can linger in the human liver for weeks to years and reactivate to cause recurrent blood-stage infection. Although they are an important target for malaria eradication, little is known about the molecular features of replicative and non-replicative intracellular liver-stage parasites and their host cell dependence. Here, we leverage a bioengineered human microliver platform to culture patient-derived P. vivax parasites for transcriptional profiling. Coupling enrichment strategies with bulk and single-cell analyses, we capture both parasite and host transcripts in individual hepatocytes throughout the course of infection. We define host- and state-dependent transcriptional signatures and identify unappreciated populations of replicative and non-replicative parasites that share features with sexual transmissive forms. We find that infection suppresses the transcription of key hepatocyte function genes and elicits an anti-parasite innate immune response. Our work provides a foundation for understanding host-parasite interactions and reveals insights into the biology of P. vivax dormancy and transmission.
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Affiliation(s)
- Liliana Mancio-Silva
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA; David H. Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA 02139, USA; Institut Pasteur, Université Paris Cité, Inserm U1201, CNRS EMR9195, Unité de Biologie des Interactions Hôte-Parasite, 75015 Paris, France.
| | - Nil Gural
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA; David H. Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA 02139, USA
| | - Eliana Real
- Institut Pasteur, Université Paris Cité, Inserm U1201, CNRS EMR9195, Unité de Biologie des Interactions Hôte-Parasite, 75015 Paris, France
| | - Marc H Wadsworth
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA; Department of Chemistry, MIT, Cambridge, MA 02139, USA
| | - Vincent L Butty
- David H. Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA 02139, USA; BioMicro Center, MIT, Cambridge, MA 02139, USA
| | - Sandra March
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA; David H. Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Niketa Nerurkar
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA; David H. Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA 02139, USA
| | - Travis K Hughes
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA; Department of Chemistry, MIT, Cambridge, MA 02139, USA
| | - Wanlapa Roobsoong
- Mahidol Vivax Research Unit, Faculty of Tropical Medicine Mahidol University, Bangkok 10400, Thailand
| | - Heather E Fleming
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA; David H. Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA 02139, USA
| | - Charlie A Whittaker
- David H. Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA 02139, USA; BioMicro Center, MIT, Cambridge, MA 02139, USA
| | - Stuart S Levine
- David H. Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA 02139, USA; BioMicro Center, MIT, Cambridge, MA 02139, USA
| | - Jetsumon Sattabongkot
- Mahidol Vivax Research Unit, Faculty of Tropical Medicine Mahidol University, Bangkok 10400, Thailand
| | - Alex K Shalek
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA; David H. Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA 02139, USA; Department of Chemistry, MIT, Cambridge, MA 02139, USA; Ragon Institute of Massachusetts General Hospital, MIT, and Harvard, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA.
| | - Sangeeta N Bhatia
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA; David H. Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA; The Wyss Institute for Biologically Inspired Engineering Harvard University Boston, MA 02215, USA.
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5
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Abstract
Advances in next-generation sequencing technologies have allowed RNA sequencing to become an increasingly time efficient, cost-effective, and accessible tool for genomic research. We present here an automated and miniaturized workflow for RNA library preparation that minimizes reagent usage and processing time required per sample to generate Illumina compatible libraries for sequencing. The reduced-volume libraries show similar behavior to full-scale libraries with comparable numbers of genes detected and reproducible clustering of samples.
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Affiliation(s)
- Samuel Mildrum
- Department of Biology, MIT BioMicro Center, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Austin Hendricks
- Department of Biology, MIT BioMicro Center, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Alexei Stortchevoi
- Department of Biology, MIT BioMicro Center, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Noelani Kamelamela
- Department of Biology, MIT BioMicro Center, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Vincent L Butty
- Department of Biology, MIT BioMicro Center, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Stuart S Levine
- Department of Biology, MIT BioMicro Center, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
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6
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Abstract
Host protein folding stress responses can play important roles in RNA virus replication and evolution. Prior work suggested a complicated interplay between the cytosolic proteostasis stress response, controlled by the transcriptional master regulator heat shock factor 1 (HSF1), and human immunodeficiency virus-1 (HIV-1). We sought to uncouple HSF1 transcription factor activity from cytotoxic proteostasis stress and thereby better elucidate the proposed role(s) of HSF1 in the HIV-1 lifecycle. To achieve this objective, we used chemical genetic, stress-independent control of HSF1 activity to establish whether and how HSF1 influences HIV-1 replication. Stress-independent HSF1 induction decreased both the total quantity and infectivity of HIV-1 virions. Moreover, HIV-1 was unable to escape HSF1-mediated restriction over the course of several serial passages. These results clarify the interplay between the host's heat shock response and HIV-1 infection and motivate continued investigation of chaperones as potential antiviral therapeutic targets.
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Affiliation(s)
- Emmanuel E. Nekongo
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Anna I. Ponomarenko
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Mahender B. Dewal
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Vincent L. Butty
- BioMicro Center, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Edward P. Browne
- Department of Medicine, University of North Carolina School of Medicine, Chapel Hill, North Carolina 27516, United States
| | - Matthew D. Shoulders
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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7
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Ben-Yair R, Butty VL, Busby M, Qiu Y, Levine SS, Goren A, Boyer LA, Burns CG, Burns CE. H3K27me3-mediated silencing of structural genes is required for zebrafish heart regeneration. Development 2019; 146:dev178632. [PMID: 31427288 PMCID: PMC6803378 DOI: 10.1242/dev.178632] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [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: 03/29/2019] [Accepted: 08/07/2019] [Indexed: 12/13/2022]
Abstract
Deciphering the genetic and epigenetic regulation of cardiomyocyte proliferation in organisms that are capable of robust cardiac renewal, such as zebrafish, represents an attractive inroad towards regenerating the human heart. Using integrated high-throughput transcriptional and chromatin analyses, we have identified a strong association between H3K27me3 deposition and reduced sarcomere and cytoskeletal gene expression in proliferative cardiomyocytes following cardiac injury in zebrafish. To move beyond an association, we generated an inducible transgenic strain expressing a mutant version of histone 3, H3.3K27M, that inhibits H3K27me3 catalysis in cardiomyocytes during the regenerative window. Hearts comprising H3.3K27M-expressing cardiomyocytes fail to regenerate, with wound edge cells showing heightened expression of structural genes and prominent sarcomeres. Although cell cycle re-entry was unperturbed, cytokinesis and wound invasion were significantly compromised. Collectively, our study identifies H3K27me3-mediated silencing of structural genes as requisite for zebrafish heart regeneration and suggests that repression of similar structural components in the border zone of an infarcted human heart might improve its regenerative capacity.
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Affiliation(s)
- Raz Ben-Yair
- Cardiovascular Research Center, Massachusetts General Hospital, Charlestown, MA 02129, USA
- Harvard Medical School, Boston, MA 02115, USA
| | - Vincent L Butty
- Departments of Biology and Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Michele Busby
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Yutong Qiu
- Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Stuart S Levine
- Departments of Biology and Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Alon Goren
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Laurie A Boyer
- Departments of Biology and Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - C Geoffrey Burns
- Cardiovascular Research Center, Massachusetts General Hospital, Charlestown, MA 02129, USA
- Harvard Medical School, Boston, MA 02115, USA
- Department of Cardiology, Boston Children's Hospital, Boston, MA 02115, USA
| | - Caroline E Burns
- Cardiovascular Research Center, Massachusetts General Hospital, Charlestown, MA 02129, USA
- Harvard Medical School, Boston, MA 02115, USA
- Department of Cardiology, Boston Children's Hospital, Boston, MA 02115, USA
- Harvard Stem Cell Institute, Cambridge, MA 02138, USA
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8
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Cheng CW, Biton M, Haber AL, Gunduz N, Eng G, Gaynor LT, Tripathi S, Calibasi-Kocal G, Rickelt S, Butty VL, Moreno M, Iqbal AM, Bauer-Rowe KE, Imada S, Ulutas MS, Mylonas C, Whary MT, Levine SS, Basbinar Y, Hynes RO, Mino-Kenudson M, Deshpande V, Boyer LA, Fox JG, Terranova C, Rai K, Piwnica-Worms H, Mihaylova MM, Regev A, Yilmaz ÖH. Ketone Body Signaling Mediates Intestinal Stem Cell Homeostasis and Adaptation to Diet. Cell 2019; 178:1115-1131.e15. [PMID: 31442404 PMCID: PMC6732196 DOI: 10.1016/j.cell.2019.07.048] [Citation(s) in RCA: 201] [Impact Index Per Article: 40.2] [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: 01/07/2019] [Revised: 06/03/2019] [Accepted: 07/25/2019] [Indexed: 01/18/2023]
Abstract
Little is known about how metabolites couple tissue-specific stem cell function with physiology. Here we show that, in the mammalian small intestine, the expression of Hmgcs2 (3-hydroxy-3-methylglutaryl-CoA synthetase 2), the gene encoding the rate-limiting enzyme in the production of ketone bodies, including beta-hydroxybutyrate (βOHB), distinguishes self-renewing Lgr5+ stem cells (ISCs) from differentiated cell types. Hmgcs2 loss depletes βOHB levels in Lgr5+ ISCs and skews their differentiation toward secretory cell fates, which can be rescued by exogenous βOHB and class I histone deacetylase (HDAC) inhibitor treatment. Mechanistically, βOHB acts by inhibiting HDACs to reinforce Notch signaling, instructing ISC self-renewal and lineage decisions. Notably, although a high-fat ketogenic diet elevates ISC function and post-injury regeneration through βOHB-mediated Notch signaling, a glucose-supplemented diet has the opposite effects. These findings reveal how control of βOHB-activated signaling in ISCs by diet helps to fine-tune stem cell adaptation in homeostasis and injury.
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Affiliation(s)
- Chia-Wei Cheng
- Koch Institute for Integrative Cancer Research at MIT, Massachusetts 02139, USA
| | - Moshe Biton
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, 02114, USA,Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA,These authors contributed equally to this work
| | - Adam L. Haber
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA,These authors contributed equally to this work
| | - Nuray Gunduz
- Koch Institute for Integrative Cancer Research at MIT, Massachusetts 02139, USA,Institute of Materials Science and Nanotechnology, National Nanotechnology Research Center (UNAM), Bilkent University, Ankara, Turkey 06800
| | - George Eng
- Koch Institute for Integrative Cancer Research at MIT, Massachusetts 02139, USA,Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Liam T. Gaynor
- Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston MA, 02215, USA
| | - Surya Tripathi
- Koch Institute for Integrative Cancer Research at MIT, Massachusetts 02139, USA
| | - Gizem Calibasi-Kocal
- Koch Institute for Integrative Cancer Research at MIT, Massachusetts 02139, USA,Dokuz Eylul University, Institute of Oncology, Department of Translational Oncology, Izmir, Turkey
| | - Steffen Rickelt
- Koch Institute for Integrative Cancer Research at MIT, Massachusetts 02139, USA
| | - Vincent L. Butty
- BioMicro Center, at MIT, Department of Biology, MIT, Cambridge, Massachusetts 02139, USA
| | - Marta Moreno
- Koch Institute for Integrative Cancer Research at MIT, Massachusetts 02139, USA
| | - Ameena M Iqbal
- Koch Institute for Integrative Cancer Research at MIT, Massachusetts 02139, USA
| | | | - Shinya Imada
- Koch Institute for Integrative Cancer Research at MIT, Massachusetts 02139, USA,Department of Gastroenterological and Transplant Surgery, Graduate School of Biomedical and Health Sciences, Hiroshima University,1-2-3 Kasumi, Minami-ku, Hiroshima, 734-8551, Japan
| | - Mehmet Sefa Ulutas
- Koch Institute for Integrative Cancer Research at MIT, Massachusetts 02139, USA,Department of Biology, Siirt University, Science and Arts Faculty, 56100 Siirt, Turkey
| | | | - Mark T. Whary
- Division of Comparative Medicine, Department of Biological Engineering, MIT, Cambridge, Massachusetts 02139, USA
| | - Stuart S. Levine
- BioMicro Center, at MIT, Department of Biology, MIT, Cambridge, Massachusetts 02139, USA
| | - Yasemin Basbinar
- Dokuz Eylul University, Institute of Oncology, Department of Translational Oncology, Izmir, Turkey
| | - Richard O. Hynes
- Koch Institute for Integrative Cancer Research at MIT, Massachusetts 02139, USA,Howard Hughes Medical Institute, Department of Biology, MIT, Cambridge, Massachusetts 02139, USA
| | - Mari Mino-Kenudson
- Department of Pathology, Massachusetts General Hospital Boston and Harvard Medical School, Boston, Massachusetts 02114, USA
| | - Vikram Deshpande
- Department of Pathology, Massachusetts General Hospital Boston and Harvard Medical School, Boston, Massachusetts 02114, USA
| | - Laurie A. Boyer
- Department of Biology, MIT, Cambridge, Massachusetts 02139, USA
| | - James G. Fox
- Division of Comparative Medicine, Department of Biological Engineering, MIT, Cambridge, Massachusetts 02139, USA
| | - Christopher Terranova
- Genomic Medicine Department, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Kunal Rai
- Genomic Medicine Department, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Helen Piwnica-Worms
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Maria M. Mihaylova
- The Ohio State Comprehensive Cancer Center, Department of Biological Chemistry and Pharmacology, Ohio State University, 308 Wiseman Hall, Columbus, OH 43210, USA
| | - Aviv Regev
- Koch Institute for Integrative Cancer Research at MIT, Massachusetts 02139, USA,Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, 02114, USA,Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
| | - Ömer H. Yilmaz
- Koch Institute for Integrative Cancer Research at MIT, Massachusetts 02139, USA,Department of Biology, MIT, Cambridge, Massachusetts 02139, USA,Department of Pathology, Massachusetts General Hospital Boston and Harvard Medical School, Boston, Massachusetts 02114, USA,Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, 02114, USA,Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA,Lead Contact,Correspondence: Ömer H. Yilmaz () (Ö.H.Y)
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9
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Struntz NB, Chen A, Deutzmann A, Wilson RM, Stefan E, Evans HL, Ramirez MA, Liang T, Caballero F, Wildschut MH, Neel DV, Freeman DB, Pop MS, McConkey M, Muller S, Curtin BH, Tseng H, Frombach KR, Butty VL, Levine SS, Feau C, Elmiligy S, Hong JA, Lewis TA, Vetere A, Clemons PA, Malstrom SE, Ebert BL, Lin CY, Felsher DW, Koehler AN. Stabilization of the Max Homodimer with a Small Molecule Attenuates Myc-Driven Transcription. Cell Chem Biol 2019; 26:711-723.e14. [DOI: 10.1016/j.chembiol.2019.02.009] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 11/27/2018] [Accepted: 02/07/2019] [Indexed: 12/13/2022]
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10
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Zhang S, Macias-Garcia A, Ulirsch JC, Velazquez J, Butty VL, Levine SS, Sankaran VG, Chen JJ. HRI coordinates translation necessary for protein homeostasis and mitochondrial function in erythropoiesis. eLife 2019; 8:46976. [PMID: 31033440 PMCID: PMC6533081 DOI: 10.7554/elife.46976] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [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: 03/19/2019] [Accepted: 04/26/2019] [Indexed: 12/05/2022] Open
Abstract
Iron and heme play central roles in the production of red blood cells, but the underlying mechanisms remain incompletely understood. Heme-regulated eIF2α kinase (HRI) controls translation by phosphorylating eIF2α. Here, we investigate the global impact of iron, heme, and HRI on protein translation in vivo in murine primary erythroblasts using ribosome profiling. We validate the known role of HRI-mediated translational stimulation of integratedstressresponse mRNAs during iron deficiency in vivo. Moreover, we find that the translation of mRNAs encoding cytosolic and mitochondrial ribosomal proteins is substantially repressed by HRI during iron deficiency, causing a decrease in cytosolic and mitochondrial protein synthesis. The absence of HRI during iron deficiency elicits a prominent cytoplasmic unfolded protein response and impairs mitochondrial respiration. Importantly, ATF4 target genes are activated during iron deficiency to maintain mitochondrial function and to enable erythroid differentiation. We further identify GRB10 as a previously unappreciated regulator of terminal erythropoiesis. Red blood cells use a molecule called hemoglobin to transport oxygen around the body. To make hemoglobin, cells require iron to build a component called heme. If an individual does not get enough iron in their diet, the body cannot produce enough red blood cells, or the cells lack hemoglobin. This condition is known as iron deficiency anemia, and it affects around one-third of the world’s population. Researchers did not know exactly how iron levels control red blood cell production, though several proteins had been identified to play important roles. Heme forms in the cell's mitochondria: the compartments in the cell that supply it with energy. When heme levels in a developing red blood cell are low, a protein called HRI reduces the production of many proteins, most importantly the proteins that make up hemoglobin. HRI also boosts the production of a protein called ATF4, which switches on a set of genes that help both the cell and its mitochondria to adapt to the lack of heme. In turn, HRI and ATF4 reduce the activity of a signaling pathway called mTORC1, which controls the production of proteins that help cells to grow and divide. To understand in more detail how iron and heme regulate the production of new red blood cells, Zhang et al. looked at immature red blood cells from the livers of developing mice. Some of the mice lacked the gene that produces HRI, and some experienced iron deficiency. Comparing gene activity in the different mice revealed that in the developing blood cells of iron-deficient mice, HRI largely reduces the rate of protein production in both the mitochondria and the wider cell. At the same time, the increased activity of ATF4 allows the mitochondria to carry on releasing energy and the cells to continue developing. Zhang et al. also found that a protein that inhibits the mTORC1 signaling pathway needs to be active for the new red blood cells to mature. Overall, the results suggest that drugs that activate HRI or block the activity of the mTORC1 pathway could help to treat anemia. The next step is to test the effects that such drugs have in anemic mice and cells from anemic people.
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Affiliation(s)
- Shuping Zhang
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, United States
| | - Alejandra Macias-Garcia
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, United States
| | - Jacob C Ulirsch
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, United States.,Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, United States.,Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, United States.,Program in Biological and Biomedical Sciences, Harvard University, Cambridge, United States
| | - Jason Velazquez
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, United States
| | - Vincent L Butty
- BioMicro Center, Massachusetts Institute of Technology, Cambridge, United States
| | - Stuart S Levine
- BioMicro Center, Massachusetts Institute of Technology, Cambridge, United States
| | - Vijay G Sankaran
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, United States.,Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, United States.,Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, United States
| | - Jane-Jane Chen
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, United States
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11
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Fletcher M, Tillman EJ, Butty VL, Levine SS, Kim DH. Global transcriptional regulation of innate immunity by ATF-7 in C. elegans. PLoS Genet 2019; 15:e1007830. [PMID: 30789901 PMCID: PMC6400416 DOI: 10.1371/journal.pgen.1007830] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [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: 11/08/2018] [Revised: 03/05/2019] [Accepted: 01/23/2019] [Indexed: 12/29/2022] Open
Abstract
The nematode Caenorhabditis elegans has emerged as a genetically tractable animal host in which to study evolutionarily conserved mechanisms of innate immune signaling. We previously showed that the PMK-1 p38 mitogen-activated protein kinase (MAPK) pathway regulates innate immunity of C. elegans through phosphorylation of the CREB/ATF bZIP transcription factor, ATF-7. Here, we have undertaken a genomic analysis of the transcriptional response of C. elegans to infection by Pseudomonas aeruginosa, combining genome-wide expression analysis by RNA-seq with ATF-7 chromatin immunoprecipitation followed by sequencing (ChIP-Seq). We observe that PMK-1-ATF-7 activity regulates a majority of all genes induced by pathogen infection, and observe ATF-7 occupancy in regulatory regions of pathogen-induced genes in a PMK-1-dependent manner. Moreover, functional analysis of a subset of these ATF-7-regulated pathogen-induced target genes supports a direct role for this transcriptional response in host defense. The genome-wide regulation through PMK-1- ATF-7 signaling reveals a striking level of control over the innate immune response to infection through a single transcriptional regulator.
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Affiliation(s)
- Marissa Fletcher
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Erik J. Tillman
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Vincent L. Butty
- BioMicro Center, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Stuart S. Levine
- BioMicro Center, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Dennis H. Kim
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
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12
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Berman CM, Papa LJ, Hendel SJ, Moore CL, Suen PH, Weickhardt AF, Doan ND, Kumar CM, Uil TG, Butty VL, Hoeben RC, Shoulders MD. An Adaptable Platform for Directed Evolution in Human Cells. J Am Chem Soc 2018; 140:18093-18103. [PMID: 30427676 DOI: 10.1021/jacs.8b10937] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The discovery and optimization of biomolecules that reliably function in metazoan cells is imperative for both the study of basic biology and the treatment of disease. We describe the development, characterization, and proof-of-concept application of a platform for directed evolution of diverse biomolecules of interest (BOIs) directly in human cells. The platform relies on a custom-designed adenovirus variant lacking multiple genes, including the essential DNA polymerase and protease genes, features that allow us to evolve BOIs encoded by genes as large as 7 kb while attaining the mutation rates and enforcing the selection pressure required for successful directed evolution. High mutagenesis rates are continuously attained by trans-complementation of a newly engineered, highly error-prone form of the adenoviral polymerase. Selection pressure that couples desired BOI functions to adenoviral propagation is achieved by linking the functionality of the encoded BOI to the production of adenoviral protease activity by the human cell. The dynamic range for directed evolution can be enhanced to several orders of magnitude via application of a small-molecule adenoviral protease inhibitor to modulate selection pressure during directed evolution experiments. This platform makes it possible, in principle, to evolve any biomolecule activity that can be coupled to adenoviral protease expression or activation by simply serially passaging adenoviral populations carrying the BOI. As proof-of-concept, we use the platform to evolve, directly in the human cell environment, several transcription factor variants that maintain high levels of function while gaining resistance to a small-molecule inhibitor. We anticipate that this platform will substantially expand the repertoire of biomolecules that can be reliably and robustly engineered for both research and therapeutic applications in metazoan systems.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Taco G Uil
- Department of Cell and Chemical Biology , Leiden University Medical Center , 2300 RC Leiden , The Netherlands
| | | | - Robert C Hoeben
- Department of Cell and Chemical Biology , Leiden University Medical Center , 2300 RC Leiden , The Netherlands
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13
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Phillips AM, Doud MB, Gonzalez LO, Butty VL, Lin YS, Bloom JD, Shoulders MD. Enhanced ER proteostasis and temperature differentially impact the mutational tolerance of influenza hemagglutinin. eLife 2018; 7:38795. [PMID: 30188321 PMCID: PMC6172027 DOI: 10.7554/elife.38795] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [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: 06/06/2018] [Accepted: 08/29/2018] [Indexed: 12/23/2022] Open
Abstract
We systematically and quantitatively evaluate whether endoplasmic reticulum (ER) proteostasis factors impact the mutational tolerance of secretory pathway proteins. We focus on influenza hemaggluttinin (HA), a viral membrane protein that folds in the host’s ER via a complex pathway. By integrating chemical methods to modulate ER proteostasis with deep mutational scanning to assess mutational tolerance, we discover that upregulation of ER proteostasis factors broadly enhances HA mutational tolerance across diverse structural elements. Remarkably, this proteostasis network-enhanced mutational tolerance occurs at the same sites where mutational tolerance is most reduced by propagation at fever-like temperature. These findings have important implications for influenza evolution, because influenza immune escape is contingent on HA possessing sufficient mutational tolerance to evade antibodies while maintaining the capacity to fold and function. More broadly, this work provides the first experimental evidence that ER proteostasis mechanisms define the mutational tolerance and, therefore, the evolution of secretory pathway proteins.
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Affiliation(s)
- Angela M Phillips
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, United States
| | - Michael B Doud
- Fred Hutchinson Cancer Research Center, Seattle, United States.,Department of Genome Sciences, University of Washington, Seattle, United States
| | - Luna O Gonzalez
- Department of Mathematics, Massachusetts Institute of Technology, Cambridge, United States
| | - Vincent L Butty
- BioMicro Center, Massachusetts Institute of Technology, Cambridge, United States
| | - Yu-Shan Lin
- Department of Chemistry, Tufts University, Medford, United States
| | - Jesse D Bloom
- Fred Hutchinson Cancer Research Center, Seattle, United States.,Department of Genome Sciences, University of Washington, Seattle, United States
| | - Matthew D Shoulders
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, United States
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14
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Phillips AM, Ponomarenko AI, Chen K, Ashenberg O, Miao J, McHugh SM, Butty VL, Whittaker CA, Moore CL, Bloom JD, Lin YS, Shoulders MD. Destabilized adaptive influenza variants critical for innate immune system escape are potentiated by host chaperones. PLoS Biol 2018; 16:e3000008. [PMID: 30222731 PMCID: PMC6160216 DOI: 10.1371/journal.pbio.3000008] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [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: 06/30/2018] [Revised: 09/27/2018] [Accepted: 08/30/2018] [Indexed: 11/24/2022] Open
Abstract
The threat of viral pandemics demands a comprehensive understanding of evolution at the host-pathogen interface. Here, we show that the accessibility of adaptive mutations in influenza nucleoprotein at fever-like temperatures is mediated by host chaperones. Particularly noteworthy, we observe that the Pro283 nucleoprotein variant, which (1) is conserved across human influenza strains, (2) confers resistance to the Myxovirus resistance protein A (MxA) restriction factor, and (3) critically contributed to adaptation to humans in the 1918 pandemic influenza strain, is rendered unfit by heat shock factor 1 inhibition-mediated host chaperone depletion at febrile temperatures. This fitness loss is due to biophysical defects that chaperones are unavailable to address when heat shock factor 1 is inhibited. Thus, influenza subverts host chaperones to uncouple the biophysically deleterious consequences of viral protein variants from the benefits of immune escape. In summary, host proteostasis plays a central role in shaping influenza adaptation, with implications for the evolution of other viruses, for viral host switching, and for antiviral drug development.
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Affiliation(s)
- Angela M. Phillips
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Anna I. Ponomarenko
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Kenny Chen
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Orr Ashenberg
- Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Jiayuan Miao
- Department of Chemistry, Tufts University, Medford, Massachusetts, United States of America
| | - Sean M. McHugh
- Department of Chemistry, Tufts University, Medford, Massachusetts, United States of America
| | - Vincent L. Butty
- BioMicro Center, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Charles A. Whittaker
- BioMicro Center, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Christopher L. Moore
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Jesse D. Bloom
- Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Yu-Shan Lin
- Department of Chemistry, Tufts University, Medford, Massachusetts, United States of America
| | - Matthew D. Shoulders
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
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15
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Richardson CE, Cunden LS, Butty VL, Nolan EM, Lippard SJ, Shoulders MD. A Novel Method for Studying Zinc Deficiency in vitro and its Application. FASEB J 2018. [DOI: 10.1096/fasebj.2018.32.1_supplement.653.6] [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]
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16
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Herbert ZT, Kershner JP, Butty VL, Thimmapuram J, Choudhari S, Alekseyev YO, Fan J, Podnar JW, Wilcox E, Gipson J, Gillaspy A, Jepsen K, BonDurant SS, Morris K, Berkeley M, LeClerc A, Simpson SD, Sommerville G, Grimmett L, Adams M, Levine SS. Cross-site comparison of ribosomal depletion kits for Illumina RNAseq library construction. BMC Genomics 2018; 19:199. [PMID: 29703133 PMCID: PMC6389247 DOI: 10.1186/s12864-018-4585-1] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Accepted: 03/08/2018] [Indexed: 01/23/2023] Open
Abstract
Background Ribosomal RNA (rRNA) comprises at least 90% of total RNA extracted from mammalian tissue or cell line samples. Informative transcriptional profiling using massively parallel sequencing technologies requires either enrichment of mature poly-adenylated transcripts or targeted depletion of the rRNA fraction. The latter method is of particular interest because it is compatible with degraded samples such as those extracted from FFPE and also captures transcripts that are not poly-adenylated such as some non-coding RNAs. Here we provide a cross-site study that evaluates the performance of ribosomal RNA removal kits from Illumina, Takara/Clontech, Kapa Biosystems, Lexogen, New England Biolabs and Qiagen on intact and degraded RNA samples. Results We find that all of the kits are capable of performing significant ribosomal depletion, though there are differences in their ease of use. All kits were able to remove ribosomal RNA to below 20% with intact RNA and identify ~ 14,000 protein coding genes from the Universal Human Reference RNA sample at >1FPKM. Analysis of differentially detected genes between kits suggests that transcript length may be a key factor in library production efficiency. Conclusions These results provide a roadmap for labs on the strengths of each of these methods and how best to utilize them. Electronic supplementary material The online version of this article (10.1186/s12864-018-4585-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Zachary T Herbert
- Molecular Biology Core Facilities at Dana-Farber Cancer Institute, Boston, MA, USA
| | - Jamie P Kershner
- BioFrontiers Institute, Next-Gen Sequencing Facility, University of Colorado Boulder, Boulder, CO, USA
| | - Vincent L Butty
- MIT BioMicro Center, Massachusetts Institute of Technology, Cambridge, MA, USA
| | | | | | - Yuriy O Alekseyev
- Microarray and Sequencing Resource Core Facility, Boston University, Boston, MA, USA.,Department of Pathology and Laboratory Medicine, Boston University, Boston, MA, USA
| | - Jun Fan
- Genomic Core Facility, Department of Biomedical Sciences, Joan C. Edwards School of Medicine, Marshall University, Huntington, WV, USA
| | - Jessica W Podnar
- Genomic Sequencing and Analysis Facility, University of Texas, Austin, TX, USA
| | - Edward Wilcox
- DNA Sequencing Center, Brigham Young University, Provo, UT, USA
| | - Jenny Gipson
- Laboratory for Molecular Biology and Cytometry, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Allison Gillaspy
- Laboratory for Molecular Biology and Cytometry, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Kristen Jepsen
- IGM Genomics Center, University of California, San Diego, La Jolla, CA, USA
| | | | - Krystalynne Morris
- Hubbard Center for Genome Studies, University of New Hampshire, Durham, NH, USA
| | - Maura Berkeley
- Molecular Biology Core Facilities at Dana-Farber Cancer Institute, Boston, MA, USA
| | - Ashley LeClerc
- Microarray and Sequencing Resource Core Facility, Boston University, Boston, MA, USA
| | - Stephen D Simpson
- Hubbard Center for Genome Studies, University of New Hampshire, Durham, NH, USA
| | - Gary Sommerville
- Molecular Biology Core Facilities at Dana-Farber Cancer Institute, Boston, MA, USA
| | - Leslie Grimmett
- Molecular Biology Core Facilities at Dana-Farber Cancer Institute, Boston, MA, USA
| | - Marie Adams
- Genomics Core Facility, Van Andel Institute, Grand Rapids, MI, USA
| | - Stuart S Levine
- MIT BioMicro Center, Massachusetts Institute of Technology, Cambridge, MA, USA.
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17
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Gural N, Mancio-Silva L, Miller AB, Galstian A, Butty VL, Levine SS, Patrapuvich R, Desai SP, Mikolajczak SA, Kappe SHI, Fleming HE, March S, Sattabongkot J, Bhatia SN. In Vitro Culture, Drug Sensitivity, and Transcriptome of Plasmodium Vivax Hypnozoites. Cell Host Microbe 2018; 23:395-406.e4. [PMID: 29478773 DOI: 10.1016/j.chom.2018.01.002] [Citation(s) in RCA: 91] [Impact Index Per Article: 15.2] [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: 07/19/2017] [Revised: 11/21/2017] [Accepted: 01/03/2018] [Indexed: 10/18/2022]
Abstract
The unique relapsing nature of Plasmodium vivax infection is a major barrier to malaria eradication. Upon infection, dormant liver-stage forms, hypnozoites, linger for weeks to months and then relapse to cause recurrent blood-stage infection. Very little is known about hypnozoite biology; definitive biomarkers are lacking and in vitro platforms that support phenotypic studies are needed. Here, we recapitulate the entire liver stage of P. vivax in vitro, using a multiwell format that incorporates micropatterned primary human hepatocyte co-cultures (MPCCs). MPCCs feature key aspects of P. vivax biology, including establishment of persistent small forms and growing schizonts, merosome release, and subsequent infection of reticulocytes. We find that the small forms exhibit previously described hallmarks of hypnozoites, and we pilot MPCCs as a tool for testing candidate anti-hypnozoite drugs. Finally, we employ a hybrid capture strategy and RNA sequencing to describe the hypnozoite transcriptome and gain insight into its biology.
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Affiliation(s)
- Nil Gural
- Harvard-MIT Department of Health Sciences and Technology, Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Boston, MA 02142, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA; Koch Institute for Integrative Cancer Research, Boston, MA 02142, USA
| | - Liliana Mancio-Silva
- Harvard-MIT Department of Health Sciences and Technology, Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Boston, MA 02142, USA; Koch Institute for Integrative Cancer Research, Boston, MA 02142, USA
| | - Alex B Miller
- Broad Institute, Boston, MA 02142, USA; Koch Institute for Integrative Cancer Research, Boston, MA 02142, USA
| | | | - Vincent L Butty
- BioMicro Center, Massachusetts Institute of Technology, Boston, MA 02142, USA
| | - Stuart S Levine
- BioMicro Center, Massachusetts Institute of Technology, Boston, MA 02142, USA
| | - Rapatbhorn Patrapuvich
- Mahidol Vivax Research Unit, Faculty of Tropical Medicine Mahidol University, Bangkok 10400, Thailand
| | | | | | | | - Heather E Fleming
- Harvard-MIT Department of Health Sciences and Technology, Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Boston, MA 02142, USA; Koch Institute for Integrative Cancer Research, Boston, MA 02142, USA
| | - Sandra March
- Harvard-MIT Department of Health Sciences and Technology, Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Boston, MA 02142, USA; Broad Institute, Boston, MA 02142, USA; Koch Institute for Integrative Cancer Research, Boston, MA 02142, USA
| | - Jetsumon Sattabongkot
- Mahidol Vivax Research Unit, Faculty of Tropical Medicine Mahidol University, Bangkok 10400, Thailand
| | - Sangeeta N Bhatia
- Harvard-MIT Department of Health Sciences and Technology, Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Boston, MA 02142, USA; Broad Institute, Boston, MA 02142, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA; Koch Institute for Integrative Cancer Research, Boston, MA 02142, USA; Department of Medicine, Brigham and Women's Hospital Boston, Boston, MA 02115, USA.
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18
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Richardson CER, Cunden LS, Butty VL, Nolan EM, Lippard SJ, Shoulders MD. A Method for Selective Depletion of Zn(II) Ions from Complex Biological Media and Evaluation of Cellular Consequences of Zn(II) Deficiency. J Am Chem Soc 2018; 140:2413-2416. [PMID: 29334734 PMCID: PMC5842789 DOI: 10.1021/jacs.7b12897] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
We describe the preparation, evaluation, and application of an S100A12 protein-conjugated solid support, hereafter the "A12-resin", that can remove 99% of Zn(II) from complex biological solutions without significantly perturbing the concentrations of other metal ions. The A12-resin can be applied to selectively deplete Zn(II) from diverse tissue culture media and from other biological fluids, including human serum. To further demonstrate the utility of this approach, we investigated metabolic, transcriptomic, and metallomic responses of HEK293 cells cultured in medium depleted of Zn(II) using S100A12. The resulting data provide insight into how cells respond to acute Zn(II) deficiency. We expect that the A12-resin will facilitate interrogation of disrupted Zn(II) homeostasis in biological settings, uncovering novel roles for Zn(II) in biology.
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Affiliation(s)
- Christopher E. R. Richardson
- Department of Chemistry, 77 Massachusetts Avenue, Massachusetts Institute of Technology, Massachusetts 02139, United States
| | - Lisa S. Cunden
- Department of Chemistry, 77 Massachusetts Avenue, Massachusetts Institute of Technology, Massachusetts 02139, United States
| | - Vincent L. Butty
- MIT BioMicroCenter, 77 Massachusetts Avenue, Massachusetts Institute of Technology, Massachusetts 02139, United States
| | - Elizabeth M. Nolan
- Department of Chemistry, 77 Massachusetts Avenue, Massachusetts Institute of Technology, Massachusetts 02139, United States
| | - Stephen J. Lippard
- Department of Chemistry, 77 Massachusetts Avenue, Massachusetts Institute of Technology, Massachusetts 02139, United States
| | - Matthew D. Shoulders
- Department of Chemistry, 77 Massachusetts Avenue, Massachusetts Institute of Technology, Massachusetts 02139, United States
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19
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Murphy PA, Butty VL, Boutz PL, Begum S, Kimble AL, Sharp PA, Burge CB, Hynes RO. Alternative RNA splicing in the endothelium mediated in part by Rbfox2 regulates the arterial response to low flow. eLife 2018; 7:29494. [PMID: 29293084 PMCID: PMC5771670 DOI: 10.7554/elife.29494] [Citation(s) in RCA: 20] [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: 06/12/2017] [Accepted: 12/30/2017] [Indexed: 12/13/2022] Open
Abstract
Low and disturbed blood flow drives the progression of arterial diseases including atherosclerosis and aneurysms. The endothelial response to flow and its interactions with recruited platelets and leukocytes determine disease progression. Here, we report widespread changes in alternative splicing of pre-mRNA in the flow-activated murine arterial endothelium in vivo. Alternative splicing was suppressed by depletion of platelets and macrophages recruited to the arterial endothelium under low and disturbed flow. Binding motifs for the Rbfox-family are enriched adjacent to many of the regulated exons. Endothelial deletion of Rbfox2, the only family member expressed in arterial endothelium, suppresses a subset of the changes in transcription and RNA splicing induced by low flow. Our data reveal an alternative splicing program activated by Rbfox2 in the endothelium on recruitment of platelets and macrophages and demonstrate its relevance in transcriptional responses during flow-driven vascular inflammation.
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Affiliation(s)
- Patrick A Murphy
- Koch Institute for Integrative Cancer Research, MIT, Cambridge, United States
| | | | - Paul L Boutz
- Koch Institute for Integrative Cancer Research, MIT, Cambridge, United States
| | - Shahinoor Begum
- Koch Institute for Integrative Cancer Research, MIT, Cambridge, United States.,Howard Hughes Medical Institute, United States
| | - Amy L Kimble
- Center for Vascular Biology, UCONN Health, Farmington, United States
| | - Phillip A Sharp
- Koch Institute for Integrative Cancer Research, MIT, Cambridge, United States.,Department of Biology, MIT, Cambridge, United States
| | | | - Richard O Hynes
- Koch Institute for Integrative Cancer Research, MIT, Cambridge, United States.,Department of Biology, MIT, Cambridge, United States.,Howard Hughes Medical Institute, United States
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20
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Phillips AM, Gonzalez LO, Nekongo EE, Ponomarenko AI, McHugh SM, Butty VL, Levine SS, Lin YS, Mirny LA, Shoulders MD. Host proteostasis modulates influenza evolution. eLife 2017; 6. [PMID: 28949290 PMCID: PMC5614556 DOI: 10.7554/elife.28652] [Citation(s) in RCA: 28] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Accepted: 08/18/2017] [Indexed: 01/02/2023] Open
Abstract
Predicting and constraining RNA virus evolution require understanding the molecular factors that define the mutational landscape accessible to these pathogens. RNA viruses typically have high mutation rates, resulting in frequent production of protein variants with compromised biophysical properties. Their evolution is necessarily constrained by the consequent challenge to protein folding and function. We hypothesized that host proteostasis mechanisms may be significant determinants of the fitness of viral protein variants, serving as a critical force shaping viral evolution. Here, we test that hypothesis by propagating influenza in host cells displaying chemically-controlled, divergent proteostasis environments. We find that both the nature of selection on the influenza genome and the accessibility of specific mutational trajectories are significantly impacted by host proteostasis. These findings provide new insights into features of host–pathogen interactions that shape viral evolution, and into the potential design of host proteostasis-targeted antiviral therapeutics that are refractory to resistance. Influenza viruses, commonly called flu, can evade our immune system and develop resistance to treatments by changing frequently. Specifically, mutations in their genome cause influenza proteins to change in ways that can help the virus evade our defences. However, these mutations come at a cost and can prevent the viral proteins from forming functional and stable three-dimensional shapes – a process known as protein folding – thereby hampering the virus’ ability to replicate. In human cells, proteins called chaperones can help our other proteins fold properly. Influenza viruses do not have their own chaperones and, instead, hijack those of their host. Host chaperones are therefore crucial to the virus’ ability to replicate. However, until now, it was not known if host chaperones can influence how these viruses evolve. Here, Phillips et al. used mammalian cells to study how host chaperones affect an evolving influenza population. First, cells were engineered to either have normal chaperone levels, elevated chaperone levels, or inactive chaperones. Next, the H3N2 influenza strain was grown in these different conditions for nearly 200 generations and sequenced to determine how the virus evolved in each distinctive host chaperone environment. Phillips et al. discovered that host chaperones affect the rate at which mutations accumulate in the influenza population, and also the types of mutations in the influenza genome. For instance, when a chaperone called Hsp90 was inactivated, mutations became prevalent in the viral population more slowly than in cells with normal or elevated chaperone levels. Moreover, some specific mutations fared better in cells with high chaperone levels, whilst others worked better in cells with inactivated chaperones. These results suggest that influenza evolution is affected by host chaperone levels in complex and important ways. Moreover, whether chaperones will promote or hinder the effects of any single mutation is difficult to predict ahead of time. This discovery is significant, as the chaperones available to influenza can vary in different tissues, organisms and infectious conditions, and may therefore influence the virus' ability to change and evolve in a context-specific manner. The findings are likely to extend to other viruses such as HIV and Ebola, which also hijack host chaperones for the same purpose. More work is now needed to systematically quantify these effects so that we can better predict how specific chaperones will affect the ability of viruses to adapt, especially in pathologically relevant conditions like fever or viral host-switching. In the future, such insights could help shape the design of treatments to which viruses do not evolve resistance.
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Affiliation(s)
- Angela M Phillips
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, United States
| | - Luna O Gonzalez
- Department of Mathematics, Massachusetts Institute of Technology, Cambridge, United States
| | - Emmanuel E Nekongo
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, United States
| | - Anna I Ponomarenko
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, United States
| | - Sean M McHugh
- Department of Chemistry, Tufts University, Medford, United States
| | - Vincent L Butty
- BioMicro Center, Massachusetts Institute of Technology, Cambridge, United States
| | - Stuart S Levine
- BioMicro Center, Massachusetts Institute of Technology, Cambridge, United States
| | - Yu-Shan Lin
- Department of Chemistry, Tufts University, Medford, United States
| | - Leonid A Mirny
- Department of Physics, Massachusetts Institute of Technology, Cambridge, United States.,Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, United States
| | - Matthew D Shoulders
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, United States
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21
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O'Meara CC, Wamstad JA, Gladstone RA, Fomovsky GM, Butty VL, Shrikumar A, Gannon JB, Boyer LA, Lee RT. Transcriptional reversion of cardiac myocyte fate during mammalian cardiac regeneration. Circ Res 2014; 116:804-15. [PMID: 25477501 DOI: 10.1161/circresaha.116.304269] [Citation(s) in RCA: 116] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
RATIONALE Neonatal mice have the capacity to regenerate their hearts in response to injury, but this potential is lost after the first week of life. The transcriptional changes that underpin mammalian cardiac regeneration have not been fully characterized at the molecular level. OBJECTIVE The objectives of our study were to determine whether myocytes revert the transcriptional phenotype to a less differentiated state during regeneration and to systematically interrogate the transcriptional data to identify and validate potential regulators of this process. METHODS AND RESULTS We derived a core transcriptional signature of injury-induced cardiac myocyte (CM) regeneration in mouse by comparing global transcriptional programs in a dynamic model of in vitro and in vivo CM differentiation, in vitro CM explant model, as well as a neonatal heart resection model. The regenerating mouse heart revealed a transcriptional reversion of CM differentiation processes, including reactivation of latent developmental programs similar to those observed during destabilization of a mature CM phenotype in the explant model. We identified potential upstream regulators of the core network, including interleukin 13, which induced CM cell cycle entry and STAT6/STAT3 signaling in vitro. We demonstrate that STAT3/periostin and STAT6 signaling are critical mediators of interleukin 13 signaling in CMs. These downstream signaling molecules are also modulated in the regenerating mouse heart. CONCLUSIONS Our work reveals new insights into the transcriptional regulation of mammalian cardiac regeneration and provides the founding circuitry for identifying potential regulators for stimulating heart regeneration.
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Affiliation(s)
- Caitlin C O'Meara
- From the Harvard Stem Cell Institute, the Brigham Regenerative Medicine Center, and the Cardiovascular Division, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, and the Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA (C.C.O.M., R.A.G., G.M.F., J.B.G., R.T.L.); and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA (J.A.W., V.L.B., A.S., L.A.B.)
| | - Joseph A Wamstad
- From the Harvard Stem Cell Institute, the Brigham Regenerative Medicine Center, and the Cardiovascular Division, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, and the Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA (C.C.O.M., R.A.G., G.M.F., J.B.G., R.T.L.); and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA (J.A.W., V.L.B., A.S., L.A.B.)
| | - Rachel A Gladstone
- From the Harvard Stem Cell Institute, the Brigham Regenerative Medicine Center, and the Cardiovascular Division, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, and the Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA (C.C.O.M., R.A.G., G.M.F., J.B.G., R.T.L.); and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA (J.A.W., V.L.B., A.S., L.A.B.)
| | - Gregory M Fomovsky
- From the Harvard Stem Cell Institute, the Brigham Regenerative Medicine Center, and the Cardiovascular Division, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, and the Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA (C.C.O.M., R.A.G., G.M.F., J.B.G., R.T.L.); and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA (J.A.W., V.L.B., A.S., L.A.B.)
| | - Vincent L Butty
- From the Harvard Stem Cell Institute, the Brigham Regenerative Medicine Center, and the Cardiovascular Division, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, and the Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA (C.C.O.M., R.A.G., G.M.F., J.B.G., R.T.L.); and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA (J.A.W., V.L.B., A.S., L.A.B.)
| | - Avanti Shrikumar
- From the Harvard Stem Cell Institute, the Brigham Regenerative Medicine Center, and the Cardiovascular Division, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, and the Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA (C.C.O.M., R.A.G., G.M.F., J.B.G., R.T.L.); and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA (J.A.W., V.L.B., A.S., L.A.B.)
| | - Joseph B Gannon
- From the Harvard Stem Cell Institute, the Brigham Regenerative Medicine Center, and the Cardiovascular Division, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, and the Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA (C.C.O.M., R.A.G., G.M.F., J.B.G., R.T.L.); and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA (J.A.W., V.L.B., A.S., L.A.B.)
| | - Laurie A Boyer
- From the Harvard Stem Cell Institute, the Brigham Regenerative Medicine Center, and the Cardiovascular Division, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, and the Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA (C.C.O.M., R.A.G., G.M.F., J.B.G., R.T.L.); and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA (J.A.W., V.L.B., A.S., L.A.B.).
| | - Richard T Lee
- From the Harvard Stem Cell Institute, the Brigham Regenerative Medicine Center, and the Cardiovascular Division, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, and the Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA (C.C.O.M., R.A.G., G.M.F., J.B.G., R.T.L.); and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA (J.A.W., V.L.B., A.S., L.A.B.).
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Thornton SR, Butty VL, Levine SS, Boyer LA. Polycomb Repressive Complex 2 regulates lineage fidelity during embryonic stem cell differentiation. PLoS One 2014; 9:e110498. [PMID: 25333635 PMCID: PMC4204901 DOI: 10.1371/journal.pone.0110498] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [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: 04/04/2014] [Accepted: 09/20/2014] [Indexed: 11/18/2022] Open
Abstract
Polycomb Repressive Complex 2 (PRC2) catalyzes histone H3 lysine 27 tri-methylation (H3K27me3), an epigenetic modification associated with gene repression. H3K27me3 is enriched at the promoters of a large cohort of developmental genes in embryonic stem cells (ESCs). Loss of H3K27me3 leads to a failure of ESCs to properly differentiate, making it difficult to determine the precise roles of PRC2 during lineage commitment. Moreover, while studies suggest that PRC2 prevents DNA methylation, how these two epigenetic regulators coordinate to regulate lineage programs is poorly understood. Using several PRC2 mutant ESC lines that maintain varying levels of H3K27me3, we found that partial maintenance of H3K27me3 allowed for proper temporal activation of lineage genes during directed differentiation of ESCs to spinal motor neurons (SMNs). In contrast, genes that function to specify other lineages failed to be repressed in these cells, suggesting that PRC2 is also necessary for lineage fidelity. We also found that loss of H3K27me3 leads to a modest gain in DNA methylation at PRC2 target regions in both ESCs and in SMNs. Our study demonstrates a critical role for PRC2 in safeguarding lineage decisions and in protecting genes against inappropriate DNA methylation.
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Affiliation(s)
- Seraphim R. Thornton
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Vincent L. Butty
- BioMicro Center, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Stuart S. Levine
- BioMicro Center, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Laurie A. Boyer
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- * E-mail:
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Subramanian V, Mazumder A, Surface LE, Butty VL, Fields PA, Alwan A, Torrey L, Thai KK, Levine SS, Bathe M, Boyer LA. H2A.Z acidic patch couples chromatin dynamics to regulation of gene expression programs during ESC differentiation. PLoS Genet 2013; 9:e1003725. [PMID: 23990805 PMCID: PMC3749939 DOI: 10.1371/journal.pgen.1003725] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [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: 01/04/2013] [Accepted: 07/01/2013] [Indexed: 12/20/2022] Open
Abstract
The histone H2A variant H2A.Z is essential for embryonic development and for proper control of developmental gene expression programs in embryonic stem cells (ESCs). Divergent regions of amino acid sequence of H2A.Z likely determine its functional specialization compared to core histone H2A. For example, H2A.Z contains three divergent residues in the essential C-terminal acidic patch that reside on the surface of the histone octamer as an uninterrupted acidic patch domain; however, we know little about how these residues contribute to chromatin structure and function. Here, we show that the divergent amino acids Gly92, Asp97, and Ser98 in the H2A.Z C-terminal acidic patch (H2A.Z(AP3)) are critical for lineage commitment during ESC differentiation. H2A.Z is enriched at most H3K4me3 promoters in ESCs including poised, bivalent promoters that harbor both activating and repressive marks, H3K4me3 and H3K27me3 respectively. We found that while H2A.Z(AP3) interacted with its deposition complex and displayed a highly similar distribution pattern compared to wild-type H2A.Z, its enrichment levels were reduced at target promoters. Further analysis revealed that H2A.Z(AP3) was less tightly associated with chromatin, suggesting that the mutant is more dynamic. Notably, bivalent genes in H2A.Z(AP3) ESCs displayed significant changes in expression compared to active genes. Moreover, bivalent genes in H2A.Z(AP3) ESCs gained H3.3, a variant associated with higher nucleosome turnover, compared to wild-type H2A.Z. We next performed single cell imaging to measure H2A.Z dynamics. We found that H2A.Z(AP3) displayed higher mobility in chromatin compared to wild-type H2A.Z by fluorescent recovery after photobleaching (FRAP). Moreover, ESCs treated with the transcriptional inhibitor flavopiridol resulted in a decrease in the H2A.Z(AP3) mobile fraction and an increase in its occupancy at target genes indicating that the mutant can be properly incorporated into chromatin. Collectively, our work suggests that the divergent residues in the H2A.Z acidic patch comprise a unique domain that couples control of chromatin dynamics to the regulation of developmental gene expression patterns during lineage commitment.
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Affiliation(s)
- Vidya Subramanian
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Aprotim Mazumder
- Laboratory for Computational Biology and Biophysics, and Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Lauren E. Surface
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Vincent L. Butty
- BioMicro Center, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Paul A. Fields
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Allison Alwan
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Lillian Torrey
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Kevin K. Thai
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Stuart S. Levine
- BioMicro Center, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Mark Bathe
- Laboratory for Computational Biology and Biophysics, and Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Laurie A. Boyer
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- * E-mail:
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24
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Klattenhoff CA, Scheuermann JC, Surface LE, Bradley RK, Fields PA, Steinhauser ML, Ding H, Butty VL, Torrey L, Haas S, Abo R, Tabebordbar M, Lee RT, Burge CB, Boyer LA. Braveheart, a long noncoding RNA required for cardiovascular lineage commitment. Cell 2013; 152:570-83. [PMID: 23352431 DOI: 10.1016/j.cell.2013.01.003] [Citation(s) in RCA: 714] [Impact Index Per Article: 64.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2012] [Revised: 11/09/2012] [Accepted: 12/20/2012] [Indexed: 11/26/2022]
Abstract
Long noncoding RNAs (lncRNAs) are often expressed in a development-specific manner, yet little is known about their roles in lineage commitment. Here, we identified Braveheart (Bvht), a heart-associated lncRNA in mouse. Using multiple embryonic stem cell (ESC) differentiation strategies, we show that Bvht is required for progression of nascent mesoderm toward a cardiac fate. We find that Bvht is necessary for activation of a core cardiovascular gene network and functions upstream of mesoderm posterior 1 (MesP1), a master regulator of a common multipotent cardiovascular progenitor. We also show that Bvht interacts with SUZ12, a component of polycomb-repressive complex 2 (PRC2), during cardiomyocyte differentiation, suggesting that Bvht mediates epigenetic regulation of cardiac commitment. Finally, we demonstrate a role for Bvht in maintaining cardiac fate in neonatal cardiomyocytes. Together, our work provides evidence for a long noncoding RNA with critical roles in the establishment of the cardiovascular lineage during mammalian development.
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Affiliation(s)
- Carla A Klattenhoff
- Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
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25
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Abstract
Polymerase colony (polony) technology amplifies multiple individual DNA molecules within a thin acrylamide gel attached to a microscope slide. Each DNA molecule included in the reaction produces an immobilized colony of double-stranded DNA. We genotype these polonies by performing single base extensions with dye-labeled nucleotides, and we demonstrate the accurate quantitation of two allelic variants. We also show that polony technology can determine the phase, or haplotype, of two single- nucleotide polymorphisms (SNPs) by coamplifying distally located targets on a single chromosomal fragment. We correctly determine the genotype and phase of three different pairs of SNPs. In one case, the distance between the two SNPs is 45 kb, the largest distance achieved to date without separating the chromosomes by cloning or somatic cell fusion. The results indicate that polony genotyping and haplotyping may play an important role in understanding the structure of genetic variation.
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Affiliation(s)
- Robi D Mitra
- Lipper Center for Computational Genetics and Department of Genetics, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA
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Butty VL, Roux-Lombard P, Garbino J, Dayer JM, Ricou B. Anti-inflammatory response after infusion of p55 soluble tumor necrosis factor receptor fusion protein for severe sepsis. Eur Cytokine Netw 2003; 14:15-9. [PMID: 12799209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/03/2023]
Abstract
OBJECTIVES To investigate the effects of Lenercept , a recombinant soluble TNF receptor p55 fused to an immunoglobulin heavy chain IgG1, on the balance of pro- and anti-inflammatory mediators in sepsis. DESIGN Post hoc analysis of a subgroup of patients enrolled in a multicenter phase III, prospective, double-blind, placebo-controlled, randomized study of Lenercept in severe sepsis. SETTING Surgical and medical intensive care units, and postoperative recovery room of a tertiary care teaching hospital. PATIENTS A total of 57 patients were enrolled in the multicenter study in our center. INTERVENTION Septic patients were randomly assigned to receive either Lenercept 0.125 mg/kg or placebo. The patients were followed for up to 28 days after randomization. MEASUREMENTS AND MAIN RESULTS Circulating levels of TNF-alpha, IL-6, TNFsR75 and IL-1Ra were measured before and after treatment. The two groups were comparable with regard to age, gender and diagnosis distribution. The total level of TNF-alpha increased significantly in treated patients, compared to patients receiving placebo. The levels of the other inflammatory mediators did not differ between the two groups CONCLUSIONS Lenercept -treated patients experienced a protracted TNF-alpha half-life, leading to higher total TNF-alpha levels throughout the study. However, the treatment had no effects on anti-inflammatory mediators. Therefore, peripheral inflammatory processes might not have been significantly modified by the treatment. This might account for the lack of efficacy this treatment in septic patients
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Affiliation(s)
- Vincent L Butty
- Department of Anesthesiology, Pharmacology and Surgical Intensive Care, Geneva University Hospital, 1211 Geneva 14, Switzerland
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