1
|
Stepanov AI, Shuvaeva AA, Putlyaeva LV, Lukyanov DK, Galiakberova AA, Gorbachev DA, Maltsev DI, Pronina V, Dylov DV, Terskikh AV, Lukyanov KA, Gurskaya NG. Tracking induced pluripotent stem cell differentiation with a fluorescent genetically encoded epigenetic probe. Cell Mol Life Sci 2024; 81:381. [PMID: 39222083 PMCID: PMC11368889 DOI: 10.1007/s00018-024-05359-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 06/11/2024] [Accepted: 07/10/2024] [Indexed: 09/04/2024]
Abstract
Epigenetic modifications (methylation, acetylation, etc.) of core histones play a key role in regulation of gene expression. Thus, the epigenome changes strongly during various biological processes such as cell differentiation and dedifferentiation. Classical methods of analysis of epigenetic modifications such as mass-spectrometry and chromatin immuno-precipitation, work with fixed cells only. Here we present a genetically encoded fluorescent probe, MPP8-Green, for detecting H3K9me3, a histone modification associated with inactive chromatin. This probe, based on the chromodomain of MPP8, allows for visualization of H3K9me3 epigenetic landscapes in single living cells. We used this probe to track changes in H3K9me3 landscapes during the differentiation of induced pluripotent stem cells (iPSCs) into induced neurons. Our findings revealed two major waves of global H3K9me3 reorganization during 4-day differentiation, namely on the first and third days, whereas nearly no changes occurred on the second and fourth days. The proposed method LiveMIEL (Live-cell Microscopic Imaging of Epigenetic Landscapes), which combines genetically encoded epigenetic probes and machine learning approaches, enables classification of multiparametric epigenetic signatures of single cells during stem cell differentiation and potentially in other biological models.
Collapse
Affiliation(s)
- Afanasii I Stepanov
- Skolkovo Institute of Science and Technology, Bolshoi Blvd. 30, Bld. 1, 121205, Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997, Moscow, Russia
| | - Alexandra A Shuvaeva
- Skolkovo Institute of Science and Technology, Bolshoi Blvd. 30, Bld. 1, 121205, Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997, Moscow, Russia
- Moscow Institute of Physics and Technology, Dolgoprudny, 141701, Russia
| | - Lidia V Putlyaeva
- Skolkovo Institute of Science and Technology, Bolshoi Blvd. 30, Bld. 1, 121205, Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997, Moscow, Russia
| | - Daniil K Lukyanov
- Skolkovo Institute of Science and Technology, Bolshoi Blvd. 30, Bld. 1, 121205, Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997, Moscow, Russia
| | - Adelya A Galiakberova
- Pirogov Russian National Research Medical University, Ostrovityanova 1, 117997, Moscow, Russia
| | - Dmitry A Gorbachev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997, Moscow, Russia
| | - Dmitry I Maltsev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997, Moscow, Russia
- Pirogov Russian National Research Medical University, Ostrovityanova 1, 117997, Moscow, Russia
- Federal Center of Brain Research and Neurotechnologies, Federal Medical Biological Agency, Moscow, 117997, Russia
| | - Valeriya Pronina
- Skolkovo Institute of Science and Technology, Bolshoi Blvd. 30, Bld. 1, 121205, Moscow, Russia
| | - Dmitry V Dylov
- Skolkovo Institute of Science and Technology, Bolshoi Blvd. 30, Bld. 1, 121205, Moscow, Russia
| | - Alexey V Terskikh
- The Scintillon Research Institute, 6404 Nancy Ridge Dr., San Diego, CA, 92121, USA
| | - Konstantin A Lukyanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997, Moscow, Russia
| | - Nadya G Gurskaya
- Skolkovo Institute of Science and Technology, Bolshoi Blvd. 30, Bld. 1, 121205, Moscow, Russia.
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997, Moscow, Russia.
- Pirogov Russian National Research Medical University, Ostrovityanova 1, 117997, Moscow, Russia.
| |
Collapse
|
2
|
Pandiloski N, Horváth V, Karlsson O, Koutounidou S, Dorazehi F, Christoforidou G, Matas-Fuentes J, Gerdes P, Garza R, Jönsson ME, Adami A, Atacho DAM, Johansson JG, Englund E, Kokaia Z, Jakobsson J, Douse CH. DNA methylation governs the sensitivity of repeats to restriction by the HUSH-MORC2 corepressor. Nat Commun 2024; 15:7534. [PMID: 39214989 PMCID: PMC11364546 DOI: 10.1038/s41467-024-50765-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 07/18/2024] [Indexed: 09/04/2024] Open
Abstract
The human silencing hub (HUSH) complex binds to transcripts of LINE-1 retrotransposons (L1s) and other genomic repeats, recruiting MORC2 and other effectors to remodel chromatin. How HUSH and MORC2 operate alongside DNA methylation, a central epigenetic regulator of repeat transcription, remains largely unknown. Here we interrogate this relationship in human neural progenitor cells (hNPCs), a somatic model of brain development that tolerates removal of DNA methyltransferase DNMT1. Upon loss of MORC2 or HUSH subunit TASOR in hNPCs, L1s remain silenced by robust promoter methylation. However, genome demethylation and activation of evolutionarily-young L1s attracts MORC2 binding, and simultaneous depletion of DNMT1 and MORC2 causes massive accumulation of L1 transcripts. We identify the same mechanistic hierarchy at pericentromeric α-satellites and clustered protocadherin genes, repetitive elements important for chromosome structure and neurodevelopment respectively. Our data delineate the epigenetic control of repeats in somatic cells, with implications for understanding the vital functions of HUSH-MORC2 in hypomethylated contexts throughout human development.
Collapse
Affiliation(s)
- Ninoslav Pandiloski
- Laboratory of Epigenetics and Chromatin Dynamics, Department of Experimental Medical Science, Wallenberg Neuroscience Center, BMC B11, Lund University, Lund, Sweden
- Laboratory of Molecular Neurogenetics, Department of Experimental Medical Science, Wallenberg Neuroscience Center, BMC A11, Lund University, Lund, Sweden
- Lund Stem Cell Center, Lund University, Lund, Sweden
| | - Vivien Horváth
- Laboratory of Molecular Neurogenetics, Department of Experimental Medical Science, Wallenberg Neuroscience Center, BMC A11, Lund University, Lund, Sweden
- Lund Stem Cell Center, Lund University, Lund, Sweden
| | - Ofelia Karlsson
- Laboratory of Molecular Neurogenetics, Department of Experimental Medical Science, Wallenberg Neuroscience Center, BMC A11, Lund University, Lund, Sweden
- Lund Stem Cell Center, Lund University, Lund, Sweden
| | - Symela Koutounidou
- Laboratory of Epigenetics and Chromatin Dynamics, Department of Experimental Medical Science, Wallenberg Neuroscience Center, BMC B11, Lund University, Lund, Sweden
- Lund Stem Cell Center, Lund University, Lund, Sweden
| | - Fereshteh Dorazehi
- Laboratory of Epigenetics and Chromatin Dynamics, Department of Experimental Medical Science, Wallenberg Neuroscience Center, BMC B11, Lund University, Lund, Sweden
- Lund Stem Cell Center, Lund University, Lund, Sweden
| | - Georgia Christoforidou
- Laboratory of Epigenetics and Chromatin Dynamics, Department of Experimental Medical Science, Wallenberg Neuroscience Center, BMC B11, Lund University, Lund, Sweden
- Lund Stem Cell Center, Lund University, Lund, Sweden
| | - Jon Matas-Fuentes
- Laboratory of Epigenetics and Chromatin Dynamics, Department of Experimental Medical Science, Wallenberg Neuroscience Center, BMC B11, Lund University, Lund, Sweden
| | - Patricia Gerdes
- Laboratory of Molecular Neurogenetics, Department of Experimental Medical Science, Wallenberg Neuroscience Center, BMC A11, Lund University, Lund, Sweden
- Lund Stem Cell Center, Lund University, Lund, Sweden
| | - Raquel Garza
- Laboratory of Molecular Neurogenetics, Department of Experimental Medical Science, Wallenberg Neuroscience Center, BMC A11, Lund University, Lund, Sweden
- Lund Stem Cell Center, Lund University, Lund, Sweden
| | | | - Anita Adami
- Laboratory of Molecular Neurogenetics, Department of Experimental Medical Science, Wallenberg Neuroscience Center, BMC A11, Lund University, Lund, Sweden
- Lund Stem Cell Center, Lund University, Lund, Sweden
| | - Diahann A M Atacho
- Laboratory of Molecular Neurogenetics, Department of Experimental Medical Science, Wallenberg Neuroscience Center, BMC A11, Lund University, Lund, Sweden
- Lund Stem Cell Center, Lund University, Lund, Sweden
| | - Jenny G Johansson
- Laboratory of Molecular Neurogenetics, Department of Experimental Medical Science, Wallenberg Neuroscience Center, BMC A11, Lund University, Lund, Sweden
| | - Elisabet Englund
- Division of Pathology, Department of Clinical Sciences, Lund University, Lund, Sweden
| | - Zaal Kokaia
- Lund Stem Cell Center, Lund University, Lund, Sweden
- Laboratory of Stem Cells and Restorative Neurology, Department of Clinical Sciences, BMC B10, Lund University, Lund, Sweden
| | - Johan Jakobsson
- Laboratory of Molecular Neurogenetics, Department of Experimental Medical Science, Wallenberg Neuroscience Center, BMC A11, Lund University, Lund, Sweden
- Lund Stem Cell Center, Lund University, Lund, Sweden
| | - Christopher H Douse
- Laboratory of Epigenetics and Chromatin Dynamics, Department of Experimental Medical Science, Wallenberg Neuroscience Center, BMC B11, Lund University, Lund, Sweden.
- Lund Stem Cell Center, Lund University, Lund, Sweden.
| |
Collapse
|
3
|
Danac JMC, Matthews RE, Gungi A, Qin C, Parsons H, Antrobus R, Timms RT, Tchasovnikarova IA. Competition between two HUSH complexes orchestrates the immune response to retroelement invasion. Mol Cell 2024; 84:2870-2881.e5. [PMID: 39013473 DOI: 10.1016/j.molcel.2024.06.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 05/31/2024] [Accepted: 06/20/2024] [Indexed: 07/18/2024]
Abstract
The human silencing hub (HUSH) preserves genome integrity through the epigenetic repression of invasive genetic elements. However, despite our understanding of HUSH as an obligate complex of three subunits, only loss of MPP8 or Periphilin, but not TASOR, triggers interferon signaling following derepression of endogenous retroelements. Here, we resolve this paradox by characterizing a second HUSH complex that shares MPP8 and Periphilin but assembles around TASOR2, an uncharacterized paralog of TASOR. Whereas HUSH represses LINE-1 retroelements marked by the repressive histone modification H3K9me3, HUSH2 is recruited by the transcription factor IRF2 to repress interferon-stimulated genes. Mechanistically, HUSH-mediated retroelement silencing sequesters the limited pool of the shared subunits MPP8 and Periphilin, preventing TASOR2 from forming HUSH2 complexes and hence relieving the HUSH2-mediated repression of interferon-stimulated genes. Thus, competition between two HUSH complexes intertwines retroelement silencing with the induction of an immune response, coupling epigenetic and immune aspects of genome defense.
Collapse
Affiliation(s)
- Joshua Miguel C Danac
- The Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK; Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK
| | - Rachael E Matthews
- The Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK; Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK
| | - Akhila Gungi
- The Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK; Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK
| | - Chuyan Qin
- The Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK; Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK
| | - Harriet Parsons
- Department of Medicine, Cambridge Institute for Medical Research, Addenbrooke's Hospital, Hills Road, Cambridge CB2 0XY, UK
| | - Robin Antrobus
- Department of Medicine, Cambridge Institute for Medical Research, Addenbrooke's Hospital, Hills Road, Cambridge CB2 0XY, UK
| | - Richard T Timms
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge CB2 0AW, UK
| | - Iva A Tchasovnikarova
- The Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK; Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK.
| |
Collapse
|
4
|
Saulnier O, Zagozewski J, Liang L, Hendrikse LD, Layug P, Gordon V, Aldinger KA, Haldipur P, Borlase S, Coudière-Morrison L, Cai T, Martell E, Gonzales NM, Palidwor G, Porter CJ, Richard S, Sharif T, Millen KJ, Doble BW, Taylor MD, Werbowetski-Ogilvie TE. A group 3 medulloblastoma stem cell program is maintained by OTX2-mediated alternative splicing. Nat Cell Biol 2024; 26:1233-1246. [PMID: 39025928 PMCID: PMC11321995 DOI: 10.1038/s41556-024-01460-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Accepted: 06/17/2024] [Indexed: 07/20/2024]
Abstract
OTX2 is a transcription factor and known driver in medulloblastoma (MB), where it is amplified in a subset of tumours and overexpressed in most cases of group 3 and group 4 MB. Here we demonstrate a noncanonical role for OTX2 in group 3 MB alternative splicing. OTX2 associates with the large assembly of splicing regulators complex through protein-protein interactions and regulates a stem cell splicing program. OTX2 can directly or indirectly bind RNA and this may be partially independent of its DNA regulatory functions. OTX2 controls a pro-tumorigenic splicing program that is mirrored in human cerebellar rhombic lip origins. Among the OTX2-regulated differentially spliced genes, PPHLN1 is expressed in the most primitive rhombic lip stem cells, and targeting PPHLN1 splicing reduces tumour growth and enhances survival in vivo. These findings identify OTX2-mediated alternative splicing as a major determinant of cell fate decisions that drive group 3 MB progression.
Collapse
Affiliation(s)
- Olivier Saulnier
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
- Genomics and Development of Childhood Cancers, Institut Curie, PSL University, Paris, France
- INSERM U830, Cancer, Heterogeneity, Instability and Plasticity, Institut Curie, PSL University, Paris, France
- SIREDO Oncology Center, Institut Curie, Paris, France
| | - Jamie Zagozewski
- Department of Biochemistry and Medical Genetics, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Lisa Liang
- Department of Biochemistry and Medical Genetics, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Liam D Hendrikse
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Paul Layug
- Department of Biochemistry and Medical Genetics, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Victor Gordon
- Department of Biochemistry and Medical Genetics, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Kimberly A Aldinger
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, USA
- Department of Pediatrics, Division of Genetic Medicine, University of Washington, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
| | - Parthiv Haldipur
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, USA
| | - Stephanie Borlase
- Department of Biochemistry and Medical Genetics, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Ludivine Coudière-Morrison
- Department of Biochemistry and Medical Genetics, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Ting Cai
- Segal Cancer Center, Lady Davis Institute for Medical Research and Gerald Bronfman Department of Oncology, McGill University, Montreal, Quebec, Canada
- Departments of Biochemistry, Human Genetics and Medicine, McGill University, Montreal, Quebec, Canada
| | - Emma Martell
- Department of Pathology, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
- Department of Human Anatomy and Cell Science, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Naomi M Gonzales
- Texas Children's Hospital, Houston, TX, USA
- Department of Pediatrics, Hematology/Oncology, Baylor College of Medicine, Houston, TX, USA
| | - Gareth Palidwor
- Ottawa Bioinformatics Core Facility, Ottawa Hospital Research Institute, Ottawa, Ontario, Canada
| | - Christopher J Porter
- Ottawa Bioinformatics Core Facility, Ottawa Hospital Research Institute, Ottawa, Ontario, Canada
| | - Stéphane Richard
- Segal Cancer Center, Lady Davis Institute for Medical Research and Gerald Bronfman Department of Oncology, McGill University, Montreal, Quebec, Canada
- Departments of Biochemistry, Human Genetics and Medicine, McGill University, Montreal, Quebec, Canada
| | - Tanveer Sharif
- Department of Pathology, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
- Department of Human Anatomy and Cell Science, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Kathleen J Millen
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, USA
- Department of Pediatrics, Division of Genetic Medicine, University of Washington, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
| | - Brad W Doble
- Department of Biochemistry and Medical Genetics, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
- Department of Pediatrics and Child Health, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Michael D Taylor
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada.
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada.
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.
- Texas Children's Hospital, Houston, TX, USA.
- Department of Pediatrics, Hematology/Oncology, Baylor College of Medicine, Houston, TX, USA.
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada.
- Department of Surgery, University of Toronto, Toronto, Ontario, Canada.
- Texas Children's Cancer and Hematology Center, Houston, TX, USA.
- Department of Neurosurgery, Baylor College of Medicine, Houston, TX, USA.
- Department of Neurosurgery, Texas Children's Hospital, Houston, TX, USA.
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA.
| | - Tamra E Werbowetski-Ogilvie
- Department of Biochemistry and Medical Genetics, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada.
- Texas Children's Hospital, Houston, TX, USA.
- Department of Pediatrics, Hematology/Oncology, Baylor College of Medicine, Houston, TX, USA.
- Texas Children's Cancer and Hematology Center, Houston, TX, USA.
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA.
| |
Collapse
|
5
|
Ahel J, Pandey A, Schwaiger M, Mohn F, Basters A, Kempf G, Andriollo A, Kaaij L, Hess D, Bühler M. ChAHP2 and ChAHP control diverse retrotransposons by complementary activities. Genes Dev 2024; 38:554-568. [PMID: 38960717 PMCID: PMC11293393 DOI: 10.1101/gad.351769.124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Accepted: 06/07/2024] [Indexed: 07/05/2024]
Abstract
Retrotransposon control in mammals is an intricate process that is effectuated by a broad network of chromatin regulatory pathways. We previously discovered ChAHP, a protein complex with repressive activity against short interspersed element (SINE) retrotransposons that is composed of the transcription factor ADNP, chromatin remodeler CHD4, and HP1 proteins. Here we identify ChAHP2, a protein complex homologous to ChAHP, in which ADNP is replaced by ADNP2. ChAHP2 is predominantly targeted to endogenous retroviruses (ERVs) and long interspersed elements (LINEs) via HP1β-mediated binding of H3K9 trimethylated histones. We further demonstrate that ChAHP also binds these elements in a manner mechanistically equivalent to that of ChAHP2 and distinct from DNA sequence-specific recruitment at SINEs. Genetic ablation of ADNP2 alleviates ERV and LINE1 repression, which is synthetically exacerbated by additional depletion of ADNP. Together, our results reveal that the ChAHP and ChAHP2 complexes function to control both nonautonomous and autonomous retrotransposons by complementary activities, further adding to the complexity of mammalian transposon control.
Collapse
Affiliation(s)
- Josip Ahel
- Friedrich Miescher Institute for Biomedical Research, Basel 4056, Switzerland
| | - Aparna Pandey
- Friedrich Miescher Institute for Biomedical Research, Basel 4056, Switzerland
| | - Michaela Schwaiger
- Friedrich Miescher Institute for Biomedical Research, Basel 4056, Switzerland
- Swiss Institute of Bioinformatics, Basel 4056, Switzerland
| | - Fabio Mohn
- Friedrich Miescher Institute for Biomedical Research, Basel 4056, Switzerland
| | - Anja Basters
- Friedrich Miescher Institute for Biomedical Research, Basel 4056, Switzerland
| | - Georg Kempf
- Friedrich Miescher Institute for Biomedical Research, Basel 4056, Switzerland
| | - Aude Andriollo
- Friedrich Miescher Institute for Biomedical Research, Basel 4056, Switzerland
- University of Basel, Basel 4003, Switzerland
| | - Lucas Kaaij
- Friedrich Miescher Institute for Biomedical Research, Basel 4056, Switzerland
| | - Daniel Hess
- Friedrich Miescher Institute for Biomedical Research, Basel 4056, Switzerland
| | - Marc Bühler
- Friedrich Miescher Institute for Biomedical Research, Basel 4056, Switzerland;
- University of Basel, Basel 4003, Switzerland
| |
Collapse
|
6
|
Rodríguez TC, Yurkovetskiy L, Nagalekshmi K, Lam CHO, Jazbec E, Maitland SA, Wolfe SA, Sontheimer EJ, Luban J. PRC1.6 localizes on chromatin with the human silencing hub (HUSH) complex for promoter-specific silencing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.12.603173. [PMID: 39026796 PMCID: PMC11257501 DOI: 10.1101/2024.07.12.603173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
An obligate step in the life cycle of HIV-1 and other retroviruses is the establishment of the provirus in target cell chromosomes. Transcriptional regulation of proviruses is complex, and understanding the mechanisms underlying this regulation has ramifications for fundamental biology, human health, and gene therapy implementation. The three core components of the Human Silencing Hub (HUSH) complex, TASOR, MPHOSPH8 (MPP8), and PPHLN1 (Periphilin 1), were identified in forward genetic screens for host genes that repress provirus expression. Subsequent loss-of-function screens revealed accessory proteins that collaborate with the HUSH complex to silence proviruses in particular contexts. To identify proteins associated with a HUSH complex-repressed provirus in human cells, we developed a technique, Provirus Proximal Proteomics, based on proximity labeling with C-BERST (dCas9-APEX2 biotinylation at genomic elements by restricted spatial tagging). Our screen exploited a lentiviral reporter that is silenced by the HUSH complex in a manner that is independent of the integration site in chromatin. Our data reveal that proviruses silenced by the HUSH complex are associated with DNA repair, mRNA processing, and transcriptional silencing proteins, including L3MBTL2, a member of the non-canonical polycomb repressive complex 1.6 (PRC1.6). A forward genetic screen confirmed that PRC1.6 components L3MBTL2 and MGA contribute to HUSH complex-mediated silencing. PRC1.6 was then shown to silence HUSH-sensitive proviruses in a promoter-specific manner. Genome wide profiling showed striking colocalization of the PRC1.6 and HUSH complexes on chromatin, primarily at sites of active promoters. Finally, PRC1.6 binding at a subset of genes that are silenced by the HUSH complex was dependent on the core HUSH complex component MPP8. These studies offer new tools with great potential for studying the transcriptional regulation of proviruses and reveal crosstalk between the HUSH complex and PRC1.6.
Collapse
Affiliation(s)
- Tomás C. Rodríguez
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | - Leonid Yurkovetskiy
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | - Karthika Nagalekshmi
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | - Chin Hung Oscar Lam
- Graduate School of Biomedical Sciences, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | - Eva Jazbec
- Graduate School of Biomedical Sciences, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | - Stacy A. Maitland
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Scot A. Wolfe
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA, USA
- Li Weibo Institute for Rare Diseases Research, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | - Erik J. Sontheimer
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
- Li Weibo Institute for Rare Diseases Research, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | - Jeremy Luban
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
- Li Weibo Institute for Rare Diseases Research, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
- Massachusetts Consortium on Pathogen Readiness, Boston, MA 02115, USA
| |
Collapse
|
7
|
Wang K, Zhu W, Huang W, Huang K, Luo H, Long L, Yi B. TRIM Expression in HNSCC: Exploring the Link Between Ubiquitination, Immune Infiltration, and Signaling Pathways Through Bioinformatics. Int J Gen Med 2024; 17:2389-2405. [PMID: 38808201 PMCID: PMC11132118 DOI: 10.2147/ijgm.s463286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Accepted: 05/13/2024] [Indexed: 05/30/2024] Open
Abstract
Objective Ubiquitination is an important post-translational modification. However, the significance of the TRIM family of E3 ubiquitin ligases in head and neck squamous cell carcinoma (HNSCC) has not been determined. In this study, the roles of TRIM E3 ubiquitin ligases in lymphovascular invasion in head and neck squamous cell carcinoma (HNSCC) were evaluated. Materials and Methods TRIM expression and related parameters were obtained from UbiBrowser2.0, UALCAN, TIMER, TISIDB, LinkedOmics, STRING, and GeneMANIA databases. Immunohistochemistry was used to confirm their expression. Results TRIM2, TRIM11, TRIM28, and TRIM56 were upregulated in HNSCC with lymphovascular invasion. TRIM expression was strongly associated with immune infiltration, including key treatment targets, like PD-1 and CTL4. Co-expressed genes and possible ubiquitination substrates included tumor-related factors. The TRIMs had predicted roles in ubiquitination-related pathways and vital signaling pathways, eg, MAPK, PI3K-Akt, and JAK-STAT signaling pathways. Conclusion Ubiquitination mediated by four TRIMs might be involved in the regulation of tumor immunity, laying the foundation for future studies of the roles of the TRIM family on the prediction and personalized medicine in HNSCC. The four TRIMs might exert oncogenic effects by promoting lymphovascular invasion in HNSCC.
Collapse
Affiliation(s)
- Kun Wang
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha, Hunan Province, People’s Republic of China
| | - Wei Zhu
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, Hunan Province, People’s Republic of China
| | - Wei Huang
- Research Center of Carcinogenesis and Targeted Therapy, Xiangya Hospital, Central South University, Changsha, Hunan Province, People’s Republic of China
| | - Kangkang Huang
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha, Hunan Province, People’s Republic of China
| | - Huidan Luo
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha, Hunan Province, People’s Republic of China
| | - Lu Long
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha, Hunan Province, People’s Republic of China
| | - Bin Yi
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha, Hunan Province, People’s Republic of China
| |
Collapse
|
8
|
Damhofer H, Tatar T, Southgate B, Scarneo S, Agger K, Shlyueva D, Uhrbom L, Morrison GM, Hughes PF, Haystead T, Pollard SM, Helin K. TAK1 inhibition leads to RIPK1-dependent apoptosis in immune-activated cancers. Cell Death Dis 2024; 15:273. [PMID: 38632238 PMCID: PMC11024179 DOI: 10.1038/s41419-024-06654-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Revised: 04/02/2024] [Accepted: 04/05/2024] [Indexed: 04/19/2024]
Abstract
Poor survival and lack of treatment response in glioblastoma (GBM) is attributed to the persistence of glioma stem cells (GSCs). To identify novel therapeutic approaches, we performed CRISPR/Cas9 knockout screens and discovered TGFβ activated kinase (TAK1) as a selective survival factor in a significant fraction of GSCs. Loss of TAK1 kinase activity results in RIPK1-dependent apoptosis via Caspase-8/FADD complex activation, dependent on autocrine TNFα ligand production and constitutive TNFR signaling. We identify a transcriptional signature associated with immune activation and the mesenchymal GBM subtype to be a characteristic of cancer cells sensitive to TAK1 perturbation and employ this signature to accurately predict sensitivity to the TAK1 kinase inhibitor HS-276. In addition, exposure to pro-inflammatory cytokines IFNγ and TNFα can sensitize resistant GSCs to TAK1 inhibition. Our findings reveal dependency on TAK1 kinase activity as a novel vulnerability in immune-activated cancers, including mesenchymal GBMs that can be exploited therapeutically.
Collapse
Affiliation(s)
- Helene Damhofer
- Division of Cancer Biology, The Institute of Cancer Research, London, UK
- Cell Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark
| | - Tülin Tatar
- Division of Cancer Biology, The Institute of Cancer Research, London, UK
- Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark
| | - Benjamin Southgate
- Centre for Regenerative Medicine, University of Edinburgh, Edinburgh, UK
| | - Scott Scarneo
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC, USA
- EydisBio Inc., Durham, NC, USA
| | - Karl Agger
- Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark
| | - Daria Shlyueva
- Cell Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark
| | - Lene Uhrbom
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Gillian M Morrison
- Centre for Regenerative Medicine, University of Edinburgh, Edinburgh, UK
| | - Philip F Hughes
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC, USA
- EydisBio Inc., Durham, NC, USA
| | - Timothy Haystead
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC, USA
- EydisBio Inc., Durham, NC, USA
| | - Steven M Pollard
- Centre for Regenerative Medicine, University of Edinburgh, Edinburgh, UK
| | - Kristian Helin
- Division of Cancer Biology, The Institute of Cancer Research, London, UK.
- Cell Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark.
| |
Collapse
|
9
|
Wang X, Sun H, Dong Y, Huang J, Bai L, Tang Z, Liu S, Chen S. Development and validation of a cuproptosis-related prognostic model for acute myeloid leukemia patients using machine learning with stacking. Sci Rep 2024; 14:2802. [PMID: 38307903 PMCID: PMC10837443 DOI: 10.1038/s41598-024-53306-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2023] [Accepted: 01/30/2024] [Indexed: 02/04/2024] Open
Abstract
Our objective is to develop a prognostic model focused on cuproptosis, aimed at predicting overall survival (OS) outcomes among Acute myeloid leukemia (AML) patients. The model utilized machine learning algorithms incorporating stacking. The GSE37642 dataset was used as the training data, and the GSE12417 and TCGA-LAML cohorts were used as the validation data. Stacking was used to merge the three prediction models, subsequently using a random survival forests algorithm to refit the final model using the stacking linear predictor and clinical factors. The prediction model, featuring stacking linear predictor and clinical factors, achieved AUC values of 0.840, 0.876 and 0.892 at 1, 2 and 3 years within the GSE37642 dataset. In external validation dataset, the corresponding AUCs were 0.741, 0.754 and 0.783. The predictive performance of the model in the external dataset surpasses that of the model simply incorporates all predictors. Additionally, the final model exhibited good calibration accuracy. In conclusion, our findings indicate that the novel prediction model refines the prognostic prediction for AML patients, while the stacking strategy displays potential for model integration.
Collapse
Affiliation(s)
- Xichao Wang
- Department of Biostatistics, School of Public Health, Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, MOE Key Laboratory of Geriatric Diseases and Immunology, Suzhou Medical College of Soochow University, Suzhou, Jiangsu, 215123, P. R. China
| | - Hao Sun
- Department of Biostatistics, School of Public Health, Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, MOE Key Laboratory of Geriatric Diseases and Immunology, Suzhou Medical College of Soochow University, Suzhou, Jiangsu, 215123, P. R. China
| | - Yongfei Dong
- Department of Biostatistics, School of Public Health, Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, MOE Key Laboratory of Geriatric Diseases and Immunology, Suzhou Medical College of Soochow University, Suzhou, Jiangsu, 215123, P. R. China
| | - Jie Huang
- Department of Biostatistics, School of Public Health, Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, MOE Key Laboratory of Geriatric Diseases and Immunology, Suzhou Medical College of Soochow University, Suzhou, Jiangsu, 215123, P. R. China
| | - Lu Bai
- Department of Biostatistics, School of Public Health, Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, MOE Key Laboratory of Geriatric Diseases and Immunology, Suzhou Medical College of Soochow University, Suzhou, Jiangsu, 215123, P. R. China
| | - Zaixiang Tang
- Department of Biostatistics, School of Public Health, Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, MOE Key Laboratory of Geriatric Diseases and Immunology, Suzhou Medical College of Soochow University, Suzhou, Jiangsu, 215123, P. R. China.
| | - Songbai Liu
- Suzhou Key Laboratory of Medical Biotechnology, Suzhou Vocational Health College, Suzhou, 215009, Jiangsu, China.
| | - Suning Chen
- National Clinical Research Center for Hematologic Diseases, The First Affiliated Hospital of Soochow University, Jiangsu Institute of Hematology, Institute of Blood and Marrow Transplantation, Collaborative Innovation Center of Hematology, Soochow University, Suzhou, China.
| |
Collapse
|
10
|
Jensvold ZD, Christenson AE, Flood JR, Lewis PW. Interplay between Two Paralogous Human Silencing Hub (HuSH) Complexes in Regulating LINE-1 Element Silencing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.28.573526. [PMID: 38313255 PMCID: PMC10836065 DOI: 10.1101/2023.12.28.573526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2024]
Abstract
The Human Silencing Hub (HuSH) complex is composed of TASOR, MPP8, and PPHLN1 subunits and serves as a conserved protein complex responsible for silencing transposable elements in vertebrate animals. Despite its importance, the regulatory mechanisms and recruitment dynamics governing this complex remain poorly understood. In this study, we have identified a second HuSH complex, termed HuSH2, centered around TASOR2, a paralog of the core TASOR protein in HuSH. Our findings indicate that every subunit in both HuSH and HuSH2 has an important role in achieving precise genomic localization to distinct, non-overlapping genomic loci. We utilized in silico protein structure prediction to simulate the interactions between MPP8 and both TASOR paralogs. Drawing on the insights gained from these predictions, we implemented amino acid substitutions that interfered with the binding of MPP8 to each HuSH complex. Leveraging these MPP8 transgenes and other constructs, we identified an important role played by the relative quantities of HuSH complexes in controlling the activity of LINE-1 elements. Furthermore, our results suggest that dynamic changes in TASOR and TASOR2 expression enable cells to finely tune the extent of HuSH-mediated silencing. Our study provides insights into the intricate interplay between HuSH complexes, illuminating their important role in the regulation of retrotransposon silencing.
Collapse
Affiliation(s)
- Zena D Jensvold
- Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin, Madison, WI 53715, USA
| | - Anna E Christenson
- Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin, Madison, WI 53715, USA
| | - Julia R Flood
- Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin, Madison, WI 53715, USA
| | - Peter W Lewis
- Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin, Madison, WI 53715, USA
| |
Collapse
|
11
|
Müller I, Helin K. Keep quiet: the HUSH complex in transcriptional silencing and disease. Nat Struct Mol Biol 2024; 31:11-22. [PMID: 38216658 DOI: 10.1038/s41594-023-01173-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 10/23/2023] [Indexed: 01/14/2024]
Abstract
The human silencing hub (HUSH) complex is an epigenetic repressor complex whose role has emerged as an important guardian of genome integrity. It protects the genome from exogenous DNA invasion and regulates endogenous retroelements by recruiting histone methyltransferases catalyzing histone 3 lysine 9 trimethylation (H3K9me3) and additional proteins involved in chromatin compaction. In particular, its regulation of transcriptionally active LINE1 retroelements, by binding to and neutralizing LINE1 transcripts, has been well characterized. HUSH is required for mouse embryogenesis and is associated with disease, in particular cancer. Here we provide insights into the structural and biochemical features of the HUSH complex. Furthermore, we discuss the molecular mechanisms by which the HUSH complex is recruited to specific genomic regions and how it silences transcription. Finally, we discuss the role of HUSH complex members in mammalian development, antiretroviral immunity, and diseases such as cancer.
Collapse
Affiliation(s)
- Iris Müller
- Cell Biology Program and Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kristian Helin
- Cell Biology Program and Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- The Institute of Cancer Research, London, UK.
| |
Collapse
|
12
|
Luo H, Wu X, Zhu XH, Yi X, Du D, Jiang DS. The functions of SET domain bifurcated histone lysine methyltransferase 1 (SETDB1) in biological process and disease. Epigenetics Chromatin 2023; 16:47. [PMID: 38057834 DOI: 10.1186/s13072-023-00519-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 10/27/2023] [Indexed: 12/08/2023] Open
Abstract
Histone methyltransferase SETDB1 (SET domain bifurcated histone lysine methyltransferase 1, also known as ESET or KMT1E) is known to be involved in the deposition of the di- and tri-methyl marks on H3K9 (H3K9me2 and H3K9me3), which are associated with transcription repression. SETDB1 exerts an essential role in the silencing of endogenous retroviruses (ERVs) in embryonic stem cells (mESCs) by tri-methylating H3K9 (H3K9me3) and interacting with DNA methyltransferases (DNMTs). Additionally, SETDB1 is engaged in regulating multiple biological processes and diseases, such as ageing, tumors, and inflammatory bowel disease (IBD), by methylating both histones and non-histone proteins. In this review, we provide an overview of the complex biology of SETDB1, review the upstream regulatory mechanisms of SETDB1 and its partners, discuss the functions and molecular mechanisms of SETDB1 in cell fate determination and stem cell, as well as in tumors and other diseases. Finally, we discuss the current challenges and prospects of targeting SETDB1 for the treatment of different diseases, and we also suggest some future research directions in the field of SETDB1 research.
Collapse
Affiliation(s)
- Hanshen Luo
- Division of Cardiovascular Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Ave., Wuhan, 430030, China
| | - Xingliang Wu
- Department of Cardiology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Xue-Hai Zhu
- Division of Cardiovascular Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Ave., Wuhan, 430030, China
- Key Laboratory of Organ Transplantation, Ministry of Education; NHC Key Laboratory of Organ Transplantation; Key Laboratory of Organ Transplantation, Chinese Academy of Medical Sciences, Wuhan, Hubei, China
| | - Xin Yi
- Department of Cardiology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Dunfeng Du
- Key Laboratory of Organ Transplantation, Ministry of Education; NHC Key Laboratory of Organ Transplantation; Key Laboratory of Organ Transplantation, Chinese Academy of Medical Sciences, Wuhan, Hubei, China.
- Institute of Organ Transplantation, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China.
| | - Ding-Sheng Jiang
- Division of Cardiovascular Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Ave., Wuhan, 430030, China.
- Key Laboratory of Organ Transplantation, Ministry of Education; NHC Key Laboratory of Organ Transplantation; Key Laboratory of Organ Transplantation, Chinese Academy of Medical Sciences, Wuhan, Hubei, China.
| |
Collapse
|
13
|
Fujimori T, Rios-Martinez C, Thurm AR, Hinks MM, Doughty BR, Sinha J, Le D, Hafner A, Greenleaf WJ, Boettiger AN, Bintu L. Single-cell chromatin state transitions during epigenetic memory formation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.03.560616. [PMID: 37873344 PMCID: PMC10592931 DOI: 10.1101/2023.10.03.560616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Repressive chromatin modifications are thought to compact chromatin to silence transcription. However, it is unclear how chromatin structure changes during silencing and epigenetic memory formation. We measured gene expression and chromatin structure in single cells after recruitment and release of repressors at a reporter gene. Chromatin structure is heterogeneous, with open and compact conformations present in both active and silent states. Recruitment of repressors associated with epigenetic memory produces chromatin compaction across 10-20 kilobases, while reversible silencing does not cause compaction at this scale. Chromatin compaction is inherited, but changes molecularly over time from histone methylation (H3K9me3) to DNA methylation. The level of compaction at the end of silencing quantitatively predicts epigenetic memory weeks later. Similarly, chromatin compaction at the Nanog locus predicts the degree of stem-cell fate commitment. These findings suggest that the chromatin state across tens of kilobases, beyond the gene itself, is important for epigenetic memory formation.
Collapse
Affiliation(s)
- Taihei Fujimori
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | | | - Abby R. Thurm
- Biophysics Program, Stanford University, Stanford, CA, USA
| | - Michaela M. Hinks
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | | | - Joydeb Sinha
- Department of Chemical & Systems Biology, Stanford University, Stanford, CA, USA
| | - Derek Le
- Department of Dermatology, Program in Epithelial Biology, Stanford University, Stanford, CA, USA
- Program in Cancer Biology, Stanford University, Stanford, CA, USA
| | - Antonina Hafner
- Department of Developmental Biology, Stanford University, Stanford, CA, USA
- Current address: Department of Discovery Oncology, Genentech, CA, USA
| | - William J. Greenleaf
- Department of Genetics, Stanford University, Stanford, CA, USA
- Department of Applied Physics, Stanford University, Stanford, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | | | - Lacramioara Bintu
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| |
Collapse
|
14
|
Zhang H, Yang T, Wu H, Yi W, Dai C, Chen X, Zhang W, Ye Y. MPP8 Governs the Activity of the LIF/STAT3 Pathway and Plays a Crucial Role in the Differentiation of Mouse Embryonic Stem Cells. Cells 2023; 12:2023. [PMID: 37626833 PMCID: PMC10453500 DOI: 10.3390/cells12162023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 08/02/2023] [Accepted: 08/04/2023] [Indexed: 08/27/2023] Open
Abstract
Mouse embryonic stem cells (mESCs) possess the remarkable characteristics of unlimited self-renewal and pluripotency, which render them highly valuable for both fundamental research and clinical applications. A comprehensive understanding of the molecular mechanisms underlying mESC function is of the utmost importance. The Human Silence Hub (HUSH) complex, comprising FAM208A, MPP8, and periphilin, constitutes an epigenetic silencing complex involved in suppressing retroviruses and transposons during early embryonic development. However, its precise role in regulating mESC pluripotency and differentiation remains elusive. In this study, we generated homogenous miniIAA7-tagged Mpp8 mouse ES cell lines. Upon induction of MPP8 protein degradation, we observed the impaired proliferation and reduced colony formation ability of mESCs. Furthermore, this study unveils the involvement of MPP8 in regulating the activity of the LIF/STAT3 signaling pathway and Nanog expression in mESCs. Finally, we provide compelling evidence that degradation of the MPP8 protein impairs the differentiation of mESC.
Collapse
Affiliation(s)
- Heyao Zhang
- Cam-Su Genomic Resource Center, Medical College of Soochow University, Suzhou 215123, China
| | - Tenghui Yang
- Cam-Su Genomic Resource Center, Medical College of Soochow University, Suzhou 215123, China
| | - Hao Wu
- Cam-Su Genomic Resource Center, Medical College of Soochow University, Suzhou 215123, China
| | - Wen Yi
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China (X.C.)
| | - Chunhong Dai
- Cam-Su Genomic Resource Center, Medical College of Soochow University, Suzhou 215123, China
| | - Xi Chen
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China (X.C.)
| | - Wensheng Zhang
- Cam-Su Genomic Resource Center, Medical College of Soochow University, Suzhou 215123, China
- Zhejiang Stem and Ageing Research (Z-StAR) Institute, International Campus, Zhejiang University, Haining 314400, China
| | - Ying Ye
- Cam-Su Genomic Resource Center, Medical College of Soochow University, Suzhou 215123, China
| |
Collapse
|
15
|
Wang J, Zhang C, Huang Y, Ruan Y, Hu Y, Wang J, Wang F, Yu M, Xu Y, Liu L, Cheng Y, Yang R, Dong Y, Wang J, Yang Y, Xiong J, Tian Y, Gao Q, Zhang J, Jian R. Parallel Genome-Wide CRISPR Screens to Identify State-Dependent Self-Renewal Regulators of Mouse Embryonic Stem Cells. Stem Cells Dev 2023; 32:450-464. [PMID: 37166379 DOI: 10.1089/scd.2023.0053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023] Open
Abstract
The pluripotency of embryonic stem cells (ESCs) is more accurately viewed as a continuous developmental process rather than a fixed state. However, the factors that play general or state-specific roles in regulating self-renewal in different pluripotency states remain poorly defined. In this study, parallel genome-wide CRISPR/Cas9 knockout (KO) screens were applied in ESCs cultured in the serum plus LIF (SL) and in the 2i plus LIF (2iL) conditions. The candidate genes were classified into seven groups based on their positive or negative effects on self-renewal, and whether this effect was general or state-specific for ESCs under SL and 2iL culture conditions. We characterized the expression and function of genes in these seven groups. The loss of function of novel pluripotent candidate genes Usp28, Zfp598, and Zfp296 was further evaluated in mouse ESCs. Consistent with our screen, the knockout of Usp28 promotes the proliferation of SL-ESCs and 2iL-ESCs, whereas Zfp598 is indispensable for the self-renewal of ESCs under both culture conditions. The cell phenotypes of Zfp296 KO ESCs under SL and 2iL culture conditions were different. Our work provided a valuable resource for dissecting the molecular regulation of ESC self-renewal in different pluripotency states.
Collapse
Affiliation(s)
- Jiangjun Wang
- Laboratory of Stem Cell and Developmental Biology, Department of Histology and Embryology, College of Basic Medical Science, Army Medical University, Chongqing, China
- Department of Cell Biology, College of Basic Medical Science, Army Medical University, Chongqing, China
| | - Chen Zhang
- Laboratory of Stem Cell and Developmental Biology, Department of Histology and Embryology, College of Basic Medical Science, Army Medical University, Chongqing, China
| | - Yi Huang
- Biomedical Analysis Center, Army Medical University, Chongqing, China
| | - Yan Ruan
- Laboratory of Stem Cell and Developmental Biology, Department of Histology and Embryology, College of Basic Medical Science, Army Medical University, Chongqing, China
| | - Yan Hu
- Department of Military Basic Training and Army Management, Army Health Service Training Base, Army Medical University, Chongqing, China
| | - Jiaqi Wang
- Laboratory of Stem Cell and Developmental Biology, Department of Histology and Embryology, College of Basic Medical Science, Army Medical University, Chongqing, China
- Department of Pathophysiology, College of High-Altitude Military Medicine, Army Medical University, Chongqing, China
| | - Fengsheng Wang
- Laboratory of Stem Cell and Developmental Biology, Department of Histology and Embryology, College of Basic Medical Science, Army Medical University, Chongqing, China
- State Key Laboratory of NBC Protection for Civilian, Beijing, China
| | - Meng Yu
- Laboratory of Stem Cell and Developmental Biology, Department of Histology and Embryology, College of Basic Medical Science, Army Medical University, Chongqing, China
- Department of Joint Surgery, Southwest Hospital, the First Hospital Affiliated to Army Medical University, Chongqing, China
| | - Yixiao Xu
- Laboratory of Stem Cell and Developmental Biology, Department of Histology and Embryology, College of Basic Medical Science, Army Medical University, Chongqing, China
| | - Lianlian Liu
- Laboratory of Stem Cell and Developmental Biology, Department of Histology and Embryology, College of Basic Medical Science, Army Medical University, Chongqing, China
| | - Yuda Cheng
- Laboratory of Stem Cell and Developmental Biology, Department of Histology and Embryology, College of Basic Medical Science, Army Medical University, Chongqing, China
| | - Ran Yang
- Laboratory of Stem Cell and Developmental Biology, Department of Histology and Embryology, College of Basic Medical Science, Army Medical University, Chongqing, China
- Department of Pathophysiology, College of High-Altitude Military Medicine, Army Medical University, Chongqing, China
| | - Yutong Dong
- Laboratory of Stem Cell and Developmental Biology, Department of Histology and Embryology, College of Basic Medical Science, Army Medical University, Chongqing, China
- Department of Military Basic Training and Army Management, Army Health Service Training Base, Army Medical University, Chongqing, China
| | - Jiali Wang
- Laboratory of Stem Cell and Developmental Biology, Department of Histology and Embryology, College of Basic Medical Science, Army Medical University, Chongqing, China
| | - Yi Yang
- Experimental Center of Basic Medicine, College of Basic Medical Science, Army Medical University, Chongqing, China
| | - Jiaxiang Xiong
- Experimental Center of Basic Medicine, College of Basic Medical Science, Army Medical University, Chongqing, China
| | - Yanping Tian
- Laboratory of Stem Cell and Developmental Biology, Department of Histology and Embryology, College of Basic Medical Science, Army Medical University, Chongqing, China
| | - Qiangguo Gao
- Department of Cell Biology, College of Basic Medical Science, Army Medical University, Chongqing, China
| | - Junlei Zhang
- Laboratory of Stem Cell and Developmental Biology, Department of Histology and Embryology, College of Basic Medical Science, Army Medical University, Chongqing, China
| | - Rui Jian
- Laboratory of Stem Cell and Developmental Biology, Department of Histology and Embryology, College of Basic Medical Science, Army Medical University, Chongqing, China
| |
Collapse
|
16
|
Hansen SL, Larsen HL, Pikkupeura LM, Maciag G, Guiu J, Müller I, Clement DL, Mueller C, Johansen JV, Helin K, Lerdrup M, Jensen KB. An organoid-based CRISPR-Cas9 screen for regulators of intestinal epithelial maturation and cell fate. SCIENCE ADVANCES 2023; 9:eadg4055. [PMID: 37436979 DOI: 10.1126/sciadv.adg4055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 06/08/2023] [Indexed: 07/14/2023]
Abstract
Generation of functionally mature organs requires exquisite control of transcriptional programs governing cell state transitions during development. Despite advances in understanding the behavior of adult intestinal stem cells and their progeny, the transcriptional regulators that control the emergence of the mature intestinal phenotype remain largely unknown. Using mouse fetal and adult small intestinal organoids, we uncover transcriptional differences between the fetal and adult state and identify rare adult-like cells present in fetal organoids. This suggests that fetal organoids have an inherent potential to mature, which is locked by a regulatory program. By implementing a CRISPR-Cas9 screen targeting transcriptional regulators expressed in fetal organoids, we establish Smarca4 and Smarcc1 as important factors safeguarding the immature progenitor state. Our approach demonstrates the utility of organoid models in the identification of factors regulating cell fate and state transitions during tissue maturation and reveals that SMARCA4 and SMARCC1 prevent precocious differentiation during intestinal development.
Collapse
Affiliation(s)
- Stine L Hansen
- Novo Nordisk Foundation Center for Stem Cell Medicine, reNEW, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen N, Denmark
| | - Hjalte L Larsen
- Novo Nordisk Foundation Center for Stem Cell Medicine, reNEW, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen N, Denmark
| | - Laura M Pikkupeura
- Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaloes Vej 5, DK-2200 Copenhagen N, Denmark
| | - Grzegorz Maciag
- Novo Nordisk Foundation Center for Stem Cell Medicine, reNEW, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen N, Denmark
| | - Jordi Guiu
- Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaloes Vej 5, DK-2200 Copenhagen N, Denmark
- Institut d'Investigació Biomèdica de Bellvitge-IDIBELL, 3a planta, Av. Granvia de l'Hospitalet 199, 08908 Hospitalet de Llobregat, Spain
| | - Iris Müller
- Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaloes Vej 5, DK-2200 Copenhagen N, Denmark
| | - Ditte L Clement
- Novo Nordisk Foundation Center for Stem Cell Medicine, reNEW, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen N, Denmark
| | - Christina Mueller
- Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaloes Vej 5, DK-2200 Copenhagen N, Denmark
| | - Jens Vilstrup Johansen
- Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaloes Vej 5, DK-2200 Copenhagen N, Denmark
| | - Kristian Helin
- Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaloes Vej 5, DK-2200 Copenhagen N, Denmark
| | - Mads Lerdrup
- The DNRF Center for Chromosome Stability, Department of Cellular and Molecular Medicine, University of Copenhagen, DK-2200 Copenhagen N, Denmark
| | - Kim B Jensen
- Novo Nordisk Foundation Center for Stem Cell Medicine, reNEW, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen N, Denmark
- Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaloes Vej 5, DK-2200 Copenhagen N, Denmark
| |
Collapse
|
17
|
McCarthy RL, Zhang J, Zaret KS. Diverse heterochromatin states restricting cell identity and reprogramming. Trends Biochem Sci 2023; 48:513-526. [PMID: 36990958 PMCID: PMC10182259 DOI: 10.1016/j.tibs.2023.02.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 02/16/2023] [Accepted: 02/24/2023] [Indexed: 03/29/2023]
Abstract
Heterochromatin is defined as a chromosomal domain harboring repressive H3K9me2/3 or H3K27me3 histone modifications and relevant factors that physically compact the chromatin. Heterochromatin can restrict where transcription factors bind, providing a barrier to gene activation and changes in cell identity. While heterochromatin thus helps maintain cell differentiation, it presents a barrier to overcome during efforts to reprogram cells for biomedical purposes. Recent findings have revealed complexity in the composition and regulation of heterochromatin, and shown that transiently disrupting the machinery of heterochromatin can enhance reprogramming. Here, we discuss how heterochromatin is established and maintained during development, and how our growing understanding of the mechanisms regulating H3K9me3 heterochromatin can be leveraged to improve our ability to direct changes in cell identity.
Collapse
Affiliation(s)
- Ryan L McCarthy
- Institute for Regenerative Medicine, Penn Epigenetics Institute, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jingchao Zhang
- Institute for Regenerative Medicine, Penn Epigenetics Institute, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Kenneth S Zaret
- Institute for Regenerative Medicine, Penn Epigenetics Institute, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
| |
Collapse
|
18
|
Spencley AL, Bar S, Swigut T, Flynn RA, Lee CH, Chen LF, Bassik MC, Wysocka J. Co-transcriptional genome surveillance by HUSH is coupled to termination machinery. Mol Cell 2023; 83:1623-1639.e8. [PMID: 37164018 PMCID: PMC10915761 DOI: 10.1016/j.molcel.2023.04.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 01/12/2023] [Accepted: 04/12/2023] [Indexed: 05/12/2023]
Abstract
The HUSH complex recognizes and silences foreign DNA such as viruses, transposons, and transgenes without prior exposure to its targets. Here, we show that endogenous targets of the HUSH complex fall into two distinct classes based on the presence or absence of H3K9me3. These classes are further distinguished by their transposon content and differential response to the loss of HUSH. A de novo genomic rearrangement at the Sox2 locus induces a switch from H3K9me3-independent to H3K9me3-associated HUSH targeting, resulting in silencing. We further demonstrate that HUSH interacts with the termination factor WDR82 and-via its component MPP8-with nascent RNA. HUSH accumulates at sites of high RNAPII occupancy including long exons and transcription termination sites in a manner dependent on WDR82 and CPSF. Together, our results uncover the functional diversity of HUSH targets and show that this vertebrate-specific complex exploits evolutionarily ancient transcription termination machinery for co-transcriptional chromatin targeting and genome surveillance.
Collapse
Affiliation(s)
- Andrew L Spencley
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, USA; Cancer Biology Program, Stanford University School of Medicine, Stanford, CA, USA
| | - Shiran Bar
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Tomek Swigut
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Ryan A Flynn
- Stem Cell Program, Boston Children's Hospital, Boston, MA, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Cameron H Lee
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Liang-Fu Chen
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Michael C Bassik
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Joanna Wysocka
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, USA; Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA; Institute of Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA; Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA.
| |
Collapse
|
19
|
Phanindhar K, Mishra RK. Auxin-inducible degron system: an efficient protein degradation tool to study protein function. Biotechniques 2023; 74:186-198. [PMID: 37191015 DOI: 10.2144/btn-2022-0108] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/17/2023] Open
Abstract
Targeted protein degradation, with its rapid protein depletion kinetics, allows the measurement of acute changes in the cell. The auxin-inducible degron (AID) system, rapidly degrades AID-tagged proteins only in the presence of auxin. The AID system being inducible makes the study of essential genes and dynamic processes like cell differentiation, cell cycle and genome organization feasible. The AID degradation system has been adapted to yeast, protozoans, C. elegans, Drosophila, zebrafish, mouse and mammalian cell lines. Using the AID system, researchers have unveiled novel functions for essential proteins at developmental stages that were previously difficult to investigate due to early lethality. This comprehensive review discusses the development, advancements, applications and drawbacks of the AID system and compares it with other available protein degradation systems.
Collapse
Affiliation(s)
- Kundurthi Phanindhar
- CSIR-Centre for Cellular & Molecular Biology (CCMB), Uppal Road, Hyderabad, 500007, India
| | - Rakesh K Mishra
- CSIR-Centre for Cellular & Molecular Biology (CCMB), Uppal Road, Hyderabad, 500007, India
- Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, 201002, India
- Tata Institute for Genetics & Society (TIGS), Bangalore, 560065, India
| |
Collapse
|
20
|
Djeghloul D, Dimond A, Cheriyamkunnel S, Kramer H, Patel B, Brown K, Montoya A, Whilding C, Wang YF, Futschik ME, Veland N, Montavon T, Jenuwein T, Merkenschlager M, Fisher AG. Loss of H3K9 trimethylation alters chromosome compaction and transcription factor retention during mitosis. Nat Struct Mol Biol 2023; 30:489-501. [PMID: 36941433 PMCID: PMC10113154 DOI: 10.1038/s41594-023-00943-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 02/13/2023] [Indexed: 03/23/2023]
Abstract
Recent studies have shown that repressive chromatin machinery, including DNA methyltransferases and polycomb repressor complexes, binds to chromosomes throughout mitosis and their depletion results in increased chromosome size. In the present study, we show that enzymes that catalyze H3K9 methylation, such as Suv39h1, Suv39h2, G9a and Glp, are also retained on mitotic chromosomes. Surprisingly, however, mutants lacking histone 3 lysine 9 trimethylation (H3K9me3) have unusually small and compact mitotic chromosomes associated with increased histone H3 phospho Ser10 (H3S10ph) and H3K27me3 levels. Chromosome size and centromere compaction in these mutants were rescued by providing exogenous first protein lysine methyltransferase Suv39h1 or inhibiting Ezh2 activity. Quantitative proteomic comparisons of native mitotic chromosomes isolated from wild-type versus Suv39h1/Suv39h2 double-null mouse embryonic stem cells revealed that H3K9me3 was essential for the efficient retention of bookmarking factors such as Esrrb. These results highlight an unexpected role for repressive heterochromatin domains in preserving transcription factor binding through mitosis and underscore the importance of H3K9me3 for sustaining chromosome architecture and epigenetic memory during cell division.
Collapse
Affiliation(s)
- Dounia Djeghloul
- Epigenetic Memory Group, MRC London Institute of Medical Sciences, Imperial College London, London, UK.
| | - Andrew Dimond
- Epigenetic Memory Group, MRC London Institute of Medical Sciences, Imperial College London, London, UK
| | - Sherry Cheriyamkunnel
- Epigenetic Memory Group, MRC London Institute of Medical Sciences, Imperial College London, London, UK
| | - Holger Kramer
- Biological Mass Spectrometry and Proteomics Facility, MRC London Institute of Medical Sciences, Imperial College London, London, UK
| | - Bhavik Patel
- Flow Cytometry Facility, MRC London Institute of Medical Sciences, Imperial College London, London, UK
| | - Karen Brown
- Epigenetic Memory Group, MRC London Institute of Medical Sciences, Imperial College London, London, UK
| | - Alex Montoya
- Biological Mass Spectrometry and Proteomics Facility, MRC London Institute of Medical Sciences, Imperial College London, London, UK
| | - Chad Whilding
- Microscopy Facility, MRC London Institute of Medical Sciences, Imperial College London, London, UK
| | - Yi-Fang Wang
- Bioinformatics, MRC London Institute of Medical Sciences, Imperial College London, London, UK
| | - Matthias E Futschik
- Bioinformatics, MRC London Institute of Medical Sciences, Imperial College London, London, UK
| | - Nicolas Veland
- Epigenetic Memory Group, MRC London Institute of Medical Sciences, Imperial College London, London, UK
| | - Thomas Montavon
- Max-Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Thomas Jenuwein
- Max-Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Matthias Merkenschlager
- Lymphocyte Development Group, MRC London Institute of Medical Sciences, Imperial College London, London, UK
| | - Amanda G Fisher
- Epigenetic Memory Group, MRC London Institute of Medical Sciences, Imperial College London, London, UK.
| |
Collapse
|
21
|
Seczynska M, Lehner PJ. The sound of silence: mechanisms and implications of HUSH complex function. Trends Genet 2023; 39:251-267. [PMID: 36754727 DOI: 10.1016/j.tig.2022.12.005] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 12/14/2022] [Accepted: 12/30/2022] [Indexed: 02/08/2023]
Abstract
The vertebrate genome is under constant threat of invasion by genetic parasites. Whether the host can immediately recognize and respond to invading elements has been unclear. The discovery of the human silencing hub (HUSH) complex, and the finding that it provides immediate protection from genome invasion by silencing products of reverse transcription, have important implications for mammalian genome evolution. In this review, we summarize recent insights into HUSH function and describe how cellular introns provide a novel means of self-nonself discrimination, allowing HUSH to recognize and transcriptionally repress a broad range of intronless genetic elements. We discuss how HUSH contributes to genome evolution, and highlight studies reporting the critical role of HUSH in development and implicating HUSH in the control of immune signaling and cancer progression.
Collapse
Affiliation(s)
- Marta Seczynska
- Cambridge Institute for Therapeutic Immunology & Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of Cambridge, Cambridge CB2 0AW, UK.
| | - Paul J Lehner
- Cambridge Institute for Therapeutic Immunology & Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of Cambridge, Cambridge CB2 0AW, UK.
| |
Collapse
|
22
|
Wong YF, Kumar Y, Proks M, Herrera JAR, Rothová MM, Monteiro RS, Pozzi S, Jennings RE, Hanley NA, Bickmore WA, Brickman JM. Expansion of ventral foregut is linked to changes in the enhancer landscape for organ-specific differentiation. Nat Cell Biol 2023; 25:481-492. [PMID: 36690849 PMCID: PMC10014581 DOI: 10.1038/s41556-022-01075-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 12/14/2022] [Indexed: 01/24/2023]
Abstract
Cell proliferation is fundamental for almost all stages of development and differentiation that require an increase in cell number. Although cell cycle phase has been associated with differentiation, the actual process of proliferation has not been considered as having a specific role. Here we exploit human embryonic stem cell-derived endodermal progenitors that we find are an in vitro model for the ventral foregut. These cells exhibit expansion-dependent increases in differentiation efficiency to pancreatic progenitors that are linked to organ-specific enhancer priming at the level of chromatin accessibility and the decommissioning of lineage-inappropriate enhancers. Our findings suggest that cell proliferation in embryonic development is about more than tissue expansion; it is required to ensure equilibration of gene regulatory networks allowing cells to become primed for future differentiation. Expansion of lineage-specific intermediates may therefore be an important step in achieving high-fidelity in vitro differentiation.
Collapse
Affiliation(s)
- Yan Fung Wong
- Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), University of Copenhagen, Copenhagen, Denmark
| | - Yatendra Kumar
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Martin Proks
- Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), University of Copenhagen, Copenhagen, Denmark
| | - Jose Alejandro Romero Herrera
- Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), University of Copenhagen, Copenhagen, Denmark
- Center for Health Data Science, University of Copenhagen, Copenhagen, Denmark
| | - Michaela Mrugala Rothová
- Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), University of Copenhagen, Copenhagen, Denmark
| | - Rita S Monteiro
- Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), University of Copenhagen, Copenhagen, Denmark
| | - Sara Pozzi
- Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), University of Copenhagen, Copenhagen, Denmark
| | - Rachel E Jennings
- Faculty of Biology, Medicine & Health, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK
| | - Neil A Hanley
- Faculty of Biology, Medicine & Health, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK
| | - Wendy A Bickmore
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK.
| | - Joshua M Brickman
- Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), University of Copenhagen, Copenhagen, Denmark.
| |
Collapse
|
23
|
Wistner SC, MacDonald IA, Stanley KA, Hathaway NA. Characterization of Hepatoma-Derived Growth Factor-Related Protein 2 Interactions with Heterochromatin. Cells 2023; 12:325. [PMID: 36672260 PMCID: PMC9856275 DOI: 10.3390/cells12020325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 01/06/2023] [Accepted: 01/09/2023] [Indexed: 01/18/2023] Open
Abstract
The expression of genetic information is tightly controlled by chromatin regulatory proteins, including those in the heterochromatin gene repression family. Many of these regulatory proteins work together on the chromatin substrate to precisely regulate gene expression during mammalian development, giving rise to many different tissues in higher organisms from a fixed genomic template. Here we identify and characterize the interactions of two related heterochromatin regulatory proteins, heterochromatin protein 1 alpha (HP1α) and M-phase phosphoprotein 8 (MPP8), with hepatoma-derived growth factor-related protein 2 (HRP2). We find in biochemical experiments that HRP2 copurifies and co-sediments with heterochromatin-associated proteins, including HP1α and MPP8. Using the Chromatin in vivo Assay in multiple cell types, we demonstrate that HP1α-mediated gene repression dynamics are altered by the presence of HRP2. Furthermore, the knockout of HRP2 in MDA-MB-231 cells results in significant changes to chromatin structure and stability, which alter gene expression patterns. Here, we detail a mechanism by which HRP2 contributes to epigenetic transcriptional regulation through engagement with heterochromatin-associated proteins to stabilize the chromatin landscape and influence gene expression.
Collapse
Affiliation(s)
- Sarah C. Wistner
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Ian A. MacDonald
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Karly A. Stanley
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Nathaniel A. Hathaway
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- UNC Lineberger Comprehensive Cancer Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| |
Collapse
|
24
|
HIF1α-AS1 is a DNA:DNA:RNA triplex-forming lncRNA interacting with the HUSH complex. Nat Commun 2022; 13:6563. [PMID: 36323673 PMCID: PMC9630315 DOI: 10.1038/s41467-022-34252-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 10/19/2022] [Indexed: 11/07/2022] Open
Abstract
DNA:DNA:RNA triplexes that are formed through Hoogsteen base-pairing of the RNA in the major groove of the DNA duplex have been observed in vitro, but the extent to which these interactions occur in cells and how they impact cellular functions remains elusive. Using a combination of bioinformatic techniques, RNA/DNA pulldown and biophysical studies, we set out to identify functionally important DNA:DNA:RNA triplex-forming long non-coding RNAs (lncRNA) in human endothelial cells. The lncRNA HIF1α-AS1 was retrieved as a top hit. Endogenous HIF1α-AS1 reduces the expression of numerous genes, including EPH Receptor A2 and Adrenomedullin through DNA:DNA:RNA triplex formation by acting as an adapter for the repressive human silencing hub complex (HUSH). Moreover, the oxygen-sensitive HIF1α-AS1 is down-regulated in pulmonary hypertension and loss-of-function approaches not only result in gene de-repression but also enhance angiogenic capacity. As exemplified here with HIF1α-AS1, DNA:DNA:RNA triplex formation is a functionally important mechanism of trans-acting gene expression control.
Collapse
|
25
|
Li J, Dai C, Xie W, Zhang H, Huang X, Chronis C, Ye Y, Zhang W. A One-step strategy to target essential factors with auxin-inducible degron system in mouse embryonic stem cells. Front Cell Dev Biol 2022; 10:964119. [PMID: 36003152 PMCID: PMC9393215 DOI: 10.3389/fcell.2022.964119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 07/11/2022] [Indexed: 11/13/2022] Open
Abstract
The self-renewal and pluripotency of embryonic stem cells (ESCs) are conferred by networks including transcription factors and histone modifiers. The Auxin-inducible degron (AID) system can rapidly and reversibly degrade its target proteins and is becoming a powerful tool to explore novel function of key pluripotent and histone modifier genes in ESCs. However, the low biallelic tagging efficiency and a basal degradation level of the current AID systems deem it unsuitable to target key pluripotent genes with tightly controlled expression levels. Here, we develop a one-step strategy to successfully target and repress the endogenous pluripotent genes in mouse ESCs and replace their expression with AID fused transgenes. Therefore, this work provides an efficient way for employing the AID system to uncover novel function of essential pluripotent and chromatin modifier genes in ESCs.
Collapse
Affiliation(s)
- Jingsheng Li
- Cam-Su Genomic Resource Center, Medical College of Soochow University, Suzhou, China
| | - Chunhong Dai
- Cam-Su Genomic Resource Center, Medical College of Soochow University, Suzhou, China
| | - Wenyan Xie
- Cam-Su Genomic Resource Center, Medical College of Soochow University, Suzhou, China
| | - Heyao Zhang
- Cam-Su Genomic Resource Center, Medical College of Soochow University, Suzhou, China
| | - Xin Huang
- Department of Computational Biology St. Jude Children’s Research Hospital, Memphis, TN, United States
| | - Constantinos Chronis
- Department of Biochemistry and Molecular Genetics University of Illinois at Chicago, Chicago, IL, United States
| | - Ying Ye
- Cam-Su Genomic Resource Center, Medical College of Soochow University, Suzhou, China
- *Correspondence: Ying Ye, ; Wensheng Zhang,
| | - Wensheng Zhang
- Cam-Su Genomic Resource Center, Medical College of Soochow University, Suzhou, China
- Department of Physiology School of Basic Medical Sciences Binzhou Medical University, Yantai, China
- *Correspondence: Ying Ye, ; Wensheng Zhang,
| |
Collapse
|
26
|
Faulkner GJ. HUSH, retrotransposon RNA, you're NEXT to decay. Mol Cell 2022; 82:1610-1612. [PMID: 35523126 DOI: 10.1016/j.molcel.2022.04.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Garland et al. (2022) discover a physical and functional connection between the HUSH silencing complex and the NEXT nuclear RNA decay complex in mouse embryonic stem cells and conclude HUSH recruits NEXT to degrade prematurely terminated retrotransposon RNAs.
Collapse
Affiliation(s)
- Geoffrey J Faulkner
- Mater Research Institute - University of Queensland, Woolloongabba, QLD, 4102, Australia; Queensland Brain Institute, University of Queensland, St. Lucia, QLD, 4067, Australia.
| |
Collapse
|
27
|
Garland W, Müller I, Wu M, Schmid M, Imamura K, Rib L, Sandelin A, Helin K, Jensen TH. Chromatin modifier HUSH co-operates with RNA decay factor NEXT to restrict transposable element expression. Mol Cell 2022; 82:1691-1707.e8. [PMID: 35349793 PMCID: PMC9433625 DOI: 10.1016/j.molcel.2022.03.004] [Citation(s) in RCA: 43] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 12/14/2021] [Accepted: 03/01/2022] [Indexed: 12/12/2022]
Abstract
Transposable elements (TEs) are widespread genetic parasites known to be kept under tight transcriptional control. Here, we describe a functional connection between the mouse-orthologous “nuclear exosome targeting” (NEXT) and “human silencing hub” (HUSH) complexes, involved in nuclear RNA decay and the epigenetic silencing of TEs, respectively. Knocking out the NEXT component ZCCHC8 in embryonic stem cells results in elevated TE RNA levels. We identify a physical interaction between ZCCHC8 and the MPP8 protein of HUSH and establish that HUSH recruits NEXT to chromatin at MPP8-bound TE loci. However, while NEXT and HUSH both dampen TE RNA expression, their activities predominantly affect shorter non-polyadenylated and full-length polyadenylated transcripts, respectively. Indeed, our data suggest that the repressive action of HUSH promotes a condition favoring NEXT RNA decay activity. In this way, transcriptional and post-transcriptional machineries synergize to suppress the genotoxic potential of TE RNAs. Garland et al. report a physical and functional connection between the NEXT complex, involved in RNA decay, and the HUSH complex, involved in chromatin regulation. Together, NEXT and HUSH cooperate to control transposable element (TE) RNA expression in embryonic stem cells, suppressing pA− and pA+ transcripts, respectively.
Collapse
Affiliation(s)
- William Garland
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark; Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Iris Müller
- Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; Novo Nordisk Foundation for Stem Cell Biology, Faculty of Health and Medical Science, University of Copenhagen, Copenhagen, Denmark; Cell Biology Program and Center for Epigenetics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Mengjun Wu
- Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; The Bioinformatics Centre, Department of Biology, University of Copenhagen, Copenhagen, Denmark; SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solna, Sweden
| | - Manfred Schmid
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Katsutoshi Imamura
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Leonor Rib
- Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; The Bioinformatics Centre, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Albin Sandelin
- Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; The Bioinformatics Centre, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Kristian Helin
- Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; Novo Nordisk Foundation for Stem Cell Biology, Faculty of Health and Medical Science, University of Copenhagen, Copenhagen, Denmark; Cell Biology Program and Center for Epigenetics, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Torben Heick Jensen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark.
| |
Collapse
|
28
|
Messling JE, Agger K, Andersen KL, Kromer K, Kuepper HM, Lund AH, Helin K. Targeting RIOK2 ATPase activity leads to decreased protein synthesis and cell death in acute myeloid leukemia. Blood 2022; 139:245-255. [PMID: 34359076 PMCID: PMC8759535 DOI: 10.1182/blood.2021012629] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 07/29/2021] [Indexed: 01/16/2023] Open
Abstract
Novel therapies for the treatment of acute myeloid leukemia (AML) are urgently needed, because current treatments do not cure most patients with AML. We report a domain-focused, kinome-wide CRISPR-Cas9 screening that identified protein kinase targets for the treatment of AML, which led to the identification of Rio-kinase 2 (RIOK2) as a potential novel target. Loss of RIOK2 led to a decrease in protein synthesis and to ribosomal instability followed by apoptosis in leukemic cells, but not in fibroblasts. Moreover, the ATPase function of RIOK2 was necessary for cell survival. When a small-molecule inhibitor was used, pharmacological inhibition of RIOK2 similarly led to loss of protein synthesis and apoptosis and affected leukemic cell growth in vivo. Our results provide proof of concept for targeting RIOK2 as a potential treatment of patients with AML.
Collapse
Affiliation(s)
- Jan-Erik Messling
- Biotech Research and Innovation Centre and
- The Novo Nordisk Foundation Center for Stem Cell Biology (DanStem), University of Copenhagen, Copenhagen, Denmark; and
| | - Karl Agger
- Biotech Research and Innovation Centre and
- The Novo Nordisk Foundation Center for Stem Cell Biology (DanStem), University of Copenhagen, Copenhagen, Denmark; and
| | | | - Kristina Kromer
- Biotech Research and Innovation Centre and
- The Novo Nordisk Foundation Center for Stem Cell Biology (DanStem), University of Copenhagen, Copenhagen, Denmark; and
| | - Hanna M Kuepper
- Biotech Research and Innovation Centre and
- The Novo Nordisk Foundation Center for Stem Cell Biology (DanStem), University of Copenhagen, Copenhagen, Denmark; and
| | | | - Kristian Helin
- Biotech Research and Innovation Centre and
- The Novo Nordisk Foundation Center for Stem Cell Biology (DanStem), University of Copenhagen, Copenhagen, Denmark; and
- Cell Biology Program and
- Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY
| |
Collapse
|
29
|
Matkovic R, Morel M, Lanciano S, Larrous P, Martin B, Bejjani F, Vauthier V, Hansen MMK, Emiliani S, Cristofari G, Gallois-Montbrun S, Margottin-Goguet F. TASOR epigenetic repressor cooperates with a CNOT1 RNA degradation pathway to repress HIV. Nat Commun 2022; 13:66. [PMID: 35013187 PMCID: PMC8748822 DOI: 10.1038/s41467-021-27650-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 11/30/2021] [Indexed: 12/17/2022] Open
Abstract
The Human Silencing Hub (HUSH) complex constituted of TASOR, MPP8 and Periphilin recruits the histone methyl-transferase SETDB1 to spread H3K9me3 repressive marks across genes and transgenes in an integration site-dependent manner. The deposition of these repressive marks leads to heterochromatin formation and inhibits gene expression, but the underlying mechanism is not fully understood. Here, we show that TASOR silencing or HIV-2 Vpx expression, which induces TASOR degradation, increases the accumulation of transcripts derived from the HIV-1 LTR promoter at a post-transcriptional level. Furthermore, using a yeast 2-hybrid screen, we identify new TASOR partners involved in RNA metabolism including the RNA deadenylase CCR4-NOT complex scaffold CNOT1. TASOR and CNOT1 synergistically repress HIV expression from its LTR. Similar to the RNA-induced transcriptional silencing complex found in fission yeast, we show that TASOR interacts with the RNA exosome and RNA Polymerase II, predominantly under its elongating state. Finally, we show that TASOR facilitates the association of RNA degradation proteins with RNA polymerase II and is detected at transcriptional centers. Altogether, we propose that HUSH operates at the transcriptional and post-transcriptional levels to repress HIV proviral expression.
Collapse
Affiliation(s)
- Roy Matkovic
- Université de Paris, Institut Cochin, INSERM, CNRS, 75014, Paris, France.
| | - Marina Morel
- Université de Paris, Institut Cochin, INSERM, CNRS, 75014, Paris, France
| | | | - Pauline Larrous
- Université de Paris, Institut Cochin, INSERM, CNRS, 75014, Paris, France
| | - Benjamin Martin
- Université de Paris, Institut Cochin, INSERM, CNRS, 75014, Paris, France
| | - Fabienne Bejjani
- Université de Paris, Institut Cochin, INSERM, CNRS, 75014, Paris, France
| | - Virginie Vauthier
- Université de Paris, Institut Cochin, INSERM, CNRS, 75014, Paris, France
| | - Maike M K Hansen
- Institute for Molecules and Materials, Radboud University, 6525 AM, Nijmegen, The Netherlands
| | - Stéphane Emiliani
- Université de Paris, Institut Cochin, INSERM, CNRS, 75014, Paris, France
| | | | | | | |
Collapse
|
30
|
Li R, Grimm SA, Wade PA. CUT&Tag-BS for simultaneous profiling of histone modification and DNA methylation with high efficiency and low cost. CELL REPORTS METHODS 2021; 1:100118. [PMID: 35028637 PMCID: PMC8754398 DOI: 10.1016/j.crmeth.2021.100118] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 09/16/2021] [Accepted: 10/25/2021] [Indexed: 11/24/2022]
Abstract
It remains a challenge to decipher the complex relationship between DNA methylation, histone modification, and the underlying DNA sequence with limited input material. Here, we developed an efficient, low-input, and low-cost method for the simultaneous profiling of genomic localization of histone modification and methylation status of the underlying DNA at single-base resolution from the same cells in a single experiment by integrating cleavage under targets and tagmentation (CUT&Tag) with tagmentation-based bisulfite sequencing (CUT&Tag-BS). We demonstrated the validity of our method using representative histone modifications of euchromatin and constitutive and facultative heterochromatin (H3K4me1, H3K9me3, and H3K27me3, respectively). Similar histone modification enrichment patterns were observed in CUT&Tag-BS compared with non-bisulfite-treated control, and H3K4me1-marked regions were found to mostly be CpG poor, lack methylation concordance, and exhibit prevalent DNA methylation heterogeneity among mouse embryonic stem cells (mESCs). We anticipate that CUT&Tag-BS will be widely applied to directly address the genomic relationship between DNA methylation and histone modification, especially in low-input scenarios with precious biological samples.
Collapse
Affiliation(s)
- Ruifang Li
- Epigenetics Innovation Lab, Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Sara A. Grimm
- Integrative Bioinformatics Support Group, Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - Paul A. Wade
- Eukaryotic Transcriptional Regulation Group, Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| |
Collapse
|
31
|
Lin J, Guo D, Liu H, Zhou W, Wang C, Müller I, Kossenkov AV, Drapkin R, Bitler BG, Helin K, Zhang R. The SETDB1-TRIM28 Complex Suppresses Antitumor Immunity. Cancer Immunol Res 2021; 9:1413-1424. [PMID: 34848497 DOI: 10.1158/2326-6066.cir-21-0754] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 10/19/2021] [Accepted: 10/25/2021] [Indexed: 01/14/2023]
Abstract
The tumor immune microenvironment is influenced by the epigenetic landscape of the tumor. Here, we have identified the SETDB1-TRIM28 complex as a critical suppressor of antitumor immunity. An epigenetic CRISPR-Cas9 screen of 1,218 chromatin regulators identified TRIM28 as a suppressor of PD-L1 expression. We then revealed that expression of the SETDB1-TRIM28 complex negatively correlated with infiltration of effector CD8+ T cells. Inhibition of SETDB1-TRIM28 simultaneously upregulated PD-L1 and activated the cyclic GMP-AMP synthase (cGAS)-stimulator of interferon genes (STING) innate immune response pathway to increase infiltration of CD8+ T cells. Mechanistically, SETDB1-TRIM28 inhibition led to micronuclei formation in the cytoplasm, which is known to activate the cGAS-STING pathway. Thus, SETDB1-TRIM28 inhibition bridges innate and adaptive immunity. Indeed, SETDB1 knockout enhanced the antitumor effects of immune checkpoint blockade with anti-PD-L1 in a mouse model of ovarian cancer in a cGAS-dependent manner. Our findings establish the SETDB1-TRIM28 complex as a regulator of antitumor immunity and demonstrate that its loss activates cGAS-STING innate immunity to boost the antitumor effects of immune checkpoint blockade.
Collapse
Affiliation(s)
- Jianhuang Lin
- Immunology, Microenvironment and Metastasis Program, The Wistar Institute, Philadelphia, Pennsylvania
| | - Dajiang Guo
- Immunology, Microenvironment and Metastasis Program, The Wistar Institute, Philadelphia, Pennsylvania
| | - Heng Liu
- Immunology, Microenvironment and Metastasis Program, The Wistar Institute, Philadelphia, Pennsylvania
| | - Wei Zhou
- Immunology, Microenvironment and Metastasis Program, The Wistar Institute, Philadelphia, Pennsylvania
| | - Chen Wang
- Immunology, Microenvironment and Metastasis Program, The Wistar Institute, Philadelphia, Pennsylvania
| | - Iris Müller
- Cell Biology Program and Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, New York.,Biotech Research & Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark.,The Novo Nordisk Foundation Center for Stem Cell Biology (DanStem), University of Copenhagen, Copenhagen, Denmark
| | - Andrew V Kossenkov
- Gene Expression and Regulation Program, The Wistar Institute, Philadelphia, Pennsylvania
| | - Ronny Drapkin
- Department of Obstetrics and Gynecology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Benjamin G Bitler
- Division of Reproductive Sciences, Department of Obstetrics and Gynecology, The University of Colorado, Aurora, Colorado
| | - Kristian Helin
- Cell Biology Program and Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, New York.,Biotech Research & Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark.,The Novo Nordisk Foundation Center for Stem Cell Biology (DanStem), University of Copenhagen, Copenhagen, Denmark
| | - Rugang Zhang
- Immunology, Microenvironment and Metastasis Program, The Wistar Institute, Philadelphia, Pennsylvania.
| |
Collapse
|
32
|
Emerging role of G9a in cancer stemness and promises as a therapeutic target. Oncogenesis 2021; 10:76. [PMID: 34775469 PMCID: PMC8590690 DOI: 10.1038/s41389-021-00370-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 10/25/2021] [Accepted: 10/28/2021] [Indexed: 12/13/2022] Open
Abstract
The histone methyltransferase G9a is well-documented for its implication in neoplastic growth. However, recent investigations have demonstrated a key involvement of this chromatin writer in maintaining the self-renewal and tumor-initiating capacities of cancer stem cells (CSCs). Direct inhibition of G9a’s catalytic activity was reported as a promising therapeutic target in multiple preclinical studies. Yet, none of the available pharmacological inhibitors of G9a activity have shown success at the early stages of clinical testing. Here, we discuss central findings of oncogenic expression and activation of G9a in CSCs from different origins, as well as the impact of the suppression of G9a histone methyltransferase activity in such contexts. We will explore the challenges posed by direct and systemic inhibition of G9a activity in the perspective of clinical translation of documented small molecules. Finally, we will discuss recent advances in drug discovery as viable strategies to develop context-specific drugs, selectively targeting G9a in CSC populations.
Collapse
|
33
|
Factors Regulating the Activity of LINE1 Retrotransposons. Genes (Basel) 2021; 12:genes12101562. [PMID: 34680956 PMCID: PMC8535693 DOI: 10.3390/genes12101562] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 09/21/2021] [Accepted: 09/22/2021] [Indexed: 12/15/2022] Open
Abstract
LINE-1 (L1) is a class of autonomous mobile genetic elements that form somatic mosaicisms in various tissues of the organism. The activity of L1 retrotransposons is strictly controlled by many factors in somatic and germ cells at all stages of ontogenesis. Alteration of L1 activity was noted in a number of diseases: in neuropsychiatric and autoimmune diseases, as well as in various forms of cancer. Altered activity of L1 retrotransposons for some pathologies is associated with epigenetic changes and defects in the genes involved in their repression. This review discusses the molecular genetic mechanisms of the retrotransposition and regulation of the activity of L1 elements. The contribution of various factors controlling the expression and distribution of L1 elements in the genome occurs at all stages of the retrotransposition. The regulation of L1 elements at the transcriptional, post-transcriptional and integration into the genome stages is described in detail. Finally, this review also focuses on the evolutionary aspects of L1 accumulation and their interplay with the host regulation system.
Collapse
|