1
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Nakagawa R, Llorian M, Varsani-Brown S, Chakravarty P, Camarillo JM, Barry D, George R, Blackledge NP, Duddy G, Kelleher NL, Klose RJ, Turner M, Calado DP. Epi-microRNA mediated metabolic reprogramming ensures affinity maturation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.31.551250. [PMID: 37609190 PMCID: PMC10441342 DOI: 10.1101/2023.07.31.551250] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
To increase antibody affinity against pathogens, positively selected GC-B cells initiate cell division in the light zone (LZ) of germinal centres (GCs). Among those, higher-affinity clones migrate to the dark zone (DZ) and vigorously proliferate by relying on oxidative phosphorylation (OXPHOS). However, it remains unknown how positively selected GC-B cells adapt their metabolism for cell division in the glycolysis-dominant, cell cycle arrest-inducing, hypoxic LZ microenvironment. Here, we show that microRNA (miR)-155 mediates metabolic reprogramming during positive selection to protect high-affinity clones. Transcriptome examination and mass spectrometry analysis revealed that miR-155 regulates H3K36me2 levels by directly repressing hypoxia-induced histone lysine demethylase, Kdm2a. This is indispensable for enhancing OXPHOS through optimizing the expression of vital nuclear mitochondrial genes under hypoxia. The miR-155-Kdm2a interaction is crucial to prevent excessive production of reactive oxygen species and apoptosis. Thus, miR-155-mediated epigenetic regulation promotes mitochondrial fitness in high-affinity clones, ensuring their expansion and consequently affinity maturation.
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2
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Moritz L, Schon SB, Rabbani M, Sheng Y, Agrawal R, Glass-Klaiber J, Sultan C, Camarillo JM, Clements J, Baldwin MR, Diehl AG, Boyle AP, O'Brien PJ, Ragunathan K, Hu YC, Kelleher NL, Nandakumar J, Li JZ, Orwig KE, Redding S, Hammoud SS. Sperm chromatin structure and reproductive fitness are altered by substitution of a single amino acid in mouse protamine 1. Nat Struct Mol Biol 2023; 30:1077-1091. [PMID: 37460896 PMCID: PMC10833441 DOI: 10.1038/s41594-023-01033-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 06/12/2023] [Indexed: 08/11/2023]
Abstract
Conventional dogma presumes that protamine-mediated DNA compaction in sperm is achieved by electrostatic interactions between DNA and the arginine-rich core of protamines. Phylogenetic analysis reveals several non-arginine residues conserved within, but not across species. The significance of these residues and their post-translational modifications are poorly understood. Here, we investigated the role of K49, a rodent-specific lysine residue in protamine 1 (P1) that is acetylated early in spermiogenesis and retained in sperm. In sperm, alanine substitution (P1(K49A)) decreases sperm motility and male fertility-defects that are not rescued by arginine substitution (P1(K49R)). In zygotes, P1(K49A) leads to premature male pronuclear decompaction, altered DNA replication, and embryonic arrest. In vitro, P1(K49A) decreases protamine-DNA binding and alters DNA compaction and decompaction kinetics. Hence, a single amino acid substitution outside the P1 arginine core is sufficient to profoundly alter protein function and developmental outcomes, suggesting that protamine non-arginine residues are essential for reproductive fitness.
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Affiliation(s)
- Lindsay Moritz
- Cellular and Molecular Biology Graduate Program, University of Michigan, Ann Arbor, MI, USA
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Samantha B Schon
- Department of Obstetrics and Gynecology, University of Michigan, Ann Arbor, MI, USA
| | - Mashiat Rabbani
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Yi Sheng
- Department of Obstetrics, Gynecology and Reproductive Sciences, Magee Womens Research Institute, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Ritvija Agrawal
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Juniper Glass-Klaiber
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Caleb Sultan
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Jeannie M Camarillo
- Departments of Chemistry, Molecular Biosciences, and the National Resource for Translational and Developmental Proteomics, Northwestern University, Evanston, IL, USA
| | - Jourdan Clements
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Michael R Baldwin
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, USA
| | - Adam G Diehl
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Alan P Boyle
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Patrick J O'Brien
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, USA
| | | | - Yueh-Chiang Hu
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Neil L Kelleher
- Departments of Chemistry, Molecular Biosciences, and the National Resource for Translational and Developmental Proteomics, Northwestern University, Evanston, IL, USA
| | - Jayakrishnan Nandakumar
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Jun Z Li
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Kyle E Orwig
- Department of Obstetrics, Gynecology and Reproductive Sciences, Magee Womens Research Institute, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Sy Redding
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Saher Sue Hammoud
- Cellular and Molecular Biology Graduate Program, University of Michigan, Ann Arbor, MI, USA.
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA.
- Department of Obstetrics and Gynecology, University of Michigan, Ann Arbor, MI, USA.
- Department of Urology, University of Michigan, Ann Arbor, MI, USA.
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3
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Leung W, Teater M, Durmaz C, Meydan C, Chivu AG, Chadburn A, Rice EJ, Muley A, Camarillo JM, Arivalagan J, Li Z, Flowers CR, Kelleher NL, Danko CG, Imielinski M, Dave SS, Armstrong SA, Mason CE, Melnick AM. SETD2 Haploinsufficiency Enhances Germinal Center-Associated AICDA Somatic Hypermutation to Drive B-cell Lymphomagenesis. Cancer Discov 2022; 12:1782-1803. [PMID: 35443279 PMCID: PMC9262862 DOI: 10.1158/2159-8290.cd-21-1514] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 03/08/2022] [Accepted: 04/18/2022] [Indexed: 01/26/2023]
Abstract
SETD2 is the sole histone methyltransferase responsible for H3K36me3, with roles in splicing, transcription initiation, and DNA damage response. Homozygous disruption of SETD2 yields a tumor suppressor effect in various cancers. However, SETD2 mutation is typically heterozygous in diffuse large B-cell lymphomas. Here we show that heterozygous Setd2 deficiency results in germinal center (GC) hyperplasia and increased competitive fitness, with reduced DNA damage checkpoint activity and apoptosis, resulting in accelerated lymphomagenesis. Impaired DNA damage sensing in Setd2-haploinsufficient germinal center B (GCB) and lymphoma cells associated with increased AICDA-induced somatic hypermutation, complex structural variants, and increased translocations including those activating MYC. DNA damage was selectively increased on the nontemplate strand, and H3K36me3 loss was associated with greater RNAPII processivity and mutational burden, suggesting that SETD2-mediated H3K36me3 is required for proper sensing of cytosine deamination. Hence, Setd2 haploinsufficiency delineates a novel GCB context-specific oncogenic pathway involving defective epigenetic surveillance of AICDA-mediated effects on transcribed genes. SIGNIFICANCE Our findings define a B cell-specific oncogenic effect of SETD2 heterozygous mutation, which unleashes AICDA mutagenesis of nontemplate strand DNA in the GC reaction, resulting in lymphomas with heavy mutational burden. GC-derived lymphomas did not tolerate SETD2 homozygous deletion, pointing to a novel context-specific therapeutic vulnerability. This article is highlighted in the In This Issue feature, p. 1599.
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Affiliation(s)
- Wilfred Leung
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, Cornell University, New York, New York
- Department of Biomedical Sciences, Cornell University, Ithaca, New York
| | - Matt Teater
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, Cornell University, New York, New York
| | - Ceyda Durmaz
- Graduate Program of Physiology, Biophysics and Systems Biology, Weill Cornell Medicine, New York, New York
| | - Cem Meydan
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, New York
- The WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, New York
| | - Alexandra G Chivu
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, New York
| | - Amy Chadburn
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York
| | - Edward J Rice
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, New York
| | - Ashlesha Muley
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, Cornell University, New York, New York
| | - Jeannie M Camarillo
- Departments of Chemistry, Molecular Biosciences and the National Resource for Translational and Developmental Proteomics, Northwestern University, Evanston, Illinois
| | - Jaison Arivalagan
- Departments of Chemistry, Molecular Biosciences and the National Resource for Translational and Developmental Proteomics, Northwestern University, Evanston, Illinois
| | - Ziyi Li
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Christopher R Flowers
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Neil L Kelleher
- Departments of Chemistry, Molecular Biosciences and the National Resource for Translational and Developmental Proteomics, Northwestern University, Evanston, Illinois
| | - Charles G Danko
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, New York
| | - Marcin Imielinski
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York
- New York Genome Center, New York, New York
- Caryl and Israel Englander Institute for Precision Medicine and Meyer Cancer Center, Weill Cornell Medicine, New York, New York
| | - Sandeep S Dave
- Center for Genomic and Computational Biology and Department of Medicine, Duke University, Durham, North Carolina
| | - Scott A Armstrong
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, New York
- The WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, New York
- The Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, New York
| | - Ari M Melnick
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, Cornell University, New York, New York
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4
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A modular single-cell pipette microfluidic chip coupling to ETAAS and ICP-MS for single cell analysis. CHINESE CHEM LETT 2021. [DOI: 10.1016/j.cclet.2021.08.024] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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5
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Villa E, Sahu U, O'Hara BP, Ali ES, Helmin KA, Asara JM, Gao P, Singer BD, Ben-Sahra I. mTORC1 stimulates cell growth through SAM synthesis and m 6A mRNA-dependent control of protein synthesis. Mol Cell 2021; 81:2076-2093.e9. [PMID: 33756106 PMCID: PMC8141029 DOI: 10.1016/j.molcel.2021.03.009] [Citation(s) in RCA: 79] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 01/21/2021] [Accepted: 03/08/2021] [Indexed: 12/13/2022]
Abstract
The mechanistic target of rapamycin complex 1 (mTORC1) regulates metabolism and cell growth in response to nutrient, growth, and oncogenic signals. We found that mTORC1 stimulates the synthesis of the major methyl donor, S-adenosylmethionine (SAM), through the control of methionine adenosyltransferase 2 alpha (MAT2A) expression. The transcription factor c-MYC, downstream of mTORC1, directly binds to intron 1 of MAT2A and promotes its expression. Furthermore, mTORC1 increases the protein abundance of Wilms' tumor 1-associating protein (WTAP), the positive regulatory subunit of the human N6-methyladenosine (m6A) RNA methyltransferase complex. Through the control of MAT2A and WTAP levels, mTORC1 signaling stimulates m6A RNA modification to promote protein synthesis and cell growth. A decline in intracellular SAM levels upon MAT2A inhibition decreases m6A RNA modification, protein synthesis rate, and tumor growth. Thus, mTORC1 adjusts m6A RNA modification through the control of SAM and WTAP levels to prime the translation machinery for anabolic cell growth.
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Affiliation(s)
- Elodie Villa
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA; Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL 60611, USA
| | - Umakant Sahu
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA; Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL 60611, USA
| | - Brendan P O'Hara
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA; Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL 60611, USA
| | - Eunus S Ali
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA; Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL 60611, USA
| | - Kathryn A Helmin
- Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, 320 East Superior Street, Chicago, IL 60611, USA
| | - John M Asara
- Mass Spectrometry Core, Beth Israel Deaconess Medical Center, Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Peng Gao
- Metabolomics Core Facility, Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL 60611, USA
| | - Benjamin D Singer
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA; Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, 320 East Superior Street, Chicago, IL 60611, USA
| | - Issam Ben-Sahra
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA; Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL 60611, USA.
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6
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Ma W, Gil HJ, Liu X, Diebold LP, Morgan MA, Oxendine-Burns MJ, Gao P, Chandel NS, Oliver G. Mitochondrial respiration controls the Prox1-Vegfr3 feedback loop during lymphatic endothelial cell fate specification and maintenance. SCIENCE ADVANCES 2021; 7:7/18/eabe7359. [PMID: 33931446 PMCID: PMC8087398 DOI: 10.1126/sciadv.abe7359] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 03/11/2021] [Indexed: 05/09/2023]
Abstract
Recent findings indicate that mitochondrial respiration regulates blood endothelial cell proliferation; however, its role in differentiating lymphatic endothelial cells (LECs) is unknown. We hypothesized that mitochondria could work as a sensor of LECs' metabolic specific needs by determining their functional requirements according to their differentiation status and local tissue microenvironment. Accordingly, we conditionally deleted the QPC subunit of mitochondrial complex III in differentiating LECs of mouse embryos. Unexpectedly, mutant mice were devoid of a lymphatic vasculature by mid-gestation, a consequence of the specific down-regulation of main LEC fate regulators, particularly Vegfr3, leading to the loss of LEC fate. Mechanistically, this is a result of reduced H3K4me3 and H3K27ac in the genomic locus of key LEC fate controllers (e.g., Vegfr3 and Prox1). Our findings indicate that by sensing the LEC differentiation status and microenvironmental metabolic conditions, mitochondrial complex III regulates the critical Prox1-Vegfr3 feedback loop and, therefore, LEC fate specification and maintenance.
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Affiliation(s)
- Wanshu Ma
- Center for Vascular and Developmental Biology, Feinberg Cardiovascular and Renal Research Institute, Northwestern University, Chicago, IL, USA
| | - Hyea Jin Gil
- Center for Vascular and Developmental Biology, Feinberg Cardiovascular and Renal Research Institute, Northwestern University, Chicago, IL, USA
| | - Xiaolei Liu
- Center for Vascular and Developmental Biology, Feinberg Cardiovascular and Renal Research Institute, Northwestern University, Chicago, IL, USA
| | - Lauren P Diebold
- Department of Medicine and Robert H. Lurie Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Marc A Morgan
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Michael J Oxendine-Burns
- Center for Vascular and Developmental Biology, Feinberg Cardiovascular and Renal Research Institute, Northwestern University, Chicago, IL, USA
| | - Peng Gao
- Robert H. Lurie Cancer Center Metabolomics Core, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Navdeep S Chandel
- Department of Medicine and Robert H. Lurie Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Robert H. Lurie Cancer Center Metabolomics Core, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Guillermo Oliver
- Center for Vascular and Developmental Biology, Feinberg Cardiovascular and Renal Research Institute, Northwestern University, Chicago, IL, USA.
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7
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An S, Camarillo JM, Huang TYT, Li D, Morris JA, Zoltek MA, Qi J, Behbahani M, Kambhampati M, Kelleher NL, Nazarian J, Thomas PM, Saratsis AM. Histone tail analysis reveals H3K36me2 and H4K16ac as epigenetic signatures of diffuse intrinsic pontine glioma. J Exp Clin Cancer Res 2020; 39:261. [PMID: 33239043 PMCID: PMC7687710 DOI: 10.1186/s13046-020-01773-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Accepted: 11/09/2020] [Indexed: 02/15/2023] Open
Abstract
BACKGROUND Diffuse intrinsic pontine glioma (DIPG) is an aggressive pediatric brainstem tumor. Most DIPGs harbor a histone H3 mutation, which alters histone post-translational modification (PTM) states and transcription. Here, we employed quantitative proteomic analysis to elucidate the impact of the H3.3K27M mutation, as well as radiation and bromodomain inhibition (BRDi) with JQ1, on DIPG PTM profiles. METHODS We performed targeted mass spectrometry on H3.3K27M mutant and wild-type tissues (n = 12) and cell lines (n = 7). RESULTS We found 29.2 and 26.4% of total H3.3K27 peptides were H3.3K27M in mutant DIPG tumor cell lines and tissue specimens, respectively. Significant differences in modification states were observed in H3.3K27M specimens, including at H3K27, H3K36, and H4K16. In addition, H3.3K27me1 and H4K16ac were the most significantly distinct modifications in H3.3K27M mutant tumors, relative to wild-type. Further, H3.3K36me2 was the most abundant co-occurring modification on the H3.3K27M mutant peptide in DIPG tissue, while H4K16ac was the most acetylated residue. Radiation treatment caused changes in PTM abundance in vitro, including increased H3K9me3. JQ1 treatment resulted in increased mono- and di-methylation of H3.1K27, H3.3K27, H3.3K36 and H4K20 in vitro. CONCLUSION Taken together, our findings provide insight into the effects of the H3K27M mutation on histone modification states and response to treatment, and suggest that H3K36me2 and H4K16ac may represent unique tumor epigenetic signatures for targeted DIPG therapy.
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Affiliation(s)
- Shejuan An
- Department of Neurological Surgery, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Jeannie M Camarillo
- Department of Chemistry, Molecular Biosciences and Proteomics Center of Excellence, Northwestern University, Evanston, IL, 60208, USA
| | - Tina Yi-Ting Huang
- Department of Neurological Surgery, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Daphne Li
- Department of Neurological Surgery, Loyola University, Chicago, IL, USA
| | - Juliette A Morris
- Department of Chemistry, Molecular Biosciences and Proteomics Center of Excellence, Northwestern University, Evanston, IL, 60208, USA
| | - Madeline A Zoltek
- Department of Chemistry, Molecular Biosciences and Proteomics Center of Excellence, Northwestern University, Evanston, IL, 60208, USA
| | - Jin Qi
- Department of Neurological Surgery, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Mandana Behbahani
- Department of Neurological Surgery, University of Illinois Chicago, Chicago, IL, USA
| | - Madhuri Kambhampati
- Research Center for Genetic Medicine, Children's National Health System, Washington, DC, USA
| | - Neil L Kelleher
- Department of Chemistry, Molecular Biosciences and Proteomics Center of Excellence, Northwestern University, Evanston, IL, 60208, USA
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Javad Nazarian
- Research Center for Genetic Medicine, Children's National Health System, Washington, DC, USA
- Department of Integrative Systems Biology, George Washington University School of Medicine and Health Sciences, Washington, DC, USA
- Department of Oncology, University Children's Hospital, Zurich, Switzerland
| | - Paul M Thomas
- Department of Chemistry, Molecular Biosciences and Proteomics Center of Excellence, Northwestern University, Evanston, IL, 60208, USA
| | - Amanda M Saratsis
- Department of Neurological Surgery, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.
- Division of Pediatric Neurosurgery, Department of Surgery, Ann & Robert H. Lurie Children's Hospital of Chicago, 225 E Chicago Avenue, Box 28., Chicago, IL, 60611-2991, USA.
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8
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Parsa S, Ortega-Molina A, Ying HY, Jiang M, Teater M, Wang J, Zhao C, Reznik E, Pasion JP, Kuo D, Mohan P, Wang S, Camarillo JM, Thomas PM, Jain N, Garcia-Bermudez J, Cho BK, Tam W, Kelleher NL, Socci N, Dogan A, De Stanchina E, Ciriello G, Green MR, Li S, Birsoy K, Melnick AM, Wendel HG. The serine hydroxymethyltransferase-2 (SHMT2) initiates lymphoma development through epigenetic tumor suppressor silencing. ACTA ACUST UNITED AC 2020; 1:653-664. [PMID: 33569544 DOI: 10.1038/s43018-020-0080-0] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Cancer cells adapt their metabolic activities to support growth and proliferation. However, increased activity of metabolic enzymes is not usually considered an initiating event in the malignant process. Here, we investigate the possible role of the enzyme serine hydroxymethyltransferase-2 (SHMT2) in lymphoma initiation. SHMT2 localizes to the most frequent region of copy number gains at chromosome 12q14.1 in lymphoma. Elevated expression of SHMT2 cooperates with BCL2 in lymphoma development; loss or inhibition of SHMT2 impairs lymphoma cell survival. SHMT2 catalyzes the conversion of serine to glycine and produces an activated one-carbon unit that can be used to support S-adenosyl methionine synthesis. SHMT2 induces changes in DNA and histone methylation patterns leading to promoter silencing of previously uncharacterized mutational genes, such as SASH1 and PTPRM. Together, our findings reveal that amplification of SHMT2 in cooperation with BCL2 is sufficient in the initiation of lymphomagenesis through epigenetic tumor suppressor silencing.
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Affiliation(s)
- Sara Parsa
- Cancer Biology and Genetics, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Ana Ortega-Molina
- Cancer Biology and Genetics, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Hsia-Yuan Ying
- Department of Medicine and Weill Cornell Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Man Jiang
- Cancer Biology and Genetics, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Matt Teater
- Department of Medicine and Weill Cornell Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Jiahui Wang
- The Jackson Laboratory Cancer Center, Farmington, CT, USA
| | - Chunying Zhao
- Cancer Biology and Genetics, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Ed Reznik
- Department of Epidemiology and Biostatistics, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Joyce P Pasion
- Cancer Biology and Genetics, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - David Kuo
- Department of Physiology, Biophysics, and Systems Biology, Weill Cornell Graduate School of Medical Sciences, New York, NY, USA
| | - Prathibha Mohan
- Cancer Biology and Genetics, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Shenqiu Wang
- Cancer Biology and Genetics, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Jeannie M Camarillo
- Department of Chemistry, Molecular Biosciences and the National Resource for Translational and Developmental Proteomics, Northwestern University, Evanston, IL, USA
| | - Paul M Thomas
- Department of Chemistry, Molecular Biosciences and the National Resource for Translational and Developmental Proteomics, Northwestern University, Evanston, IL, USA
| | - Neeraj Jain
- Department of Lymphoma and Myeloma, University of Texas MD Anderson Cancer Center, Houston, TX, USA.,Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Javier Garcia-Bermudez
- Laboratory of Metabolic Regulation and Genetics, Rockefeller University, New York, NY, USA
| | - Byoung-Kyu Cho
- Department of Chemistry, Molecular Biosciences and the National Resource for Translational and Developmental Proteomics, Northwestern University, Evanston, IL, USA
| | - Wayne Tam
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Neil L Kelleher
- Department of Chemistry, Molecular Biosciences and the National Resource for Translational and Developmental Proteomics, Northwestern University, Evanston, IL, USA
| | - Nicholas Socci
- Cancer Biology and Genetics, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Ahmet Dogan
- Hematopathology Service, Departments of Pathology and Laboratory Medicine, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Elisa De Stanchina
- Cancer Biology and Genetics, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Giovanni Ciriello
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Michael R Green
- Department of Lymphoma and Myeloma, University of Texas MD Anderson Cancer Center, Houston, TX, USA.,Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Sheng Li
- The Jackson Laboratory Cancer Center, Farmington, CT, USA
| | - Kivanc Birsoy
- Laboratory of Metabolic Regulation and Genetics, Rockefeller University, New York, NY, USA
| | - Ari M Melnick
- Department of Medicine and Weill Cornell Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Hans-Guido Wendel
- Cancer Biology and Genetics, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
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