1
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Acton OJ, Sheppard D, Kunzelmann S, Caswell SJ, Nans A, Burgess AJO, Kelly G, Morris ER, Rosenthal PB, Taylor IA. Platform-directed allostery and quaternary structure dynamics of SAMHD1 catalysis. Nat Commun 2024; 15:3775. [PMID: 38710701 PMCID: PMC11074143 DOI: 10.1038/s41467-024-48237-w] [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: 11/03/2023] [Accepted: 04/25/2024] [Indexed: 05/08/2024] Open
Abstract
SAMHD1 regulates cellular nucleotide homeostasis, controlling dNTP levels by catalysing their hydrolysis into 2'-deoxynucleosides and triphosphate. In differentiated CD4+ macrophage and resting T-cells SAMHD1 activity results in the inhibition of HIV-1 infection through a dNTP blockade. In cancer, SAMHD1 desensitizes cells to nucleoside-analogue chemotherapies. Here we employ time-resolved cryogenic-EM imaging and single-particle analysis to visualise assembly, allostery and catalysis by this multi-subunit enzyme. Our observations reveal how dynamic conformational changes in the SAMHD1 quaternary structure drive the catalytic cycle. We capture five states at high-resolution in a live catalytic reaction, revealing how allosteric activators support assembly of a stable SAMHD1 tetrameric core and how catalysis is driven by the opening and closing of active sites through pairwise coupling of active sites and order-disorder transitions in regulatory domains. This direct visualisation of enzyme catalysis dynamics within an allostery-stabilised platform sets a precedent for mechanistic studies into the regulation of multi-subunit enzymes.
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Affiliation(s)
- Oliver J Acton
- Macromolecular Structure Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
- Structural Biology of Cells and Viruses Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
- AstraZeneca, The Discovery Centre, 1 Francis Crick Avenue, Cambridge, CB2 0AA, UK
| | - Devon Sheppard
- Macromolecular Structure Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Simone Kunzelmann
- Structural Biology Science Technology Platform, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Sarah J Caswell
- Macromolecular Structure Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
- AstraZeneca, The Discovery Centre, 1 Francis Crick Avenue, Cambridge, CB2 0AA, UK
| | - Andrea Nans
- Structural Biology Science Technology Platform, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Ailidh J O Burgess
- Macromolecular Structure Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Geoff Kelly
- The Medical Research Council Biomedical NMR Centre, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Elizabeth R Morris
- Macromolecular Structure Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
- Department of Biosciences, University of Durham, Durham, DH1 3LE, UK
| | - Peter B Rosenthal
- Structural Biology of Cells and Viruses Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.
| | - Ian A Taylor
- Macromolecular Structure Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.
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2
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Yang K, Jeltema D, Yan N. Innate immune sensing of macromolecule homeostasis. Adv Immunol 2024; 161:17-51. [PMID: 38763701 DOI: 10.1016/bs.ai.2024.03.004] [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: 05/21/2024]
Abstract
The innate immune system uses a distinct set of germline-encoded pattern recognition receptors to recognize molecular patterns initially thought to be unique to microbial invaders, named pathogen-associated molecular patterns. The concept was later further developed to include similar molecular patterns originating from host cells during tissue damage, known as damage-associated molecular patterns. However, recent advances in the mechanism of monogenic inflammatory diseases have highlighted a much more expansive repertoire of cellular functions that are monitored by innate immunity. Here, we summarize several examples in which an innate immune response is triggered when homeostasis of macromolecule in the cell is disrupted in non-infectious or sterile settings. These ever-growing sensing mechanisms expand the repertoire of innate immune recognition, positioning it not only as a key player in host defense but also as a gatekeeper of cellular homeostasis. Therapeutics inspired by these advances to restore cellular homeostasis and correct the immune system could have far-reaching implications.
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Affiliation(s)
- Kun Yang
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Devon Jeltema
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Nan Yan
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX, United States.
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3
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Daddacha W, Monroe D, Schlafstein A, Withers A, Thompson E, Danelia D, Luong N, Sesay F, Rath S, Usoro E, Essien M, Jung A, Jiang J, Hu J, Mahboubi B, Williams A, Steinbeck J, Yang X, Buchwald Z, Dynan W, Switchenko J, Kim B, Khan M, Jaye D, Yu D. SAMHD1 expression contributes to doxorubicin resistance and predicts survival outcomes in diffuse large B-cell lymphoma patients. NAR Cancer 2024; 6:zcae007. [PMID: 38406263 PMCID: PMC10894040 DOI: 10.1093/narcan/zcae007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 01/31/2024] [Accepted: 02/22/2024] [Indexed: 02/27/2024] Open
Abstract
Diffuse large B-cell lymphoma (DLBCL) is a commonly diagnosed, aggressive non-Hodgkin's lymphoma. While R-CHOP chemoimmunotherapy is potentially curative, about 40% of DLBCL patients will fail, highlighting the need to identify biomarkers to optimize management. SAMHD1 has a dNTPase-independent role in promoting resection to facilitate DNA double-strand break (DSB) repair by homologous recombination. We evaluated the relationship of SAMHD1 levels with sensitivity to DSB-sensitizing agents in DLBCL cells and the association of SAMHD1 expression with clinical outcomes in 79 DLBCL patients treated with definitive therapy and an independent cohort dataset of 234 DLBCL patients. Low SAMHD1 expression, Vpx-mediated, or siRNA-mediated degradation/depletion in DLBCL cells was associated with greater sensitivity to doxorubicin and PARP inhibitors. On Kaplan-Meier log-rank survival analysis, low SAMHD1 expression was associated with improved overall survival (OS), which on subset analysis remained significant only in patients with advanced stage (III-IV) and moderate to high risk (2-5 International Prognostic Index (IPI)). The association of low SAMHD1 expression with improved OS remained significant on multivariate analysis independent of other adverse factors, including IPI, and was validated in an independent cohort. Our findings suggest that SAMHD1 expression mediates doxorubicin resistance and may be an important prognostic biomarker in advanced, higher-risk DLBCL patients.
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Affiliation(s)
- Waaqo Daddacha
- Department of Biochemistry and Molecular Biology, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA
| | - Dominique Monroe
- Department of Biochemistry and Molecular Biology, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA
| | - Ashley J Schlafstein
- Department of Radiation Oncology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Allison E Withers
- Department of Radiation Oncology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Elizabeth B Thompson
- Department of Radiation Oncology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Diana Danelia
- Department of Radiation Oncology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Nho C Luong
- Department of Radiation Oncology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Fatmata Sesay
- Department of Radiation Oncology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Sandip K Rath
- Department of Radiation Oncology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Edidiong R Usoro
- Department of Biochemistry and Molecular Biology, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA
| | - Mark E Essien
- Department of Radiation Oncology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Andrew T Jung
- Department of Radiation Oncology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Jinmeng G Jiang
- Department of Radiation Oncology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Jiaxuan Hu
- Department of Radiation Oncology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Bijan Mahboubi
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Arilyn Williams
- Department of Biochemistry and Molecular Biology, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA
| | - Julia E Steinbeck
- Department of Biochemistry and Molecular Biology, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA
| | - Xiaofeng Yang
- Department of Radiation Oncology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Zachary S Buchwald
- Department of Radiation Oncology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - William S Dynan
- Department of Radiation Oncology, Emory University School of Medicine, Atlanta, GA 30322, USA
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Jeffrey M Switchenko
- Department of Biostatistics and Bioinformatics, Rollins School of Public Health and Winship Cancer Institute, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Baek Kim
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Mohammad K Khan
- Department of Radiation Oncology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - David L Jaye
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - David S Yu
- Department of Radiation Oncology, Emory University School of Medicine, Atlanta, GA 30322, USA
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4
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Zhang SM, Paulin CB, Shu H, Yagüe-Capilla M, Michel M, Marttila P, Ortis F, Bwanika HC, Dirks C, Venkatram RP, Wiita E, Jemth AS, Almlöf I, Loseva O, Hormann FM, Koolmeister T, Linde E, Lee S, Llona-Minguez S, Haraldsson M, Axelsson H, Strömberg K, Homan EJ, Scobie M, Lundbäck T, Helleday T, Rudd SG. Identification and evaluation of small-molecule inhibitors against the dNTPase SAMHD1 via a comprehensive screening funnel. iScience 2024; 27:108907. [PMID: 38318365 PMCID: PMC10839966 DOI: 10.1016/j.isci.2024.108907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Revised: 09/05/2023] [Accepted: 01/10/2024] [Indexed: 02/07/2024] Open
Abstract
SAMHD1 is a dNTP triphosphohydrolase governing nucleotide pool homeostasis and can detoxify chemotherapy metabolites controlling their clinical responses. To understand SAMHD1 biology and investigate the potential of targeting SAMHD1 as neoadjuvant to current chemotherapies, we set out to discover selective small-molecule inhibitors. Here, we report a discovery pipeline encompassing a biochemical screening campaign and a set of complementary biochemical, biophysical, and cell-based readouts for rigorous characterization of the screen output. The identified small molecules, TH6342 and analogs, accompanied by inactive control TH7126, demonstrated specific, low μM potency against both physiological and oncology-drug-derived substrates. By coupling kinetic studies with thermal shift assays, we reveal the inhibitory mechanism of TH6342 and analogs, which engage pre-tetrameric SAMHD1 and deter oligomerization and allosteric activation without occupying nucleotide-binding pockets. Altogether, our study diversifies inhibitory modes against SAMHD1, and the discovery pipeline reported herein represents a thorough framework for future SAMHD1 inhibitor development.
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Affiliation(s)
- Si Min Zhang
- Science for Life Laboratory (SciLifeLab), Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden
| | - Cynthia B.J. Paulin
- Science for Life Laboratory (SciLifeLab), Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden
| | - Huazhang Shu
- Science for Life Laboratory (SciLifeLab), Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden
| | - Miriam Yagüe-Capilla
- Science for Life Laboratory (SciLifeLab), Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden
| | - Maurice Michel
- Science for Life Laboratory (SciLifeLab), Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden
| | - Petra Marttila
- Science for Life Laboratory (SciLifeLab), Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden
| | - Florian Ortis
- Science for Life Laboratory (SciLifeLab), Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden
| | - Henri Colyn Bwanika
- Science for Life Laboratory (SciLifeLab), Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden
| | - Christopher Dirks
- Science for Life Laboratory (SciLifeLab), Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden
| | - Rajagopal Papagudi Venkatram
- Science for Life Laboratory (SciLifeLab), Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden
| | - Elisée Wiita
- Science for Life Laboratory (SciLifeLab), Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden
| | - Ann-Sofie Jemth
- Science for Life Laboratory (SciLifeLab), Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden
| | - Ingrid Almlöf
- Science for Life Laboratory (SciLifeLab), Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden
| | - Olga Loseva
- Science for Life Laboratory (SciLifeLab), Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden
| | - Femke M. Hormann
- Science for Life Laboratory (SciLifeLab), Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden
| | - Tobias Koolmeister
- Science for Life Laboratory (SciLifeLab), Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden
| | - Erika Linde
- Science for Life Laboratory (SciLifeLab), Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden
| | - Sun Lee
- Science for Life Laboratory (SciLifeLab), Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden
| | - Sabin Llona-Minguez
- Science for Life Laboratory (SciLifeLab), Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden
| | - Martin Haraldsson
- Chemical Biology Consortium Sweden, Science for Life Laboratory (SciLifeLab), Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 171 65 Stockholm, Sweden
| | - Hanna Axelsson
- Chemical Biology Consortium Sweden, Science for Life Laboratory (SciLifeLab), Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 171 65 Stockholm, Sweden
| | - Kia Strömberg
- Science for Life Laboratory (SciLifeLab), Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden
| | - Evert J. Homan
- Science for Life Laboratory (SciLifeLab), Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden
| | - Martin Scobie
- Science for Life Laboratory (SciLifeLab), Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden
| | - Thomas Lundbäck
- Chemical Biology Consortium Sweden, Science for Life Laboratory (SciLifeLab), Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 171 65 Stockholm, Sweden
| | - Thomas Helleday
- Science for Life Laboratory (SciLifeLab), Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden
- Weston Park Cancer Centre, Department of Oncology and Metabolism, University of Sheffield, Sheffield S10 2RX, UK
| | - Sean G. Rudd
- Science for Life Laboratory (SciLifeLab), Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden
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5
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McCown C, Yu CH, Ivanov DN. Allosteric substrate activation of SAMHD1 shapes deoxynucleotide triphosphate imbalances by interconnecting the depletion and biosynthesis of different dNTPs. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.14.567083. [PMID: 38014186 PMCID: PMC10680743 DOI: 10.1101/2023.11.14.567083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
SAMHD1 is a dNTPase that impedes replication of HIV-1 in myeloid cells and resting T lymphocytes. Here we elucidate the substrate activation mechanism of SAMHD1 that depends on dNTP binding at allosteric sites and the concomitant tetramerization of the enzyme. The study reveals that SAMHD1 activation involves an inactive tetrameric intermediate with partial occupancy of the allosteric sites. The equilibrium between the inactive and active tetrameric states, which is coupled to cooperative binding/dissociation of at least two allosteric dNTP ligands, controls the dNTPase activity of the enzyme, which, in addition, depends on the identity of the dNTPs occupying the four allosteric sites of the active tetramer. We show how such allosteric regulation determines deoxynucleotide triphosphate levels established in the dynamic equilibria between dNTP production and SAMHD1-catalyzed depletion. Notably, the mechanism enables a distinctive functionality of SAMHD1, which we call facilitated dNTP depletion, whereby elevated biosynthesis of some dNTPs results in more efficient depletion of others. The regulatory relationship between the biosynthesis and depletion of different dNTPs sheds light on the emerging role of SAMHD1 in the biology of dNTP homeostasis with implications for HIV/AIDS, innate antiviral immunity, T cell disorders, telomere maintenance and therapeutic efficacy of nucleoside analogs.
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6
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Maehigashi T, Lim C, Wade LR, Bowen NE, Knecht KM, Alvarez NN, Kelly WG, Schinazi RF, Kim DH, Xiong Y, Kim B. Biochemical functions and structure of Caenorhabditis elegans ZK177.8 protein: Aicardi-Goutières syndrome SAMHD1 dNTPase ortholog. J Biol Chem 2023; 299:105148. [PMID: 37567474 PMCID: PMC10485159 DOI: 10.1016/j.jbc.2023.105148] [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: 02/02/2023] [Revised: 08/02/2023] [Accepted: 08/04/2023] [Indexed: 08/13/2023] Open
Abstract
Mutations in sterile alpha motif domain and histidine-aspartate domain-containing protein 1 (SAMHD1) are found in a neurodevelopmental disorder, Aicardi-Goutières syndrome, and cancers, and SAMHD1, which is a deoxynucleoside triphosphate (dNTP) triphosphorylase, was identified as a myeloid-specific HIV-1 restriction factor. Here, we characterized the enzymology and structure of an SAMHD1 ortholog of Caenorhabditis elegans, ZK177.8, which also reportedly induces developmental defects upon gene knockdown. We found ZK177.8 protein is a dNTPase allosterically regulated by dGTP. The active site of ZK177.8 recognizes both 2' OH and triphosphate moieties of dNTPs but not base moiety. The dGTP activator induces the formation of the enzymatically active ZK177.8 tetramers, and ZK177.8 protein lowers cellular dNTP levels in a human monocytic cell line. Finally, ZK177.8 tetramers display very similar X-ray crystal structure with human and mouse SAMHD1s except that its lack of the canonical sterile alpha motif domain. This striking conservation in structure, function, and allosteric regulatory mechanism for the hydrolysis of the DNA building blocks supports their host developmental roles.
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Affiliation(s)
- Tatsuya Maehigashi
- Department of Pediatrics, School of Medicine, Emory University, Atlanta, Georgia, USA
| | - Christopher Lim
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA
| | - Lydia R Wade
- Department of Pediatrics, School of Medicine, Emory University, Atlanta, Georgia, USA
| | - Nicole E Bowen
- Department of Pediatrics, School of Medicine, Emory University, Atlanta, Georgia, USA
| | - Kirsten M Knecht
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA
| | - Natalie N Alvarez
- Department of Pediatrics, School of Medicine, Emory University, Atlanta, Georgia, USA
| | - William G Kelly
- Department of Biology, Emory University, Atlanta, Georgia, USA
| | - Raymond F Schinazi
- Department of Pediatrics, School of Medicine, Emory University, Atlanta, Georgia, USA; Center for ViroScience and Cure, Children's Healthcare of Atlanta, Atlanta, Georgia, USA
| | - Dong-Hyun Kim
- Neurobiota Research Center, College of Pharmacy, Kyung-Hee University, Seoul, South Korea
| | - Yong Xiong
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA.
| | - Baek Kim
- Department of Pediatrics, School of Medicine, Emory University, Atlanta, Georgia, USA; Center for ViroScience and Cure, Children's Healthcare of Atlanta, Atlanta, Georgia, USA.
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7
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An S, Vo TTL, Son T, Choi H, Kim J, Lee J, Kim BH, Choe M, Ha E, Surh YJ, Kim KW, Seo JH. SAMHD1-induced endosomal FAK signaling promotes human renal clear cell carcinoma metastasis by activating Rac1-mediated lamellipodia protrusion. Exp Mol Med 2023; 55:779-793. [PMID: 37009792 PMCID: PMC10167369 DOI: 10.1038/s12276-023-00961-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 12/22/2022] [Accepted: 12/27/2022] [Indexed: 04/04/2023] Open
Abstract
Human sterile α motif and HD domain-containing protein 1 (SAMHD1) has deoxyribonucleoside triphosphohydrolase (dNTPase) activity that allows it to defend against human immunodeficiency virus type I (HIV-1) infections and regulate the cell cycle. Although SAMHD1 mutations have been identified in various cancer types, their role in cancer is unclear. Here, we aimed to investigate the oncogenic role of SAMHD1 in human clear cell renal cell carcinoma (ccRCC), particularly as a core molecule promoting cancer cell migration. We found that SAMHD1 participated in endocytosis and lamellipodia formation. Mechanistically, SAMHD1 contributed to the formation of the endosomal complex by binding to cortactin. Thereafter, SAMHD1-stimulated endosomal focal adhesion kinase (FAK) signaling activated Rac1, which promoted lamellipodia formation on the plasma membrane and enhanced the motility of ccRCC cells. Finally, we observed a strong correlation between SAMHD1 expression and the activation of FAK and cortactin in tumor tissues obtained from patients with ccRCC. In brief, these findings reveal that SAMHD1 is an oncogene that plays a pivotal role in ccRCC cell migration through the endosomal FAK-Rac1 signaling pathway.
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Affiliation(s)
- Sunho An
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Tam Thuy Lu Vo
- Department of Biochemistry, School of Medicine, Keimyung University, Daegu, 42601, Republic of Korea
| | - Taekwon Son
- Korea Brain Bank, Korea Brain Research Institute, Daegu, 42601, Republic of Korea
| | - Hoon Choi
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Jinyoung Kim
- Department of Internal Medicine, School of Medicine, Keimyung University, Daegu, 42601, Republic of Korea
| | - Juyeon Lee
- Department of Biochemistry, School of Medicine, Keimyung University, Daegu, 42601, Republic of Korea
| | - Byung Hoon Kim
- Department of Urology, School of Medicine, Keimyung University, Daegu, 42601, Republic of Korea
| | - Misun Choe
- Department of Pathology, School of Medicine, Keimyung University, Daegu, 42601, Republic of Korea
| | - Eunyoung Ha
- Department of Biochemistry, School of Medicine, Keimyung University, Daegu, 42601, Republic of Korea
| | - Young-Joon Surh
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul, 08826, South Korea.
| | - Kyu-Won Kim
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul, 08826, South Korea.
| | - Ji Hae Seo
- Department of Biochemistry, School of Medicine, Keimyung University, Daegu, 42601, Republic of Korea.
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8
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D'Aronco G, Ferraro P, Sassano V, Dagostino C, Biancotto M, Palumbo E, Presot E, Russo A, Bianchi V, Rampazzo C. SAMHD1 restricts the deoxyguanosine triphosphate pool contributing to telomere stability in telomerase-positive cells. FASEB J 2023; 37:e22883. [PMID: 36934410 DOI: 10.1096/fj.202300122r] [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: 01/23/2023] [Revised: 02/26/2023] [Accepted: 03/07/2023] [Indexed: 03/20/2023]
Abstract
SAMHD1 (Sterile alpha motif and histidine/aspartic acid domain-containing protein 1) is a dNTP triphosphohydrolase crucial in the maintenance of balanced cellular dNTP pools, which support genome integrity. In SAMHD1 deficient fibroblasts isolated from Aicardi-Goutières Syndrome (AGS) patients, all four DNA precursors are increased and markedly imbalanced with the largest effect on dGTP, a key player in the modulation of telomerase processivity. Here, we present data showing that SAMHD1, by restricting the dGTP pool, contributes to telomere maintenance in hTERT-immortalized human fibroblasts from AGS patients as well as in telomerase positive cancer cell lines. Only in cells expressing telomerase, the lack of SAMHD1 causes excessive lengthening of telomeres and telomere fragility, whereas primary fibroblasts lacking both SAMHD1 and telomerase enter normally into senescence. Telomere lengthening observed in SAMHD1 deficient but telomerase proficient cells is a gradual process, in accordance with the intrinsic property of telomerase of adding only a few tens of nucleotides for each cycle. Therefore, only a prolonged exposure to high dGTP content causes telomere over-elongation. hTERT-immortalized AGS fibroblasts display also high fragility of chromosome ends, a marker of telomere replication stress. These results not only demonstrate the functional importance of dGTP cellular level but also reveal the critical role played by SAMHD1 in restraining telomerase processivity and safeguarding telomere stability.
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Affiliation(s)
| | - Paola Ferraro
- Department of Biology, University of Padova, Padova, Italy
| | | | | | | | - Elisa Palumbo
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | - Ettore Presot
- Department of Biology, University of Padova, Padova, Italy
| | - Antonella Russo
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | - Vera Bianchi
- Department of Biology, University of Padova, Padova, Italy
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9
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Pillalamarri V, Shi W, Say C, Yang S, Lane J, Guallar E, Pankratz N, Arking DE. Whole-exome sequencing in 415,422 individuals identifies rare variants associated with mitochondrial DNA copy number. HGG ADVANCES 2023; 4:100147. [PMID: 36311265 PMCID: PMC9615038 DOI: 10.1016/j.xhgg.2022.100147] [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: 07/06/2022] [Accepted: 09/23/2022] [Indexed: 10/14/2022] Open
Abstract
Inter-individual variation in the number of copies of the mitochondrial genome, called mitochondrial DNA copy number (mtDNA-CN), reflects mitochondrial function and has been associated with various aging-related diseases. We examined 415,422 exomes of self-reported White ancestry individuals from the UK Biobank and tested the impact of rare variants, at the level of single variants and through aggregate variant-set tests, on mtDNA-CN. A survey across nine variant sets tested enrichment of putatively causal variants and identified 14 genes at experiment-wide significance and three genes at marginal significance. These included associations at known mtDNA depletion syndrome genes (mtDNA helicase TWNK, p = 1.1 × 10-30; mitochondrial transcription factor TFAM, p = 4.3 × 10-15; mtDNA maintenance exonuclease MGME1, p = 2.0 × 10-6) and the V617F dominant gain-of-function mutation in the tyrosine kinase JAK2 (p = 2.7 × 10-17), associated with myeloproliferative disease. Novel genes included the ATP-dependent protease CLPX (p = 8.4 × 10-9), involved in mitochondrial proteome quality, and the mitochondrial adenylate kinase AK2 (p = 4.7 × 10-8), involved in hematopoiesis. The most significant association was a missense variant in SAMHD1 (p = 4.2 × 10-28), found on a rare, 1.2-Mb shared ancestral haplotype on chromosome 20. SAMHD1 encodes a cytoplasmic host restriction factor involved in viral defense response and the mitochondrial nucleotide salvage pathway, and is associated with Aicardi-Goutières syndrome 5, a childhood encephalopathy and chronic inflammatory response disorder. Rare variants were enriched in Mendelian mtDNA depletion syndrome loci, and these variants implicated core processes in mtDNA replication, nucleoid structure formation, and maintenance. These data indicate that strong-effect mutations from the nuclear genome contribute to the genetic architecture of mtDNA-CN.
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Affiliation(s)
- Vamsee Pillalamarri
- McKusick-Nathans Institute, Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Predoctoral Program in Human Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Maryland Genetics Epidemiology and Medicine Training Program, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Wen Shi
- McKusick-Nathans Institute, Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Conrad Say
- McKusick-Nathans Institute, Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Stephanie Yang
- McKusick-Nathans Institute, Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Vertex Pharmaceuticals, Inc., Boston, MA 02210, USA
| | - John Lane
- Department of Laboratory Medicine and Pathology, University of Minnesota Medical School, Minneapolis, MN 55455, USA
| | - Eliseo Guallar
- Departments of Epidemiology and Medicine and Welch Center for Prevention, Epidemiology and Clinical Research, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Nathan Pankratz
- Department of Laboratory Medicine and Pathology, University of Minnesota Medical School, Minneapolis, MN 55455, USA
| | - Dan E. Arking
- McKusick-Nathans Institute, Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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10
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Schumann T, Ramon SC, Schubert N, Mayo MA, Hega M, Maser KI, Ada SR, Sydow L, Hajikazemi M, Badstübner M, Müller P, Ge Y, Shakeri F, Buness A, Rupf B, Lienenklaus S, Utess B, Muhandes L, Haase M, Rupp L, Schmitz M, Gramberg T, Manel N, Hartmann G, Zillinger T, Kato H, Bauer S, Gerbaulet A, Paeschke K, Roers A, Behrendt R. Deficiency for SAMHD1 activates MDA5 in a cGAS/STING-dependent manner. J Exp Med 2022; 220:213670. [PMID: 36346347 PMCID: PMC9648672 DOI: 10.1084/jem.20220829] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 09/01/2022] [Accepted: 10/06/2022] [Indexed: 11/09/2022] Open
Abstract
Defects in nucleic acid metabolizing enzymes can lead to spontaneous but selective activation of either cGAS/STING or RIG-like receptor (RLR) signaling, causing type I interferon-driven inflammatory diseases. In these pathophysiological conditions, activation of the DNA sensor cGAS and IFN production are linked to spontaneous DNA damage. Physiological, or tonic, IFN signaling on the other hand is essential to functionally prime nucleic acid sensing pathways. Here, we show that low-level chronic DNA damage in mice lacking the Aicardi-Goutières syndrome gene SAMHD1 reduced tumor-free survival when crossed to a p53-deficient, but not to a DNA mismatch repair-deficient background. Increased DNA damage did not result in higher levels of type I interferon. Instead, we found that the chronic interferon response in SAMHD1-deficient mice was driven by the MDA5/MAVS pathway but required functional priming through the cGAS/STING pathway. Our work positions cGAS/STING upstream of tonic IFN signaling in Samhd1-deficient mice and highlights an important role of the pathway in physiological and pathophysiological innate immune priming.
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Affiliation(s)
- Tina Schumann
- Institute for Immunology, Medical Faculty Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Santiago Costas Ramon
- Institute for Immunology, Medical Faculty Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Nadja Schubert
- Institute for Immunology, Medical Faculty Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Mohamad Aref Mayo
- Institute for Clinical Chemistry and Clinical Pharmacology, University Hospital Bonn, Bonn, Germany
| | - Melanie Hega
- Institute for Clinical Chemistry and Clinical Pharmacology, University Hospital Bonn, Bonn, Germany
| | - Katharina Isabell Maser
- Institute for Clinical Chemistry and Clinical Pharmacology, University Hospital Bonn, Bonn, Germany
| | - Servi-Remzi Ada
- Institute for Immunology, Medical Faculty Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Lukas Sydow
- Institute for Immunology, Medical Faculty Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Mona Hajikazemi
- Clinic of Internal Medicine III, Oncology, Hematology, Rheumatology and Clinical Immunology, University Hospital Bonn, Bonn, Germany
| | - Markus Badstübner
- Institute for Immunology, Medical Faculty Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Patrick Müller
- Institute for Clinical Chemistry and Clinical Pharmacology, University Hospital Bonn, Bonn, Germany
| | - Yan Ge
- Institute for Immunology, Medical Faculty Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany,Institute for Immunology, University Hospital Heidelberg, Heidelberg, Germany
| | - Farhad Shakeri
- Institute for Medical Biometry, Informatics and Epidemiology, Medical Faculty, University of Bonn, Bonn, Germany,Institute for Genomic Statistics and Bioinformatics, Medical Faculty, University of Bonn, Bonn, Germany
| | - Andreas Buness
- Institute for Medical Biometry, Informatics and Epidemiology, Medical Faculty, University of Bonn, Bonn, Germany,Institute for Genomic Statistics and Bioinformatics, Medical Faculty, University of Bonn, Bonn, Germany
| | - Benjamin Rupf
- Institute for Immunology, Philipps-University Marburg, Marburg, Germany
| | - Stefan Lienenklaus
- Institute of Laboratory Animal Science, Hannover Medical School, Hannover, Germany
| | - Barbara Utess
- Institute for Immunology, Medical Faculty Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Lina Muhandes
- Institute for Immunology, Medical Faculty Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany,Institute for Clinical Chemistry and Clinical Pharmacology, University Hospital Bonn, Bonn, Germany
| | - Michael Haase
- Department of Pediatric Surgery, University Hospital Dresden, Dresden, Germany
| | - Luise Rupp
- Institute for Immunology, Medical Faculty Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Marc Schmitz
- Institute for Immunology, Medical Faculty Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany,National Center for Tumor Diseases, Partner Site Dresden, Dresden, Germany,German Cancer Consortium, Partner Site Dresden, and German Cancer Research Center, Heidelberg, Germany
| | - Thomas Gramberg
- Institute of Clinical and Molecular Virology, Friedrich-Alexander University Erlangen-Nürnberg, Erlangen, Germany
| | - Nicolas Manel
- Institut national de la santé et de la recherche médicale U932, Institut Curie, Paris Sciences et Lettres Research University, Paris, France
| | - Gunther Hartmann
- Institute for Clinical Chemistry and Clinical Pharmacology, University Hospital Bonn, Bonn, Germany
| | - Thomas Zillinger
- Institute for Clinical Chemistry and Clinical Pharmacology, University Hospital Bonn, Bonn, Germany
| | - Hiroki Kato
- Institute of Cardiovascular Immunology, Medical Faculty, University Hospital Bonn, Bonn, Germany
| | - Stefan Bauer
- Institute for Immunology, Philipps-University Marburg, Marburg, Germany
| | - Alexander Gerbaulet
- Institute for Immunology, Medical Faculty Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Katrin Paeschke
- Clinic of Internal Medicine III, Oncology, Hematology, Rheumatology and Clinical Immunology, University Hospital Bonn, Bonn, Germany
| | - Axel Roers
- Institute for Immunology, Medical Faculty Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany,Institute for Immunology, University Hospital Heidelberg, Heidelberg, Germany
| | - Rayk Behrendt
- Institute for Immunology, Medical Faculty Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany,Institute for Clinical Chemistry and Clinical Pharmacology, University Hospital Bonn, Bonn, Germany,Correspondence to Rayk Behrendt:
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11
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Kapoor-Vazirani P, Rath SK, Liu X, Shu Z, Bowen NE, Chen Y, Haji-Seyed-Javadi R, Daddacha W, Minten EV, Danelia D, Farchi D, Duong DM, Seyfried NT, Deng X, Ortlund EA, Kim B, Yu DS. SAMHD1 deacetylation by SIRT1 promotes DNA end resection by facilitating DNA binding at double-strand breaks. Nat Commun 2022; 13:6707. [PMID: 36344525 PMCID: PMC9640623 DOI: 10.1038/s41467-022-34578-x] [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: 01/21/2022] [Accepted: 10/29/2022] [Indexed: 11/09/2022] Open
Abstract
Sterile alpha motif and HD domain-containing protein 1 (SAMHD1) has a dNTPase-independent function in promoting DNA end resection to facilitate DNA double-strand break (DSB) repair by homologous recombination (HR); however, it is not known if upstream signaling events govern this activity. Here, we show that SAMHD1 is deacetylated by the SIRT1 sirtuin deacetylase, facilitating its binding with ssDNA at DSBs, to promote DNA end resection and HR. SIRT1 complexes with and deacetylates SAMHD1 at conserved lysine 354 (K354) specifically in response to DSBs. K354 deacetylation by SIRT1 promotes DNA end resection and HR but not SAMHD1 tetramerization or dNTPase activity. Mechanistically, K354 deacetylation by SIRT1 promotes SAMHD1 recruitment to DSBs and binding to ssDNA at DSBs, which in turn facilitates CtIP ssDNA binding, leading to promotion of genome integrity. These findings define a mechanism governing the dNTPase-independent resection function of SAMHD1 by SIRT1 deacetylation in promoting HR and genome stability.
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Affiliation(s)
- Priya Kapoor-Vazirani
- Department of Radiation Oncology and Winship Cancer Institute, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Sandip K Rath
- Department of Radiation Oncology and Winship Cancer Institute, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Xu Liu
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Zhen Shu
- Department of Radiation Oncology and Winship Cancer Institute, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Nicole E Bowen
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Yitong Chen
- Department of Radiation Oncology and Winship Cancer Institute, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Ramona Haji-Seyed-Javadi
- Department of Radiation Oncology and Winship Cancer Institute, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Waaqo Daddacha
- Department of Biochemistry and Molecular Biology, Medical College of Georgia at Augusta University, Augusta, GA, 30912, USA
| | - Elizabeth V Minten
- Department of Radiation Oncology and Winship Cancer Institute, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Diana Danelia
- Department of Radiation Oncology and Winship Cancer Institute, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Daniela Farchi
- Department of Radiation Oncology and Winship Cancer Institute, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Duc M Duong
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Nicholas T Seyfried
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Xingming Deng
- Department of Radiation Oncology and Winship Cancer Institute, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Eric A Ortlund
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Baek Kim
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - David S Yu
- Department of Radiation Oncology and Winship Cancer Institute, Emory University School of Medicine, Atlanta, GA, 30322, USA.
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12
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Helleday T, Rudd SG. Targeting the DNA damage response and repair in cancer through nucleotide metabolism. Mol Oncol 2022; 16:3792-3810. [PMID: 35583750 PMCID: PMC9627788 DOI: 10.1002/1878-0261.13227] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 05/05/2022] [Accepted: 05/17/2022] [Indexed: 12/24/2022] Open
Abstract
The exploitation of the DNA damage response and DNA repair proficiency of cancer cells is an important anticancer strategy. The replication and repair of DNA are dependent upon the supply of deoxynucleoside triphosphate (dNTP) building blocks, which are produced and maintained by nucleotide metabolic pathways. Enzymes within these pathways can be promising targets to selectively induce toxic DNA lesions in cancer cells. These same pathways also activate antimetabolites, an important group of chemotherapies that disrupt both nucleotide and DNA metabolism to induce DNA damage in cancer cells. Thus, dNTP metabolic enzymes can also be targeted to refine the use of these chemotherapeutics, many of which remain standard of care in common cancers. In this review article, we will discuss both these approaches exemplified by the enzymes MTH1, MTHFD2 and SAMHD1. © 2022 The Authors. Molecular Oncology published by John Wiley & Sons Ltd on behalf of Federation of European Biochemical Societies.
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Affiliation(s)
- Thomas Helleday
- Science for Life LaboratoryDepartment of Oncology‐PathologyKarolinska InstitutetStockholmSweden,Department of Oncology and Metabolism, Weston Park Cancer CentreUniversity of SheffieldUK
| | - Sean G. Rudd
- Science for Life LaboratoryDepartment of Oncology‐PathologyKarolinska InstitutetStockholmSweden
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13
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Xiong F, Wang Q, Wu GH, Liu WZ, Wang B, Chen YJ. Direct and indirect effects of IFN-α2b in malignancy treatment: not only an archer but also an arrow. Biomark Res 2022; 10:69. [PMID: 36104718 PMCID: PMC9472737 DOI: 10.1186/s40364-022-00415-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 08/22/2022] [Indexed: 12/02/2022] Open
Abstract
Interferon-α2b (IFN-α2b) is a highly active cytokine that belongs to the interferon-α (IFN-α) family. IFN-α2b has beneficial antiviral, antitumour, antiparasitic and immunomodulatory activities. Direct and indirect antiproliferative effects of IFN-α2b have been found to occur via multiple pathways, mainly the JAK-STAT pathway, in certain cancers. This article reviews mechanistic studies and clinical trials on IFN-α2b. Potential regulators of the function of IFN-α2b were also reviewed, which could be utilized to relieve the poor response to IFN-α2b. IFN-α2b can function not only by enhancing the systematic immune response but also by directly killing tumour cells. Different parts of JAK-STAT pathway activated by IFN-α2b, such as interferon alpha and beta receptors (IFNARs), Janus kinases (JAKs) and IFN‐stimulated gene factor 3 (ISGF3), might serve as potential target for enhancing the pharmacological action of IFN-α2b. Despite some issues that remain to be solved, based on current evidence, IFN-α2b can inhibit disease progression and improve the survival of patients with certain types of malignant tumours. More efforts should be made to address potential adverse effects and complications.
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14
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You D, Zhang S, Yan S, Ding Y, Li C, Cheng X, Wu L, Wang W, Zhang T, Li Z, He Y. SAMHD1 as a prognostic and predictive biomarker in stage II colorectal cancer: A multicenter cohort study. Front Oncol 2022; 12:939982. [PMID: 35978833 PMCID: PMC9376296 DOI: 10.3389/fonc.2022.939982] [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: 05/09/2022] [Accepted: 07/11/2022] [Indexed: 11/19/2022] Open
Abstract
Background The identification of high-risk population patients is key to the personalized treatment options for the stage II colorectal cancers. The use of proteomics in the prognosis of patients with stage II colorectal cancer remains unclear. Methods Using quantitative proteomics, we analyzed proteins that are differentially expressed in the tumor and adjacent normal tissues of 11 paired colorectal cancer patients with and without recurrence selected by a nested case-control design. Of the 21 identified proteins, we selected one candidate protein. The association of the corresponding gene of the selected protein with overall survival (OS) and adjuvant chemotherapy was analyzed using two independent cohorts of patients with stages II colorectal cancer. Results Sterile α motif and histidine-aspartate domain-containing protein 1 (SAMHD1) was selected as the candidate biomarker. A group of 124 patients (12.5%) were stratified into SAMHD1-high subgroup. The 5-year OS rate of SAMHD1-high patients was lower than that of SAMHD1-low patients with stage II colorectal cancer (discovery cohort: hazard ratio [HR] = 2.89, 95% confidence interval [CI], 1.17-7.18, P = 0.016; validation cohort: HR = 2.25, 95% CI, 1.17-4.34, P = 0.013). The Cox multivariate analysis yielded similar results. In a pooled database, the 5-year OS rate was significantly different between patients with and without adjuvant chemotherapy among stage II SAMHD1-low tumors than in patients with stage II SAMHD1-high tumors (88% vs. 77%, P = 0.032). Conclusions SAMHD1-high expression could help in identifying patients with stage II colorectal cancer with poor prognosis and less benefit from adjuvant chemotherapy.
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Affiliation(s)
- Dingyun You
- Department of Dental Research, The Affiliated Stomatological Hospital of Kunming Medical University, Kunming, China
- Yunnan Key Laboratory of Stomatology, Kunming Medical University, Kunming, China
- Yunnan Key Laboratory of Stem Cell and Regenerative Medicine, Biomedical Engineering Research Center, Kunming Medical University, Kunming, China
| | - Shuai Zhang
- Department of Biostatistics, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Shan Yan
- Yunnan Key Laboratory of Stem Cell and Regenerative Medicine, Biomedical Engineering Research Center, Kunming Medical University, Kunming, China
| | - Yingying Ding
- Department of Radiology, The Third Affiliated Hospital of Kunming Medical University, Yunnan Cancer Hospital, Yunnan Cancer Center, Kunming, China
| | - Chunxia Li
- Department of Biostatistics, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Xianshuo Cheng
- Department of Colorectal Surgery, The Third Affiliated Hospital of Kunming Medical University, Yunnan Cancer Hospital, Yunnan Cancer Center, Kunming, China
| | - Lin Wu
- Department of Pathology, The Third Affiliated Hospital of Kunming Medical University, Yunnan Cancer Hospital, Yunnan Cancer Center, Kunming, China
| | - Weizhou Wang
- Department of Orthopedics, The First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Tao Zhang
- Department of Biostatistics, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, China
- *Correspondence: Yongwen He, ; Zhenhui Li, ; Tao Zhang,
| | - Zhenhui Li
- Department of Radiology, The Third Affiliated Hospital of Kunming Medical University, Yunnan Cancer Hospital, Yunnan Cancer Center, Kunming, China
- *Correspondence: Yongwen He, ; Zhenhui Li, ; Tao Zhang,
| | - Yongwen He
- Department of Dental Research, The Affiliated Stomatological Hospital of Kunming Medical University, Kunming, China
- *Correspondence: Yongwen He, ; Zhenhui Li, ; Tao Zhang,
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15
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Bowen NE, Oo A, Kim B. Mechanistic Interplay between HIV-1 Reverse Transcriptase Enzyme Kinetics and Host SAMHD1 Protein: Viral Myeloid-Cell Tropism and Genomic Mutagenesis. Viruses 2022; 14:v14081622. [PMID: 35893688 PMCID: PMC9331428 DOI: 10.3390/v14081622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 07/21/2022] [Accepted: 07/22/2022] [Indexed: 11/23/2022] Open
Abstract
Human immunodeficiency virus type 1 (HIV-1) reverse transcriptase (RT) has been the primary interest among studies on antiviral discovery, viral replication kinetics, drug resistance, and viral evolution. Following infection and entry into target cells, the HIV-1 core disassembles, and the viral RT concomitantly converts the viral RNA into double-stranded proviral DNA, which is integrated into the host genome. The successful completion of the viral life cycle highly depends on the enzymatic DNA polymerase activity of RT. Furthermore, HIV-1 RT has long been known as an error-prone DNA polymerase due to its lack of proofreading exonuclease properties. Indeed, the low fidelity of HIV-1 RT has been considered as one of the key factors in the uniquely high rate of mutagenesis of HIV-1, which leads to efficient viral escape from immune and therapeutic antiviral selective pressures. Interestingly, a series of studies on the replication kinetics of HIV-1 in non-dividing myeloid cells and myeloid specific host restriction factor, SAM domain, and HD domain-containing protein, SAMHD1, suggest that the myeloid cell tropism and high rate of mutagenesis of HIV-1 are mechanistically connected. Here, we review not only HIV-1 RT as a key antiviral target, but also potential evolutionary and mechanistic crosstalk among the unique enzymatic features of HIV-1 RT, the replication kinetics of HIV-1, cell tropism, viral genetic mutation, and host SAMHD1 protein.
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Affiliation(s)
- Nicole E. Bowen
- Department of Pediatrics, School of Medicine, Emory University, Atlanta, GA 30329, USA; (N.E.B.); (A.O.)
| | - Adrian Oo
- Department of Pediatrics, School of Medicine, Emory University, Atlanta, GA 30329, USA; (N.E.B.); (A.O.)
| | - Baek Kim
- Department of Pediatrics, School of Medicine, Emory University, Atlanta, GA 30329, USA; (N.E.B.); (A.O.)
- Center for Drug Discovery, Children’s Healthcare of Atlanta, Atlanta, GA 30329, USA
- Correspondence:
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16
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Zhang Z, Li P, Sun P. Expression of SAMHD1 and its mutation on prognosis of colon cancer. Oncol Lett 2022; 24:303. [PMID: 35949607 PMCID: PMC9353240 DOI: 10.3892/ol.2022.13423] [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: 02/26/2022] [Accepted: 05/31/2022] [Indexed: 12/24/2022] Open
Abstract
The expression of sterile α motif and histidine/aspartic acid domain-containing protein 1 (SAMHD1) and its mutation play a key role in the prognosis of colon cancer. The aim of the present study was to investigate the mechanism and the role of SAMHD1 in colon cancer. Microarray data from 187 patients with colon cancer and 45 adjacent normal tissue obtained from the Gene Expression Omnibus (GEO) were analyzed. A protein-protein interaction (PPI) network was constructed to identify key genes associated with colon cancer prognosis. Cox proportional hazard regression and survival analyses were performed to identify the potential for SAMHD1 to serve as a prognostic biomarker. Immunohistochemistry (IHC) and immunofluorescence (IF) were performed to assess the expression levels and distribution of SAMHD1 in tissues and cells. Western blotting (WB) and Cell Counting Kit-8 (CCK-8) assays were used to identify the proliferation and apoptotic effects of SAMHD1 on HT-29 (Cas9-SAMHD1) cell lines. A total of 6,905 consistently differentially expressed genes were identified in the GEO database. Through the PPI network, SAMHD1 was found to be associated with Kirsten rat sarcoma virus (KRAS). SAMHD1 expression was negatively associated with KRAS. Proportional hazards regression and survival analyses demonstrated that low expression of SAMHD1 was associated with increased patient mortality. IHC and IF results demonstrated that SAMHD1 expression in patients with colon cancer was decreased compared with controls (both P<0.05). CCK-8 and WB results showed that proliferation was significantly promoted, and the expression levels of apoptosis-related proteins were significantly inhibited in the D137N and D311A groups as a result of a mutation in the deoxynucleoside triphosphohydrolase (dNTPase) site (both P<0.05 vs. wild-type). Proliferation was inhibited and apoptosis-related protein expression levels were promoted in the wild-type (WT) and D137N groups following 20 µg/ml 5-fluorouracil (5-FU) treatment (both P<0.05). WB and CCK-8 results showed cell proliferation was promoted and cell apoptosis-related protein expression was inhibited in the D137N group following treatment with 20 µg/ml 5-FU (all P<0.05) compared with the WT group. In conclusion, SAMHD1 expression was low in colon cancer. The dNTPase function of SAMHD1 may inhibit colon cancer cell proliferation and may enhance apoptosis. In addition, first-line chemotherapy with 5-FU has a time-dependent effect, which may provide novel options for clinical treatment of colon cancer.
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Affiliation(s)
- Zhou Zhang
- Translational Medical Centre, Wuxi No. 2 People's Hospital, Affiliated Wuxi Clinical College of Nantong University, Wuxi, Jiangsu 214002, P.R. China
| | - Ping Li
- Department of Pathology, Wuxi No. 2 People's Hospital, Affiliated Wuxi Clinical College of Nantong University, Wuxi, Jiangsu 214002, P.R. China
| | - Ping Sun
- Department of Pathology, Wuxi No. 2 People's Hospital, Affiliated Wuxi Clinical College of Nantong University, Wuxi, Jiangsu 214002, P.R. China
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17
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Targeting SAMHD1: to overcome multiple anti-cancer drugs resistance in hematological malignancies. Genes Dis 2022. [DOI: 10.1016/j.gendis.2022.06.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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18
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Jin Z, Kang J, Yu T. Feature selection and classification over the network with missing node observations. Stat Med 2022; 41:1242-1262. [PMID: 34816464 PMCID: PMC9773124 DOI: 10.1002/sim.9267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 09/14/2021] [Accepted: 10/29/2021] [Indexed: 12/25/2022]
Abstract
Jointly analyzing transcriptomic data and the existing biological networks can yield more robust and informative feature selection results, as well as better understanding of the biological mechanisms. Selecting and classifying node features over genome-scale networks has become increasingly important in genomic biology and genomic medicine. Existing methods have some critical drawbacks. The first is they do not allow flexible modeling of different subtypes of selected nodes. The second is they ignore nodes with missing values, very likely to increase bias in estimation. To address these limitations, we propose a general modeling framework for Bayesian node classification (BNC) with missing values. A new prior model is developed for the class indicators incorporating the network structure. For posterior computation, we resort to the Swendsen-Wang algorithm for efficiently updating class indicators. BNC can naturally handle missing values in the Bayesian modeling framework, which improves the node classification accuracy and reduces the bias in estimating gene effects. We demonstrate the advantages of our methods via extensive simulation studies and the analysis of the cutaneous melanoma dataset from The Cancer Genome Atlas.
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Affiliation(s)
| | - Jian Kang
- Department of Biostatistics, University of Michigan, Ann Arbor, Michigan
| | - Tianwei Yu
- School of Data Science and Warshel Institute, The Chinese University of Hong Kong - Shenzhen, and Shenzhen Research Institute of Big Data, Shenzhen, China
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19
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Modulation of DNA Damage Response by SAM and HD Domain Containing Deoxynucleoside Triphosphate Triphosphohydrolase (SAMHD1) Determines Prognosis and Treatment Efficacy in Different Solid Tumor Types. Cancers (Basel) 2022; 14:cancers14030641. [PMID: 35158911 PMCID: PMC8833711 DOI: 10.3390/cancers14030641] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 01/19/2022] [Accepted: 01/21/2022] [Indexed: 12/31/2022] Open
Abstract
SAMHD1 is a deoxynucleotide triphosphate (dNTP) triphosphohydrolase with important roles in the control of cell proliferation and apoptosis, either through the regulation of intracellular dNTPs levels or the modulation of the DNA damage response. However, SAMHD1's role in cancer evolution is still unknown. We performed the first in-depth study of SAMHD1's role in advanced solid tumors, by analyzing samples of 128 patients treated with chemotherapy agents based on platinum derivatives and/or antimetabolites, developing novel in vitro knock-out models to explore the mechanisms driving SAMHD1 function in cancer. Low (or no) expression of SAMHD1 was associated with a positive prognosis in breast, ovarian, and non-small cell lung cancer (NSCLC) cancer patients. A predictive value was associated with low-SAMHD1 expression in NSCLC and ovarian patients treated with antimetabolites in combination with platinum derivatives. In vitro, SAMHD1 knock-out cells showed increased γ-H2AX and apoptosis, suggesting that SAMHD1 depletion induces DNA damage leading to cell death. In vitro treatment with platinum-derived drugs significantly enhanced γ-H2AX and apoptotic markers expression in knock-out cells, indicating a synergic effect of SAMHD1 depletion and platinum-based treatment. SAMHD1 expression represents a new strong prognostic and predictive biomarker in solid tumors and, thus, modulation of the SAMHD1 function may constitute a promising target for the improvement of cancer therapy.
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20
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Wang T, Yue W, Tang G, Ye M, Yu J, Liu B, Jiao L, Liu X, Yin S, Chen J, Gao L, Yang J, He M. SAMHD1 Mutations and Expression in Mantle Cell Lymphoma Patients. Front Oncol 2021; 11:763151. [PMID: 34976810 PMCID: PMC8719590 DOI: 10.3389/fonc.2021.763151] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 11/16/2021] [Indexed: 12/27/2022] Open
Abstract
SAMHD1 (sterile alpha motif domain and histidine-aspartate domain-containing protein 1) is a deoxynucleoside triphosphate triphosphohydrolase regulating innate immune and modulating DNA damage signaling. It plays an important role in the development of some tumors. SAMHD1 was also reported as a barrier to cytarabine, a common chemotherapy drug for mantle cell lymphoma (MCL), and as a biomarker of grim prognosis for acute myelocytic leukemia (AML) patients. However, SAMHD1 expression and function in MCL have not been well-defined. In the present study, we evaluated SAMHD1 expression by immunohistochemistry and its gene structure by Sanger sequencing in MCL. Our results showed that SAMHD1 was positive in 36 (62.1%) patients. Importantly, SAMHD1-positive patients were associated with lower chemotherapy response rate (p = 0.023) and shorter overall survival (p = 0.039) than SAMHD1-negative cases. These results suggest that SAMHD1 is an adverse biomarker for MCL patients, which is due to the high expression of SAMHD1 and rapid cell proliferation. These findings were confirmed in an in vitro study using the siRNA technique. Silencing the SAMHD1 gene in the MCL cell line Jeko-1 significantly decreased cell proliferation and increased cell apoptosis. The MCL cell line with SAMHD1 knockdown showed lower Ki-67 proliferation index, higher caspase-3, and higher sensitivity to cytarabine. Furthermore, for the first time, four previously unreported missense mutations (S302Y, Y432C, E449G, and R451H) in exon 8 and exon 12 of the SAMHD1 gene were discovered by sequencing. The mutations had not been found to corelate with SAMHD1 protein expression detected by immunohistochemistry. The biological functions of this mutated SAMHD1 remain to be investigated.
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Affiliation(s)
- Tao Wang
- Department of Hematology, Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Wenqin Yue
- Department of Hematology, Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Gusheng Tang
- Department of Hematology, Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Mingyu Ye
- Department of Hematology, Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Jiechen Yu
- Department of Hematology, Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Bin Liu
- Department of Hematology, Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Lijuan Jiao
- Department of Pathology, Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Xuefei Liu
- Department of Pathology, Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Shuyi Yin
- Department of Pathology, Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Jie Chen
- Department of Hematology, Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Lei Gao
- Department of Hematology, Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Jianmin Yang
- Department of Hematology, Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Miaoxia He
- Department of Pathology, Changhai Hospital, Second Military Medical University, Shanghai, China
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21
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Canino F, Moscetti L, Borghi V, Dominici M, Piacentini F. Palbociclib in a patient with HR+/HER2- advanced breast cancer and HIV1 infection: a case report. BREAST CANCER MANAGEMENT 2021. [DOI: 10.2217/bmt-2021-0006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The use of drugs that affect the cell cycle represents one of the common strategies for the control of some unrelated pathologies, such as chronic viral HIV infections or cancer. The authors report the case of a patient followed for a hormone receptor-positive (HR+)/HER2 negative (HER2-) advanced breast cancer, treated with hormone therapy and CDK 4/6 inhibitors, and a concomitant HIV infection under antiretroviral treatment. The authors consider the function of the sterile alpha motif and HD domain-containing protein-1 (SAMHD1) enzyme, its implications in the control of viral replication and the correlation between its activity and the mechanism of action of the CDK 4/6 inhibitor palbociclib.
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Affiliation(s)
- Fabio Canino
- Division of Oncology, Department of Oncology & Hematology, University Hospital of Modena, Modena, Italy
| | - Luca Moscetti
- Division of Oncology, Department of Oncology & Hematology, University Hospital of Modena, Modena, Italy
| | - Vanni Borghi
- Division of Infectious Diseases, Department of Specialized Medicine, University Hospital of Modena, Modena, Italy
| | - Massimo Dominici
- Division of Oncology, Department of Medical & Surgical Sciences for Children & Adults, University Hospital of Modena, Italy
| | - Federico Piacentini
- Division of Oncology, Department of Medical & Surgical Sciences for Children & Adults, University Hospital of Modena, Italy
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22
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Ranjbarian F, Sharma S, Falappa G, Taruschio W, Chabes A, Hofer A. Isocratic HPLC analysis for the simultaneous determination of dNTPs, rNTPs and ADP in biological samples. Nucleic Acids Res 2021; 50:e18. [PMID: 34850106 PMCID: PMC8860589 DOI: 10.1093/nar/gkab1117] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 09/22/2021] [Accepted: 10/26/2021] [Indexed: 11/18/2022] Open
Abstract
Information about the cellular concentrations of deoxyribonucleoside triphosphates (dNTPs) is instrumental for mechanistic studies of DNA replication and for understanding diseases caused by defects in dNTP metabolism. The dNTPs are measured by methods based on either HPLC or DNA polymerization. An advantage with the HPLC-based techniques is that the parallel analysis of ribonucleoside triphosphates (rNTPs) can serve as an internal quality control of nucleotide integrity and extraction efficiency. We have developed a Freon-free trichloroacetic acid-based method to extract cellular nucleotides and an isocratic reverse phase HPLC-based technique that is able to separate dNTPs, rNTPs and ADP in a single run. The ability to measure the ADP levels improves the control of nucleotide integrity, and the use of an isocratic elution overcomes the shifting baseline problems in previously developed gradient-based reversed phase protocols for simultaneously measuring dNTPs and rNTPs. An optional DNA-polymerase-dependent step is used for confirmation that the dNTP peaks do not overlap with other components of the extracts, further increasing the reliability of the analysis. The method is compatible with a wide range of biological samples and has a sensitivity better than other UV-based HPLC protocols, closely matching that of mass spectrometry-based detection.
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Affiliation(s)
- Farahnaz Ranjbarian
- Dept. Medical Biochemistry and Biophysics, Umeå University, SE-901 87 Umeå, Sweden
| | - Sushma Sharma
- Dept. Medical Biochemistry and Biophysics, Umeå University, SE-901 87 Umeå, Sweden
| | - Giulia Falappa
- Dept. Medical Biochemistry and Biophysics, Umeå University, SE-901 87 Umeå, Sweden
| | - Walter Taruschio
- Dept. Medical Biochemistry and Biophysics, Umeå University, SE-901 87 Umeå, Sweden
| | - Andrei Chabes
- Dept. Medical Biochemistry and Biophysics, Umeå University, SE-901 87 Umeå, Sweden
| | - Anders Hofer
- Dept. Medical Biochemistry and Biophysics, Umeå University, SE-901 87 Umeå, Sweden
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23
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Shi K, Lin W, Zhao XM. Identifying Molecular Biomarkers for Diseases With Machine Learning Based on Integrative Omics. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2021; 18:2514-2525. [PMID: 32305934 DOI: 10.1109/tcbb.2020.2986387] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Molecular biomarkers are certain molecules or set of molecules that can be of help for diagnosis or prognosis of diseases or disorders. In the past decades, thanks to the advances in high-throughput technologies, a huge amount of molecular 'omics' data, e.g., transcriptomics and proteomics, have been accumulated. The availability of these omics data makes it possible to screen biomarkers for diseases or disorders. Accordingly, a number of computational approaches have been developed to identify biomarkers by exploring the omics data. In this review, we present a comprehensive survey on the recent progress of identification of molecular biomarkers with machine learning approaches. Specifically, we categorize the machine learning approaches into supervised, un-supervised and recommendation approaches, where the biomarkers including single genes, gene sets and small gene networks. In addition, we further discuss potential problems underlying bio-medical data that may pose challenges for machine learning, and provide possible directions for future biomarker identification.
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24
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Bowen NE, Temple J, Shepard C, Oo A, Arizaga F, Kapoor-Vazirani P, Persaud M, Yu CH, Kim DH, Schinazi RF, Ivanov DN, Diaz-Griffero F, Yu DS, Xiong Y, Kim B. Structural and functional characterization explains loss of dNTPase activity of the cancer-specific R366C/H mutant SAMHD1 proteins. J Biol Chem 2021; 297:101170. [PMID: 34492268 PMCID: PMC8497992 DOI: 10.1016/j.jbc.2021.101170] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 08/20/2021] [Accepted: 08/23/2021] [Indexed: 01/09/2023] Open
Abstract
Elevated intracellular levels of dNTPs have been shown to be a biochemical marker of cancer cells. Recently, a series of mutations in the multifunctional dNTP triphosphohydrolase (dNTPase), sterile alpha motif and histidine-aspartate domain-containing protein 1 (SAMHD1), have been reported in various cancers. Here, we investigated the structure and functions of SAMHD1 R366C/H mutants, found in colon cancer and leukemia. Unlike many other cancer-specific mutations, the SAMHD1 R366 mutations do not alter cellular protein levels of the enzyme. However, R366C/H mutant proteins exhibit a loss of dNTPase activity, and their X-ray structures demonstrate the absence of dGTP substrate in their active site, likely because of a loss of interaction with the γ-phosphate of the substrate. The R366C/H mutants failed to reduce intracellular dNTP levels and restrict HIV-1 replication, functions of SAMHD1 that are dependent on the ability of the enzyme to hydrolyze dNTPs. However, these mutants retain dNTPase-independent functions, including mediating dsDNA break repair, interacting with CtIP and cyclin A2, and suppressing innate immune responses. Finally, SAMHD1 degradation in human primary-activated/dividing CD4+ T cells further elevates cellular dNTP levels. This study suggests that the loss of SAMHD1 dNTPase activity induced by R366 mutations can mechanistically contribute to the elevated dNTP levels commonly found in cancer cells.
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Affiliation(s)
- Nicole E Bowen
- Department of Pediatrics, School of Medicine, Emory University, Atlanta, Georgia, USA
| | - Joshua Temple
- Department of Molecular Biophysics and Biochemistry, School of Medicine, Yale University, New Haven, Connecticut, USA
| | - Caitlin Shepard
- Department of Pediatrics, School of Medicine, Emory University, Atlanta, Georgia, USA
| | - Adrian Oo
- Department of Pediatrics, School of Medicine, Emory University, Atlanta, Georgia, USA
| | - Fidel Arizaga
- Department of Molecular Biophysics and Biochemistry, School of Medicine, Yale University, New Haven, Connecticut, USA
| | - Priya Kapoor-Vazirani
- Department of Radiation Oncology, School of Medicine, Emory University, Atlanta, Georgia, USA
| | - Mirjana Persaud
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Corey H Yu
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, Texas, USA
| | - Dong-Hyun Kim
- School of Pharmacy, Kyung-Hee University, Seoul, South Korea
| | - Raymond F Schinazi
- Department of Pediatrics, School of Medicine, Emory University, Atlanta, Georgia, USA
| | - Dmitri N Ivanov
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, Texas, USA
| | - Felipe Diaz-Griffero
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York, USA
| | - David S Yu
- Department of Radiation Oncology, School of Medicine, Emory University, Atlanta, Georgia, USA
| | - Yong Xiong
- Department of Molecular Biophysics and Biochemistry, School of Medicine, Yale University, New Haven, Connecticut, USA.
| | - Baek Kim
- Department of Pediatrics, School of Medicine, Emory University, Atlanta, Georgia, USA; Children's Healthcare of Atlanta, Atlanta, Georgia, USA.
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25
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Nucleotide Pool Imbalance and Antibody Gene Diversification. Vaccines (Basel) 2021; 9:vaccines9101050. [PMID: 34696158 PMCID: PMC8538681 DOI: 10.3390/vaccines9101050] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 09/13/2021] [Accepted: 09/17/2021] [Indexed: 01/10/2023] Open
Abstract
The availability and adequate balance of deoxyribonucleoside triphosphate (dNTP) is an important determinant of both the fidelity and the processivity of DNA polymerases. Therefore, maintaining an optimal balance of the dNTP pool is critical for genomic stability in replicating and quiescent cells. Since DNA synthesis is required not only in genomic replication but also in DNA damage repair and recombination, the abnormalities in the dNTP pool affect a wide range of chromosomal activities. The generation of antibody diversity relies on antigen-independent V(D)J recombination, as well as antigen-dependent somatic hypermutation and class switch recombination. These processes involve diverse sets of DNA polymerases, which are affected by the dNTP pool imbalances. This review discusses the role of the optimal dNTP pool balance in the diversification of antibody encoding genes.
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26
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Schott K, Majer C, Bulashevska A, Childs L, Schmidt MHH, Rajalingam K, Munder M, König R. SAMHD1 in cancer: curse or cure? J Mol Med (Berl) 2021; 100:351-372. [PMID: 34480199 PMCID: PMC8843919 DOI: 10.1007/s00109-021-02131-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 07/15/2021] [Accepted: 08/12/2021] [Indexed: 12/12/2022]
Abstract
Human sterile α motif and HD domain-containing protein 1 (SAMHD1), originally described as the major cellular deoxyribonucleoside triphosphate triphosphohydrolase (dNTPase) balancing the intracellular deoxynucleotide (dNTP) pool, has come recently into focus of cancer research. As outlined in this review, SAMHD1 has been reported to be mutated in a variety of cancer types and the expression of SAMHD1 is dysregulated in many cancers. Therefore, SAMHD1 is regarded as a tumor suppressor in certain tumors. Moreover, it has been proposed that SAMHD1 might fulfill the requirements of a driver gene in tumor development or might promote a so-called mutator phenotype. Besides its role as a dNTPase, several novel cellular functions of SAMHD1 have come to light only recently, including a role as negative regulator of innate immune responses and as facilitator of DNA end resection during DNA replication and repair. Therefore, SAMHD1 can be placed at the crossroads of various cellular processes. The present review summarizes the negative role of SAMHD1 in chemotherapy sensitivity, highlights reported SAMHD1 mutations found in various cancer types, and aims to discuss functional consequences as well as underlying mechanisms of SAMHD1 dysregulation potentially involved in cancer development.
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Affiliation(s)
- Kerstin Schott
- Host-Pathogen Interactions, Paul-Ehrlich-Institut, Langen, Germany
| | - Catharina Majer
- Host-Pathogen Interactions, Paul-Ehrlich-Institut, Langen, Germany
| | - Alla Bulashevska
- Host-Pathogen Interactions, Paul-Ehrlich-Institut, Langen, Germany
| | - Liam Childs
- Host-Pathogen Interactions, Paul-Ehrlich-Institut, Langen, Germany
| | - Mirko H H Schmidt
- Institute of Anatomy, Medical Faculty Carl Gustav Carus, Technische Universität Dresden School of Medicine, Dresden, Germany
| | - Krishnaraj Rajalingam
- Cell Biology Unit, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
- University Cancer Center Mainz, University Medical Center Mainz, Mainz, Germany
| | - Markus Munder
- Third Department of Medicine, University Medical Center, Johannes Gutenberg University, Mainz, Germany
| | - Renate König
- Host-Pathogen Interactions, Paul-Ehrlich-Institut, Langen, Germany.
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27
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Soriano I, Vazquez E, De Leon N, Bertrand S, Heitzer E, Toumazou S, Bo Z, Palles C, Pai CC, Humphrey TC, Tomlinson I, Cotterill S, Kearsey SE. Expression of the cancer-associated DNA polymerase ε P286R in fission yeast leads to translesion synthesis polymerase dependent hypermutation and defective DNA replication. PLoS Genet 2021; 17:e1009526. [PMID: 34228709 PMCID: PMC8284607 DOI: 10.1371/journal.pgen.1009526] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Revised: 07/16/2021] [Accepted: 06/11/2021] [Indexed: 12/15/2022] Open
Abstract
Somatic and germline mutations in the proofreading domain of the replicative DNA polymerase ε (POLE-exonuclease domain mutations, POLE-EDMs) are frequently found in colorectal and endometrial cancers and, occasionally, in other tumours. POLE-associated cancers typically display hypermutation, and a unique mutational signature, with a predominance of C > A transversions in the context TCT and C > T transitions in the context TCG. To understand better the contribution of hypermutagenesis to tumour development, we have modelled the most recurrent POLE-EDM (POLE-P286R) in Schizosaccharomyces pombe. Whole-genome sequencing analysis revealed that the corresponding pol2-P287R allele also has a strong mutator effect in vivo, with a high frequency of base substitutions and relatively few indel mutations. The mutations are equally distributed across different genomic regions, but in the immediate vicinity there is an asymmetry in AT frequency. The most abundant base-pair changes are TCT > TAT transversions and, in contrast to human mutations, TCG > TTG transitions are not elevated, likely due to the absence of cytosine methylation in fission yeast. The pol2-P287R variant has an increased sensitivity to elevated dNTP levels and DNA damaging agents, and shows reduced viability on depletion of the Pfh1 helicase. In addition, S phase is aberrant and RPA foci are elevated, suggestive of ssDNA or DNA damage, and the pol2-P287R mutation is synthetically lethal with rad3 inactivation, indicative of checkpoint activation. Significantly, deletion of genes encoding some translesion synthesis polymerases, most notably Pol κ, partially suppresses pol2-P287R hypermutation, indicating that polymerase switching contributes to this phenotype.
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Affiliation(s)
- Ignacio Soriano
- ZRAB, University of Oxford, Oxford, United Kingdom
- Edinburgh Cancer Research Centre, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, United Kingdom
| | - Enrique Vazquez
- Genomics Unit, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
| | - Nagore De Leon
- ZRAB, University of Oxford, Oxford, United Kingdom
- Edinburgh Cancer Research Centre, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, United Kingdom
| | | | - Ellen Heitzer
- Institute of Human Genetics, Diagnostic & Research Center for Molecular BioMedicine, Medical University of Graz, Graz, Austria
| | - Sophia Toumazou
- ZRAB, University of Oxford, Oxford, United Kingdom
- MRC Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford, United Kingdom
| | - Zhihan Bo
- ZRAB, University of Oxford, Oxford, United Kingdom
| | - Claire Palles
- Gastrointestinal Cancer Genetics Laboratory, Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Chen-Chun Pai
- MRC Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford, United Kingdom
| | - Timothy C. Humphrey
- MRC Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford, United Kingdom
| | - Ian Tomlinson
- Edinburgh Cancer Research Centre, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, United Kingdom
| | - Sue Cotterill
- St. George’s, University of London, Cranmer Terrace, Tooting, London, United Kingdom
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28
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Lamb NA, Bard JE, Buck MJ, Surtees JA. A selection-based next generation sequencing approach to develop robust, genotype-specific mutation profiles in Saccharomyces cerevisiae. G3 GENES|GENOMES|GENETICS 2021; 11:6204636. [PMID: 33784385 PMCID: PMC8495734 DOI: 10.1093/g3journal/jkab099] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 03/11/2021] [Indexed: 11/13/2022]
Abstract
Distinct mutation signatures arise from environmental exposures and/or from defects in metabolic pathways that promote genome stability. The presence of a particular mutation signature can therefore predict the underlying mechanism of mutagenesis. These insults to the genome often alter dNTP pools, which itself impacts replication fidelity. Therefore, the impact of altered dNTP pools should be considered when making mechanistic predictions based on mutation signatures. We developed a targeted deep-sequencing approach on the CAN1 gene in Saccharomyces cerevisiae to define information-rich mutational profiles associated with distinct rnr1 backgrounds. Mutations in the activity and selectivity sites of rnr1 lead to elevated and/or unbalanced dNTP levels, which compromises replication fidelity and increases mutation rates. The mutation spectra of rnr1Y285F and rnr1Y285A alleles were characterized previously; our analysis was consistent with this prior work but the sequencing depth achieved in our study allowed a significantly more robust and nuanced computational analysis of the variants observed, generating profiles that integrated information about mutation spectra, position effects, and sequence context. This approach revealed previously unidentified, genotype-specific mutation profiles in the presence of even modest changes in dNTP pools. Furthermore, we identified broader sequence contexts and nucleotide motifs that influenced variant profiles in different rnr1 backgrounds, which allowed specific mechanistic predictions about the impact of altered dNTP pools on replication fidelity.
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Affiliation(s)
- Natalie A Lamb
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo (SUNY), Buffalo, NY 14203, USA
| | - Jonathan E Bard
- University at Buffalo Genomics and Bioinformatics Core, Buffalo, NY 14203, USA
- Genetics, Genomics and Bioinformatics Graduate Program, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo (SUNY), Buffalo, NY 14203, USA
| | - Michael J Buck
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo (SUNY), Buffalo, NY 14203, USA
- Genetics, Genomics and Bioinformatics Graduate Program, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo (SUNY), Buffalo, NY 14203, USA
| | - Jennifer A Surtees
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo (SUNY), Buffalo, NY 14203, USA
- Genetics, Genomics and Bioinformatics Graduate Program, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo (SUNY), Buffalo, NY 14203, USA
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29
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Morris ER, Kunzelmann S, Caswell SJ, Purkiss AG, Kelly G, Taylor IA. Probing the Catalytic Mechanism and Inhibition of SAMHD1 Using the Differential Properties of R p- and S p-dNTPαS Diastereomers. Biochemistry 2021; 60:1682-1698. [PMID: 33988981 PMCID: PMC8173608 DOI: 10.1021/acs.biochem.0c00944] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
SAMHD1 is a fundamental regulator of cellular dNTPs that catalyzes their hydrolysis into 2'-deoxynucleoside and triphosphate, restricting the replication of viruses, including HIV-1, in CD4+ myeloid lineage and resting T-cells. SAMHD1 mutations are associated with the autoimmune disease Aicardi-Goutières syndrome (AGS) and certain cancers. More recently, SAMHD1 has been linked to anticancer drug resistance and the suppression of the interferon response to cytosolic nucleic acids after DNA damage. Here, we probe dNTP hydrolysis and inhibition of SAMHD1 using the Rp and Sp diastereomers of dNTPαS nucleotides. Our biochemical and enzymological data show that the α-phosphorothioate substitution in Sp-dNTPαS but not Rp-dNTPαS diastereomers prevents Mg2+ ion coordination at both the allosteric and catalytic sites, rendering SAMHD1 unable to form stable, catalytically active homotetramers or hydrolyze substrate dNTPs at the catalytic site. Furthermore, we find that Sp-dNTPαS diastereomers competitively inhibit dNTP hydrolysis, while Rp-dNTPαS nucleotides stabilize tetramerization and are hydrolyzed with similar kinetic parameters to cognate dNTPs. For the first time, we present a cocrystal structure of SAMHD1 with a substrate, Rp-dGTPαS, in which an Fe-Mg-bridging water species is poised for nucleophilic attack on the Pα. We conclude that it is the incompatibility of Mg2+, a hard Lewis acid, and the α-phosphorothioate thiol, a soft Lewis base, that prevents the Sp-dNTPαS nucleotides coordinating in a catalytically productive conformation. On the basis of these data, we present a model for SAMHD1 stereospecific hydrolysis of Rp-dNTPαS nucleotides and for a mode of competitive inhibition by Sp-dNTPαS nucleotides that competes with formation of the enzyme-substrate complex.
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Affiliation(s)
- Elizabeth R Morris
- Macromolecular Structure Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, U.K
| | - Simone Kunzelmann
- Structural Biology Science Technology Platform, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, U.K
| | - Sarah J Caswell
- Macromolecular Structure Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, U.K
| | - Andrew G Purkiss
- Structural Biology Science Technology Platform, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, U.K
| | - Geoff Kelly
- The Medical Research Council Biomedical NMR Centre, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, U.K
| | - Ian A Taylor
- Macromolecular Structure Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, U.K
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30
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Gazquez-Gutierrez A, Witteveldt J, R Heras S, Macias S. Sensing of transposable elements by the antiviral innate immune system. RNA (NEW YORK, N.Y.) 2021; 27:rna.078721.121. [PMID: 33888553 PMCID: PMC8208052 DOI: 10.1261/rna.078721.121] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 04/17/2021] [Indexed: 05/15/2023]
Abstract
Around half of the genome in mammals is composed of transposable elements (TEs) such as DNA transposons and retrotransposons. Several mechanisms have evolved to prevent their activity and the detrimental impact of their insertional mutagenesis. Despite these potentially negative effects, TEs are essential drivers of evolution, and in certain settings, beneficial to their hosts. For instance, TEs have rewired the antiviral gene regulatory network and are required for early embryonic development. However, due to structural similarities between TE-derived and viral nucleic acids, cells can misidentify TEs as invading viruses and trigger the major antiviral innate immune pathway, the type I interferon (IFN) response. This review will focus on the different settings in which the role of TE-mediated IFN activation has been documented, including cancer and senescence. Importantly, TEs may also play a causative role in the development of complex autoimmune diseases characterised by constitutive type I IFN activation. All these observations suggest the presence of strong but opposing forces driving the coevolution of TEs and antiviral defence. A better biological understanding of the TE replicative cycle as well as of the antiviral nucleic acid sensing mechanisms will provide insights into how these two biological processes interact and will help to design better strategies to treat human diseases characterised by aberrant TE expression and/or type I IFN activation.
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Affiliation(s)
| | - Jeroen Witteveldt
- University of Edinburgh - Institute of Immunology and Infection Research
| | - Sara R Heras
- GENYO. Centre for Genomics and Oncological Research, Pfizer University of Granada
| | - Sara Macias
- Institute of Immunology and Infection Research
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31
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Park K, Ryoo J, Jeong H, Kim M, Lee S, Hwang SY, Ahn J, Kim D, Moon HC, Baek D, Kim K, Park HY, Ahn K. Aicardi-Goutières syndrome-associated gene SAMHD1 preserves genome integrity by preventing R-loop formation at transcription-replication conflict regions. PLoS Genet 2021; 17:e1009523. [PMID: 33857133 PMCID: PMC8078737 DOI: 10.1371/journal.pgen.1009523] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 04/27/2021] [Accepted: 03/29/2021] [Indexed: 12/25/2022] Open
Abstract
The comorbid association of autoimmune diseases with cancers has been a major obstacle to successful anti-cancer treatment. Cancer survival rate decreases significantly in patients with preexisting autoimmunity. However, to date, the molecular and cellular profiles of such comorbidities are poorly understood. We used Aicardi-Goutières syndrome (AGS) as a model autoimmune disease and explored the underlying mechanisms of genome instability in AGS-associated-gene-deficient patient cells. We found that R-loops are highly enriched at transcription-replication conflict regions of the genome in fibroblast of patients bearing SAMHD1 mutation, which is the AGS-associated-gene mutation most frequently reported with tumor and malignancies. In SAMHD1-depleted cells, R-loops accumulated with the concomitant activation of DNA damage responses. Removal of R-loops in SAMHD1 deficiency reduced cellular responses to genome instability. Furthermore, downregulation of SAMHD1 expression is associated with various types of cancer and poor survival rate. Our findings suggest that SAMHD1 functions as a tumor suppressor by resolving R-loops, and thus, SAMHD1 and R-loop may be novel diagnostic markers and targets for patient stratification in anti-cancer therapy. Mutations in SAMHD1 cause Aicardi-Goutières syndrome (AGS), a monogenic lupus-like autoimmune disease. Among AGS-associated genes, SAMHD1 is most frequently mutates in various types of tumors and malignancies, suggesting that it is biologically relevant to cancer development. Here, we show that SAMHD1 resolves R-loops induced by transcription-replication conflicts, thereby contributing to the maintenance of genome stability. Our findings provide insight into the molecular and mechanical understanding of the autoimmunity and cancer comorbidity, and suggest that SAMHD1 and R-loops are potential and reliable biomarkers in anti-cancer therapeutics.
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Affiliation(s)
- Kiwon Park
- Center for RNA Research, Institute for Basic Science, Seoul, Republic of Korea
- School of Biological Sciences, Seoul National University, Seoul, Republic of Korea
| | - Jeongmin Ryoo
- Department of Hematology, Oncology and Stem Cell transplantation, Comprehensive Cancer center Freiburg, University of Freiburg, Freiburg, Germany
| | - Heena Jeong
- Center for RNA Research, Institute for Basic Science, Seoul, Republic of Korea
- School of Biological Sciences, Seoul National University, Seoul, Republic of Korea
| | - Minsu Kim
- Center for RNA Research, Institute for Basic Science, Seoul, Republic of Korea
- School of Biological Sciences, Seoul National University, Seoul, Republic of Korea
| | - Sungwon Lee
- Center for RNA Research, Institute for Basic Science, Seoul, Republic of Korea
- School of Biological Sciences, Seoul National University, Seoul, Republic of Korea
| | - Sung-Yeon Hwang
- Center for RNA Research, Institute for Basic Science, Seoul, Republic of Korea
- School of Biological Sciences, Seoul National University, Seoul, Republic of Korea
| | - Jiyoung Ahn
- Biomedical Research Institute, Seoul National University Hospital, Seoul, Republic of Korea
| | - Doyeon Kim
- School of Biological Sciences, Seoul National University, Seoul, Republic of Korea
| | - Hyungseok C. Moon
- Department of Physics and Astronomy, Seoul National University, Seoul, Republic of Korea
| | - Daehyun Baek
- School of Biological Sciences, Seoul National University, Seoul, Republic of Korea
| | - Kwangsoo Kim
- Transdisciplinary Department of Medicine & Advanced Technology, Seoul National University Hospital, Seoul, Republic of Korea
| | - Hye Yoon Park
- Department of Physics and Astronomy, Seoul National University, Seoul, Republic of Korea
| | - Kwangseog Ahn
- Center for RNA Research, Institute for Basic Science, Seoul, Republic of Korea
- School of Biological Sciences, Seoul National University, Seoul, Republic of Korea
- * E-mail:
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32
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Dual roles of SAMHD1 in tumor development and chemoresistance to anticancer drugs. Oncol Lett 2021; 21:451. [PMID: 33907561 PMCID: PMC8063254 DOI: 10.3892/ol.2021.12712] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 03/10/2021] [Indexed: 11/05/2022] Open
Abstract
Human sterile alpha motif and HD-domain-containing protein 1 (SAMHD1) has been identified as a GTP or dGTP-dependent deoxynucleotide triphosphohydrolase (dNTPase) and acts as an antiviral factor against certain retroviruses and DNA viruses. Genetic mutation in SAMHD1 causes the inflammatory Aicardi-Goutières Syndrome and abnormal intracellular deoxyribonucleoside triphosphates (dNTPs) pool. At present, the role of SAMHD1 in numerous types of cancer, such as chronic lymphocytic leukemia, lung cancer and colorectal cancer, is highly studied. Furthermore, it has been found that methylation, acetylation and phosphorylation are involved in the regulation of SAMHD1 expression, and that genetic mutations can cause changes in its activities, including dNTPase activity, long interspersed element type 1 (LINE-1) suppression and DNA damage repair, which could lead to uncontrolled cell cycle progression and cancer development. In addition, SAMHD1 has been reported to have a negative regulatory role in the chemosensitivity to anticancer drugs through its dNTPase activity. The present review aimed to summarize the regulation of SAMHD1 expression in cancer and its function in tumor growth and chemotherapy sensitivity, and discussed controversial points and future directions.
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33
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Akimova E, Gassner FJ, Schubert M, Rebhandl S, Arzt C, Rauscher S, Tober V, Zaborsky N, Greil R, Geisberger R. SAMHD1 restrains aberrant nucleotide insertions at repair junctions generated by DNA end joining. Nucleic Acids Res 2021; 49:2598-2608. [PMID: 33591315 PMCID: PMC7969033 DOI: 10.1093/nar/gkab051] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 01/15/2021] [Accepted: 01/19/2021] [Indexed: 12/15/2022] Open
Abstract
Aberrant end joining of DNA double strand breaks leads to chromosomal rearrangements and to insertion of nuclear or mitochondrial DNA into breakpoints, which is commonly observed in cancer cells and constitutes a major threat to genome integrity. However, the mechanisms that are causative for these insertions are largely unknown. By monitoring end joining of different linear DNA substrates introduced into HEK293 cells, as well as by examining end joining of CRISPR/Cas9 induced DNA breaks in HEK293 and HeLa cells, we provide evidence that the dNTPase activity of SAMHD1 impedes aberrant DNA resynthesis at DNA breaks during DNA end joining. Hence, SAMHD1 expression or low intracellular dNTP levels lead to shorter repair joints and impede insertion of distant DNA regions prior end repair. Our results reveal a novel role for SAMHD1 in DNA end joining and provide new insights into how loss of SAMHD1 may contribute to genome instability and cancer development.
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Affiliation(s)
- Ekaterina Akimova
- Department of Internal Medicine III with Haematology, Medical Oncology, Haemostaseology, Infectiology and Rheumatology, Oncologic Center, Paracelsus Medical University, Salzburg, Austria.,Salzburg Cancer Research Institute - Laboratory for Immunological and Molecular Cancer Research (SCRI-LIMCR); Cancer Cluster Salzburg, 5020 Salzburg, Austria.,Department of Biosciences, Paris Lodron University of Salzburg, 5020 Salzburg, Austria
| | - Franz Josef Gassner
- Department of Internal Medicine III with Haematology, Medical Oncology, Haemostaseology, Infectiology and Rheumatology, Oncologic Center, Paracelsus Medical University, Salzburg, Austria.,Salzburg Cancer Research Institute - Laboratory for Immunological and Molecular Cancer Research (SCRI-LIMCR); Cancer Cluster Salzburg, 5020 Salzburg, Austria
| | - Maria Schubert
- Department of Internal Medicine III with Haematology, Medical Oncology, Haemostaseology, Infectiology and Rheumatology, Oncologic Center, Paracelsus Medical University, Salzburg, Austria.,Salzburg Cancer Research Institute - Laboratory for Immunological and Molecular Cancer Research (SCRI-LIMCR); Cancer Cluster Salzburg, 5020 Salzburg, Austria
| | - Stefan Rebhandl
- Department of Internal Medicine III with Haematology, Medical Oncology, Haemostaseology, Infectiology and Rheumatology, Oncologic Center, Paracelsus Medical University, Salzburg, Austria.,Salzburg Cancer Research Institute - Laboratory for Immunological and Molecular Cancer Research (SCRI-LIMCR); Cancer Cluster Salzburg, 5020 Salzburg, Austria
| | - Claudia Arzt
- Department of Internal Medicine III with Haematology, Medical Oncology, Haemostaseology, Infectiology and Rheumatology, Oncologic Center, Paracelsus Medical University, Salzburg, Austria.,Salzburg Cancer Research Institute - Laboratory for Immunological and Molecular Cancer Research (SCRI-LIMCR); Cancer Cluster Salzburg, 5020 Salzburg, Austria
| | - Stefanie Rauscher
- Department of Internal Medicine III with Haematology, Medical Oncology, Haemostaseology, Infectiology and Rheumatology, Oncologic Center, Paracelsus Medical University, Salzburg, Austria.,Salzburg Cancer Research Institute - Laboratory for Immunological and Molecular Cancer Research (SCRI-LIMCR); Cancer Cluster Salzburg, 5020 Salzburg, Austria.,Department of Biosciences, Paris Lodron University of Salzburg, 5020 Salzburg, Austria
| | - Vanessa Tober
- Department of Internal Medicine III with Haematology, Medical Oncology, Haemostaseology, Infectiology and Rheumatology, Oncologic Center, Paracelsus Medical University, Salzburg, Austria.,Salzburg Cancer Research Institute - Laboratory for Immunological and Molecular Cancer Research (SCRI-LIMCR); Cancer Cluster Salzburg, 5020 Salzburg, Austria.,Department of Biosciences, Paris Lodron University of Salzburg, 5020 Salzburg, Austria
| | - Nadja Zaborsky
- Department of Internal Medicine III with Haematology, Medical Oncology, Haemostaseology, Infectiology and Rheumatology, Oncologic Center, Paracelsus Medical University, Salzburg, Austria.,Salzburg Cancer Research Institute - Laboratory for Immunological and Molecular Cancer Research (SCRI-LIMCR); Cancer Cluster Salzburg, 5020 Salzburg, Austria
| | - Richard Greil
- Department of Internal Medicine III with Haematology, Medical Oncology, Haemostaseology, Infectiology and Rheumatology, Oncologic Center, Paracelsus Medical University, Salzburg, Austria.,Salzburg Cancer Research Institute - Laboratory for Immunological and Molecular Cancer Research (SCRI-LIMCR); Cancer Cluster Salzburg, 5020 Salzburg, Austria
| | - Roland Geisberger
- Department of Internal Medicine III with Haematology, Medical Oncology, Haemostaseology, Infectiology and Rheumatology, Oncologic Center, Paracelsus Medical University, Salzburg, Austria.,Salzburg Cancer Research Institute - Laboratory for Immunological and Molecular Cancer Research (SCRI-LIMCR); Cancer Cluster Salzburg, 5020 Salzburg, Austria
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34
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SAMHD1 … and Viral Ways around It. Viruses 2021; 13:v13030395. [PMID: 33801276 PMCID: PMC7999308 DOI: 10.3390/v13030395] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 02/24/2021] [Accepted: 02/25/2021] [Indexed: 12/19/2022] Open
Abstract
The SAM and HD domain-containing protein 1 (SAMHD1) is a dNTP triphosphohydrolase that plays a crucial role for a variety of different cellular functions. Besides balancing intracellular dNTP concentrations, facilitating DNA damage repair, and dampening excessive immune responses, SAMHD1 has been shown to act as a major restriction factor against various virus species. In addition to its well-described activity against retroviruses such as HIV-1, SAMHD1 has been identified to reduce the infectivity of different DNA viruses such as the herpesviruses CMV and EBV, the poxvirus VACV, or the hepadnavirus HBV. While some viruses are efficiently restricted by SAMHD1, others have developed evasion mechanisms that antagonize the antiviral activity of SAMHD1. Within this review, we summarize the different cellular functions of SAMHD1 and highlight the countermeasures viruses have evolved to neutralize the restriction factor SAMHD1.
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35
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Wu Y, Niu Y, Wu Y, Chen X, Shen X, Gao W. SAMHD1 can suppress lung adenocarcinoma progression through the negative regulation of STING. J Thorac Dis 2021; 13:189-201. [PMID: 33569199 PMCID: PMC7867844 DOI: 10.21037/jtd-20-1889] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Background The sterile alpha motif (SAM) domain and histidine-aspartate (HD) domain-containing protein 1 (SAMHD1) has been specifically linked to lung cancer. However, the underlying mechanisms in regulating lung adenocarcinoma (LAC) are unclear. The aim of this study was to assess the specific regulation between SAMHD1 and LAC. Methods We retrospectively reviewed 238 patients who underwent surgery for LAC between January 2018 and December 2019. The expression of SAMHD1 was detected by quantitative reverse-transcription polymerase chain reaction (RT-qPCR) in tumors and paired adjacent tissues. A lentivirus was used to overexpress SAMHD1 and stimulator of interferon genes (STING) in A549 cells; and RT-qPCR and western blot analysis were performed to verify their levels. Cell proliferation was evaluated via 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay and Celigo imaging cytometry. Cell apoptosis was detected by Annexin V staining. Overexpressed SAMHD1 suppressed LAC progression in a xenograft model. The DNA damage response inhibitor (DDRi) was used to assess the cell proliferation and apoptosis rate in SAMHD1-overexpressing A549 cells and the control group. A rescue experiment was carried out to evaluate the potential influence of SAMHD1 and STING. Results A low expression of SAMHD1 was associated with advanced disease. Overexpression of SAMHD1 decreased cell proliferation and invasion in A549 cells, and the apoptosis rate was significantly higher in the overexpressed SAMHD1 cells than those in the control group. The overexpression of SAMHD1 inhibited tumor progression in the xenograft model. The expression of STING was lower in SAMHD1-overexpressing A549 cells than those in the wild-type group. Furthermore, the inhibited cellular behaviors of LAC cells resulting from the stable SAMHD1 expression were partially reversed after STING overexpression. Treatment with DDRi could inhibit cancer cell progression. Conclusions Upregulation of SAMHD1 could suppress the progression of LAC in vivo and in vitro through the negative regulation of STING.
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Affiliation(s)
- Yun Wu
- Department of Thoracic Surgery, Shanghai Key Laboratory of Clinical Geriatric Medicine, Huadong Hospital Affiliated with Fudan University, Shanghai, China
| | - Yuxu Niu
- Department of Thoracic Surgery, Shanghai Key Laboratory of Clinical Geriatric Medicine, Huadong Hospital Affiliated with Fudan University, Shanghai, China
| | - Yue Wu
- Department of Thoracic Surgery, Shanghai Key Laboratory of Clinical Geriatric Medicine, Huadong Hospital Affiliated with Fudan University, Shanghai, China
| | - Xiaoyu Chen
- Department of Thoracic Surgery, Shanghai Key Laboratory of Clinical Geriatric Medicine, Huadong Hospital Affiliated with Fudan University, Shanghai, China
| | - Xiaoyong Shen
- Department of Thoracic Surgery, Shanghai Key Laboratory of Clinical Geriatric Medicine, Huadong Hospital Affiliated with Fudan University, Shanghai, China
| | - Wen Gao
- Department of Thoracic Surgery, Shanghai Key Laboratory of Clinical Geriatric Medicine, Huadong Hospital Affiliated with Fudan University, Shanghai, China
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36
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De Meo S, Dell'Oste V, Molfetta R, Tassinari V, Lotti LV, Vespa S, Pignoloni B, Covino DA, Fantuzzi L, Bona R, Zingoni A, Nardone I, Biolatti M, Coscia A, Paolini R, Benkirane M, Edfors F, Sandalova T, Achour A, Hiscott J, Landolfo S, Santoni A, Cerboni C. SAMHD1 phosphorylation and cytoplasmic relocalization after human cytomegalovirus infection limits its antiviral activity. PLoS Pathog 2020; 16:e1008855. [PMID: 32986788 PMCID: PMC7544099 DOI: 10.1371/journal.ppat.1008855] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 10/08/2020] [Accepted: 08/03/2020] [Indexed: 12/16/2022] Open
Abstract
SAMHD1 is a host restriction factor that functions to restrict both retroviruses and DNA viruses, based on its nuclear deoxynucleotide triphosphate (dNTP) hydrolase activity that limits availability of intracellular dNTP pools. In the present study, we demonstrate that SAMHD1 expression was increased following human cytomegalovirus (HCMV) infection, with only a modest effect on infectious virus production. SAMHD1 was rapidly phosphorylated at residue T592 after infection by cellular cyclin-dependent kinases, especially Cdk2, and by the viral kinase pUL97, resulting in a significant fraction of phosho-SAMHD1 being relocalized to the cytoplasm of infected fibroblasts, in association with viral particles and dense bodies. Thus, our findings indicate that HCMV-dependent SAMHD1 cytoplasmic delocalization and inactivation may represent a potential novel mechanism of HCMV evasion from host antiviral restriction activities.
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Affiliation(s)
- Simone De Meo
- Department of Molecular Medicine, "Sapienza" University of Rome, Rome, Italy
| | - Valentina Dell'Oste
- Department of Public Health and Pediatric Sciences, University of Turin, Turin, Italy
| | - Rosa Molfetta
- Department of Molecular Medicine, "Sapienza" University of Rome, Rome, Italy
| | - Valentina Tassinari
- Department of Molecular Medicine, "Sapienza" University of Rome, Rome, Italy
| | | | - Simone Vespa
- Laboratory of General Pathology, Center of Aging Science and Translational Medicine (CeSI-MeT) and Department of Medical, Oral and Biotechnological Sciences G. d'Annunzio University, Chieti, Italy
| | - Benedetta Pignoloni
- Department of Molecular Medicine, "Sapienza" University of Rome, Rome, Italy
| | | | - Laura Fantuzzi
- National Center for Global Health, Istituto Superiore di Sanità, Rome, Italy
| | - Roberta Bona
- National Center for Global Health, Istituto Superiore di Sanità, Rome, Italy
| | - Alessandra Zingoni
- Department of Molecular Medicine, "Sapienza" University of Rome, Rome, Italy
| | - Ilaria Nardone
- Department of Molecular Medicine, "Sapienza" University of Rome, Rome, Italy
| | - Matteo Biolatti
- Department of Public Health and Pediatric Sciences, University of Turin, Turin, Italy
| | - Alessandra Coscia
- Neonatal Unit, Department of Public Health and Pediatric Sciences, University of Turin, Turin, Italy
| | - Rossella Paolini
- Department of Molecular Medicine, "Sapienza" University of Rome, Rome, Italy
| | - Monsef Benkirane
- Institut de Génétique Humaine, Laboratoire de Virologie Moléculaire, CNRS-Université de Montpellier, Montpellier, France
| | - Fredrik Edfors
- Science for Life Laboratory, Department of Medicine Solna, Karolinska Institute, and Division of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - Tatyana Sandalova
- Science for Life Laboratory, Department of Medicine Solna, Karolinska Institute, and Division of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - Adnane Achour
- Science for Life Laboratory, Department of Medicine Solna, Karolinska Institute, and Division of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - John Hiscott
- Istituto Pasteur Italia-Cenci Bolognetti Foundation, Rome, Italy
| | - Santo Landolfo
- Department of Public Health and Pediatric Sciences, University of Turin, Turin, Italy
| | - Angela Santoni
- Department of Molecular Medicine, "Sapienza" University of Rome, Rome, Italy
- IRCCS, Neuromed, Pozzilli, Isernia, Italy
| | - Cristina Cerboni
- Department of Molecular Medicine, "Sapienza" University of Rome, Rome, Italy
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37
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Nishimura T, Végvári Á, Nakamura H, Kato H, Saji H. Mutant Proteomics of Lung Adenocarcinomas Harboring Different EGFR Mutations. Front Oncol 2020; 10:1494. [PMID: 32983988 PMCID: PMC7477350 DOI: 10.3389/fonc.2020.01494] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 07/13/2020] [Indexed: 12/28/2022] Open
Abstract
Epidermal growth factor receptor EGFR major driver mutations may affect downstream molecular networks and pathways, which would influence treatment outcomes of non-small cell lung cancer (NSCLC). This study aimed to unveil profiles of mutant proteins expressed in lung adenocarcinomas of 36 patients harboring representative driver EGFR mutations (Ex19del, nine; L858R, nine; no Ex19del/L858R, 18). Surprisingly, the orthogonal partial least squares discriminant analysis performed for identified mutant proteins demonstrated the profound differences in distance among the different EGFR mutation groups, suggesting that cancer cells harboring L858R or Ex19del emerge from cellular origins different from L858R/Ex19del-negative cells. Weighted gene coexpression network analysis, together with over-representative analysis, identified 18 coexpressed modules and their eigen proteins. Pathways enriched differentially for both the L858R and Ex19del mutations included carboxylic acid metabolic process, cell cycle, developmental biology, cellular responses to stress, mitotic prophase, cell proliferation, growth, epithelial to mesenchymal transition (EMT), and immune system. The IPA causal network analysis identified the highly activated networks of PARPBP, HOXA1, and APH1 under the L858R mutation, whereas those of ASGR1, APEX1, BUB1, and MAPK10 were highly activated under the Ex19del mutation. Interestingly, the downregulated causal network of osimertinib intervention showed the highest significance in overlap p-value among most causal networks predicted under the L858R mutation. We also identified the causal network of MAPK interacting serine/threonine kinase 1/2 (MNK1/2) highly activated differentially under the L858R mutation. Tumor-suppressor AMOT, a component of the Hippo pathways, was highly inhibited commonly under both L858R and Ex19del mutations. Our results could identify disease-related protein molecular networks from the landscape of single amino acid variants. Our findings may help identify potential therapeutic targets and develop therapeutic strategies to improve patient outcomes.
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Affiliation(s)
- Toshihide Nishimura
- Department of Translational Medicine Informatics, St. Marianna University School of Medicine, Kawasaki, Japan.,Department of Chest Surgery, St. Marianna University School of Medicine, Kawasaki, Japan
| | - Ákos Végvári
- Division of Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Haruhiko Nakamura
- Department of Chest Surgery, St. Marianna University School of Medicine, Kawasaki, Japan
| | - Harubumi Kato
- Division of Thoracic and Thyroid Surgery, Tokyo Medical University, Tokyo, Japan.,Research Institute of Health and Welfare Sciences, Graduate School, International University of Health and Welfare, Tokyo, Japan
| | - Hisashi Saji
- Department of Chest Surgery, St. Marianna University School of Medicine, Kawasaki, Japan
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Sharma S, Koolmeister C, Tran P, Nilsson AK, Larsson NG, Chabes A. Proofreading deficiency in mitochondrial DNA polymerase does not affect total dNTP pools in mouse embryos. Nat Metab 2020; 2:673-675. [PMID: 32778836 DOI: 10.1038/s42255-020-0264-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 07/14/2020] [Indexed: 02/06/2023]
Affiliation(s)
- Sushma Sharma
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
| | - Camilla Koolmeister
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- Max Planck Institute for Biology of Ageing - Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Phong Tran
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
| | - Anna Karin Nilsson
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
| | - Nils-Göran Larsson
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- Max Planck Institute for Biology of Ageing - Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Andrei Chabes
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden.
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39
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Rothenburger T, McLaughlin KM, Herold T, Schneider C, Oellerich T, Rothweiler F, Feber A, Fenton TR, Wass MN, Keppler OT, Michaelis M, Cinatl J. SAMHD1 is a key regulator of the lineage-specific response of acute lymphoblastic leukaemias to nelarabine. Commun Biol 2020; 3:324. [PMID: 32581304 PMCID: PMC7314829 DOI: 10.1038/s42003-020-1052-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Accepted: 06/02/2020] [Indexed: 12/31/2022] Open
Abstract
The nucleoside analogue nelarabine, the prodrug of arabinosylguanine (AraG), is effective against T-cell acute lymphoblastic leukaemia (T-ALL) but not against B-cell ALL (B-ALL). The underlying mechanisms have remained elusive. Here, data from pharmacogenomics studies and a panel of ALL cell lines reveal an inverse correlation between nelarabine sensitivity and the expression of SAMHD1, which can hydrolyse and inactivate triphosphorylated nucleoside analogues. Lower SAMHD1 abundance is detected in T-ALL than in B-ALL in cell lines and patient-derived leukaemic blasts. Mechanistically, T-ALL cells display increased SAMHD1 promoter methylation without increased global DNA methylation. SAMHD1 depletion sensitises B-ALL cells to AraG, while ectopic SAMHD1 expression in SAMHD1-null T-ALL cells induces AraG resistance. SAMHD1 has a larger impact on nelarabine/AraG than on cytarabine in ALL cells. Opposite effects are observed in acute myeloid leukaemia cells, indicating entity-specific differences. In conclusion, SAMHD1 promoter methylation and, in turn, SAMHD1 expression levels determine ALL cell response to nelarabine.
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Affiliation(s)
- Tamara Rothenburger
- Institut für Medizinische Virologie, Klinikum der Goethe-Universität, Paul Ehrlich-Straße 40, 60596, Frankfurt am Main, Germany
| | | | - Tobias Herold
- Department of Medicine III, University Hospital, LMU Munich, Marchioninistraße 15, 81377, Munich, Germany
- Research Unit Apoptosis in Hematopoietic Stem Cells, Helmholtz Zentrum München, German Research Center for Environmental Health (HMGU), Feodor-Lynenstraße 21, 81377, Munich, Germany
| | - Constanze Schneider
- Institut für Medizinische Virologie, Klinikum der Goethe-Universität, Paul Ehrlich-Straße 40, 60596, Frankfurt am Main, Germany
- Department of Medicine II, Hematology/Oncology, Goethe-Universität, Frankfurt am Main, Germany; Frankfurt Cancer Institute, Goethe University, Theodor-Stern-Kai 7, 60590, Frankfurt am Main, Germany
| | - Thomas Oellerich
- Department of Medicine II, Hematology/Oncology, Goethe-Universität, Theodor-Stern-Kai 7, 60590, Frankfurt am Main, Germany
- Frankfurt Cancer Institute, Goethe University, Theodor-Stern-Kai 7, 60590, Frankfurt am Main, Germany
- German Cancer Consortium/German Cancer Research Center, Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Florian Rothweiler
- Institut für Medizinische Virologie, Klinikum der Goethe-Universität, Paul Ehrlich-Straße 40, 60596, Frankfurt am Main, Germany
| | - Andrew Feber
- Division of Surgery and Interventional Science, University College London, Gower Street, London, WC1E 6BT, UK
| | - Tim R Fenton
- School of Biosciences, University of Kent, Canterbury, CT2 7NJ, UK
| | - Mark N Wass
- School of Biosciences, University of Kent, Canterbury, CT2 7NJ, UK
| | - Oliver T Keppler
- Faculty of Medicine, Max von Pettenkofer Institute, Virology, LMU München, Pettenkoferstraße 9a, 80336, Munich, Germany
| | - Martin Michaelis
- School of Biosciences, University of Kent, Canterbury, CT2 7NJ, UK.
| | - Jindrich Cinatl
- Institut für Medizinische Virologie, Klinikum der Goethe-Universität, Paul Ehrlich-Straße 40, 60596, Frankfurt am Main, Germany.
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Morris ER, Caswell SJ, Kunzelmann S, Arnold LH, Purkiss AG, Kelly G, Taylor IA. Crystal structures of SAMHD1 inhibitor complexes reveal the mechanism of water-mediated dNTP hydrolysis. Nat Commun 2020; 11:3165. [PMID: 32576829 PMCID: PMC7311409 DOI: 10.1038/s41467-020-16983-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 06/03/2020] [Indexed: 12/29/2022] Open
Abstract
SAMHD1 regulates cellular 2'-deoxynucleoside-5'-triphosphate (dNTP) homeostasis by catalysing the hydrolysis of dNTPs into 2'-deoxynucleosides and triphosphate. In CD4+ myeloid lineage and resting T-cells, SAMHD1 blocks HIV-1 and other viral infections by depletion of the dNTP pool to a level that cannot support replication. SAMHD1 mutations are associated with the autoimmune disease Aicardi-Goutières syndrome and hypermutated cancers. Furthermore, SAMHD1 sensitises cancer cells to nucleoside-analogue anti-cancer therapies and is linked with DNA repair and suppression of the interferon response to cytosolic nucleic acids. Nevertheless, despite its requirement in these processes, the fundamental mechanism of SAMHD1-catalysed dNTP hydrolysis remained unknown. Here, we present structural and enzymological data showing that SAMHD1 utilises an active site, bi-metallic iron-magnesium centre that positions a hydroxide nucleophile in-line with the Pα-O5' bond to catalyse phosphoester bond hydrolysis. This precise molecular mechanism for SAMHD1 catalysis, reveals how SAMHD1 down-regulates cellular dNTP and modulates the efficacy of nucleoside-based anti-cancer and anti-viral therapies.
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Affiliation(s)
- Elizabeth R Morris
- Macromolecular Structure Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Sarah J Caswell
- Macromolecular Structure Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.,AstraZeneca, 50F49, Mereside, Alderley Park, Macclesfield, Cheshire, SK10 4TG, UK
| | - Simone Kunzelmann
- Structural Biology Science Technology Platform, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Laurence H Arnold
- Macromolecular Structure Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.,Pelago Bioscience, Banvaktsvägen 20, 171 48, Solna, Sweden
| | - Andrew G Purkiss
- Structural Biology Science Technology Platform, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Geoff Kelly
- The Medical Research Council Biomedical NMR Centre, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Ian A Taylor
- Macromolecular Structure Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.
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41
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Elimination of rNMPs from mitochondrial DNA has no effect on its stability. Proc Natl Acad Sci U S A 2020; 117:14306-14313. [PMID: 32513727 PMCID: PMC7322039 DOI: 10.1073/pnas.1916851117] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Mammalian mitochondria contain their own genome (mtDNA) that encodes key subunits of the machinery that produces the majority of the cell’s energy. mtDNA integrity is crucial for normal energy production, and its loss due to deletions or point mutations can lead to various human disorders and might contribute to aging. We asked whether ribonucleotides—the building blocks of RNA and an established threat to nuclear genome stability—contribute to the loss of mtDNA integrity observed during aging. We show that the persistent presence of ribonucleotides in mtDNA over the course of the mouse life span has no major impact on mtDNA stability. This indicates that the physiological level of ribonucleotides does not pose a serious threat to mtDNA quality. Ribonucleotides (rNMPs) incorporated in the nuclear genome are a well-established threat to genome stability and can result in DNA strand breaks when not removed in a timely manner. However, the presence of a certain level of rNMPs is tolerated in mitochondrial DNA (mtDNA) although aberrant mtDNA rNMP content has been identified in disease models. We investigated the effect of incorporated rNMPs on mtDNA stability over the mouse life span and found that the mtDNA rNMP content increased during early life. The rNMP content of mtDNA varied greatly across different tissues and was defined by the rNTP/dNTP ratio of the tissue. Accordingly, mtDNA rNMPs were nearly absent in SAMHD1−/− mice that have increased dNTP pools. The near absence of rNMPs did not, however, appreciably affect mtDNA copy number or the levels of mtDNA molecules with deletions or strand breaks in aged animals near the end of their life span. The physiological rNMP load therefore does not contribute to the progressive loss of mtDNA quality that occurs as mice age.
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42
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Husain A, Xu J, Fujii H, Nakata M, Kobayashi M, Wang JY, Rehwinkel J, Honjo T, Begum NA. SAMHD1-mediated dNTP degradation is required for efficient DNA repair during antibody class switch recombination. EMBO J 2020; 39:e102931. [PMID: 32511795 DOI: 10.15252/embj.2019102931] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 05/04/2020] [Accepted: 05/08/2020] [Indexed: 12/12/2022] Open
Abstract
Sterile alpha motif and histidine-aspartic acid domain-containing protein 1 (SAMHD1), a dNTP triphosphohydrolase, regulates the levels of cellular dNTPs through their hydrolysis. SAMHD1 protects cells from invading viruses that depend on dNTPs to replicate and is frequently mutated in cancers and Aicardi-Goutières syndrome, a hereditary autoimmune encephalopathy. We discovered that SAMHD1 localizes at the immunoglobulin (Ig) switch region, and serves as a novel DNA repair regulator of Ig class switch recombination (CSR). Depletion of SAMHD1 impaired not only CSR but also IgH/c-Myc translocation. Consistently, we could inhibit these two processes by elevating the cellular nucleotide pool. A high frequency of nucleotide insertion at the break-point junctions is a notable feature in SAMHD1 deficiency during activation-induced cytidine deaminase-mediated genomic instability. Interestingly, CSR induced by staggered but not blunt, double-stranded DNA breaks was impaired by SAMHD1 depletion, which was accompanied by enhanced nucleotide insertions at recombination junctions. We propose that SAMHD1-mediated dNTP balance regulates dNTP-sensitive DNA end-processing enzyme and promotes CSR and aberrant genomic rearrangements by suppressing the insertional DNA repair pathway.
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Affiliation(s)
- Afzal Husain
- Department of Immunology and Genomic Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Jianliang Xu
- Department of Immunology and Genomic Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Hodaka Fujii
- Department of Biochemistry and Genome Biology, Hirosaki University Graduate School of Medicine, Hirosaki, Aomori, Japan.,Combined Program on Microbiology and Immunology, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan
| | - Mikiyo Nakata
- Department of Immunology and Genomic Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Maki Kobayashi
- Department of Immunology and Genomic Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Ji-Yang Wang
- Department of Immunology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Jan Rehwinkel
- Medical Research Council Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Tasuku Honjo
- Department of Immunology and Genomic Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Nasim A Begum
- Department of Immunology and Genomic Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
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43
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Davenne T, Klintman J, Sharma S, Rigby RE, Blest HTW, Cursi C, Bridgeman A, Dadonaite B, De Keersmaecker K, Hillmen P, Chabes A, Schuh A, Rehwinkel J. SAMHD1 Limits the Efficacy of Forodesine in Leukemia by Protecting Cells against the Cytotoxicity of dGTP. Cell Rep 2020; 31:107640. [PMID: 32402273 PMCID: PMC7225753 DOI: 10.1016/j.celrep.2020.107640] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 03/12/2020] [Accepted: 04/22/2020] [Indexed: 12/12/2022] Open
Abstract
The anti-leukemia agent forodesine causes cytotoxic overload of intracellular deoxyguanosine triphosphate (dGTP) but is efficacious only in a subset of patients. We report that SAMHD1, a phosphohydrolase degrading deoxyribonucleoside triphosphate (dNTP), protects cells against the effects of dNTP imbalances. SAMHD1-deficient cells induce intrinsic apoptosis upon provision of deoxyribonucleosides, particularly deoxyguanosine (dG). Moreover, dG and forodesine act synergistically to kill cells lacking SAMHD1. Using mass cytometry, we find that these compounds kill SAMHD1-deficient malignant cells in patients with chronic lymphocytic leukemia (CLL). Normal cells and CLL cells from patients without SAMHD1 mutation are unaffected. We therefore propose to use forodesine as a precision medicine for leukemia, stratifying patients by SAMHD1 genotype or expression.
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Affiliation(s)
- Tamara Davenne
- Medical Research Council Human Immunology Unit, Medical Research Council Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, UK; Laboratory for Disease Mechanisms in Cancer, Department of Oncology, KU Leuven and Leuven Cancer Institute (LKI), Herestraat 49, 3000 Leuven, Belgium
| | - Jenny Klintman
- Molecular Diagnostic Centre, Department of Oncology, University of Oxford, Oxford OX3 7DQ, UK
| | - Sushma Sharma
- Department of Medical Biochemistry and Biophysics and Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, 901 87 Umeå, Sweden
| | - Rachel E Rigby
- Medical Research Council Human Immunology Unit, Medical Research Council Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Henry T W Blest
- Medical Research Council Human Immunology Unit, Medical Research Council Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Chiara Cursi
- Medical Research Council Human Immunology Unit, Medical Research Council Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Anne Bridgeman
- Medical Research Council Human Immunology Unit, Medical Research Council Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Bernadeta Dadonaite
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Kim De Keersmaecker
- Laboratory for Disease Mechanisms in Cancer, Department of Oncology, KU Leuven and Leuven Cancer Institute (LKI), Herestraat 49, 3000 Leuven, Belgium
| | - Peter Hillmen
- St James' Institute of Oncology, St James' University Hospital, Leeds LS9 7TF, UK
| | - Andrei Chabes
- Department of Medical Biochemistry and Biophysics and Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, 901 87 Umeå, Sweden
| | - Anna Schuh
- Molecular Diagnostic Centre, Department of Oncology, University of Oxford, Oxford OX3 7DQ, UK; Department of Oncology, Old Road Campus Research Building, University of Oxford, Oxford OX3 7DQ, UK; Department of Haematology, Oxford University Hospitals NHS Trust, Oxford OX3 7JL, UK
| | - Jan Rehwinkel
- Medical Research Council Human Immunology Unit, Medical Research Council Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, UK.
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Patil S, Subbannayya T, Mohan SV, Babu N, Advani J, Sathe G, Rajagopalan P, Patel K, Bhandi S, Solanki H, Sidransky D, Gowda H, Chatterjee A, Ferrari M. Proteomic Changes in Oral Keratinocytes Chronically Exposed to Shisha (Water Pipe). OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2020; 23:86-97. [PMID: 30767727 DOI: 10.1089/omi.2018.0173] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Shisha (water pipe) smoking is falsely believed to be a hazard-free habit and has become a major public health concern. Studies have reported shisha smoking to be associated with oral lesions, as well as carcinomas of the lung, esophagus, bladder, and pancreas. A deeper understanding of the underlying molecular mechanisms would contribute to identification of biomarkers for targeted public health screening, therapeutic innovation, and better prognosis of associated diseases. In this study, we have established an in vitro chronic cellular model of shisha-exposed oral keratinocytes to study the effect of shisha on oral cells. Normal nontransformed, immortalized oral keratinocytes were chronically exposed to shisha extract for 8 months. This resulted in significant increase in cellular proliferation and cell invasion in shisha-exposed cells compared to the parental cells. Quantitative proteomic analysis of OKF6/TERT1-Parental and OKF6/TERT1-Shisha cells resulted in the identification of 5515 proteins. Forty-three differentially expressed proteins were found to be common across all conditions. Bioinformatic analysis of the dysregulated proteins identified in the proteomic study revealed dysregulation of interferon pathway, upregulation of proteins involved in cell growth, and downregulation of immune processes. The present findings reveal that chronic exposure of normal oral keratinocytes to shisha leads to cellular transformation and dysregulation of immune response. To the best of our knowledge, this is the first report that has developed a model of oral keratinocytes chronically exposed to shisha and identified proteomic alterations associated with shisha exposure. However, further research is required to evaluate the health burden of shisha smoking.
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Affiliation(s)
- Shankargouda Patil
- 1 Department of Medical Biotechnologies, School of Dental Medicine, University of Siena, Siena, Italy.,2 Department of Maxillofacial Surgery and Diagnostic Sciences, Division of Oral Pathology, College of Dentistry, Jazan University, Jazan, Saudi Arabia
| | | | | | - Niraj Babu
- 3 Institute of Bioinformatics, Bangalore, India.,4 Manipal Academy of Higher Education, Manipal, India
| | | | | | | | | | - Shilpa Bhandi
- 5 Department of Restorative Dental Sciences, Division of Operative Dentistry, College of Dentistry, Jazan University, Jazan, Saudi Arabia
| | | | - David Sidransky
- 6 Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Harsha Gowda
- 3 Institute of Bioinformatics, Bangalore, India.,4 Manipal Academy of Higher Education, Manipal, India
| | - Aditi Chatterjee
- 3 Institute of Bioinformatics, Bangalore, India.,4 Manipal Academy of Higher Education, Manipal, India
| | - Marco Ferrari
- 1 Department of Medical Biotechnologies, School of Dental Medicine, University of Siena, Siena, Italy.,7 Department of Restorative Dentistry, School of Dentistry, University of Leeds, Leeds, West Yorkshire, United Kingdom
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45
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SAMHD1 Functions and Human Diseases. Viruses 2020; 12:v12040382. [PMID: 32244340 PMCID: PMC7232136 DOI: 10.3390/v12040382] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 03/27/2020] [Accepted: 03/28/2020] [Indexed: 12/12/2022] Open
Abstract
Deoxynucleoside triphosphate (dNTP) molecules are essential for the replication and maintenance of genomic information in both cells and a variety of viral pathogens. While the process of dNTP biosynthesis by cellular enzymes, such as ribonucleotide reductase (RNR) and thymidine kinase (TK), has been extensively investigated, a negative regulatory mechanism of dNTP pools was recently found to involve sterile alpha motif (SAM) domain and histidine-aspartate (HD) domain-containing protein 1, SAMHD1. When active, dNTP triphosphohydrolase activity of SAMHD1 degrades dNTPs into their 2'-deoxynucleoside (dN) and triphosphate subparts, steadily depleting intercellular dNTP pools. The differential expression levels and activation states of SAMHD1 in various cell types contributes to unique dNTP pools that either aid (i.e., dividing T cells) or restrict (i.e., nondividing macrophages) viral replication that consumes cellular dNTPs. Genetic mutations in SAMHD1 induce a rare inflammatory encephalopathy called Aicardi-Goutières syndrome (AGS), which phenotypically resembles viral infection. Recent publications have identified diverse roles for SAMHD1 in double-stranded break repair, genome stability, and the replication stress response through interferon signaling. Finally, a series of SAMHD1 mutations were also reported in various cancer cell types while why SAMHD1 is mutated in these cancer cells remains to investigated. Here, we reviewed a series of studies that have begun illuminating the highly diverse roles of SAMHD1 in virology, immunology, and cancer biology.
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46
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Pharmacological Modulation of SAMHD1 Activity by CDK4/6 Inhibitors Improves Anticancer Therapy. Cancers (Basel) 2020; 12:cancers12030713. [PMID: 32197329 PMCID: PMC7140116 DOI: 10.3390/cancers12030713] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 03/09/2020] [Accepted: 03/16/2020] [Indexed: 01/16/2023] Open
Abstract
Sterile alpha motif and histidine-aspartic acid domain-containing protein 1 (SAMHD1) is a dNTP triphosphohydrolase involved in the regulation of the intracellular dNTP pool, linked to viral restriction, cancer development and autoimmune disorders. SAMHD1 function is regulated by phosphorylation through a mechanism controlled by cyclin-dependent kinases and tightly linked to cell cycle progression. Recently, SAMHD1 has been shown to decrease the efficacy of nucleotide analogs used as chemotherapeutic drugs. Here, we demonstrate that SAMHD1 can enhance or decrease the efficacy of various classes of anticancer drug, including nucleotide analogues, but also anti-folate drugs and CDK inhibitors. Importantly, we show that selective CDK4/6 inhibitors are pharmacological activators of SAMHD1 that act by inhibiting its inactivation by phosphorylation. Combinations of a CDK4/6 inhibitor with nucleoside or folate antimetabolites potently enhanced drug efficacy, resulting in highly synergic drug combinations (CI < 0.04). Mechanistic analyses reveal that cell cycle-controlled modulation of SAMHD1 function is the central process explaining changes in anticancer drug efficacy, therefore providing functional proof of the potential of CDK4/6 inhibitors as a new class of adjuvants to boost chemotherapeutic regimens. The evaluation of SAMHD1 expression in cancer tissues allowed for the identification of cancer types that would benefit from the pharmacological modulation of SAMHD1 function. In conclusion, these results indicate that the modulation of SAMHD1 function may represent a promising strategy for the improvement of current antimetabolite-based treatments.
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47
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Zhang Z, Zheng L, Yu Y, Wu J, Yang F, Xu Y, Guo Q, Wu X, Cao S, Cao L, Song X. Involvement of SAMHD1 in dNTP homeostasis and the maintenance of genomic integrity and oncotherapy (Review). Int J Oncol 2020; 56:879-888. [PMID: 32319570 DOI: 10.3892/ijo.2020.4988] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Accepted: 02/07/2020] [Indexed: 11/06/2022] Open
Abstract
Sterile alpha motif and histidine/aspartic acid domain‑containing protein 1 (SAMHD1), the only deoxynucleotide triphosphate (dNTP) hydrolase in eukaryotes, plays a crucial role in regulating the dynamic balance and ratio of cellular dNTP pools. Furthermore, SAMHD1 has been reported to be involved in the pathological process of several diseases. Homozygous SAMHD1 mutations have been identified in immune system disorders, such as autoimmune disease Aicardi‑Goutières syndrome (AGS), whose primary pathogenesis is associated with the abnormal accumulation and disproportion of dNTPs. SAMHD1 is also considered to be an intrinsic virus‑restriction factor by suppressing the viral infection process, including reverse transcription, replication, packaging and transmission. In addition, SAMHD1 has been shown to promote genome integrity during homologous recombination following DNA damage, thus being considered a promising candidate for oncotherapy applications. The present review summarizes the molecular mechanisms of SAMHD1 regarding the regulation of dNTP homeostasis and DNA damage response. Additionally, its potential effects on tumorigenesis and oncotherapy are reported.
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Affiliation(s)
- Zhou Zhang
- College of Basic Medical Science, Institute of Translational Medicine, China Medical University, Shenyang, Liaoning 110122, P.R. China
| | - Lixia Zheng
- College of Basic Medical Science, Institute of Translational Medicine, China Medical University, Shenyang, Liaoning 110122, P.R. China
| | - Yang Yu
- College of Basic Medical Science, Institute of Translational Medicine, China Medical University, Shenyang, Liaoning 110122, P.R. China
| | - Jinying Wu
- College of Basic Medical Science, Institute of Translational Medicine, China Medical University, Shenyang, Liaoning 110122, P.R. China
| | - Fan Yang
- College of Basic Medical Science, Institute of Translational Medicine, China Medical University, Shenyang, Liaoning 110122, P.R. China
| | - Yingxi Xu
- College of Basic Medical Science, Institute of Translational Medicine, China Medical University, Shenyang, Liaoning 110122, P.R. China
| | - Qiqiang Guo
- College of Basic Medical Science, Institute of Translational Medicine, China Medical University, Shenyang, Liaoning 110122, P.R. China
| | - Xuan Wu
- College of Basic Medical Science, Institute of Translational Medicine, China Medical University, Shenyang, Liaoning 110122, P.R. China
| | - Sunrun Cao
- College of Basic Medical Science, Institute of Translational Medicine, China Medical University, Shenyang, Liaoning 110122, P.R. China
| | - Liu Cao
- College of Basic Medical Science, Institute of Translational Medicine, China Medical University, Shenyang, Liaoning 110122, P.R. China
| | - Xiaoyu Song
- College of Basic Medical Science, Institute of Translational Medicine, China Medical University, Shenyang, Liaoning 110122, P.R. China
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48
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Vosberg S, Greif PA. Clonal evolution of acute myeloid leukemia from diagnosis to relapse. Genes Chromosomes Cancer 2019; 58:839-849. [PMID: 31478278 PMCID: PMC6852285 DOI: 10.1002/gcc.22806] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 08/19/2019] [Accepted: 08/21/2019] [Indexed: 12/13/2022] Open
Abstract
Based on the individual genetic profile, acute myeloid leukemia (AML) patients are classified into clinically meaningful molecular subtypes. However, the mutational profile within these groups is highly heterogeneous and multiple AML subclones may exist in a single patient in parallel. Distinct alterations of single cells may be key factors in providing the fitness to survive in this highly competitive environment. Although the majority of AML patients initially respond to induction chemotherapy and achieve a complete remission, most patients will eventually relapse. These points toward an evolutionary process transforming treatment-sensitive cells into treatment-resistant cells. As described by Charles Darwin, evolution by natural selection is the selection of individuals that are optimally adapted to their environment, based on the random acquisition of heritable changes. By changing their mutational profile, AML cell populations are able to adapt to the new environment defined by chemotherapy treatment, ultimately leading to cell survival and regrowth. In this review, we will summarize the current knowledge about clonal evolution in AML, describe different models of clonal evolution, and provide the methodological background that allows the detection of clonal evolution in individual AML patients. During the last years, numerous studies have focused on delineating the molecular patterns that are associated with AML relapse, each focusing on a particular genetic subgroup of AML. Finally, we will review the results of these studies in the light of Darwinian evolution and discuss open questions regarding the molecular background of relapse development.
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Affiliation(s)
- Sebastian Vosberg
- Department of Medicine IIIUniversity Hospital, LMU MunichMunichGermany
- Experimental Leukemia and Lymphoma Research (ELLF)University Hospital, LMU MunichMunichGermany
- German Cancer Consortium (DKTK)HeidelbergGermany
- German Cancer Research Center (DKFZ)HeidelbergGermany
| | - Philipp A. Greif
- Department of Medicine IIIUniversity Hospital, LMU MunichMunichGermany
- Experimental Leukemia and Lymphoma Research (ELLF)University Hospital, LMU MunichMunichGermany
- German Cancer Consortium (DKTK)HeidelbergGermany
- German Cancer Research Center (DKFZ)HeidelbergGermany
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49
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Franzolin E, Coletta S, Ferraro P, Pontarin G, D'Aronco G, Stevanoni M, Palumbo E, Cagnin S, Bertoldi L, Feltrin E, Valle G, Russo A, Bianchi V, Rampazzo C. SAMHD1‐deficient fibroblasts from Aicardi‐Goutières Syndrome patients can escape senescence and accumulate mutations. FASEB J 2019; 34:631-647. [DOI: 10.1096/fj.201902508r] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 10/30/2019] [Accepted: 11/04/2019] [Indexed: 01/16/2023]
Affiliation(s)
| | - Sara Coletta
- Department of Biology University of Padova Padova Italy
| | - Paola Ferraro
- Department of Biology University of Padova Padova Italy
| | | | | | | | - Elisa Palumbo
- Department of Molecular Medicine University of Padova Padova Italy
| | - Stefano Cagnin
- Department of Biology University of Padova Padova Italy
- CRIBI Biotechnology Center University of Padova Padova Italy
- CIR‐Myo Myology Center University of Padova Padova Italy
| | | | - Erika Feltrin
- Department of Biology University of Padova Padova Italy
| | - Giorgio Valle
- Department of Biology University of Padova Padova Italy
| | - Antonella Russo
- Department of Molecular Medicine University of Padova Padova Italy
| | - Vera Bianchi
- Department of Biology University of Padova Padova Italy
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50
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Chowell D, Krishna C, Pierini F, Makarov V, Rizvi NA, Kuo F, Morris LGT, Riaz N, Lenz TL, Chan TA. Evolutionary divergence of HLA class I genotype impacts efficacy of cancer immunotherapy. Nat Med 2019; 25:1715-1720. [PMID: 31700181 DOI: 10.1038/s41591-019-0639-4] [Citation(s) in RCA: 165] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Accepted: 10/03/2019] [Indexed: 12/22/2022]
Abstract
Functional diversity of the highly polymorphic human leukocyte antigen class I (HLA-I) genes underlies successful immunologic control of both infectious disease and cancer. The divergent allele advantage hypothesis dictates that an HLA-I genotype with two alleles with sequences that are more divergent enables presentation of more diverse immunopeptidomes1-3. However, the effect of sequence divergence between HLA-I alleles-a quantifiable measure of HLA-I evolution-on the efficacy of immune checkpoint inhibitor (ICI) treatment for cancer remains unknown. In the present study the germline HLA-I evolutionary divergence (HED) of patients with cancer treated with ICIs was determined by quantifying the physiochemical sequence divergence between HLA-I alleles of each patient's genotype. HED was a strong determinant of survival after treatment with ICIs. Even among patients fully heterozygous at HLA-I, patients with an HED in the upper quartile respond better to ICIs than patients with a low HED. Furthermore, HED strongly impacts the diversity of tumor, viral and self-immunopeptidomes and intratumoral T cell receptor clonality. Similar to tumor mutation burden, HED is a fundamental metric of diversity at the major histocompatibility complex-peptide complex, which dictates ICI efficacy. The data link divergent HLA allele advantage to immunotherapy efficacy and unveil how ICI response relies on the evolved efficiency of HLA-mediated immunity.
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Affiliation(s)
- Diego Chowell
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Immunogenomics and Precision Oncology Platform, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Chirag Krishna
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Federica Pierini
- Research Group for Evolutionary Immunogenomics, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Vladimir Makarov
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Immunogenomics and Precision Oncology Platform, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Naiyer A Rizvi
- Department of Medicine, Columbia University Medical Center, New York, NY, USA
| | - Fengshen Kuo
- Immunogenomics and Precision Oncology Platform, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Luc G T Morris
- Immunogenomics and Precision Oncology Platform, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nadeem Riaz
- Immunogenomics and Precision Oncology Platform, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Tobias L Lenz
- Research Group for Evolutionary Immunogenomics, Max Planck Institute for Evolutionary Biology, Plön, Germany.
| | - Timothy A Chan
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA. .,Immunogenomics and Precision Oncology Platform, Memorial Sloan Kettering Cancer Center, New York, NY, USA. .,Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA. .,Weill Cornell School of Medicine, New York, NY, USA.
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