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Ye Z, Shi Y, Lees-Miller SP, Tainer JA. Function and Molecular Mechanism of the DNA Damage Response in Immunity and Cancer Immunotherapy. Front Immunol 2021; 12:797880. [PMID: 34970273 PMCID: PMC8712645 DOI: 10.3389/fimmu.2021.797880] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 11/15/2021] [Indexed: 12/21/2022] Open
Abstract
The DNA damage response (DDR) is an organized network of multiple interwoven components evolved to repair damaged DNA and maintain genome fidelity. Conceptually the DDR includes damage sensors, transducer kinases, and effectors to maintain genomic stability and accurate transmission of genetic information. We have recently gained a substantially improved molecular and mechanistic understanding of how DDR components are interconnected to inflammatory and immune responses to stress. DDR shapes both innate and adaptive immune pathways: (i) in the context of innate immunity, DDR components mainly enhance cytosolic DNA sensing and its downstream STimulator of INterferon Genes (STING)-dependent signaling; (ii) in the context of adaptive immunity, the DDR is needed for the assembly and diversification of antigen receptor genes that is requisite for T and B lymphocyte development. Imbalances between DNA damage and repair impair tissue homeostasis and lead to replication and transcription stress, mutation accumulation, and even cell death. These impacts from DDR defects can then drive tumorigenesis, secretion of inflammatory cytokines, and aberrant immune responses. Yet, DDR deficiency or inhibition can also directly enhance innate immune responses. Furthermore, DDR defects plus the higher mutation load in tumor cells synergistically produce primarily tumor-specific neoantigens, which are powerfully targeted in cancer immunotherapy by employing immune checkpoint inhibitors to amplify immune responses. Thus, elucidating DDR-immune response interplay may provide critical connections for harnessing immunomodulatory effects plus targeted inhibition to improve efficacy of radiation and chemotherapies, of immune checkpoint blockade, and of combined therapeutic strategies.
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Affiliation(s)
- Zu Ye
- Department of Molecular and Cellular Oncology, and Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Yin Shi
- Department of Immunology, Zhejiang University School of Medicine, Hangzhou, China
- Division of Pediatrics, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Susan P. Lees-Miller
- Department of Biochemistry and Molecular Biology, Robson DNA Science Centre, Charbonneau Cancer Institute, University of Calgary, Calgary, AB, Canada
| | - John A. Tainer
- Department of Molecular and Cellular Oncology, and Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
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Chen X, Xu X, Chen Y, Cheung JC, Wang H, Jiang J, de Val N, Fox T, Gellert M, Yang W. Structure of an activated DNA-PK and its implications for NHEJ. Mol Cell 2020; 81:801-810.e3. [PMID: 33385326 DOI: 10.1016/j.molcel.2020.12.015] [Citation(s) in RCA: 77] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 11/17/2020] [Accepted: 12/07/2020] [Indexed: 02/06/2023]
Abstract
DNA-dependent protein kinase (DNA-PK), like all phosphatidylinositol 3-kinase-related kinases (PIKKs), is composed of conserved FAT and kinase domains (FATKINs) along with solenoid structures made of HEAT repeats. These kinases are activated in response to cellular stress signals, but the mechanisms governing activation and regulation remain unresolved. For DNA-PK, all existing structures represent inactive states with resolution limited to 4.3 Å at best. Here, we report the cryoelectron microscopy (cryo-EM) structures of DNA-PKcs (DNA-PK catalytic subunit) bound to a DNA end or complexed with Ku70/80 and DNA in both inactive and activated forms at resolutions of 3.7 Å overall and 3.2 Å for FATKINs. These structures reveal the sequential transition of DNA-PK from inactive to activated forms. Most notably, activation of the kinase involves previously unknown stretching and twisting within individual solenoid segments and loosens DNA-end binding. This unprecedented structural plasticity of helical repeats may be a general regulatory mechanism of HEAT-repeat proteins.
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Affiliation(s)
- Xuemin Chen
- Laboratory of Molecular Biology, NIDDK, National Institutes of Health, Bethesda, MD 20892, USA
| | - Xiang Xu
- Laboratory of Molecular Biology, NIDDK, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yun Chen
- Laboratory of Molecular Biology, NIDDK, National Institutes of Health, Bethesda, MD 20892, USA
| | - Joyce C Cheung
- Laboratory of Molecular Biology, NIDDK, National Institutes of Health, Bethesda, MD 20892, USA
| | - Huaibin Wang
- Laboratory of Cell and Molecular Biology, NIDDK, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jiansen Jiang
- Laboratory of Membrane Proteins and Structural Biology, NHLBI, National Institutes of Health, Bethesda, MD 20892, USA
| | - Natalia de Val
- Cancer Research Technology Program Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., Frederick, MD 21701, USA
| | - Tara Fox
- Cancer Research Technology Program Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., Frederick, MD 21701, USA
| | - Martin Gellert
- Laboratory of Molecular Biology, NIDDK, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Wei Yang
- Laboratory of Molecular Biology, NIDDK, National Institutes of Health, Bethesda, MD 20892, USA.
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Lees-Miller JP, Cobban A, Katsonis P, Bacolla A, Tsutakawa SE, Hammel M, Meek K, Anderson DW, Lichtarge O, Tainer JA, Lees-Miller SP. Uncovering DNA-PKcs ancient phylogeny, unique sequence motifs and insights for human disease. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2020; 163:87-108. [PMID: 33035590 PMCID: PMC8021618 DOI: 10.1016/j.pbiomolbio.2020.09.010] [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] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Revised: 09/12/2020] [Accepted: 09/29/2020] [Indexed: 01/26/2023]
Abstract
DNA-dependent protein kinase catalytic subunit (DNA-PKcs) is a key member of the phosphatidylinositol-3 kinase-like (PIKK) family of protein kinases with critical roles in DNA-double strand break repair, transcription, metastasis, mitosis, RNA processing, and innate and adaptive immunity. The absence of DNA-PKcs from many model organisms has led to the assumption that DNA-PKcs is a vertebrate-specific PIKK. Here, we find that DNA-PKcs is widely distributed in invertebrates, fungi, plants, and protists, and that threonines 2609, 2638, and 2647 of the ABCDE cluster of phosphorylation sites are highly conserved amongst most Eukaryotes. Furthermore, we identify highly conserved amino acid sequence motifs and domains that are characteristic of DNA-PKcs relative to other PIKKs. These include residues in the Forehead domain and a novel motif we have termed YRPD, located in an α helix C-terminal to the ABCDE phosphorylation site loop. Combining sequence with biochemistry plus structural data on human DNA-PKcs unveils conserved sequence and conformational features with functional insights and implications. The defined generally progressive DNA-PKcs sequence diversification uncovers conserved functionality supported by Evolutionary Trace analysis, suggesting that for many organisms both functional sites and evolutionary pressures remain identical due to fundamental cell biology. The mining of cancer genomic data and germline mutations causing human inherited disease reveal that robust DNA-PKcs activity in tumors is detrimental to patient survival, whereas germline mutations compromising function are linked to severe immunodeficiency and neuronal degeneration. We anticipate that these collective results will enable ongoing DNA-PKcs functional analyses with biological and medical implications.
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Affiliation(s)
- James P Lees-Miller
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, T2N 4N1, Canada
| | - Alexander Cobban
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, T2N 4N1, Canada
| | - Panagiotis Katsonis
- Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Albino Bacolla
- Departments of Cancer Biology and of Molecular and Cellular Oncology, University of Texas MD Anderson Cancer Center, 6767 Bertner Avenue, Houston, TX, 77030, USA
| | - Susan E Tsutakawa
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Michal Hammel
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Katheryn Meek
- College of Veterinary Medicine, Department of Microbiology & Molecular Genetics, And Department of Pathobiology & Diagnostic Investigation, Michigan State University, East Lansing, MI, 48824, USA
| | - Dave W Anderson
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, T2N 4N1, Canada
| | - Olivier Lichtarge
- Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - John A Tainer
- Departments of Cancer Biology and of Molecular and Cellular Oncology, University of Texas MD Anderson Cancer Center, 6767 Bertner Avenue, Houston, TX, 77030, USA; Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
| | - Susan P Lees-Miller
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, T2N 4N1, Canada.
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