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Thomas C, Avalos-Irving L, Victorino J, Green S, Andrews M, Rodrigues N, Ebirim S, Mudd A, Towle-Weicksel JB. Melanoma-Derived DNA Polymerase Theta Variants Exhibit Altered DNA Polymerase Activity. Biochemistry 2024; 63:1107-1117. [PMID: 38671548 PMCID: PMC11080051 DOI: 10.1021/acs.biochem.3c00670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 04/19/2024] [Accepted: 04/22/2024] [Indexed: 04/28/2024]
Abstract
DNA polymerase θ (Pol θ or POLQ) is primarily involved in repairing double-stranded breaks in DNA through an alternative pathway known as microhomology-mediated end joining (MMEJ) or theta-mediated end joining (TMEJ). Unlike other DNA repair polymerases, Pol θ is thought to be highly error-prone yet critical for cell survival. We have identified several POLQ gene variants from human melanoma tumors that experience altered DNA polymerase activity, including a propensity for incorrect nucleotide selection and reduced polymerization rates compared to WT Pol θ. Variants are 30-fold less efficient at incorporating a nucleotide during repair and up to 70-fold less accurate at selecting the correct nucleotide opposite a templating base. This suggests that aberrant Pol θ has reduced DNA repair capabilities and may also contribute to increased mutagenesis. Moreover, the variants were identified in established tumors, suggesting that cancer cells may use mutated polymerases to promote metastasis and drug resistance.
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Affiliation(s)
- Corey Thomas
- Department of Physical Sciences, Rhode Island College, 600 Mount Pleasant Avenue, Providence, Rhode Island 02908, United States
| | - Lisbeth Avalos-Irving
- Department of Physical Sciences, Rhode Island College, 600 Mount Pleasant Avenue, Providence, Rhode Island 02908, United States
| | - Jorge Victorino
- Department of Physical Sciences, Rhode Island College, 600 Mount Pleasant Avenue, Providence, Rhode Island 02908, United States
| | - Sydney Green
- Department of Physical Sciences, Rhode Island College, 600 Mount Pleasant Avenue, Providence, Rhode Island 02908, United States
| | - Morgan Andrews
- Department of Physical Sciences, Rhode Island College, 600 Mount Pleasant Avenue, Providence, Rhode Island 02908, United States
| | - Naisha Rodrigues
- Department of Physical Sciences, Rhode Island College, 600 Mount Pleasant Avenue, Providence, Rhode Island 02908, United States
| | - Sarah Ebirim
- Department of Physical Sciences, Rhode Island College, 600 Mount Pleasant Avenue, Providence, Rhode Island 02908, United States
| | - Ayden Mudd
- Department of Physical Sciences, Rhode Island College, 600 Mount Pleasant Avenue, Providence, Rhode Island 02908, United States
| | - Jamie B. Towle-Weicksel
- Department of Physical Sciences, Rhode Island College, 600 Mount Pleasant Avenue, Providence, Rhode Island 02908, United States
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Thomas C, Avalos-Irving L, Victorino J, Green S, Andrews M, Rodrigues N, Ebirim S, Mudd A, Towle-Weicksel JB. Melanoma-derived DNA polymerase theta variants exhibit altered DNA polymerase activity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.14.566933. [PMID: 38014040 PMCID: PMC10680777 DOI: 10.1101/2023.11.14.566933] [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
DNA Polymerase θ (Pol θ or POLQ) is primarily involved in repairing double-stranded breaks in DNA through the alternative pathway known as microhomology-mediated end joining (MMEJ) or theta-mediated end joining (TMEJ). Unlike other DNA repair polymerases, Pol θ is thought to be highly error prone, yet critical for cell survival. We have identified several mutations in the POLQ gene from human melanoma tumors. Through biochemical analysis, we have demonstrated that all three cancer-associated variants experienced altered DNA polymerase activity including a propensity for incorrect nucleotide selection and reduced polymerization rates compared to WT Pol θ. Moreover, the variants are 30 fold less efficient at incorporating a nucleotide during repair and up to 70 fold less accurate at selecting the correct nucleotide opposite a templating base. Taken together, this suggests that aberrant Pol θ has reduced DNA repair capabilities and may also contribute to increased mutagenesis. While this may be beneficial to normal cell survival, the variants were identified in established tumors suggesting that cancer cells may use this promiscuous polymerase to its advantage to promote metastasis and drug resistance.
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Venkadakrishnan J, Lahane G, Dhar A, Xiao W, Bhat KM, Pandita TK, Bhat A. Implications of Translesion DNA Synthesis Polymerases on Genomic Stability and Human Health. Mol Cell Biol 2023; 43:401-425. [PMID: 37439479 PMCID: PMC10448981 DOI: 10.1080/10985549.2023.2224199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 05/03/2023] [Accepted: 06/01/2023] [Indexed: 07/14/2023] Open
Abstract
Replication fork arrest-induced DNA double strand breaks (DSBs) caused by lesions are effectively suppressed in cells due to the presence of a specialized mechanism, commonly referred to as DNA damage tolerance (DDT). In eukaryotic cells, DDT is facilitated through translesion DNA synthesis (TLS) carried out by a set of DNA polymerases known as TLS polymerases. Another parallel mechanism, referred to as homology-directed DDT, is error-free and involves either template switching or fork reversal. The significance of the DDT pathway is well established. Several diseases have been attributed to defects in the TLS pathway, caused either by mutations in the TLS polymerase genes or dysregulation. In the event of a replication fork encountering a DNA lesion, cells switch from high-fidelity replicative polymerases to low-fidelity TLS polymerases, which are associated with genomic instability linked with several human diseases including, cancer. The role of TLS polymerases in chemoresistance has been recognized in recent years. In addition to their roles in the DDT pathway, understanding noncanonical functions of TLS polymerases is also a key to unraveling their importance in maintaining genomic stability. Here we summarize the current understanding of TLS pathway in DDT and its implication for human health.
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Affiliation(s)
| | - Ganesh Lahane
- Department of Pharmacy, Birla Institute of Technology and Sciences Pilani, Hyderabad Campus, Hyderabad, India
| | - Arti Dhar
- Department of Pharmacy, Birla Institute of Technology and Sciences Pilani, Hyderabad Campus, Hyderabad, India
| | - Wei Xiao
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, Canada
| | - Krishna Moorthi Bhat
- Department of Molecular Medicine, University of South Florida, Tampa, Florida, USA
| | - Tej K. Pandita
- Center for Genomics and Precision Medicine, Texas A&M College of Medicine, Houston, Texas, USA
| | - Audesh Bhat
- Center for Molecular Biology, Central University of Jammu, UT Jammu and Kashmir, India
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Multifaceted Nature of DNA Polymerase θ. Int J Mol Sci 2023; 24:ijms24043619. [PMID: 36835031 PMCID: PMC9962433 DOI: 10.3390/ijms24043619] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Revised: 01/26/2023] [Accepted: 02/02/2023] [Indexed: 02/15/2023] Open
Abstract
DNA polymerase θ belongs to the A family of DNA polymerases and plays a key role in DNA repair and damage tolerance, including double-strand break repair and DNA translesion synthesis. Pol θ is often overexpressed in cancer cells and promotes their resistance to chemotherapeutic agents. In this review, we discuss unique biochemical properties and structural features of Pol θ, its multiple roles in protection of genome stability and the potential of Pol θ as a target for cancer treatment.
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Bai H, Xia S, Zhu L, Dong Y, Liu C, Li N, Liu H, Xiao J. Altered polymerase theta expression promotes chromosomal instability in salivary adenoid cystic carcinoma. J Cell Mol Med 2022; 26:3931-3949. [PMID: 35726713 PMCID: PMC9279586 DOI: 10.1111/jcmm.17429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 05/10/2022] [Accepted: 05/20/2022] [Indexed: 11/28/2022] Open
Abstract
Genomic instability (GIN) plays a key role in cancer progression. The disorders of polymerase theta (POLQ) were reported to contribute to GIN and progression in many cancers. Here, we found that POLQ over‐expression was related to salivary adenoid cystic carcinoma (SACC) progression and poor prognosis. Then, we investigated the role and mechanism of POLQ in the GIN in SACC. GIN was assessed by chromosome staining with DAPI and Giemsa, as well as qRT‐PCR of the mitosis‐related gene expression. Meanwhile, PCR‐SSCP was used to evaluate microsatellite instability. Modulation of POLQ expression increased chromosomal instability and enhanced the sensitivity to etoposide without impacting microsatellite stability. Mechanistically, POLQ regulated genome stability by promoting the expression of the error‐prone alt‐NHEJ‐related protein PARP1, and down‐regulating c‐NHEJ‐ and HR‐related proteins KU70 and RAD51. In vitro CCK, Transwell assays and in vivo murine xenograft models indicated that the PARP inhibitor olaparib suppressed SACC growth in the case of etoposide‐induced DNA damage. Bioinformatic analysis identified CEBPB as a potential POLQ‐regulating transcription factor. In summary, our research provides new insights into the mechanisms of SACC chromosomal instability and identifies new potential targets for SACC treatment.
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Affiliation(s)
- Han Bai
- College of Stomatology, Dalian Medical University, Dalian, China
| | - Shilin Xia
- Clinical Laboratory of Integrative Medicine, The First Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Lei Zhu
- College of Stomatology, Dalian Medical University, Dalian, China
| | - Yan Dong
- College of Stomatology, Dalian Medical University, Dalian, China
| | - Chao Liu
- College of Stomatology, Dalian Medical University, Dalian, China
| | - Nan Li
- College of Stomatology, Dalian Medical University, Dalian, China.,Liaoning Province Key Laboratory of Organism Microecology and Disease Control, Dalian, China
| | - Han Liu
- College of Stomatology, Dalian Medical University, Dalian, China.,Liaoning Province Key Laboratory of Organism Microecology and Disease Control, Dalian, China
| | - Jing Xiao
- College of Stomatology, Dalian Medical University, Dalian, China.,Liaoning Province Key Laboratory of Organism Microecology and Disease Control, Dalian, China
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Zahn KE, Jensen RB. Polymerase θ Coordinates Multiple Intrinsic Enzymatic Activities during DNA Repair. Genes (Basel) 2021; 12:1310. [PMID: 34573292 PMCID: PMC8470613 DOI: 10.3390/genes12091310] [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: 07/13/2021] [Revised: 08/19/2021] [Accepted: 08/20/2021] [Indexed: 11/16/2022] Open
Abstract
The POLQ gene encodes DNA polymerase θ, a 2590 amino acid protein product harboring DNA-dependent ATPase, template-dependent DNA polymerase, dNTP-dependent endonuclease, and 5'-dRP lyase functions. Polymerase θ participates at an essential step of a DNA double-strand break repair pathway able to join 5'-resected substrates by locating and pairing microhomologies present in 3'-overhanging single-stranded tails, cleaving the extraneous 3'-DNA by dNTP-dependent end-processing, before extending the nascent 3' end from the microhomology annealing site. Metazoans require polymerase θ for full resistance to DNA double-strand break inducing agents but can survive knockout of the POLQ gene. Cancer cells with compromised homologous recombination, or other DNA repair defects, over-utilize end-joining by polymerase θ and often over-express the POLQ gene. This dependency points to polymerase θ as an ideal drug target candidate and multiple drug-development programs are now preparing to enter clinical trials with small-molecule inhibitors. Specific inhibitors of polymerase θ would not only be predicted to treat BRCA-mutant cancers, but could thwart accumulated resistance to current standard-of-care cancer therapies and overcome PARP-inhibitor resistance in patients. This article will discuss synthetic lethal strategies targeting polymerase θ in DNA damage-response-deficient cancers and summarize data, describing molecular structures and enzymatic functions.
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Affiliation(s)
- Karl E. Zahn
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, CT 06520, USA
- Repare Therapeutics, 7210 Rue Frederick Banting, Montreal, QC H4S 2A1, Canada
| | - Ryan B. Jensen
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, CT 06520, USA
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Zahn KE, Jensen RB, Wood RD, Doublié S. WITHDRAWN: Human DNA polymerase θ harbors DNA end-trimming activity critical for DNA repair. Mol Cell 2021; 81:1534-1547.e4. [PMID: 33577776 PMCID: PMC8231307 DOI: 10.1016/j.molcel.2021.01.021] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 11/24/2020] [Accepted: 01/15/2021] [Indexed: 12/12/2022]
Abstract
Cancers with hereditary defects in homologous recombination rely on DNA polymerase θ (pol θ) for repair of DNA double-strand breaks. During end joining, pol θ aligns microhomology tracts internal to 5'-resected broken ends. An unidentified nuclease trims the 3' ends before synthesis can occur. Here we report that a nuclease activity, which differs from the proofreading activity often associated with DNA polymerases, is intrinsic to the polymerase domain of pol θ. Like the DNA synthesis activity, the nuclease activity requires conserved metal-binding residues, metal ions, and dNTPs and is inhibited by ddNTPs or chain-terminated DNA. Our data indicate that pol θ repurposes metal ions in the polymerase active site for endonucleolytic cleavage and that the polymerase-active and end-trimming conformations of the enzyme are distinct. We reveal a nimble strategy of substrate processing that allows pol θ to trim or extend DNA depending on the DNA repair context.
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Affiliation(s)
- Karl E Zahn
- Department of Microbiology and Molecular Genetics, University of Vermont, 89 Beaumont Ave., Burlington, VT 05405, USA; Department of Therapeutic Radiology, Yale University, New Haven, CT 06510, USA
| | - Ryan B Jensen
- Department of Therapeutic Radiology, Yale University, New Haven, CT 06510, USA
| | - Richard D Wood
- Department of Epigenetics & Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX 78957, USA.
| | - Sylvie Doublié
- Department of Microbiology and Molecular Genetics, University of Vermont, 89 Beaumont Ave., Burlington, VT 05405, USA.
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Nayak S, Calvo JA, Cantor SB. Targeting translesion synthesis (TLS) to expose replication gaps, a unique cancer vulnerability. Expert Opin Ther Targets 2021; 25:27-36. [PMID: 33416413 DOI: 10.1080/14728222.2021.1864321] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
Introduction: Translesion synthesis (TLS) is a DNA damage tolerance (DDT) mechanism that employs error-prone polymerases to bypass replication blocking DNA lesions, contributing to a gain in mutagenesis and chemo-resistance. However, recent findings illustrate an emerging role for TLS in replication gap suppression (RGS), distinct from its role in post-replication gap filling. Here, TLS protects cells from replication stress (RS)-induced toxic single-stranded DNA (ssDNA) gaps that accumulate in the wake of active replication. Intriguingly, TLS-mediated RGS is specifically observed in several cancer cell lines and contributes to their survival. Thus, targeting TLS has the potential to uniquely eradicate tumors without harming non-cancer tissues. Areas Covered: This review provides an innovative perspective on the role of TLS beyond its canonical function of lesion bypass or post-replicative gap filling. We provide a comprehensive analysis that underscores the emerging role of TLS as a cancer adaptation necessary to overcome the replication stress response (RSR), an anti-cancer barrier. Expert Opinion: TLS RGS is critical for tumorigenesis and is a new hallmark of cancer. Although the exact mechanism and extent of TLS dependency in cancer is still emerging, TLS inhibitors have shown promise as an anti-cancer therapy in selectively targeting this unique cancer vulnerability.
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Affiliation(s)
- Sumeet Nayak
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School , Worcester, MA USA
| | - Jennifer A Calvo
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School , Worcester, MA USA
| | - Sharon B Cantor
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School , Worcester, MA USA
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