1
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Do BT, Hsu PP, Vermeulen SY, Wang Z, Hirz T, Abbott KL, Aziz N, Replogle JM, Bjelosevic S, Paolino J, Nelson SA, Block S, Darnell AM, Ferreira R, Zhang H, Milosevic J, Schmidt DR, Chidley C, Harris IS, Weissman JS, Pikman Y, Stegmaier K, Cheloufi S, Su XA, Sykes DB, Vander Heiden MG. Nucleotide depletion promotes cell fate transitions by inducing DNA replication stress. Dev Cell 2024:S1534-5807(24)00327-7. [PMID: 38823395 DOI: 10.1016/j.devcel.2024.05.010] [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: 01/30/2024] [Revised: 04/14/2024] [Accepted: 05/09/2024] [Indexed: 06/03/2024]
Abstract
Control of cellular identity requires coordination of developmental programs with environmental factors such as nutrient availability, suggesting that perturbing metabolism can alter cell state. Here, we find that nucleotide depletion and DNA replication stress drive differentiation in human and murine normal and transformed hematopoietic systems, including patient-derived acute myeloid leukemia (AML) xenografts. These cell state transitions begin during S phase and are independent of ATR/ATM checkpoint signaling, double-stranded DNA break formation, and changes in cell cycle length. In systems where differentiation is blocked by oncogenic transcription factor expression, replication stress activates primed regulatory loci and induces lineage-appropriate maturation genes despite the persistence of progenitor programs. Altering the baseline cell state by manipulating transcription factor expression causes replication stress to induce genes specific for alternative lineages. The ability of replication stress to selectively activate primed maturation programs across different contexts suggests a general mechanism by which changes in metabolism can promote lineage-appropriate cell state transitions.
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Affiliation(s)
- Brian T Do
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Harvard-MIT Health Sciences and Technology, Cambridge, MA 02139, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Peggy P Hsu
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Dana-Farber Cancer Institute, Boston, MA 02115, USA; Massachusetts General Hospital Cancer Center, Boston, MA 02113, USA; Rogel Cancer Center and Division of Hematology and Oncology, Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA.
| | - Sidney Y Vermeulen
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Zhishan Wang
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Taghreed Hirz
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA 02113, USA; Harvard Stem Cell Institute, Cambridge, MA 02139, USA
| | - Keene L Abbott
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Najihah Aziz
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA 02113, USA; Harvard Stem Cell Institute, Cambridge, MA 02139, USA
| | - Joseph M Replogle
- Whitehead Institute for Biomedical Research, Cambridge, MA 02139, USA; Medical Scientist Training Program, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Stefan Bjelosevic
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Pediatric Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, Boston, MA 02115, USA; Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Jonathan Paolino
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, Boston, MA 02115, USA; Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Samantha A Nelson
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Samuel Block
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Alicia M Darnell
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Raphael Ferreira
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Hanyu Zhang
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA 02113, USA; Harvard Stem Cell Institute, Cambridge, MA 02139, USA
| | - Jelena Milosevic
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA 02113, USA; Harvard Stem Cell Institute, Cambridge, MA 02139, USA
| | - Daniel R Schmidt
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Radiation Oncology, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA
| | - Christopher Chidley
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Isaac S Harris
- Wilmot Cancer Institute, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Jonathan S Weissman
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Whitehead Institute for Biomedical Research, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, Cambridge, MA 02139, USA
| | - Yana Pikman
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, Boston, MA 02115, USA; Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Kimberly Stegmaier
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Pediatric Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, Boston, MA 02115, USA; Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Sihem Cheloufi
- Department of Biochemistry, University of California, Riverside, Riverside, CA 92521, USA; Stem Cell Center, University of California, Riverside, Riverside, CA 92521, USA; Center for RNA Biology and Medicine, Riverside, CA 92521, USA
| | - Xiaofeng A Su
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - David B Sykes
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA 02113, USA; Harvard Stem Cell Institute, Cambridge, MA 02139, USA
| | - Matthew G Vander Heiden
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Dana-Farber Cancer Institute, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
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2
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D'Ordine AM, Jogl G, Sedivy JM. Identification and characterization of small molecule inhibitors of the LINE-1 retrotransposon endonuclease. Nat Commun 2024; 15:3883. [PMID: 38719805 PMCID: PMC11078990 DOI: 10.1038/s41467-024-48066-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: 07/12/2023] [Accepted: 04/18/2024] [Indexed: 05/12/2024] Open
Abstract
The long interspersed nuclear element-1 (LINE-1 or L1) retrotransposon is the only active autonomously replicating retrotransposon in the human genome. L1 harms the cell by inserting new copies, generating DNA damage, and triggering inflammation. Therefore, L1 inhibition could be used to treat many diseases associated with these processes. Previous research has focused on inhibition of the L1 reverse transcriptase due to the prevalence of well-characterized inhibitors of related viral enzymes. Here we present the L1 endonuclease as another target for reducing L1 activity. We characterize structurally diverse small molecule endonuclease inhibitors using computational, biochemical, and biophysical methods. We also show that these inhibitors reduce L1 retrotransposition, L1-induced DNA damage, and inflammation reinforced by L1 in senescent cells. These inhibitors could be used for further pharmacological development and as tools to better understand the life cycle of this element and its impact on disease processes.
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Affiliation(s)
- Alexandra M D'Ordine
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI, USA
- Center on the Biology of Aging, Brown University, Providence, RI, USA
| | - Gerwald Jogl
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI, USA.
- Center on the Biology of Aging, Brown University, Providence, RI, USA.
| | - John M Sedivy
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI, USA.
- Center on the Biology of Aging, Brown University, Providence, RI, USA.
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3
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Kojima K, Ohkubo H, Kawasumi R, Hirota K. Pold4 subunit of replicative polymerase δ promotes fork slowing at broken templates. DNA Repair (Amst) 2024; 139:103688. [PMID: 38678695 DOI: 10.1016/j.dnarep.2024.103688] [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: 10/25/2023] [Revised: 02/25/2024] [Accepted: 04/23/2024] [Indexed: 05/01/2024]
Abstract
Single-strand breaks (SSBs) are the most frequent type of lesion, and replication across such lesions leads to double-strand breaks (DSBs). DSBs that arise during replication are repaired by homologous recombination (HR) and are suppressed by fork reversal. Poly[ADP-ribose] polymerase I (PARP1) and the proofreading exonuclease activity of replicative polymerase ε (Polε) are required for fork reversal when leading strand replication encounters SSBs. However, the mechanism underlying fork reversal at the SSB during lagging-strand replication remains elusive. We here demonstrate that the Pold4 subunit of replicative polymerase δ (Polδ) plays a role in promoting fork reversal during lagging strand replication on a broken template. POLD4-/- cells exhibited heightened sensitivity to camptothecin (CPT) but not to other DNA-damaging agents compared to wild-type cells. This selective CPT sensitivity in POLD4-/- cells suggests that Pold4 suppresses DSBs during replication, as CPT induces significant SSBs during replication, which subsequently lead to DSBs. To explore the functional interactions among Pold4, Polε exonuclease, and PARP1 in DSB suppression, we generated PARP1-/-, POLD4-/-, Polε exonuclease-deficient POLE1exo-/-, PARP1-/-/POLD4-/-, and POLD4-/-/POLE1exo-/- cells. These epistasis analyses showed that Pold4 is involved in the PARP1-Polε exonuclease-mediated fork reversal following CPT treatment. These results suggest that Pold4 aids in fork reversal when lagging strand replication stalls on a broken template. In conclusion, the Pold4 subunit of Polδ has roles in the PARP1-Polε exonuclease-mediated fork reversal, contributing to the suppression of DSBs.
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Affiliation(s)
- Kota Kojima
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, Minamiosawa 1-1, Hachioji-shi, Tokyo 192-0397, Japan
| | - Hiromori Ohkubo
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, Minamiosawa 1-1, Hachioji-shi, Tokyo 192-0397, Japan
| | - Ryotaro Kawasumi
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, Minamiosawa 1-1, Hachioji-shi, Tokyo 192-0397, Japan
| | - Kouji Hirota
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, Minamiosawa 1-1, Hachioji-shi, Tokyo 192-0397, Japan.
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4
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Qin Y, Ren J, Yu H, He X, Cheng S, Chen W, Yang Z, Sun F, Wang C, Yuan S, Chen P, Wu D, Ren F, Huang A, Chen J. HOXA-AS2 Epigenetically Inhibits HBV Transcription by Recruiting the MTA1-HDAC1/2 Deacetylase Complex to cccDNA Minichromosome. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2306810. [PMID: 38647380 DOI: 10.1002/advs.202306810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 03/27/2024] [Indexed: 04/25/2024]
Abstract
Persistent transcription of HBV covalently closed circular DNA (cccDNA) is critical for chronic HBV infection. Silencing cccDNA transcription through epigenetic mechanisms offers an effective strategy to control HBV. Long non-coding RNAs (lncRNAs), as important epigenetic regulators, have an unclear role in cccDNA transcription regulation. In this study, lncRNA sequencing (lncRNA seq) is conducted on five pairs of HBV-positive and HBV-negative liver tissue. Through analysis, HOXA-AS2 (HOXA cluster antisense RNA 2) is identified as a significantly upregulated lncRNA in HBV-infected livers. Further experiments demonstrate that HBV DNA polymerase (DNA pol) induces HOXA-AS2 after establishing persistent high-level HBV replication. Functional studies reveal that HOXA-AS2 physically binds to cccDNA and significantly inhibits its transcription. Mechanistically, HOXA-AS2 recruits the MTA1-HDAC1/2 deacetylase complex to cccDNA minichromosome by physically interacting with metastasis associated 1 (MTA1) subunit, resulting in reduced acetylation of histone H3 at lysine 9 (H3K9ac) and lysine 27 (H3K27ac) associated with cccDNA and subsequently suppressing cccDNA transcription. Altogether, the study reveals a mechanism to self-limit HBV replication, wherein the upregulation of lncRNA HOXA-AS2, induced by HBV DNA pol, can epigenetically suppress cccDNA transcription.
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Affiliation(s)
- YiPing Qin
- Institute for Viral Hepatitis, Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), Department of Infectious Diseases, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, 400010, China
- Chongqing Key Laboratory of Translational Research for Cancer Metastasis and Individualized Treatment, Chongqing University Cancer Hospital, Chongqing, 400030, China
| | - JiHua Ren
- Institute for Viral Hepatitis, Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), Department of Infectious Diseases, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, 400010, China
| | - HaiBo Yu
- Institute for Viral Hepatitis, Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), Department of Infectious Diseases, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, 400010, China
| | - Xin He
- Institute for Viral Hepatitis, Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), Department of Infectious Diseases, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, 400010, China
| | - ShengTao Cheng
- Institute for Viral Hepatitis, Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), Department of Infectious Diseases, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, 400010, China
| | - WeiXian Chen
- Institute for Viral Hepatitis, Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), Department of Infectious Diseases, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, 400010, China
| | - Zhen Yang
- Institute for Viral Hepatitis, Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), Department of Infectious Diseases, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, 400010, China
| | - FengMing Sun
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, China
| | - ChunDuo Wang
- Institute for Viral Hepatitis, Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), Department of Infectious Diseases, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, 400010, China
| | - SiYu Yuan
- Institute for Viral Hepatitis, Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), Department of Infectious Diseases, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, 400010, China
| | - Peng Chen
- Institute for Viral Hepatitis, Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), Department of Infectious Diseases, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, 400010, China
| | - DaiQing Wu
- Institute for Viral Hepatitis, Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), Department of Infectious Diseases, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, 400010, China
| | - Fang Ren
- Institute for Viral Hepatitis, Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), Department of Infectious Diseases, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, 400010, China
| | - AiLong Huang
- Institute for Viral Hepatitis, Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), Department of Infectious Diseases, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, 400010, China
| | - Juan Chen
- Institute for Viral Hepatitis, Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), Department of Infectious Diseases, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, 400010, China
- State Key Laboratory of Ultrasound in Medicine and Engineering, College of Biomedical Engineering, Chongqing Medical University, Chongqing, 400016, China
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5
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Carvajal-Moreno J, Wang X, Hernandez VA, Mondal M, Zhao X, Yalowich JC, Elton TS. Use of CRISPR/Cas9 with Homology-Directed Repair to Gene-Edit Topoisomerase II β in Human Leukemia K562 Cells: Generation of a Resistance Phenotype. J Pharmacol Exp Ther 2024; 389:186-196. [PMID: 38508753 PMCID: PMC11026151 DOI: 10.1124/jpet.123.002038] [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: 11/21/2023] [Revised: 02/27/2024] [Accepted: 02/27/2024] [Indexed: 03/22/2024] Open
Abstract
DNA topoisomerase IIβ (TOP2β/180; 180 kDa) is a nuclear enzyme that regulates DNA topology by generation of short-lived DNA double-strand breaks, primarily during transcription. TOP2β/180 can be a target for DNA damage-stabilizing anticancer drugs, whose efficacy is often limited by chemoresistance. Our laboratory previously demonstrated reduced levels of TOP2β/180 (and the paralog TOP2α/170) in an acquired etoposide-resistant human leukemia (K562) clonal cell line, K/VP.5, in part due to overexpression of microRNA-9-3p/5p impacting post-transcriptional events. To evaluate the effect on drug sensitivity upon reduction/elimination of TOP2β/180, a premature stop codon was generated at the TOP2β/180 gene exon 19/intron 19 boundary (AGAA//GTAA→ATAG//GTAA) in parental K562 cells (which contain four TOP2β/180 alleles) by CRISPR/Cas9 editing with homology-directed repair to disrupt production of full-length TOP2β/180. Gene-edited clones were identified and verified by quantitative polymerase chain reaction and Sanger sequencing, respectively. Characterization of TOP2β/180 gene-edited clones, with one or all four TOP2β/180 alleles mutated, revealed partial or complete loss of TOP2β mRNA/protein, respectively. The loss of TOP2β/180 protein correlated with decreased (2-{4-[(7-chloro-2-quinoxalinyl)oxy]phenoxy}propionic acid)-induced DNA damage and partial resistance in growth inhibition assays. Partial resistance to mitoxantrone was also noted in the gene-edited clone with all four TOP2β/180 alleles modified. No cross-resistance to etoposide or mAMSA was noted in the gene-edited clones. Results demonstrated the role of TOP2β/180 in drug sensitivity/resistance in K562 cells and revealed differential paralog activity of TOP2-targeted agents. SIGNIFICANCE STATEMENT: Data indicated that CRISPR/Cas9 editing of the exon 19/intron 19 boundary in the TOP2β/180 gene to introduce a premature stop codon resulted in partial to complete disruption of TOP2β/180 expression in human leukemia (K562) cells depending on the number of edited alleles. Edited clones were partially resistant to mitoxantrone and XK469, while lacking resistance to etoposide and mAMSA. Results demonstrated the import of TOP2β/180 in drug sensitivity/resistance in K562 cells and revealed differential paralog activity of TOP2-targeted agents.
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Affiliation(s)
- Jessika Carvajal-Moreno
- Division of Pharmaceutics and Pharmacology, College of Pharmacy, The Ohio State University, Columbus, Ohio
| | - Xinyi Wang
- Division of Pharmaceutics and Pharmacology, College of Pharmacy, The Ohio State University, Columbus, Ohio
| | - Victor A Hernandez
- Division of Pharmaceutics and Pharmacology, College of Pharmacy, The Ohio State University, Columbus, Ohio
| | - Milon Mondal
- Division of Pharmaceutics and Pharmacology, College of Pharmacy, The Ohio State University, Columbus, Ohio
| | - Xinyu Zhao
- Division of Pharmaceutics and Pharmacology, College of Pharmacy, The Ohio State University, Columbus, Ohio
| | - Jack C Yalowich
- Division of Pharmaceutics and Pharmacology, College of Pharmacy, The Ohio State University, Columbus, Ohio
| | - Terry S Elton
- Division of Pharmaceutics and Pharmacology, College of Pharmacy, The Ohio State University, Columbus, Ohio
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6
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Rona G, Miwatani-Minter B, Zhang Q, Goldberg HV, Kerzhnerman MA, Howard JB, Simoneschi D, Lane E, Hobbs JW, Sassani E, Wang AA, Keegan S, Laverty DJ, Piett CG, Pongor LS, Xu ML, Andrade J, Thomas A, Sicinski P, Askenazi M, Ueberheide B, Fenyö D, Nagel ZD, Pagano M. CDK-independent role of D-type cyclins in regulating DNA mismatch repair. Mol Cell 2024; 84:1224-1242.e13. [PMID: 38458201 PMCID: PMC10997477 DOI: 10.1016/j.molcel.2024.02.010] [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: 07/10/2023] [Revised: 01/04/2024] [Accepted: 02/09/2024] [Indexed: 03/10/2024]
Abstract
Although mismatch repair (MMR) is essential for correcting DNA replication errors, it can also recognize other lesions, such as oxidized bases. In G0 and G1, MMR is kept in check through unknown mechanisms as it is error-prone during these cell cycle phases. We show that in mammalian cells, D-type cyclins are recruited to sites of oxidative DNA damage in a PCNA- and p21-dependent manner. D-type cyclins inhibit the proteasomal degradation of p21, which competes with MMR proteins for binding to PCNA, thereby inhibiting MMR. The ability of D-type cyclins to limit MMR is CDK4- and CDK6-independent and is conserved in G0 and G1. At the G1/S transition, the timely, cullin-RING ubiquitin ligase (CRL)-dependent degradation of D-type cyclins and p21 enables MMR activity to efficiently repair DNA replication errors. Persistent expression of D-type cyclins during S-phase inhibits the binding of MMR proteins to PCNA, increases the mutational burden, and promotes microsatellite instability.
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Affiliation(s)
- Gergely Rona
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA; Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY 10016, USA; Howard Hughes Medical Institute, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Bearach Miwatani-Minter
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA; Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Qingyue Zhang
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA; Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Hailey V Goldberg
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA; Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Marc A Kerzhnerman
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA; Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Jesse B Howard
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA; Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Daniele Simoneschi
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA; Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Ethan Lane
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA; Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - John W Hobbs
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA; Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Elizabeth Sassani
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA; Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Andrew A Wang
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA; Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Sarah Keegan
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA; Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY 10016, USA; Institute for Systems Genetics, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Daniel J Laverty
- Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Cortt G Piett
- Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Lorinc S Pongor
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA; Cancer Genomics and Epigenetics Core Group, Hungarian Centre of Excellence for Molecular Medicine, Szeged 6728, Hungary
| | - Miranda Li Xu
- Department of Cancer Biology, Dana-Farber Cancer Institute, and Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Joshua Andrade
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA; Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Anish Thomas
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Piotr Sicinski
- Department of Cancer Biology, Dana-Farber Cancer Institute, and Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02215, USA; Department of Histology and Embryology, Center for Biostructure Research, Medical University of Warsaw, Chalubinskiego 5, 02-004 Warsaw, Poland
| | - Manor Askenazi
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA; Biomedical Hosting LLC, 33 Lewis Avenue, Arlington, MA 02474, USA
| | - Beatrix Ueberheide
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA; Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - David Fenyö
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA; Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY 10016, USA; Institute for Systems Genetics, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Zachary D Nagel
- Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Michele Pagano
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA; Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY 10016, USA; Howard Hughes Medical Institute, NYU Grossman School of Medicine, New York, NY 10016, USA.
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7
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Beattie UK, Estrada RS, Gormally BMG, Reed JM, McVey M, Romero LM. Investigating the effects of acute and chronic stress on DNA damage. JOURNAL OF EXPERIMENTAL ZOOLOGY. PART A, ECOLOGICAL AND INTEGRATIVE PHYSIOLOGY 2024; 341:256-263. [PMID: 38221843 DOI: 10.1002/jez.2778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 12/19/2023] [Accepted: 12/25/2023] [Indexed: 01/16/2024]
Abstract
A hallmark of the vertebrate stress response is a rapid increase in glucocorticoids and catecholamines; however, this does not mean that these mediators are the best, or should be the only, metric measured when studying stress. Instead, it is becoming increasingly clear that assaying a suite of downstream metrics is necessary in stress physiology. One component of this suite could be assessing double-stranded DNA damage (dsDNA damage), which has recently been shown to increase in blood with both acute and chronic stress in house sparrows (Passer domesticus). To further understand the relationship between stress and dsDNA damage, we designed two experiments to address the following questions: (1) how does dsDNA damage with chronic stress vary across tissues? (2) does the increase in dsDNA damage during acute stress come from one arm of the stress response or both? We found that (1) dsDNA damage affects tissues differently during chronic stress and (2) the hypothalamic-pituitary-adrenal axis influences dsDNA damage with acute stress, but the sympathetic-adreno-medullary system does not. Surprisingly, our data are not explained by studies on changes in hormone receptor levels with chronic stress, so the underlying mechanism remains unclear.
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Affiliation(s)
- Ursula K Beattie
- Department of Biology, Tufts University, Medford, Massachusetts, USA
| | - Rodolfo S Estrada
- Department of Biology, Tufts University, Medford, Massachusetts, USA
| | - Brenna M G Gormally
- Department of Biology, Tufts University, Medford, Massachusetts, USA
- Seventh College, University of California San Diego, San Diego, California, USA
| | - J Michael Reed
- Department of Biology, Tufts University, Medford, Massachusetts, USA
| | - Mitch McVey
- Department of Biology, Tufts University, Medford, Massachusetts, USA
| | - L Michael Romero
- Department of Biology, Tufts University, Medford, Massachusetts, USA
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8
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Dong H, He X, Zhang L, Chen W, Lin YC, Liu SB, Wang H, Nguyen LXT, Li M, Zhu Y, Zhao D, Ghoda L, Serody J, Vincent B, Luznik L, Gojo I, Zeidner J, Su R, Chen J, Sharma R, Pirrotte P, Wu X, Hu W, Han W, Shen B, Kuo YH, Jin J, Salhotra A, Wang J, Marcucci G, Luo YL, Li L. Targeting PRMT9-mediated arginine methylation suppresses cancer stem cell maintenance and elicits cGAS-mediated anticancer immunity. NATURE CANCER 2024; 5:601-624. [PMID: 38413714 PMCID: PMC11056319 DOI: 10.1038/s43018-024-00736-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Accepted: 01/26/2024] [Indexed: 02/29/2024]
Abstract
Current anticancer therapies cannot eliminate all cancer cells, which hijack normal arginine methylation as a means to promote their maintenance via unknown mechanisms. Here we show that targeting protein arginine N-methyltransferase 9 (PRMT9), whose activities are elevated in blasts and leukemia stem cells (LSCs) from patients with acute myeloid leukemia (AML), eliminates disease via cancer-intrinsic mechanisms and cancer-extrinsic type I interferon (IFN)-associated immunity. PRMT9 ablation in AML cells decreased the arginine methylation of regulators of RNA translation and the DNA damage response, suppressing cell survival. Notably, PRMT9 inhibition promoted DNA damage and activated cyclic GMP-AMP synthase, which underlies the type I IFN response. Genetically activating cyclic GMP-AMP synthase in AML cells blocked leukemogenesis. We also report synergy of a PRMT9 inhibitor with anti-programmed cell death protein 1 in eradicating AML. Overall, we conclude that PRMT9 functions in survival and immune evasion of both LSCs and non-LSCs; targeting PRMT9 may represent a potential anticancer strategy.
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Affiliation(s)
- Haojie Dong
- Department of Hematological Malignancies Translational Science, Gehr Family Center for Leukemia Research, Hematologic Malignancies and Stem Cell Transplantation Institute, Beckman Research Institute, City of Hope Medical Center, Duarte, CA, USA
| | - Xin He
- Department of Hematological Malignancies Translational Science, Gehr Family Center for Leukemia Research, Hematologic Malignancies and Stem Cell Transplantation Institute, Beckman Research Institute, City of Hope Medical Center, Duarte, CA, USA
| | - Lei Zhang
- Department of Hematological Malignancies Translational Science, Gehr Family Center for Leukemia Research, Hematologic Malignancies and Stem Cell Transplantation Institute, Beckman Research Institute, City of Hope Medical Center, Duarte, CA, USA
| | - Wei Chen
- Integrative Genomics Core, Beckman Research Institute, City of Hope Medical Center, Duarte, CA, USA
| | - Yi-Chun Lin
- Department of Pharmaceutical Sciences, College of Pharmacy, Western University of Health Sciences, Pomona, CA, USA
| | - Song-Bai Liu
- Suzhou Key Laboratory of Medical Biotechnology, Suzhou Vocational Health College, Suzhou, People's Republic of China
| | - Huafeng Wang
- Department of Hematology, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, People's Republic of China
| | - Le Xuan Truong Nguyen
- Department of Hematological Malignancies Translational Science, Gehr Family Center for Leukemia Research, Hematologic Malignancies and Stem Cell Transplantation Institute, Beckman Research Institute, City of Hope Medical Center, Duarte, CA, USA
| | - Min Li
- Division of Biostatistics, Department of Computational and Quantitative Medicine, Beckman Research Institute, City of Hope Medical Center, Duarte, CA, USA
| | - Yinghui Zhu
- Department of Hematological Malignancies Translational Science, Gehr Family Center for Leukemia Research, Hematologic Malignancies and Stem Cell Transplantation Institute, Beckman Research Institute, City of Hope Medical Center, Duarte, CA, USA
| | - Dandan Zhao
- Department of Hematological Malignancies Translational Science, Gehr Family Center for Leukemia Research, Hematologic Malignancies and Stem Cell Transplantation Institute, Beckman Research Institute, City of Hope Medical Center, Duarte, CA, USA
| | - Lucy Ghoda
- Department of Hematological Malignancies Translational Science, Gehr Family Center for Leukemia Research, Hematologic Malignancies and Stem Cell Transplantation Institute, Beckman Research Institute, City of Hope Medical Center, Duarte, CA, USA
| | - Jonathan Serody
- Department of Medicine, Division of Hematology, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
- Department of Microbiology and Immunology and Department of Pathology and Laboratory Medicine, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Benjamin Vincent
- Department of Medicine, Division of Hematology, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
- Department of Microbiology and Immunology, Computational Medicine Program, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
| | - Leo Luznik
- Department of Oncology and Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Ivana Gojo
- Department of Oncology and Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Joshua Zeidner
- Department of Medicine, Division of Hematology, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
| | - Rui Su
- Department of Systems Biology, Beckman Research Institute, City of Hope Medical Center, Duarte, CA, USA
| | - Jianjun Chen
- Department of Systems Biology, Beckman Research Institute, City of Hope Medical Center, Duarte, CA, USA
| | - Ritin Sharma
- Cancer & Cell Biology Division, The Translational Genomics Research Institute, Phoenix, AZ, USA
- Integrated Mass Spectrometry Shared Resource, City of Hope Medical Center, Duarte, CA, USA
| | - Patrick Pirrotte
- Cancer & Cell Biology Division, The Translational Genomics Research Institute, Phoenix, AZ, USA
- Integrated Mass Spectrometry Shared Resource, City of Hope Medical Center, Duarte, CA, USA
| | - Xiwei Wu
- Integrative Genomics Core, Beckman Research Institute, City of Hope Medical Center, Duarte, CA, USA
- Department of Computational and Quantitative Medicine, Beckman Research Institute, City of Hope Medical Center, Duarte, CA, USA
| | - Weidong Hu
- Department of Immunology and Theranostics, Beckman Research Institute, City of Hope Medical Center, Duarte, CA, USA
| | - Weidong Han
- Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, People's Republic of China
| | - Binghui Shen
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope Medical Center, Duarte, CA, USA
| | - Ya-Huei Kuo
- Department of Hematological Malignancies Translational Science, Gehr Family Center for Leukemia Research, Hematologic Malignancies and Stem Cell Transplantation Institute, Beckman Research Institute, City of Hope Medical Center, Duarte, CA, USA
| | - Jie Jin
- Department of Hematology, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, People's Republic of China
| | - Amandeep Salhotra
- Department of Hematology and HCT, City of Hope Medical Center, Duarte, CA, USA
| | - Jeffrey Wang
- Department of Pharmaceutical Sciences, College of Pharmacy, Western University of Health Sciences, Pomona, CA, USA
| | - Guido Marcucci
- Department of Hematological Malignancies Translational Science, Gehr Family Center for Leukemia Research, Hematologic Malignancies and Stem Cell Transplantation Institute, Beckman Research Institute, City of Hope Medical Center, Duarte, CA, USA
- Department of Hematology and HCT, City of Hope Medical Center, Duarte, CA, USA
| | - Yun Lyna Luo
- Department of Pharmaceutical Sciences, College of Pharmacy, Western University of Health Sciences, Pomona, CA, USA
| | - Ling Li
- Department of Hematological Malignancies Translational Science, Gehr Family Center for Leukemia Research, Hematologic Malignancies and Stem Cell Transplantation Institute, Beckman Research Institute, City of Hope Medical Center, Duarte, CA, USA.
- Department of Pediatrics, Beckman Research Institute, City of Hope Medical Center, Duarte, CA, USA.
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9
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Woolley PR, Wen X, Conway OM, Ender NA, Lee JH, Paull TT. Regulation of transcription patterns, poly(ADP-ribose), and RNA-DNA hybrids by the ATM protein kinase. Cell Rep 2024; 43:113896. [PMID: 38442018 PMCID: PMC11022685 DOI: 10.1016/j.celrep.2024.113896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 01/11/2024] [Accepted: 02/15/2024] [Indexed: 03/07/2024] Open
Abstract
The ataxia telangiectasia mutated (ATM) protein kinase is a master regulator of the DNA damage response and also an important sensor of oxidative stress. Analysis of gene expression in ataxia-telangiectasia (A-T) patient brain tissue shows that large-scale transcriptional changes occur in patient cerebellum that correlate with the expression level and guanine-cytosine (GC) content of transcribed genes. In human neuron-like cells in culture, we map locations of poly(ADP-ribose) and RNA-DNA hybrid accumulation genome-wide with ATM inhibition and find that these marks also coincide with high transcription levels, active transcription histone marks, and high GC content. Antioxidant treatment reverses the accumulation of R-loops in transcribed regions, consistent with the central role of reactive oxygen species in promoting these lesions. Based on these results, we postulate that transcription-associated lesions accumulate in ATM-deficient cells and that the single-strand breaks and PARylation at these sites ultimately generate changes in transcription that compromise cerebellum function and lead to neurodegeneration over time in A-T patients.
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Affiliation(s)
- Phillip R Woolley
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Xuemei Wen
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Olivia M Conway
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Nicolette A Ender
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Ji-Hoon Lee
- Department of Biological Sciences, Research Center of Ecomimetics, Chonnam National University, Gwangju 61186, Republic of Korea.
| | - Tanya T Paull
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA.
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10
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Bachus S, Akkerman N, Fulham L, Graves D, Helwer R, Rempel J, Pelka P. ARGLU1 enhances promoter-proximal pausing of RNA polymerase II and stimulates DNA damage repair. Nucleic Acids Res 2024:gkae208. [PMID: 38520408 DOI: 10.1093/nar/gkae208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 03/05/2024] [Accepted: 03/11/2024] [Indexed: 03/25/2024] Open
Abstract
Arginine and glutamate rich 1 (ARGLU1) is a poorly understood cellular protein with functions in RNA splicing and transcription. Computational prediction suggests that ARGLU1 contains intrinsically disordered regions and lacks any known structural or functional domains. We used adenovirus Early protein 1A (E1A) to probe for critical regulators of important cellular pathways and identified ARGLU1 as a significant player in transcription and the DNA damage response pathway. Transcriptional effects induced by ARGLU1 occur via enhancement of promoter-proximal RNA polymerase II pausing, likely by inhibiting the interaction between JMJD6 and BRD4. When overexpressed, ARGLU1 increases the growth rate of cancer cells, while its knockdown leads to growth arrest. Significantly, overexpression of ARGLU1 increased cancer cell resistance to genotoxic drugs and promoted DNA damage repair. These results identify new roles for ARGLU1 in cancer cell survival and the DNA damage repair pathway, with potential clinical implications for chemotherapy resistance.
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Affiliation(s)
- Scott Bachus
- Department of Microbiology, University of Manitoba, 45 Chancellor's Circle, Buller Building Room 427, Winnipeg, MB R3T 2N2, Canada
| | - Nikolas Akkerman
- Department of Microbiology, University of Manitoba, 45 Chancellor's Circle, Buller Building Room 427, Winnipeg, MB R3T 2N2, Canada
| | - Lauren Fulham
- Department of Microbiology, University of Manitoba, 45 Chancellor's Circle, Buller Building Room 427, Winnipeg, MB R3T 2N2, Canada
| | - Drayson Graves
- Department of Microbiology, University of Manitoba, 45 Chancellor's Circle, Buller Building Room 427, Winnipeg, MB R3T 2N2, Canada
| | - Rafe Helwer
- Department of Microbiology, University of Manitoba, 45 Chancellor's Circle, Buller Building Room 427, Winnipeg, MB R3T 2N2, Canada
| | - Jordan Rempel
- Department of Microbiology, University of Manitoba, 45 Chancellor's Circle, Buller Building Room 427, Winnipeg, MB R3T 2N2, Canada
| | - Peter Pelka
- Department of Microbiology, University of Manitoba, 45 Chancellor's Circle, Buller Building Room 427, Winnipeg, MB R3T 2N2, Canada
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, 45 Chancellor's Circle, Buller Building Room 427, Winnipeg, MB R3T 2N2, Canada
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11
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Leventhal MJ, Zanella CA, Kang B, Peng J, Gritsch D, Liao Z, Bukhari H, Wang T, Pao PC, Danquah S, Benetatos J, Nehme R, Farhi S, Tsai LH, Dong X, Scherzer CR, Feany MB, Fraenkel E. A systems-biology approach connects aging mechanisms with Alzheimer's disease pathogenesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.17.585262. [PMID: 38559190 PMCID: PMC10980014 DOI: 10.1101/2024.03.17.585262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Age is the strongest risk factor for developing Alzheimer's disease, the most common neurodegenerative disorder. However, the mechanisms connecting advancing age to neurodegeneration in Alzheimer's disease are incompletely understood. We conducted an unbiased, genome-scale, forward genetic screen for age-associated neurodegeneration in Drosophila to identify the underlying biological processes required for maintenance of aging neurons. To connect genetic screen hits to Alzheimer's disease pathways, we measured proteomics, phosphoproteomics, and metabolomics in Drosophila models of Alzheimer's disease. We further identified Alzheimer's disease human genetic variants that modify expression in disease-vulnerable neurons. Through multi-omic, multi-species network integration of these data, we identified relationships between screen hits and tau-mediated neurotoxicity. Furthermore, we computationally and experimentally identified relationships between screen hits and DNA damage in Drosophila and human iPSC-derived neural progenitor cells. Our work identifies candidate pathways that could be targeted to attenuate the effects of age on neurodegeneration and Alzheimer's disease.
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Affiliation(s)
- Matthew J Leventhal
- MIT Ph.D. Program in Computational and Systems Biology, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Camila A Zanella
- Department of Pathology, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Byunguk Kang
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Spatial Technology Platform, Broad Institute of Harvard and MIT, Cambridge, MA USA
| | - Jiajie Peng
- Precision Neurology Program, Brigham and Women’s Hospital and Harvard Medical school, Boston, MA, USA
- APDA Center for Advanced Parkinson’s Disease Research, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - David Gritsch
- Precision Neurology Program, Brigham and Women’s Hospital and Harvard Medical school, Boston, MA, USA
- APDA Center for Advanced Parkinson’s Disease Research, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Zhixiang Liao
- Precision Neurology Program, Brigham and Women’s Hospital and Harvard Medical school, Boston, MA, USA
- APDA Center for Advanced Parkinson’s Disease Research, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Hassan Bukhari
- Department of Pathology, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Tao Wang
- Precision Neurology Program, Brigham and Women’s Hospital and Harvard Medical school, Boston, MA, USA
- APDA Center for Advanced Parkinson’s Disease Research, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
- Present address: School of Computer Science, Northwestern Polytechnical University, Xi’an, China
| | - Ping-Chieh Pao
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Serwah Danquah
- Spatial Technology Platform, Broad Institute of Harvard and MIT, Cambridge, MA USA
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Joseph Benetatos
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Ralda Nehme
- Spatial Technology Platform, Broad Institute of Harvard and MIT, Cambridge, MA USA
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Samouil Farhi
- Spatial Technology Platform, Broad Institute of Harvard and MIT, Cambridge, MA USA
| | - Li-Huei Tsai
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Xianjun Dong
- Precision Neurology Program, Brigham and Women’s Hospital and Harvard Medical school, Boston, MA, USA
- APDA Center for Advanced Parkinson’s Disease Research, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Clemens R Scherzer
- Precision Neurology Program, Brigham and Women’s Hospital and Harvard Medical school, Boston, MA, USA
- APDA Center for Advanced Parkinson’s Disease Research, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
- Present address: Stephen and Denise Adams Center of Yale School of Medicine, CT, USA
| | - Mel B Feany
- Department of Pathology, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Ernest Fraenkel
- MIT Ph.D. Program in Computational and Systems Biology, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Lead contact
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12
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Benedetti F, Silvestri G, Denaro F, Finesso G, Contreras-Galindo R, Munawwar A, Williams S, Davis H, Bryant J, Wang Y, Radaelli E, Rathinam CV, Gallo RC, Zella D. Mycoplasma DnaK expression increases cancer development in vivo upon DNA damage. Proc Natl Acad Sci U S A 2024; 121:e2320859121. [PMID: 38412130 DOI: 10.1073/pnas.2320859121] [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: 11/27/2023] [Accepted: 01/24/2024] [Indexed: 02/29/2024] Open
Abstract
Well-controlled repair mechanisms are involved in the maintenance of genomic stability, and their failure can precipitate DNA abnormalities and elevate tumor risk. In addition, the tumor microenvironment, enriched with factors inducing oxidative stress and affecting cell cycle checkpoints, intensifies DNA damage when repair pathways falter. Recent research has unveiled associations between certain bacteria, including Mycoplasmas, and various cancers, and the causative mechanism(s) are under active investigation. We previously showed that Mycoplasma fermentans DnaK, an HSP70 family chaperone protein, hampers the activity of proteins like PARP1 and p53, crucial for genomic integrity. Moreover, our analysis of its interactome in human cancer cell lines revealed DnaK's engagement with several components of DNA-repair machinery. Finally, in vivo experiments performed in our laboratory using a DnaK knock-in mouse model generated by our group demonstrated that DnaK exposure led to increased DNA copy number variants, indicative of genomic instability. We present here evidence that expression of DnaK is linked to increased i) incidence of tumors in vivo upon exposure to urethane, a DNA damaging agent; ii) spontaneous DNA damage ex vivo; and iii) expression of proinflammatory cytokines ex vivo, variations in reactive oxygen species levels, and increased β-galactosidase activity across tissues. Moreover, DnaK was associated with increased centromeric instability. Overall, these findings highlight the significance of Mycoplasma DnaK in the etiology of cancer and other genetic disorders providing a promising target for prevention, diagnostics, and therapeutics.
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Affiliation(s)
- Francesca Benedetti
- Institute of Human Virology and Global Virus Network Center, University of Maryland School of Medicine, Baltimore, MD 21201
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD 21201
| | - Giovannino Silvestri
- Institute of Human Virology and Global Virus Network Center, University of Maryland School of Medicine, Baltimore, MD 21201
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD 21201
| | - Frank Denaro
- Department of Biology, Morgan State University, Baltimore, MD 21251
| | - Giovanni Finesso
- Comparative Pathology Core, Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | | | - Arshi Munawwar
- Institute of Human Virology and Global Virus Network Center, University of Maryland School of Medicine, Baltimore, MD 21201
| | - Sumiko Williams
- Institute of Human Virology and Global Virus Network Center, University of Maryland School of Medicine, Baltimore, MD 21201
- Department of Biology, Morgan State University, Baltimore, MD 21251
| | - Harry Davis
- Institute of Human Virology and Global Virus Network Center, University of Maryland School of Medicine, Baltimore, MD 21201
| | - Joseph Bryant
- Institute of Human Virology and Global Virus Network Center, University of Maryland School of Medicine, Baltimore, MD 21201
| | - Yin Wang
- Institute of Human Virology and Global Virus Network Center, University of Maryland School of Medicine, Baltimore, MD 21201
- Department of Surgery, School of Medicine, University of Maryland School of Medicine, Baltimore, MD 21201
| | - Enrico Radaelli
- Comparative Pathology Core, Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Chozha V Rathinam
- Institute of Human Virology and Global Virus Network Center, University of Maryland School of Medicine, Baltimore, MD 21201
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD 21201
| | - Robert C Gallo
- Institute of Human Virology and Global Virus Network Center, University of Maryland School of Medicine, Baltimore, MD 21201
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD 21201
| | - Davide Zella
- Institute of Human Virology and Global Virus Network Center, University of Maryland School of Medicine, Baltimore, MD 21201
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD 21201
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13
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Conti BA, Ruiz PD, Broton C, Blobel NJ, Kottemann MC, Sridhar S, Lach FP, Wiley TF, Sasi NK, Carroll T, Smogorzewska A. RTF2 controls replication repriming and ribonucleotide excision at the replisome. Nat Commun 2024; 15:1943. [PMID: 38431617 PMCID: PMC10908796 DOI: 10.1038/s41467-024-45947-z] [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: 11/09/2023] [Accepted: 02/07/2024] [Indexed: 03/05/2024] Open
Abstract
DNA replication through a challenging genomic landscape is coordinated by the replisome, which must adjust to local conditions to provide appropriate replication speed and respond to lesions that hinder its progression. We have previously shown that proteasome shuttle proteins, DNA Damage Inducible 1 and 2 (DDI1/2), regulate Replication Termination Factor 2 (RTF2) levels at stalled replisomes, allowing fork stabilization and restart. Here, we show that during unperturbed replication, RTF2 regulates replisome localization of RNase H2, a heterotrimeric enzyme that removes RNA from RNA-DNA heteroduplexes. RTF2, like RNase H2, is essential for mammalian development and maintains normal replication speed. However, persistent RTF2 and RNase H2 at stalled replication forks prevent efficient replication restart, which is dependent on PRIM1, the primase component of DNA polymerase α-primase. Our data show a fundamental need for RTF2-dependent regulation of replication-coupled ribonucleotide removal and reveal the existence of PRIM1-mediated direct replication restart in mammalian cells.
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Affiliation(s)
- Brooke A Conti
- Laboratory of Genome Maintenance, The Rockefeller University, New York, NY, 10065, USA
| | - Penelope D Ruiz
- Laboratory of Genome Maintenance, The Rockefeller University, New York, NY, 10065, USA
| | - Cayla Broton
- Laboratory of Genome Maintenance, The Rockefeller University, New York, NY, 10065, USA
| | - Nicolas J Blobel
- Laboratory of Genome Maintenance, The Rockefeller University, New York, NY, 10065, USA
| | - Molly C Kottemann
- Laboratory of Genome Maintenance, The Rockefeller University, New York, NY, 10065, USA
| | - Sunandini Sridhar
- Laboratory of Genome Maintenance, The Rockefeller University, New York, NY, 10065, USA
| | - Francis P Lach
- Laboratory of Genome Maintenance, The Rockefeller University, New York, NY, 10065, USA
| | - Tom F Wiley
- Laboratory of Genome Maintenance, The Rockefeller University, New York, NY, 10065, USA
| | - Nanda K Sasi
- Laboratory for Cell Biology and Genetics, The Rockefeller University, New York, NY, 10065, USA
| | - Thomas Carroll
- Bioinformatics, The Rockefeller University, New York, NY, 10065, USA
| | - Agata Smogorzewska
- Laboratory of Genome Maintenance, The Rockefeller University, New York, NY, 10065, USA.
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14
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García-delaTorre P, Rivero-Segura NA, Sánchez-García S, Becerril-Rojas K, Sandoval-Rodriguez FE, Castro-Morales D, Cruz-Lopez M, Vazquez-Moreno M, Rincón-Heredia R, Ramirez-Garcia P, Gomez-Verjan JC. GrimAge is elevated in older adults with mild COVID-19 an exploratory analysis. GeroScience 2024:10.1007/s11357-024-01095-2. [PMID: 38358578 DOI: 10.1007/s11357-024-01095-2] [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: 12/06/2023] [Accepted: 02/07/2024] [Indexed: 02/16/2024] Open
Abstract
COVID-19 has been contained; however, the side effects associated with its infection continue to be a challenge for public health, particularly for older adults. On the other hand, epigenetic status contributes to the inter-individual health status and is associated with COVID-19 severity. Nevertheless, current studies focus only on severe COVID-19. Considering that most of the worldwide population developed mild COVID-19 infection. In the present exploratory study, we aim to analyze the association of mild COVID-19 with epigenetic ages (HorvathAge, HannumAge, GrimAge, PhenoAge, SkinAge, and DNAmTL) and clinical variables obtained from a Mexican cohort of older adults. We found that all epigenetic ages significantly differ from the chronological age, but only GrimAge is elevated. Additionally, both the intrinsic epigenetic age acceleration (IEAA) and the extrinsic epigenetic age acceleration (EEAA) are accelerated in all patients. Moreover, we found that immunological estimators and DNA damage were associated with PhenoAge, SkinBloodHorvathAge, and HorvathAge, suggesting that the effects of mild COVID-19 on the epigenetic clocks are mainly associated with inflammation and immunology changes. In conclusion, our results show that the effects of mild COVID-19 on the epigenetic clock are mainly associated with the immune system and an increase in GrimAge, IEAA, and EEAA.
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Affiliation(s)
- Paola García-delaTorre
- Unidad de Investigación Médica en Enfermedades Neurológicas, Hospital de Especialidades, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico City, México
| | | | - Sergio Sánchez-García
- Unidad de Investigación Epidemiológica y en Servicios de Salud, Área de Envejecimiento, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, 06720, Mexico City, Mexico
| | | | | | - Diana Castro-Morales
- Dirección de Investigación, Instituto Nacional de Geriatría (INGER), 10200, Mexico City, Mexico
| | - Miguel Cruz-Lopez
- Unidad de Investigación Médica en Bioquímica, Hospital de Especialidades, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, 06720, Mexico City, Mexico
| | - Miguel Vazquez-Moreno
- Unidad de Investigación Médica en Bioquímica, Hospital de Especialidades, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, 06720, Mexico City, Mexico
| | - Ruth Rincón-Heredia
- Unidad de Imagenología, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510, Mexico City, Mexico
| | - Perla Ramirez-Garcia
- Dirección de Investigación, Instituto Nacional de Geriatría (INGER), 10200, Mexico City, Mexico
| | - Juan Carlos Gomez-Verjan
- Dirección de Investigación, Instituto Nacional de Geriatría (INGER), 10200, Mexico City, Mexico.
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15
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Rosellini M, Omer EA, Schulze A, Ali NT, Boulos JC, Marini F, Küpper JH, Efferth T. Impact of plastic-related compounds on the gene expression signature of HepG2 cells transfected with CYP3A4. Arch Toxicol 2024; 98:525-536. [PMID: 38160208 PMCID: PMC10794370 DOI: 10.1007/s00204-023-03648-4] [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: 10/11/2023] [Accepted: 11/16/2023] [Indexed: 01/03/2024]
Abstract
The presence of plastic and microplastic within the oceans as well as in marine flora and fauna have caused a multitude of problems that have been the topic of numerous investigations for many years. However, their impact on human health remains largely unknown. Such plastic and microplastic particles have been detected in blood and placenta, underlining their ability to enter the human body. Plastics also contain other compounds, such as plasticizers, antioxidants, or dyes, whose impact on human health is currently being studied. Critical enzymes within the metabolism of endogenous molecules, especially of xenobiotics, are the cytochrome P450 monooxygenases (CYPs). Although their importance in maintaining cellular balance has been confirmed, their interactions with plastics and related products are poorly understood. In this study, the possible relationship between different plastic-related compounds and CYP3A4 as one of the most important CYPs was analyzed using hepatic cells overexpressing this enzyme. Beginning with virtual compound screening and molecular docking of more than 1000 plastic-related compounds, several candidates were identified to interact with CYP3A4. In a second step, RNA-sequencing was used to study in detail the transcriptome-wide gene expression levels affected by the selected compounds. Three candidate molecules ((2,2'-methylenebis(6-tert-butyl-4-methylphenol), 1,1-bis(3,5-di-tert-butyl-2-hydroxyphenyl)ethane, and 2,2'-methylenebis(6-cyclohexyl-4-methylphenol)) had an excellent binding affinity to CYP3A4 in-silico as well as cytotoxic effects and interactions with several metabolic pathways in-vitro. We identified common pathways influenced by all three selected plastic-related compounds. In particular, the suppression of pathways related to mitosis and 'DNA-templated DNA replication' which were confirmed by cell cycle analysis and single-cell gel electrophoresis. Furthermore, several mis-regulated metabolic and inflammation-related pathways were identified, suggesting the induction of hepatotoxicity at different levels. These findings imply that these compounds may cause liver problems subsequently affecting the entire organism.
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Affiliation(s)
- Matteo Rosellini
- Department of Pharmaceutical Biology, Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University, Staudinger Weg 5, 55128, Mainz, Germany
| | - Ejlal A Omer
- Department of Pharmaceutical Biology, Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University, Staudinger Weg 5, 55128, Mainz, Germany
| | - Alicia Schulze
- Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI), Medical Center of the Johannes Gutenberg University, 55122, Mainz, Germany
| | - Nadeen T Ali
- Department of Pharmaceutical Biology, Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University, Staudinger Weg 5, 55128, Mainz, Germany
| | - Joelle C Boulos
- Department of Pharmaceutical Biology, Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University, Staudinger Weg 5, 55128, Mainz, Germany
| | - Federico Marini
- Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI), Medical Center of the Johannes Gutenberg University, 55122, Mainz, Germany
- Research Center for Immunotherapy (FZI), Langenbeckstraße 1, 55131, Mainz, Germany
| | - Jan-Heiner Küpper
- Institute of Biotechnology, Brandenburg University of Technology Cottbus-Senftenberg, 03046, Senftenberg, Germany
| | - Thomas Efferth
- Department of Pharmaceutical Biology, Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University, Staudinger Weg 5, 55128, Mainz, Germany.
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16
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Chang JHM, Xue Z, Bauer J, Wehle B, Hendrix DA, Catalano T, Hurowitz JA, Nekvasil H, Demple B. Artificial Space Weathering to Mimic Solar Wind Enhances the Toxicity of Lunar Dust Simulants in Human Lung Cells. GEOHEALTH 2024; 8:e2023GH000840. [PMID: 38312735 PMCID: PMC10835080 DOI: 10.1029/2023gh000840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 12/01/2023] [Accepted: 12/07/2023] [Indexed: 02/06/2024]
Abstract
During NASA's Apollo missions, inhalation of dust particles from lunar regolith was identified as a potential occupational hazard for astronauts. These fine particles adhered tightly to spacesuits and were unavoidably brought into the living areas of the spacecraft. Apollo astronauts reported that exposure to the dust caused intense respiratory and ocular irritation. This problem is a potential challenge for the Artemis Program, which aims to return humans to the Moon for extended stays in this decade. Since lunar dust is "weathered" by space radiation, solar wind, and the incessant bombardment of micrometeorites, we investigated whether treatment of lunar regolith simulants to mimic space weathering enhanced their toxicity. Two such simulants were employed in this research, Lunar Mare Simulant-1 (LMS-1), and Lunar Highlands Simulant-1 (LHS-1), which were added to cultures of human lung epithelial cells (A549) to simulate lung exposure to the dusts. In addition to pulverization, previously shown to increase dust toxicity sharply, the simulants were exposed to hydrogen gas at high temperature as a proxy for solar wind exposure. This treatment further increased the toxicity of both simulants, as measured by the disruption of mitochondrial function, and damage to DNA both in mitochondria and in the nucleus. By testing the effects of supplementing the cells with an antioxidant (N-acetylcysteine), we showed that a substantial component of this toxicity arises from free radicals. It remains to be determined to what extent the radicals arise from the dust itself, as opposed to their active generation by inflammatory processes in the treated cells.
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Affiliation(s)
- J H M Chang
- Department of Pharmacological Sciences Renaissance School of Medicine Stony Brook University Stony Brook NY USA
| | - Z Xue
- Department of Pharmacological Sciences Renaissance School of Medicine Stony Brook University Stony Brook NY USA
| | - J Bauer
- Department of Pharmacological Sciences Renaissance School of Medicine Stony Brook University Stony Brook NY USA
| | - B Wehle
- Department of Pharmacological Sciences Renaissance School of Medicine Stony Brook University Stony Brook NY USA
| | - D A Hendrix
- Department of Geosciences Stony Brook University Stony Brook NY USA
- National High Magnetic Field Laboratory Florida State University Tallahassee FL USA
| | - T Catalano
- Department of Geosciences Stony Brook University Stony Brook NY USA
| | - J A Hurowitz
- Department of Geosciences Stony Brook University Stony Brook NY USA
| | - H Nekvasil
- Department of Geosciences Stony Brook University Stony Brook NY USA
| | - B Demple
- Departments of Pharmacological Sciences and of Radiation Oncology Renaissance School of Medicine Stony Brook University Stony Brook NY USA
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17
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Marto CM, Laranjo M, Gonçalves AC, Paula A, Jorge J, Caetano-Oliveira R, Sousa MI, Oliveiros B, Ramalho-Santos J, Sarmento-Ribeiro AB, Marques-Ferreira M, Cabrita A, Botelho MF, Carrilho E. In Vitro Characterization of Reversine-Treated Gingival Fibroblasts and Their Safety Evaluation after In Vivo Transplantation. Pharmaceutics 2024; 16:207. [PMID: 38399261 PMCID: PMC10892828 DOI: 10.3390/pharmaceutics16020207] [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: 12/20/2023] [Revised: 01/18/2024] [Accepted: 01/25/2024] [Indexed: 02/25/2024] Open
Abstract
Reversine is a purine derivative that has been investigated with regard to its biological effects, such as its anticancer properties and, mostly, its ability to induce the dedifferentiation of adult cells, increasing their plasticity. The obtained dedifferentiated cells have a high potential for use in regenerative procedures, such as regenerative dentistry (RD). Instead of replacing the lost or damaged oral tissues with synthetic materials, RD uses stem cells combined with matrices and an appropriate microenvironment to achieve tissue regeneration. However, the currently available stem cell sources present limitations, thus restricting the potential of RD. Based on this problem, new sources of stem cells are fundamental. This work aims to characterize mouse gingival fibroblasts (GFs) after dedifferentiation with reversine. Different administration protocols were tested, and the cells obtained were evaluated regarding their cell metabolism, protein and DNA contents, cell cycle changes, morphology, cell death, genotoxicity, and acquisition of stem cell characteristics. Additionally, their teratoma potential was evaluated after in vivo transplantation. Reversine caused toxicity at higher concentrations, with decreased cell metabolic activity and protein content. The cells obtained displayed polyploidy, a cycle arrest in the G2/M phase, and showed an enlarged size. Additionally, apoptosis and genotoxicity were found at higher reversine concentrations. A subpopulation of the GFs possessed stem properties, as supported by the increased expression of CD90, CD105, and TERT, the existence of a CD106+ population, and their trilineage differentiation capacity. The dedifferentiated cells did not induce teratoma formation. The extensive characterization performed shows that significant functional, morphological, and genetic changes occur during the dedifferentiation process. The dedifferentiated cells have some stem-like characteristics, which are of interest for RD.
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Affiliation(s)
- Carlos Miguel Marto
- Institute of Experimental Pathology, Faculty of Medicine, University of Coimbra, 3000-548 Coimbra, Portugal
- Institute of Biophysics, Faculty of Medicine, University of Coimbra, 3000-548 Coimbra, Portugal
- Institute of Integrated Clinical Practice and Laboratory of Evidence-Based and Precision Dentistry, Faculty of Medicine, University of Coimbra, 3000-075 Coimbra, Portugal (E.C.)
- Coimbra Institute for Clinical and Biomedical Research (iCBR), Area of Environment, Genetics and Oncobiology (CIMAGO), Faculty of Medicine, University of Coimbra, 3000-548 Coimbra, Portugal; (A.C.G.); (B.O.); (M.M.-F.)
- Centre for Innovative Biomedicine and Biotechnology (CIBB), University of Coimbra, 3000-548 Coimbra, Portugal
- Clinical Academic Center of Coimbra (CACC), 3004-561 Coimbra, Portugal
| | - Mafalda Laranjo
- Institute of Biophysics, Faculty of Medicine, University of Coimbra, 3000-548 Coimbra, Portugal
- Coimbra Institute for Clinical and Biomedical Research (iCBR), Area of Environment, Genetics and Oncobiology (CIMAGO), Faculty of Medicine, University of Coimbra, 3000-548 Coimbra, Portugal; (A.C.G.); (B.O.); (M.M.-F.)
- Centre for Innovative Biomedicine and Biotechnology (CIBB), University of Coimbra, 3000-548 Coimbra, Portugal
- Clinical Academic Center of Coimbra (CACC), 3004-561 Coimbra, Portugal
| | - Ana Cristina Gonçalves
- Coimbra Institute for Clinical and Biomedical Research (iCBR), Area of Environment, Genetics and Oncobiology (CIMAGO), Faculty of Medicine, University of Coimbra, 3000-548 Coimbra, Portugal; (A.C.G.); (B.O.); (M.M.-F.)
- Centre for Innovative Biomedicine and Biotechnology (CIBB), University of Coimbra, 3000-548 Coimbra, Portugal
- Clinical Academic Center of Coimbra (CACC), 3004-561 Coimbra, Portugal
- Laboratory of Oncobiology and Hematology (LOH) and University Clinic of Hematology, Faculty of Medicine, University of Coimbra, 3000-548 Coimbra, Portugal
| | - Anabela Paula
- Institute of Integrated Clinical Practice and Laboratory of Evidence-Based and Precision Dentistry, Faculty of Medicine, University of Coimbra, 3000-075 Coimbra, Portugal (E.C.)
- Coimbra Institute for Clinical and Biomedical Research (iCBR), Area of Environment, Genetics and Oncobiology (CIMAGO), Faculty of Medicine, University of Coimbra, 3000-548 Coimbra, Portugal; (A.C.G.); (B.O.); (M.M.-F.)
- Centre for Innovative Biomedicine and Biotechnology (CIBB), University of Coimbra, 3000-548 Coimbra, Portugal
- Clinical Academic Center of Coimbra (CACC), 3004-561 Coimbra, Portugal
| | - Joana Jorge
- Coimbra Institute for Clinical and Biomedical Research (iCBR), Area of Environment, Genetics and Oncobiology (CIMAGO), Faculty of Medicine, University of Coimbra, 3000-548 Coimbra, Portugal; (A.C.G.); (B.O.); (M.M.-F.)
- Centre for Innovative Biomedicine and Biotechnology (CIBB), University of Coimbra, 3000-548 Coimbra, Portugal
- Clinical Academic Center of Coimbra (CACC), 3004-561 Coimbra, Portugal
- Laboratory of Oncobiology and Hematology (LOH) and University Clinic of Hematology, Faculty of Medicine, University of Coimbra, 3000-548 Coimbra, Portugal
| | - Rui Caetano-Oliveira
- Coimbra Institute for Clinical and Biomedical Research (iCBR), Area of Environment, Genetics and Oncobiology (CIMAGO), Faculty of Medicine, University of Coimbra, 3000-548 Coimbra, Portugal; (A.C.G.); (B.O.); (M.M.-F.)
- Pathology Department, Centro Hospitalar e Universitário de Coimbra, 3000-075 Coimbra, Portugal
- Germano de Sousa—Centro de Diagnóstico Histopatológico CEDAP, University of Coimbra, 3000-377 Coimbra, Portugal
| | - Maria Inês Sousa
- Centre for Innovative Biomedicine and Biotechnology (CIBB), University of Coimbra, 3000-548 Coimbra, Portugal
- Department of Life Sciences, University of Coimbra, 3000-456 Coimbra, Portugal
- CNC—Center for Neuroscience and Cell Biology, University of Coimbra, 3000-548 Coimbra, Portugal
| | - Bárbara Oliveiros
- Coimbra Institute for Clinical and Biomedical Research (iCBR), Area of Environment, Genetics and Oncobiology (CIMAGO), Faculty of Medicine, University of Coimbra, 3000-548 Coimbra, Portugal; (A.C.G.); (B.O.); (M.M.-F.)
- Centre for Innovative Biomedicine and Biotechnology (CIBB), University of Coimbra, 3000-548 Coimbra, Portugal
- Clinical Academic Center of Coimbra (CACC), 3004-561 Coimbra, Portugal
- Laboratory of Biostatistics and Medical Informatics, Faculty of Medicine, University of Coimbra, 3000-548 Coimbra, Portugal
| | - João Ramalho-Santos
- Centre for Innovative Biomedicine and Biotechnology (CIBB), University of Coimbra, 3000-548 Coimbra, Portugal
- Department of Life Sciences, University of Coimbra, 3000-456 Coimbra, Portugal
- CNC—Center for Neuroscience and Cell Biology, University of Coimbra, 3000-548 Coimbra, Portugal
| | - Ana Bela Sarmento-Ribeiro
- Coimbra Institute for Clinical and Biomedical Research (iCBR), Area of Environment, Genetics and Oncobiology (CIMAGO), Faculty of Medicine, University of Coimbra, 3000-548 Coimbra, Portugal; (A.C.G.); (B.O.); (M.M.-F.)
- Centre for Innovative Biomedicine and Biotechnology (CIBB), University of Coimbra, 3000-548 Coimbra, Portugal
- Clinical Academic Center of Coimbra (CACC), 3004-561 Coimbra, Portugal
- Laboratory of Oncobiology and Hematology (LOH) and University Clinic of Hematology, Faculty of Medicine, University of Coimbra, 3000-548 Coimbra, Portugal
| | - Manuel Marques-Ferreira
- Coimbra Institute for Clinical and Biomedical Research (iCBR), Area of Environment, Genetics and Oncobiology (CIMAGO), Faculty of Medicine, University of Coimbra, 3000-548 Coimbra, Portugal; (A.C.G.); (B.O.); (M.M.-F.)
- Centre for Innovative Biomedicine and Biotechnology (CIBB), University of Coimbra, 3000-548 Coimbra, Portugal
- Clinical Academic Center of Coimbra (CACC), 3004-561 Coimbra, Portugal
- Institute of Endodontics, Faculty of Medicine, University of Coimbra, 3000-075 Coimbra, Portugal
| | - António Cabrita
- Institute of Experimental Pathology, Faculty of Medicine, University of Coimbra, 3000-548 Coimbra, Portugal
| | - Maria Filomena Botelho
- Institute of Biophysics, Faculty of Medicine, University of Coimbra, 3000-548 Coimbra, Portugal
- Coimbra Institute for Clinical and Biomedical Research (iCBR), Area of Environment, Genetics and Oncobiology (CIMAGO), Faculty of Medicine, University of Coimbra, 3000-548 Coimbra, Portugal; (A.C.G.); (B.O.); (M.M.-F.)
- Centre for Innovative Biomedicine and Biotechnology (CIBB), University of Coimbra, 3000-548 Coimbra, Portugal
- Clinical Academic Center of Coimbra (CACC), 3004-561 Coimbra, Portugal
| | - Eunice Carrilho
- Institute of Integrated Clinical Practice and Laboratory of Evidence-Based and Precision Dentistry, Faculty of Medicine, University of Coimbra, 3000-075 Coimbra, Portugal (E.C.)
- Coimbra Institute for Clinical and Biomedical Research (iCBR), Area of Environment, Genetics and Oncobiology (CIMAGO), Faculty of Medicine, University of Coimbra, 3000-548 Coimbra, Portugal; (A.C.G.); (B.O.); (M.M.-F.)
- Centre for Innovative Biomedicine and Biotechnology (CIBB), University of Coimbra, 3000-548 Coimbra, Portugal
- Clinical Academic Center of Coimbra (CACC), 3004-561 Coimbra, Portugal
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18
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Rona G, Miwatani-Minter B, Zhang Q, Goldberg HV, Kerzhnerman MA, Howard JB, Simoneschi D, Lane E, Hobbs JW, Sassani E, Wang AA, Keegan S, Laverty DJ, Piett CG, Pongor LS, Xu ML, Andrade J, Thomas A, Sicinski P, Askenazi M, Ueberheide B, Fenyö D, Nagel ZD, Pagano M. D-type cyclins regulate DNA mismatch repair in the G1 and S phases of the cell cycle, maintaining genome stability. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.12.575420. [PMID: 38260436 PMCID: PMC10802603 DOI: 10.1101/2024.01.12.575420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
The large majority of oxidative DNA lesions occurring in the G1 phase of the cell cycle are repaired by base excision repair (BER) rather than mismatch repair (MMR) to avoid long resections that can lead to genomic instability and cell death. However, the molecular mechanisms dictating pathway choice between MMR and BER have remained unknown. Here, we show that, during G1, D-type cyclins are recruited to sites of oxidative DNA damage in a PCNA- and p21-dependent manner. D-type cyclins shield p21 from its two ubiquitin ligases CRL1SKP2 and CRL4CDT2 in a CDK4/6-independent manner. In turn, p21 competes through its PCNA-interacting protein degron with MMR components for their binding to PCNA. This inhibits MMR while not affecting BER. At the G1/S transition, the CRL4AMBRA1-dependent degradation of D-type cyclins renders p21 susceptible to proteolysis. These timely degradation events allow the proper binding of MMR proteins to PCNA, enabling the repair of DNA replication errors. Persistent expression of cyclin D1 during S-phase increases the mutational burden and promotes microsatellite instability. Thus, the expression of D-type cyclins inhibits MMR in G1, whereas their degradation is necessary for proper MMR function in S.
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Affiliation(s)
- Gergely Rona
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA
- Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY 10016, USA
- Howard Hughes Medical Institute, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Bearach Miwatani-Minter
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA
- Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Qingyue Zhang
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA
- Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Hailey V. Goldberg
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA
- Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Marc A. Kerzhnerman
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA
- Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Jesse B. Howard
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA
- Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Daniele Simoneschi
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA
- Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Ethan Lane
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA
- Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - John W. Hobbs
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA
- Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Elizabeth Sassani
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA
- Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Andrew A. Wang
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA
- Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Sarah Keegan
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA
- Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY 10016, USA
- Institute for Systems Genetics, NYU Grossman School of Medicine, New York, NY 10016, USA
| | | | - Cortt G. Piett
- Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Lorinc S. Pongor
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
- Hungarian Centre of Excellence for Molecular Medicine, University of Szeged, Szeged, H-6728, Hungary
| | - Miranda Li Xu
- Department of Cancer Biology, Dana-Farber Cancer Institute, and Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Joshua Andrade
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA
- Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Anish Thomas
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Piotr Sicinski
- Department of Cancer Biology, Dana-Farber Cancer Institute, and Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02215, USA
- Department of Histology and Embryology, Center for Biostructure Research, Medical University of Warsaw, Chalubinskiego 5, 02-004 Warsaw, Poland
| | - Manor Askenazi
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA
- Biomedical Hosting LLC, 33 Lewis Avenue, Arlington, MA 02474, USA
| | - Beatrix Ueberheide
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA
- Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - David Fenyö
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA
- Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY 10016, USA
- Institute for Systems Genetics, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Zachary D. Nagel
- Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Michele Pagano
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA
- Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY 10016, USA
- Howard Hughes Medical Institute, NYU Grossman School of Medicine, New York, NY 10016, USA
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19
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Jiao X, Di Sante G, Casimiro MC, Tantos A, Ashton AW, Li Z, Quach Y, Bhargava D, Di Rocco A, Pupo C, Crosariol M, Lazar T, Tompa P, Wang C, Yu Z, Zhang Z, Aldaaysi K, Vadlamudi R, Mann M, Skordalakes E, Kossenkov A, Du Y, Pestell RG. A cyclin D1 intrinsically disordered domain accesses modified histone motifs to govern gene transcription. Oncogenesis 2024; 13:4. [PMID: 38191593 PMCID: PMC10774418 DOI: 10.1038/s41389-023-00502-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 11/09/2023] [Accepted: 12/05/2023] [Indexed: 01/10/2024] Open
Abstract
The essential G1-cyclin, CCND1, is frequently overexpressed in cancer, contributing to tumorigenesis by driving cell-cycle progression. D-type cyclins are rate-limiting regulators of G1-S progression in mammalian cells via their ability to bind and activate CDK4 and CDK6. In addition, cyclin D1 conveys kinase-independent transcriptional functions of cyclin D1. Here we report that cyclin D1 associates with H2BS14 via an intrinsically disordered domain (IDD). The same region of cyclin D1 was necessary for the induction of aneuploidy, induction of the DNA damage response, cyclin D1-mediated recruitment into chromatin, and CIN gene transcription. In response to DNA damage H2BS14 phosphorylation occurs, resulting in co-localization with γH2AX in DNA damage foci. Cyclin D1 ChIP seq and γH2AX ChIP seq revealed ~14% overlap. As the cyclin D1 IDD functioned independently of the CDK activity to drive CIN, the IDD domain may provide a rationale new target to complement CDK-extinction strategies.
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Affiliation(s)
- Xuanmao Jiao
- Baruch S. Blumberg Institute, Doylestown, PA, 18902, USA
- Xavier University School of Medicine at Aruba, Oranjestad, Aruba
| | | | - Mathew C Casimiro
- Baruch S. Blumberg Institute, Doylestown, PA, 18902, USA
- Department of Science and Mathematics, Abraham Baldwin Agricultural College, Tifton, GA, 31794, USA
| | - Agnes Tantos
- Institute of Enzymology, Hun-Ren Research Centre for Natural Sciences, Budapest, Hungary
| | - Anthony W Ashton
- Baruch S. Blumberg Institute, Doylestown, PA, 18902, USA
- Xavier University School of Medicine at Aruba, Oranjestad, Aruba
- Division of Cardiovascular Medicine, Lankenau Institute for Medical Research, Wynnewood, PA, 19003, USA
| | - Zhiping Li
- Baruch S. Blumberg Institute, Doylestown, PA, 18902, USA
- Xavier University School of Medicine at Aruba, Oranjestad, Aruba
| | - Yen Quach
- Xavier University School of Medicine at Aruba, Oranjestad, Aruba
| | | | | | - Claudia Pupo
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, PA, 19107, USA
| | - Marco Crosariol
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, PA, 19107, USA
| | - Tamas Lazar
- VIB-VUB Center for Structural Biology, Vrije Universiteit Brussel, Brussels, 1050, Belgium
| | - Peter Tompa
- Institute of Enzymology, Hun-Ren Research Centre for Natural Sciences, Budapest, Hungary
- VIB-VUB Center for Structural Biology, Vrije Universiteit Brussel, Brussels, 1050, Belgium
| | - Chenguang Wang
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, PA, 19107, USA
| | - Zuoren Yu
- Research Center for Translational Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, 200120, China
| | - Zhao Zhang
- Baruch S. Blumberg Institute, Doylestown, PA, 18902, USA
| | - Kawthar Aldaaysi
- Xavier University School of Medicine at Aruba, Oranjestad, Aruba
| | - Ratna Vadlamudi
- Department of Obstetrics and Gynecology, University of Texas Health Sciences Center, San Antonio, TX, 78229, USA
| | - Monica Mann
- Department of Obstetrics and Gynecology, University of Texas Health Sciences Center, San Antonio, TX, 78229, USA
| | | | | | - Yanming Du
- Baruch S. Blumberg Institute, Doylestown, PA, 18902, USA
| | - Richard G Pestell
- Baruch S. Blumberg Institute, Doylestown, PA, 18902, USA.
- Xavier University School of Medicine at Aruba, Oranjestad, Aruba.
- The Wistar Institute, Philadelphia, PA, 19107, USA.
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20
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Zhang W, Yang Z, Wang W, Sun Q. Primase promotes the competition between transcription and replication on the same template strand resulting in DNA damage. Nat Commun 2024; 15:73. [PMID: 38168108 PMCID: PMC10761990 DOI: 10.1038/s41467-023-44443-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 12/13/2023] [Indexed: 01/05/2024] Open
Abstract
Transcription-replication conflicts (TRCs), especially Head-On TRCs (HO-TRCs) can introduce R-loops and DNA damage, however, the underlying mechanisms are still largely unclear. We previously identified a chloroplast-localized RNase H1 protein AtRNH1C that can remove R-loops and relax HO-TRCs for genome integrity. Through the mutagenesis screen, we identify a mutation in chloroplast-localized primase ATH that weakens the binding affinity of DNA template and reduces the activities of RNA primer synthesis and delivery. This slows down DNA replication, and reduces competition of transcription-replication, thus rescuing the developmental defects of atrnh1c. Strand-specific DNA damage sequencing reveals that HO-TRCs cause DNA damage at the end of the transcription unit in the lagging strand and overexpression of ATH can boost HO-TRCs and exacerbates DNA damage. Furthermore, mutation of plastid DNA polymerase Pol1A can similarly rescue the defects in atrnh1c mutants. Taken together these results illustrate a potentially conserved mechanism among organisms, of which the primase activity can promote the occurrence of transcription-replication conflicts leading to HO-TRCs and genome instability.
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Affiliation(s)
- Weifeng Zhang
- Center for Plant Biology, School of Life Sciences, Tsinghua University, 100084, Beijing, China
- Tsinghua-Peking Center for Life Sciences, 100084, Beijing, China
| | - Zhuo Yang
- Center for Plant Biology, School of Life Sciences, Tsinghua University, 100084, Beijing, China
- Tsinghua-Peking Center for Life Sciences, 100084, Beijing, China
| | - Wenjie Wang
- Center for Plant Biology, School of Life Sciences, Tsinghua University, 100084, Beijing, China
- Tsinghua-Peking Center for Life Sciences, 100084, Beijing, China
| | - Qianwen Sun
- Center for Plant Biology, School of Life Sciences, Tsinghua University, 100084, Beijing, China.
- Tsinghua-Peking Center for Life Sciences, 100084, Beijing, China.
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21
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da Costa RL, Souza IC, Morozesk M, de Carvalho LB, Carvalho CDS, Monferrán MV, Wunderlin DA, Fernandes MN, Monteiro DA. Toxic, genotoxic, mutagenic, and bioaccumulative effects of metal mixture from settleable particulate matter on American bullfrog tadpoles (Lithobates catesbeianus). ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 340:122846. [PMID: 37926415 DOI: 10.1016/j.envpol.2023.122846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Revised: 10/29/2023] [Accepted: 10/30/2023] [Indexed: 11/07/2023]
Abstract
Amphibians are more susceptible to environmental stressors than other vertebrates due to their semipermeable skin and physiological adaptations to living in very specific microhabitats. Therefore, the aim of the present study was to investigate the effects of a metal mixture from settleable particulate matter (SePM) released from metallurgical industries on Lithobates catesbeianus tadpoles. Endpoints analyzed included metal bioconcentration, morphological (biometrical indices), hematological parameters (hemoglobin and blood cell count), and erythrocyte DNA damage (genotoxicity and mutagenicity). American bullfrog tadpoles (Gosner's stage 25) were kept under control condition (no contaminant addition) or exposed to a sub-lethal and environmentally relevant concentration (1 g.L-1) of SePM for 96 h. Tadpoles exposed to SePM exhibited elevated whole blood levels of Fe56, AL, Sn, Pb, Zn, Cr, Cu, Ti, Rb, V, Ce, La, Ag, As. SePM-exposed tadpoles showed a significant decrease in condition factor (12%) and increases in hepatosomatic index (25%), hemoglobin concentration (17%), and total leukocytes (82%), thrombocytes (90%), and monocytes (78%) abundance. In addition, exposed tadpoles showed higher MN and ENAs (340 and 140%, respectively) frequencies, and erythrocyte DNA damage with approximately 1.2- to 1.8-fold increases in comet parameters. Taken together, these results suggest that the multimetal mixture found in SePM is potentially genotoxic and mutagenic to L. catesbeianus tadpoles, induces stress associated with hematological changes, and negatively affects growth. Although such contamination occurs at sublethal levels, regulatory standards are needed to control the emission of SePM and protect amphibian populations.
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Affiliation(s)
- Regiane Luiza da Costa
- Departamento de Ciências Fisiológicas (DCF), Centro de Ciências Biológicas e da Saúde (CCBS), Universidade Federal de São Carlos (UFSCar), 13565-905, São Carlos, São Paulo, Brazil; Programa de Pós-Graduação Em Ciências Ambientais (PPGCAm), Centro de Ciências Biológicas e da Saúde (CCBS), Universidade Federal de São Carlos (UFSCar), Brazil
| | - Iara Costa Souza
- Departamento de Ciências Fisiológicas (DCF), Centro de Ciências Biológicas e da Saúde (CCBS), Universidade Federal de São Carlos (UFSCar), 13565-905, São Carlos, São Paulo, Brazil
| | - Mariana Morozesk
- Departamento de Ciências Fisiológicas (DCF), Centro de Ciências Biológicas e da Saúde (CCBS), Universidade Federal de São Carlos (UFSCar), 13565-905, São Carlos, São Paulo, Brazil
| | - Luana Beserra de Carvalho
- Departamento de Ciências Fisiológicas (DCF), Centro de Ciências Biológicas e da Saúde (CCBS), Universidade Federal de São Carlos (UFSCar), 13565-905, São Carlos, São Paulo, Brazil; Programa de Pós-Graduação Em Ciências Ambientais (PPGCAm), Centro de Ciências Biológicas e da Saúde (CCBS), Universidade Federal de São Carlos (UFSCar), 13565-905, São Carlos, São Paulo, Brazil
| | - Cleoni Dos Santos Carvalho
- Departamento de Biologia (DBio), Centro de Ciências Humanas e Biológicas (CCHB), Universidade Federal de São Carlos (UFSCar), 18052-780, São Carlos, São Paulo, Brazil
| | - Magdalena Victoria Monferrán
- ICYTAC, Instituto de Ciencia y Tecnología de Alimentos Córdoba, CONICET and Dpto. Qca. Orgánica, Fac. Cs. Químicas, Universidad Nacional de Córdoba, Ciudad Universitaria, 5000, Córdoba, Argentina
| | - Daniel Alberto Wunderlin
- ICYTAC, Instituto de Ciencia y Tecnología de Alimentos Córdoba, CONICET and Dpto. Qca. Orgánica, Fac. Cs. Químicas, Universidad Nacional de Córdoba, Ciudad Universitaria, 5000, Córdoba, Argentina
| | - Marisa Narciso Fernandes
- Departamento de Ciências Fisiológicas (DCF), Centro de Ciências Biológicas e da Saúde (CCBS), Universidade Federal de São Carlos (UFSCar), 13565-905, São Carlos, São Paulo, Brazil
| | - Diana Amaral Monteiro
- Departamento de Ciências Fisiológicas (DCF), Centro de Ciências Biológicas e da Saúde (CCBS), Universidade Federal de São Carlos (UFSCar), 13565-905, São Carlos, São Paulo, Brazil.
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Marçal R, Sousa P, Marques A, Pereira V, Guilherme S, Barreto A, Costas B, Rocha RJM, Pacheco M. Exploring the Antioxidant and Genoprotective Potential of Salicornia ramosissima Incorporation in the Diet of the European Seabass ( Dicentrarchus labrax). Animals (Basel) 2023; 14:93. [PMID: 38200822 PMCID: PMC10778275 DOI: 10.3390/ani14010093] [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: 11/14/2023] [Revised: 12/14/2023] [Accepted: 12/16/2023] [Indexed: 01/12/2024] Open
Abstract
The identification of novel feed materials as a source of functional ingredients is a topical priority in the finfish aquaculture sector. Due to the agrotechnical practices associated and phytochemical profiling, halophytes emerge as a new source of feedstuff for aquafeeds, with the potential to boost productivity and environmental sustainability. Therefore, the present study aimed to assess the potential of Salicornia ramosissima incorporation (2.5, 5, and 10%), for 2 months, in the diet of juvenile European seabass, seeking antioxidant (in the liver, gills, and blood) and genoprotective (DNA and chromosomal integrity in blood) benefits. Halophyte inclusion showed no impairments on growth performance. Moreover, a tissue-specific antioxidant improvement was apparent, namely through the GSH-related defense subsystem, but revealing multiple and complex mechanisms. A genotoxic trigger (regarded as a pro-genoprotective mechanism) was identified in the first month of supplementation. A clear protection of DNA integrity was detected in the second month, for all the supplementation levels (and the most prominent melioration at 10%). Overall, these results pointed out a functionality of S. ramosissima-supplemented diets and a promising way to improve aquaculture practices, also unraveling a complementary novel, low-value raw material, and a path to its valorization.
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Affiliation(s)
- Raquel Marçal
- CESAM—Centre for Environmental and Marine Studies and Department of Biology, University of Aveiro, 3810-193 Aveiro, Portugal; (P.S.); (A.M.); (V.P.); (S.G.); (M.P.)
| | - Pedro Sousa
- CESAM—Centre for Environmental and Marine Studies and Department of Biology, University of Aveiro, 3810-193 Aveiro, Portugal; (P.S.); (A.M.); (V.P.); (S.G.); (M.P.)
| | - Ana Marques
- CESAM—Centre for Environmental and Marine Studies and Department of Biology, University of Aveiro, 3810-193 Aveiro, Portugal; (P.S.); (A.M.); (V.P.); (S.G.); (M.P.)
| | - Vitória Pereira
- CESAM—Centre for Environmental and Marine Studies and Department of Biology, University of Aveiro, 3810-193 Aveiro, Portugal; (P.S.); (A.M.); (V.P.); (S.G.); (M.P.)
| | - Sofia Guilherme
- CESAM—Centre for Environmental and Marine Studies and Department of Biology, University of Aveiro, 3810-193 Aveiro, Portugal; (P.S.); (A.M.); (V.P.); (S.G.); (M.P.)
| | - André Barreto
- Riasearch, Lda., 3870-168 Murtosa, Portugal; (A.B.); (R.J.M.R.)
| | - Benjamin Costas
- Centro Interdisciplinar de Investigação Marinha e Ambiental (CIIMAR), Universidade do Porto, 4450-208 Matosinhos, Portugal;
- School of Medicine and Biomedical Sciences (ICBAS-UP), University of Porto, 4050-313 Porto, Portugal
| | - Rui J. M. Rocha
- Riasearch, Lda., 3870-168 Murtosa, Portugal; (A.B.); (R.J.M.R.)
| | - Mário Pacheco
- CESAM—Centre for Environmental and Marine Studies and Department of Biology, University of Aveiro, 3810-193 Aveiro, Portugal; (P.S.); (A.M.); (V.P.); (S.G.); (M.P.)
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23
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Parambil AM, Prasad A, Tomar AK, Ghosh I, Rajamani P. Biogenic carbon dots: a novel mechanistic approach to combat multidrug-resistant critical pathogens on the global priority list. J Mater Chem B 2023; 12:202-221. [PMID: 38073612 DOI: 10.1039/d3tb02374e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2023]
Abstract
This study delves into investigating alternative methodologies for anti-microbial therapy by focusing on the mechanistic assessment of carbon dots (CDs) synthesized from F. benghalensis L. extracts. These biogenic CDs have shown remarkable broad-spectrum anti-bacterial activity even against multi-drug resistant (MDR) bacterial strains, prompting a deeper examination of their potential as novel anti-microbial agents. The study highlights the significant detrimental impact of CDs on bacterial cells through oxidative damage, which disrupts the delicate balance of ROS control within the cells. Notably, even at low doses, the anti-bacterial activity of CDs against MDR strains of P. aeruginosa and E. cloacae is highly effective, demonstrating their promise as potent antimicrobial agents. The research sheds light on the capacity of CDs to generate ROS, leading to membrane lipid peroxidation, loss of membrane potential, and rupture of bacterial cell membranes, resulting in cytoplasmic leakage. SEM and TEM analysis revealed time-dependent cell surface, morphological, and ultrastructural changes such as elongation of the cells, irregular surface protrusion, cell wall and cell membrane disintegration, internalization, and aggregations of CDs. These mechanisms offer a comprehensive explanation of how CDs exert their anti-bacterial effects. We also determined the status of plasma membrane integrity and evaluated live (viable) and dead cells upon CD exposure by flow cytometry. Furthermore, comet assay, biochemical assays, and SDS PAGE identify DNA damage, carbohydrate and protein leakage, and distinct differences in protein expression, adding another layer of understanding to the mechanisms behind CDs' anti-bacterial activity. These findings pave the way for future research on managing ROS levels and developing CDs with enhanced anti-bacterial properties, presenting a breakthrough in anti-microbial therapy.
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Affiliation(s)
- Ajith Manayil Parambil
- School of Environmental Sciences, Jawaharlal Nehru University (JNU), New Delhi 110067, India.
| | - Abhinav Prasad
- School of Environmental Sciences, Jawaharlal Nehru University (JNU), New Delhi 110067, India.
| | - Anuj Kumar Tomar
- School of Environmental Sciences, Jawaharlal Nehru University (JNU), New Delhi 110067, India.
| | - Ilora Ghosh
- School of Environmental Sciences, Jawaharlal Nehru University (JNU), New Delhi 110067, India.
| | - Paulraj Rajamani
- School of Environmental Sciences, Jawaharlal Nehru University (JNU), New Delhi 110067, India.
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Galvan GC, Friedrich NA, Das S, Daniels JP, Pollan S, Dambal S, Suzuki R, Sanders SE, You S, Tanaka H, Lee YJ, Yuan W, de Bono JS, Vasilevskaya I, Knudsen KE, Freeman MR, Freedland SJ. 27-hydroxycholesterol and DNA damage repair: implication in prostate cancer. Front Oncol 2023; 13:1251297. [PMID: 38188290 PMCID: PMC10771304 DOI: 10.3389/fonc.2023.1251297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Accepted: 12/04/2023] [Indexed: 01/09/2024] Open
Abstract
Introduction We previously reported that cholesterol homeostasis in prostate cancer (PC) is regulated by 27-hydroxycholesterol (27HC) and that CYP27A1, the enzyme that converts cholesterol to 27HC, is frequently lost in PCs. We observed that restoring the CYP27A1/27HC axis inhibited PC growth. In this study, we investigated the mechanism of 27HC-mediated anti-PC effects. Methods We employed in vitro models and human transcriptomics data to investigate 27HC mechanism of action in PC. LNCaP (AR+) and DU145 (AR-) cells were treated with 27HC or vehicle. Transcriptome profiling was performed using the Affymetrix GeneChip™ microarray system. Differential expression was determined, and gene set enrichment analysis was done using the GSEA software with hallmark gene sets from MSigDB. Key changes were validated at mRNA and protein levels. Human PC transcriptomes from six datasets were analyzed to determine the correlation between CYP27A1 and DNA repair gene expression signatures. DNA damage was assessed via comet assays. Results Transcriptome analysis revealed 27HC treatment downregulated Hallmark pathways related to DNA damage repair, decreased expression of FEN1 and RAD51, and induced "BRCAness" by downregulating genes involved in homologous recombination regulation in LNCaP cells. Consistently, we found a correlation between higher CYP27A1 expression (i.e., higher intracellular 27HC) and decreased expression of DNA repair gene signatures in castration-sensitive PC (CSPC) in human PC datasets. However, such correlation was less clear in metastatic castration-resistant PC (mCRPC). 27HC increased expression of DNA damage repair markers in PC cells, notably in AR+ cells, but no consistent effects in AR- cells and decreased expression in non-neoplastic prostate epithelial cells. While testing the clinical implications of this, we noted that 27HC treatment increased DNA damage in LNCaP cells via comet assays. Effects were reversible by adding back cholesterol, but not androgens. Finally, in combination with olaparib, a PARP inhibitor, we showed additive DNA damage effects. Discussion These results suggest 27HC induces "BRCAness", a functional state thought to increase sensitivity to PARP inhibitors, and leads to increased DNA damage, especially in CSPC. Given the emerging appreciation that defective DNA damage repair can drive PC growth, future studies are needed to test whether 27HC creates a synthetic lethality to PARP inhibitors and DNA damaging agents in CSPC.
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Affiliation(s)
- Gloria Cecilia Galvan
- Department of Urology, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, United States
| | - Nadine A. Friedrich
- Department of Urology, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, United States
| | - Sanjay Das
- Department of Urology, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, United States
- Department of Urology, University of California, Los Angeles, Los Angeles, CA, United States
- Urology Section, Department of Surgery, Veterans Affairs Health Care System, Durham, NC, United States
| | - James P. Daniels
- Department of Urology, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, United States
| | - Sara Pollan
- Department of Urology, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, United States
| | - Shweta Dambal
- Department of Pathology, Duke University School of Medicine, Durham, NC, United States
| | - Ryusuke Suzuki
- Department of Surgery, Cedars-Sinai Medical Center, Los Angeles, CA, United States
| | - Sergio E. Sanders
- Department of Urology, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, United States
| | - Sungyong You
- Department of Urology, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, United States
| | - Hisashi Tanaka
- Department of Surgery, Cedars-Sinai Medical Center, Los Angeles, CA, United States
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, United States
| | - Yeon-Joo Lee
- Department of Urology, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, United States
| | - Wei Yuan
- Cancer Biomarkers Team, Division of Clinical Studies, The Institute of Cancer Research, London, United Kingdom
| | - Johann S. de Bono
- Cancer Biomarkers Team, Division of Clinical Studies, The Institute of Cancer Research, London, United Kingdom
- Prostate Cancer Targeted Therapy Group and Drug Development Unit, The Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Irina Vasilevskaya
- Department of Cancer Biology at Thomas Jefferson University, Philadelphia, PA, United States
| | - Karen E. Knudsen
- Department of Cancer Biology at Thomas Jefferson University, Philadelphia, PA, United States
| | - Michael R. Freeman
- Department of Urology, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, United States
| | - Stephen J. Freedland
- Department of Urology, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, United States
- Urology Section, Department of Surgery, Veterans Affairs Health Care System, Durham, NC, United States
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25
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Jenkins SV, Jung S, Jamshidi-Parsian A, Borrelli MJ, Dings RPM, Griffin RJ. Morphological Effects and In Vitro Biological Mechanisms of Radiation-Induced Cell Killing by Gold Nanomaterials. ACS APPLIED MATERIALS & INTERFACES 2023; 15:58241-58250. [PMID: 38059477 DOI: 10.1021/acsami.3c15358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/08/2023]
Abstract
Gold nanomaterials have been shown to augment radiation therapy both in vitro and in vivo. However, studies on these materials are mostly phenomenological due to nanoparticle heterogeneity and the complexity of biological systems. Even accurate quantification of the particle dose still results in bulk average biases; the effect on individual cells is not measured but rather the effect on the overall population. To perform quantitative nanobiology, we coated glass coverslips uniformly at varying densities with Au nanoparticle preparations with different morphologies (45 nm cages, 25 nm spheres, and 30 nm rods). Consequently, the effect of a specific number of particles per unit area in contact with breast cancer cells growing on the coated surfaces was ascertained. Gold nanocages showed the highest degree of radiosensitization on a per particle basis, followed by gold nanospheres and gold nanorods, respectively. All three materials showed little cytotoxic effect at 0 Gy, but clonogenic survival decreased proportionally with the radiation dose and particle coverage density. A similar trend was seen in vivo in the combined treatment antitumor response in 4T1 tumor-bearing animals. The presence of gold affected the type and quantity of reactive oxygen species generated, specifically superoxide and hydroxyl radicals, and the concentration of nanocages correlated with the development of more numerous double-stranded DNA breaks and increased protein oxidation as measured by carbonylation. This work demonstrates the dependence on morphology and concentration of radiation enhancement by gold nanomaterials and may lead to a novel method to differentiate intra- and extracellular functionalities of gold nanomedicine treatment strategies. It further provides insights that can guide the rational development of gold nanomaterial-based radiosensitizers for clinical use.
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Affiliation(s)
- Samir V Jenkins
- Department of Radiation Oncology, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, United States
| | - Seunghyun Jung
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Azemat Jamshidi-Parsian
- Department of Radiation Oncology, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, United States
| | - Michael J Borrelli
- Department of Radiology, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, United States
| | - Ruud P M Dings
- Department of Radiation Oncology, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, United States
| | - Robert J Griffin
- Department of Radiation Oncology, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, United States
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Woolley PR, Wen X, Conway OM, Ender NA, Lee JH, Paull TT. Regulation of transcription patterns, poly-ADP-ribose, and RNA-DNA hybrids by the ATM protein kinase. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.06.570417. [PMID: 38106035 PMCID: PMC10723464 DOI: 10.1101/2023.12.06.570417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
The ATM protein kinase is a master regulator of the DNA damage response and also an important sensor of oxidative stress. Analysis of gene expression in Ataxia-telangiectasia patient brain tissue shows that large-scale transcriptional changes occur in patient cerebellum that correlate with expression level and GC content of transcribed genes. In human neuron-like cells in culture we map locations of poly-ADP-ribose and RNA-DNA hybrid accumulation genome-wide with ATM inhibition and find that these marks also coincide with high transcription levels, active transcription histone marks, and high GC content. Antioxidant treatment reverses the accumulation of R-loops in transcribed regions, consistent with the central role of ROS in promoting these lesions. Based on these results we postulate that transcription-associated lesions accumulate in ATM-deficient cells and that the single-strand breaks and PARylation at these sites ultimately generate changes in transcription that compromise cerebellum function and lead to neurodegeneration over time in A-T patients.
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Affiliation(s)
- Phillip R. Woolley
- The University of Texas at Austin, Department of Molecular Biosciences, Austin, TX, 78712
| | - Xuemei Wen
- The University of Texas at Austin, Department of Molecular Biosciences, Austin, TX, 78712
| | - Olivia M. Conway
- The University of Texas at Austin, Department of Molecular Biosciences, Austin, TX, 78712
| | - Nicolette A. Ender
- The University of Texas at Austin, Department of Molecular Biosciences, Austin, TX, 78712
| | - Ji-Hoon Lee
- Department of Biological Sciences, Research Center of Ecomimetics, Chonnam National University, Gwangju, 61186, Republic of Korea
| | - Tanya T. Paull
- The University of Texas at Austin, Department of Molecular Biosciences, Austin, TX, 78712
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27
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Zhao S, Francois A, Kidane D. Inhibition of DHODH Enhances Replication-Associated Genomic Instability and Promotes Sensitivity in Endometrial Cancer. Cancers (Basel) 2023; 15:5727. [PMID: 38136273 PMCID: PMC10741824 DOI: 10.3390/cancers15245727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 11/28/2023] [Accepted: 12/04/2023] [Indexed: 12/24/2023] Open
Abstract
Endometrial carcinoma (EC) is the most common gynecological malignancy in the United States. De novo pyrimidine synthesis pathways generate nucleotides that are required for DNA synthesis. Approximately 38% of human endometrial tumors present with an overexpression of human dihydroorotate dehydrogenase (DHODH). However, the role of DHODH in cancer cell DNA replication and its impact on modulating a treatment response is currently unknown. Here, we report that endometrial tumors with overexpression of DHODH are associated with a high mutation count and chromosomal instability. Furthermore, tumors with an overexpression of DHODH show significant co-occurrence with mutations in DNA replication polymerases, which result in a histologically high-grade endometrial tumor. An in vitro experiment demonstrated that the inhibition of DHODH in endometrial cancer cell lines significantly induced replication-associated DNA damage and hindered replication fork progression. Furthermore, endometrial cancer cells were sensitive to the DHODH inhibitor either alone or in combination with the Poly (ADP-ribose) polymerase 1 inhibitor. Our findings may have important clinical implications for utilizing DHODH as a potential target to enhance cytotoxicity in high-grade endometrial tumors.
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Affiliation(s)
- Shengyuan Zhao
- Division of Pharmacology and Toxicology, Dell Pediatric Research Institute, College of Pharmacy, The University of Texas at Austin, 1400 Barbara Jordan Blvd. R1800, Austin, TX 78723, USA
| | - Aaliyah Francois
- Division of Pharmacology and Toxicology, Dell Pediatric Research Institute, College of Pharmacy, The University of Texas at Austin, 1400 Barbara Jordan Blvd. R1800, Austin, TX 78723, USA
| | - Dawit Kidane
- Division of Pharmacology and Toxicology, Dell Pediatric Research Institute, College of Pharmacy, The University of Texas at Austin, 1400 Barbara Jordan Blvd. R1800, Austin, TX 78723, USA
- Department of Physiology and Biophysics, College of Medicine, Howard University, 520 W Street N.W., Washington, DC 20059, USA
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28
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Zhou M, Boulos JC, Klauck SM, Efferth T. The cardiac glycoside ZINC253504760 induces parthanatos-type cell death and G2/M arrest via downregulation of MEK1/2 phosphorylation in leukemia cells. Cell Biol Toxicol 2023; 39:2971-2997. [PMID: 37322258 PMCID: PMC10693532 DOI: 10.1007/s10565-023-09813-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: 02/23/2023] [Accepted: 05/23/2023] [Indexed: 06/17/2023]
Abstract
Overcoming multidrug resistance (MDR) represents a major obstacle in cancer chemotherapy. Cardiac glycosides (CGs) are efficient in the treatment of heart failure and recently emerged in a new role in the treatment of cancer. ZINC253504760, a synthetic cardenolide that is structurally similar to well-known GCs, digitoxin and digoxin, has not been investigated yet. This study aims to investigate the cytotoxicity of ZINC253504760 on MDR cell lines and its molecular mode of action for cancer treatment. Four drug-resistant cell lines (P-glycoprotein-, ABCB5-, and EGFR-overexpressing cells, and TP53-knockout cells) did not show cross-resistance to ZINC253504760 except BCRP-overexpressing cells. Transcriptomic profiling indicated that cell death and survival as well as cell cycle (G2/M damage) were the top cellular functions affected by ZINC253504760 in CCRF-CEM cells, while CDK1 was linked with the downregulation of MEK and ERK. With flow cytometry, ZINC253504760 induced G2/M phase arrest. Interestingly, ZINC253504760 induced a novel state-of-the-art mode of cell death (parthanatos) through PARP and PAR overexpression as shown by western blotting, apoptosis-inducing factor (AIF) translocation by immunofluorescence, DNA damage by comet assay, and mitochondrial membrane potential collapse by flow cytometry. These results were ROS-independent. Furthermore, ZINC253504760 is an ATP-competitive MEK inhibitor evidenced by its interaction with the MEK phosphorylation site as shown by molecular docking in silico and binding to recombinant MEK by microscale thermophoresis in vitro. To the best of our knowledge, this is the first time to describe a cardenolide that induces parthanatos in leukemia cells, which may help to improve efforts to overcome drug resistance in cancer. A cardiac glycoside compound ZINC253504760 displayed cytotoxicity against different multidrug-resistant cell lines. ZINC253504760 exhibited cytotoxicity in CCRF-CEM leukemia cells by predominantly inducing a new mode of cell death (parthanatos). ZINC253504760 downregulated MEK1/2 phosphorylation and further affected ERK activation, which induced G2/M phase arrest.
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Affiliation(s)
- Min Zhou
- Department of Pharmaceutical Biology, Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University-Mainz, Staudinger Weg 5, 55128, Mainz, Germany
| | - Joelle C Boulos
- Department of Pharmaceutical Biology, Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University-Mainz, Staudinger Weg 5, 55128, Mainz, Germany
| | - Sabine M Klauck
- Division of Cancer Genome Research, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), National Center for Tumor Disease (NCT), 69120, Heidelberg, Germany
| | - Thomas Efferth
- Department of Pharmaceutical Biology, Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University-Mainz, Staudinger Weg 5, 55128, Mainz, Germany.
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29
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Isobe S, Nair RV, Kang HY, Wang L, Moonen JR, Shinohara T, Cao A, Taylor S, Otsuki S, Marciano DP, Harper RL, Adil MS, Zhang C, Lago-Docampo M, Körbelin J, Engreitz JM, Snyder MP, Rabinovitch M. Reduced FOXF1 links unrepaired DNA damage to pulmonary arterial hypertension. Nat Commun 2023; 14:7578. [PMID: 37989727 PMCID: PMC10663616 DOI: 10.1038/s41467-023-43039-y] [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: 12/06/2022] [Accepted: 10/30/2023] [Indexed: 11/23/2023] Open
Abstract
Pulmonary arterial hypertension (PAH) is a progressive disease in which pulmonary arterial (PA) endothelial cell (EC) dysfunction is associated with unrepaired DNA damage. BMPR2 is the most common genetic cause of PAH. We report that human PAEC with reduced BMPR2 have persistent DNA damage in room air after hypoxia (reoxygenation), as do mice with EC-specific deletion of Bmpr2 (EC-Bmpr2-/-) and persistent pulmonary hypertension. Similar findings are observed in PAEC with loss of the DNA damage sensor ATM, and in mice with Atm deleted in EC (EC-Atm-/-). Gene expression analysis of EC-Atm-/- and EC-Bmpr2-/- lung EC reveals reduced Foxf1, a transcription factor with selectivity for lung EC. Reducing FOXF1 in control PAEC induces DNA damage and impaired angiogenesis whereas transfection of FOXF1 in PAH PAEC repairs DNA damage and restores angiogenesis. Lung EC targeted delivery of Foxf1 to reoxygenated EC-Bmpr2-/- mice repairs DNA damage, induces angiogenesis and reverses pulmonary hypertension.
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Affiliation(s)
- Sarasa Isobe
- Basic Science and Engineering (BASE) Initiative at the Betty Irene Moore Children's Heart Center, Lucile Packard Children's Hospital, Stanford University School of Medicine, Stanford, CA, USA
- Vera Moulton Wall Center for Pulmonary Vascular Diseases, Stanford University, Stanford, CA, USA
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, USA
- Department of Pediatrics - Cardiology, Stanford University School of Medicine, Stanford, CA, USA
| | - Ramesh V Nair
- Stanford Center for Genomics and Personalized Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Helen Y Kang
- Basic Science and Engineering (BASE) Initiative at the Betty Irene Moore Children's Heart Center, Lucile Packard Children's Hospital, Stanford University School of Medicine, Stanford, CA, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Lingli Wang
- Basic Science and Engineering (BASE) Initiative at the Betty Irene Moore Children's Heart Center, Lucile Packard Children's Hospital, Stanford University School of Medicine, Stanford, CA, USA
- Vera Moulton Wall Center for Pulmonary Vascular Diseases, Stanford University, Stanford, CA, USA
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, USA
- Department of Pediatrics - Cardiology, Stanford University School of Medicine, Stanford, CA, USA
| | - Jan-Renier Moonen
- Basic Science and Engineering (BASE) Initiative at the Betty Irene Moore Children's Heart Center, Lucile Packard Children's Hospital, Stanford University School of Medicine, Stanford, CA, USA
- Vera Moulton Wall Center for Pulmonary Vascular Diseases, Stanford University, Stanford, CA, USA
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, USA
- Department of Pediatrics - Cardiology, Stanford University School of Medicine, Stanford, CA, USA
| | - Tsutomu Shinohara
- Basic Science and Engineering (BASE) Initiative at the Betty Irene Moore Children's Heart Center, Lucile Packard Children's Hospital, Stanford University School of Medicine, Stanford, CA, USA
- Vera Moulton Wall Center for Pulmonary Vascular Diseases, Stanford University, Stanford, CA, USA
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, USA
- Department of Pediatrics - Cardiology, Stanford University School of Medicine, Stanford, CA, USA
| | - Aiqin Cao
- Basic Science and Engineering (BASE) Initiative at the Betty Irene Moore Children's Heart Center, Lucile Packard Children's Hospital, Stanford University School of Medicine, Stanford, CA, USA
- Vera Moulton Wall Center for Pulmonary Vascular Diseases, Stanford University, Stanford, CA, USA
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, USA
- Department of Pediatrics - Cardiology, Stanford University School of Medicine, Stanford, CA, USA
| | - Shalina Taylor
- Vera Moulton Wall Center for Pulmonary Vascular Diseases, Stanford University, Stanford, CA, USA
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, USA
- Department of Pediatrics - Cardiology, Stanford University School of Medicine, Stanford, CA, USA
| | - Shoichiro Otsuki
- Vera Moulton Wall Center for Pulmonary Vascular Diseases, Stanford University, Stanford, CA, USA
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, USA
- Department of Pediatrics - Cardiology, Stanford University School of Medicine, Stanford, CA, USA
| | - David P Marciano
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Rebecca L Harper
- Vera Moulton Wall Center for Pulmonary Vascular Diseases, Stanford University, Stanford, CA, USA
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, USA
- Department of Pediatrics - Cardiology, Stanford University School of Medicine, Stanford, CA, USA
| | - Mir S Adil
- Basic Science and Engineering (BASE) Initiative at the Betty Irene Moore Children's Heart Center, Lucile Packard Children's Hospital, Stanford University School of Medicine, Stanford, CA, USA
- Vera Moulton Wall Center for Pulmonary Vascular Diseases, Stanford University, Stanford, CA, USA
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, USA
- Department of Pediatrics - Cardiology, Stanford University School of Medicine, Stanford, CA, USA
| | - Chongyang Zhang
- Basic Science and Engineering (BASE) Initiative at the Betty Irene Moore Children's Heart Center, Lucile Packard Children's Hospital, Stanford University School of Medicine, Stanford, CA, USA
- Vera Moulton Wall Center for Pulmonary Vascular Diseases, Stanford University, Stanford, CA, USA
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, USA
- Department of Pediatrics - Cardiology, Stanford University School of Medicine, Stanford, CA, USA
| | - Mauro Lago-Docampo
- Basic Science and Engineering (BASE) Initiative at the Betty Irene Moore Children's Heart Center, Lucile Packard Children's Hospital, Stanford University School of Medicine, Stanford, CA, USA
- Vera Moulton Wall Center for Pulmonary Vascular Diseases, Stanford University, Stanford, CA, USA
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, USA
- Department of Pediatrics - Cardiology, Stanford University School of Medicine, Stanford, CA, USA
| | - Jakob Körbelin
- Department of Oncology, Hematology and Bone Marrow Transplantation, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Jesse M Engreitz
- Basic Science and Engineering (BASE) Initiative at the Betty Irene Moore Children's Heart Center, Lucile Packard Children's Hospital, Stanford University School of Medicine, Stanford, CA, USA
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Michael P Snyder
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Marlene Rabinovitch
- Basic Science and Engineering (BASE) Initiative at the Betty Irene Moore Children's Heart Center, Lucile Packard Children's Hospital, Stanford University School of Medicine, Stanford, CA, USA.
- Vera Moulton Wall Center for Pulmonary Vascular Diseases, Stanford University, Stanford, CA, USA.
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, USA.
- Department of Pediatrics - Cardiology, Stanford University School of Medicine, Stanford, CA, USA.
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30
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Rodríguez-Pena E, Suárez D, Estévez-Pérez G, Verísimo P, Barreira N, Fernández L, González-Tizón A, Martínez-Lage A. Influence of Storage Time on the DNA Integrity and Viability of Spermatozoa of the Spider Crab Maja brachydactyla. Animals (Basel) 2023; 13:3555. [PMID: 38003172 PMCID: PMC10668756 DOI: 10.3390/ani13223555] [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: 10/20/2023] [Revised: 11/04/2023] [Accepted: 11/15/2023] [Indexed: 11/26/2023] Open
Abstract
Natural populations of the spider crab Maja brachydactyla constitute a fishery resource of great economic importance in many countries. As in the rest of eubrachyurans, the females of this species have ventral-type seminal receptacles where they store sperm from copulations. Sperm can be stored in these structures for months and even years before egg fertilisation, with the consequent degradation of the sperm cells during the time. In this work, we analyse the viability and the possible genetic damage in sperm accumulated in the seminal receptacles of M. brachydactyla females as a function of the storage time (from 0 to 14 months) using the comet assay technique. On one hand, we developed an algorithm for comet image analysis that improves the comet segmentation compared with the free software Open comet v1.3.1 (97% vs. 76% of detection). In addition, our software allows the manual modification of the contours wrongly delimited via the automatic tool. On the other hand, our data show a sharp decline in sperm viability and DNA integrity in the first four months of storage, which could lead to a decrease in the fecundity rate and/or viability of the embryos or larvae from the second and third clutches of the annual cycle if the repair capacity in these gametic cells is low.
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Affiliation(s)
- Elba Rodríguez-Pena
- CICA (Centro Interdisciplinar de Química e Bioloxía), University of A Coruña, 15071 A Coruña, Spain; (E.R.-P.); (A.G.-T.)
| | - Diego Suárez
- Department of Computer Science, University of A Coruña, 15071 A Coruña, Spain; (D.S.); (N.B.)
| | | | - Patricia Verísimo
- Centro Oceanográfico de Santander (IEO-CSIC), 39004 Santander, Spain;
| | - Noelia Barreira
- Department of Computer Science, University of A Coruña, 15071 A Coruña, Spain; (D.S.); (N.B.)
- CITIC (Research Center of Information and Communication Technologies), University of A Coruña, 15071 A Coruña, Spain
| | - Luis Fernández
- Department of Biology, University of A Coruña, 15071 A Coruña, Spain;
| | - Ana González-Tizón
- CICA (Centro Interdisciplinar de Química e Bioloxía), University of A Coruña, 15071 A Coruña, Spain; (E.R.-P.); (A.G.-T.)
- Department of Biology, University of A Coruña, 15071 A Coruña, Spain;
| | - Andrés Martínez-Lage
- CICA (Centro Interdisciplinar de Química e Bioloxía), University of A Coruña, 15071 A Coruña, Spain; (E.R.-P.); (A.G.-T.)
- Department of Biology, University of A Coruña, 15071 A Coruña, Spain;
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31
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Manohar S, Estrada ME, Uliana F, Vuina K, Alvarez PM, de Bruin RAM, Neurohr GE. Genome homeostasis defects drive enlarged cells into senescence. Mol Cell 2023; 83:4032-4046.e6. [PMID: 37977116 PMCID: PMC10659931 DOI: 10.1016/j.molcel.2023.10.018] [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: 09/12/2022] [Revised: 06/30/2023] [Accepted: 10/16/2023] [Indexed: 11/19/2023]
Abstract
Cellular senescence refers to an irreversible state of cell-cycle arrest and plays important roles in aging and cancer biology. Because senescence is associated with increased cell size, we used reversible cell-cycle arrests combined with growth rate modulation to study how excessive growth affects proliferation. We find that enlarged cells upregulate p21, which limits cell-cycle progression. Cells that re-enter the cell cycle encounter replication stress that is well tolerated in physiologically sized cells but causes severe DNA damage in enlarged cells, ultimately resulting in mitotic failure and permanent cell-cycle withdrawal. We demonstrate that enlarged cells fail to recruit 53BP1 and other non-homologous end joining (NHEJ) machinery to DNA damage sites and fail to robustly initiate DNA damage-dependent p53 signaling, rendering them highly sensitive to genotoxic stress. We propose that an impaired DNA damage response primes enlarged cells for persistent replication-acquired damage, ultimately leading to cell division failure and permanent cell-cycle exit.
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Affiliation(s)
- Sandhya Manohar
- Institute for Biochemistry, Department of Biology, ETH Zürich 8093, Zürich, Zürich, Switzerland
| | - Marianna E Estrada
- Institute for Biochemistry, Department of Biology, ETH Zürich 8093, Zürich, Zürich, Switzerland
| | - Federico Uliana
- Institute for Biochemistry, Department of Biology, ETH Zürich 8093, Zürich, Zürich, Switzerland
| | - Karla Vuina
- Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, UK
| | - Patricia Moyano Alvarez
- Institute for Biochemistry, Department of Biology, ETH Zürich 8093, Zürich, Zürich, Switzerland
| | - Robertus A M de Bruin
- Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, UK; UCL Cancer Institute, University College London, London WC1E 6BT, UK
| | - Gabriel E Neurohr
- Institute for Biochemistry, Department of Biology, ETH Zürich 8093, Zürich, Zürich, Switzerland.
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32
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Carpenter MA, Temiz NA, Ibrahim MA, Jarvis MC, Brown MR, Argyris PP, Brown WL, Starrett GJ, Yee D, Harris RS. Mutational impact of APOBEC3A and APOBEC3B in a human cell line and comparisons to breast cancer. PLoS Genet 2023; 19:e1011043. [PMID: 38033156 PMCID: PMC10715669 DOI: 10.1371/journal.pgen.1011043] [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: 07/31/2023] [Revised: 12/12/2023] [Accepted: 10/30/2023] [Indexed: 12/02/2023] Open
Abstract
A prominent source of mutation in cancer is single-stranded DNA cytosine deamination by cellular APOBEC3 enzymes, which results in signature C-to-T and C-to-G mutations in TCA and TCT motifs. Although multiple enzymes have been implicated, reports conflict and it is unclear which protein(s) are responsible. Here we report the development of a selectable system to quantify genome mutation and demonstrate its utility by comparing the mutagenic activities of three leading candidates-APOBEC3A, APOBEC3B, and APOBEC3H. The human cell line, HAP1, is engineered to express the thymidine kinase (TK) gene of HSV-1, which confers sensitivity to ganciclovir. Expression of APOBEC3A and APOBEC3B, but not catalytic mutant controls or APOBEC3H, triggers increased frequencies of TK mutation and similar TC-biased cytosine mutation profiles in the selectable TK reporter gene. Whole genome sequences from independent clones enabled an analysis of thousands of single base substitution mutations and extraction of local sequence preferences with APOBEC3A preferring YTCW motifs 70% of the time and APOBEC3B 50% of the time (Y = C/T; W = A/T). Signature comparisons with breast tumor whole genome sequences indicate that most malignancies manifest intermediate percentages of APOBEC3 signature mutations in YTCW motifs, mostly between 50 and 70%, suggesting that both enzymes contribute in a combinatorial manner to the overall mutation landscape. Although the vast majority of APOBEC3A- and APOBEC3B-induced single base substitution mutations occur outside of predicted chromosomal DNA hairpin structures, whole genome sequence analyses and supporting biochemical studies also indicate that both enzymes are capable of deaminating the single-stranded loop regions of DNA hairpins at elevated rates. These studies combine to help resolve a long-standing etiologic debate on the source of APOBEC3 signature mutations in cancer and indicate that future diagnostic and therapeutic efforts should focus on both APOBEC3A and APOBEC3B.
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Affiliation(s)
- Michael A. Carpenter
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, United States of America
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, United States of America
- Howard Hughes Medical Institute, University of Minnesota, Minneapolis, Minnesota, United States of America
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, Texas, United States of America
- Howard Hughes Medical Institute, University of Texas Health San Antonio, San Antonio, Texas, United States of America
| | - Nuri A. Temiz
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, United States of America
- Institute for Health Informatics, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Mahmoud A. Ibrahim
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, Texas, United States of America
| | - Matthew C. Jarvis
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, United States of America
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Margaret R. Brown
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, United States of America
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Prokopios P. Argyris
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, United States of America
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, United States of America
- Howard Hughes Medical Institute, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - William L. Brown
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, United States of America
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Gabriel J. Starrett
- Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland, United States of America
| | - Douglas Yee
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, United States of America
- Department of Medicine, University of Minnesota Medical School, Minneapolis, Minnesota, United States of America
| | - Reuben S. Harris
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, United States of America
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, United States of America
- Howard Hughes Medical Institute, University of Minnesota, Minneapolis, Minnesota, United States of America
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, Texas, United States of America
- Howard Hughes Medical Institute, University of Texas Health San Antonio, San Antonio, Texas, United States of America
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33
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Ceylan T, Akin AT, Karabulut D, Tan FC, Taşkiran M, Yakan B. Therapeutic effect of thymoquinone on brain damage caused by nonylphenol exposure in rats. J Biochem Mol Toxicol 2023; 37:e23471. [PMID: 37466128 DOI: 10.1002/jbt.23471] [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: 11/25/2022] [Revised: 06/24/2023] [Accepted: 07/08/2023] [Indexed: 07/20/2023]
Abstract
Nonylphenol (NP), causes various harmful effects such as cognitive impairment and neurotoxicity. Thymoquinone (TQ), has antioxidant, anti-inflammatory, and neuroprotective properties. In this study, our aim is to investigate the effects of TQ on the brain damage caused by NP. Corn oil was applied to the control group. NP (100 mg/kg/day) was administered to the NP and NP + TQ groups for 21 days. TQ (5 mg/kg/day) was administered to the NP + TQ and TQ groups for 7 after 21 days. At the end of the experiment, the new object recognition test was applied to the rats and the rats were killed and their brain tissues were removed. Sections taken from brain tissues were stained with hematoxylin-eosin for histopathological evaluation. In addition, neuronal nuclei (NeuN), glial fibrillary acidic protein (GFAP), Cas-3, and nerve growth factor (NGF) immunoreactivities were evaluated in brain tissue sections. In addition, malondialdehyde (MDA), superoxide dismutase (SOD), and catalase (CAT) activities were determined. Comet assay was applied to determine DNA damage in cells. The results of our study showed that NP, caused behavioral disorders and damage to the cerebral cortex in rats. This damage in the form of neuron degeneration seen in the cortex was associated with apoptosis involving Cas-3 activation, increased DNA damage, and free oxygen radicals. NP, SOD, and CAT caused a decrease in enzyme activities. In addition, the cellular protein NeuN was decreased, astrocytosis-associated GFAP was increased, and growth factor NGF was decreased. When all our evaluations are taken together, treatment with TQ showed an ameliorative effect on the behavioral impairment and brain damage caused by NP exposure.
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Affiliation(s)
- Tayfun Ceylan
- Department of Histology and Embryology, Faculty of Dentistry, Cappadocia University, Nevsehir, Turkey
- Department of Histology and Embryology, Faculty of Medicine, Erciyes University, Kayseri, Turkey
| | - Ali Tuğrul Akin
- Department of Medical Biology, Faculty of Medicine, Istinye University, Istanbul, Turkey
| | - Derya Karabulut
- Department of Histology and Embryology, Faculty of Medicine, Erciyes University, Kayseri, Turkey
| | - Fazile Cantürk Tan
- Department of Biophysics, Faculty of Medicine, Erciyes University, Kayseri, Turkey
| | - Mehmet Taşkiran
- Department of Biology, Faculty of Science, Erciyes University, Kayseri, Turkey
| | - Birkan Yakan
- Department of Histology and Embryology, Faculty of Medicine, Erciyes University, Kayseri, Turkey
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34
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Mann CA, Carvajal Moreno JJ, Lu Y, Dellos-Nolan S, Wozniak DJ, Yalowich JC, Mitton-Fry MJ. Novel bacterial topoisomerase inhibitors: unique targeting activities of amide enzyme-binding motifs for tricyclic analogs. Antimicrob Agents Chemother 2023; 67:e0048223. [PMID: 37724886 PMCID: PMC10583662 DOI: 10.1128/aac.00482-23] [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: 04/13/2023] [Accepted: 07/14/2023] [Indexed: 09/21/2023] Open
Abstract
Antimicrobial resistance has made a sizeable impact on public health and continues to threaten the effectiveness of antibacterial therapies. Novel bacterial topoisomerase inhibitors (NBTIs) are a promising class of antibacterial agents with a unique binding mode and distinct pharmacology that enables them to evade existing resistance mechanisms. The clinical development of NBTIs has been plagued by several issues, including cardiovascular safety. Herein, we report a sub-series of tricyclic NBTIs bearing an amide linkage that displays promising antibacterial activity, potent dual-target inhibition of DNA gyrase and topoisomerase IV (TopoIV), as well as improved cardiovascular safety and metabolic profiles. These amide NBTIs induced both single- and double-strand breaks in pBR322 DNA mediated by Staphylococcus aureus DNA gyrase, in contrast to prototypical NBTIs that cause only single-strand breaks. Unexpectedly, amides 1a and 1b targeted human topoisomerase IIα (TOP2α) causing both single- and double-strand breaks in pBR322 DNA, and induced DNA strand breaks in intact human leukemia K562 cells. In addition, anticancer drug-resistant K/VP.5 cells containing decreased levels of TOP2α were cross-resistant to amides 1a and 1b. Together, these results demonstrate broad spectrum antibacterial properties of selected tricyclic NBTIs, desirable safety profiles, an unusual ability to induce DNA double-stranded breaks, and activity against human TOP2α. Future work will be directed toward optimization and development of tricyclic NBTIs with potent and selective activity against bacteria. Finally, the current results may provide an additional avenue for development of selective anticancer agents.
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Affiliation(s)
- Chelsea A. Mann
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, Ohio, USA
| | - Jessika J. Carvajal Moreno
- Division of Pharmaceutics and Pharmacology, College of Pharmacy, The Ohio State University, Columbus, Ohio, USA
| | - Yanran Lu
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, Ohio, USA
| | - Sheri Dellos-Nolan
- Department of Microbial Infection and Immunity, College of Medicine, The Ohio State University, Columbus, Ohio, USA
| | - Daniel J. Wozniak
- Department of Microbial Infection and Immunity, College of Medicine, The Ohio State University, Columbus, Ohio, USA
| | - Jack C. Yalowich
- Division of Pharmaceutics and Pharmacology, College of Pharmacy, The Ohio State University, Columbus, Ohio, USA
| | - Mark J. Mitton-Fry
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, Ohio, USA
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Chen X, Liu C, Zhao H, Zhong Y, Xu Y, Wang Y. Deep learning-assisted high-content screening identifies isoliquiritigenin as an inhibitor of DNA double-strand breaks for preventing doxorubicin-induced cardiotoxicity. Biol Direct 2023; 18:63. [PMID: 37807075 PMCID: PMC10561451 DOI: 10.1186/s13062-023-00412-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 08/30/2023] [Indexed: 10/10/2023] Open
Abstract
BACKGROUND Anthracyclines including doxorubicin are essential components of many cancer chemotherapy regimens, but their cardiotoxicity severely limits their use. New strategies for treating anthracycline-induced cardiotoxicity (AIC) are still needed. Anthracycline-induced DNA double-strand break (DSB) is the major cause of its cardiotoxicity. However, DSB-based drug screening for AIC has not been performed possibly due to the limited throughput of common assays for detecting DSB. To discover new therapeutic candidates for AIC, here we established a method to rapidly visualize and accurately evaluate the intranuclear anthracycline-induced DSB, and performed a screening for DSB inhibitors. RESULTS First, we constructed a cardiomyocyte cell line stably expressing EGFP-53BP1, in which the formation of EGFP-53BP1 foci faithfully marked the doxorubicin-induced DSB, providing a faster and visible approach to detecting DSB. To quantify the DSB, we used a deep learning-based image analysis method, which showed the better ability to distinguish different cell populations undergoing different treatments of doxorubicin or reference compounds, compared with the traditional threshold-based method. Subsequently, we applied the deep learning-assisted high-content screening method to 315 compounds and found three compounds (kaempferol, kaempferide, and isoliquiritigenin) that exert cardioprotective effects in vitro. Among them, the protective effect of isoliquiritigenin is accompanied by the up-regulation of HO-1, down-regulation of peroxynitrite and topo II, and the alleviation of doxorubicin-induced DSB and apoptosis. The results of animal experiments also showed that isoliquiritigenin maintained the myocardial tissue structure and cardiac function in vivo. Moreover, isoliquiritigenin did not affect the killing of HeLa and MDA-MB-436 cancer cells by doxorubicin and thus has the potential to be a lead compound to exert cardioprotective effects without affecting the antitumor effect of doxorubicin. CONCLUSIONS Our findings provided a new method for the drug discovery for AIC, which combines phenotypic screening with artificial intelligence. The results suggested that isoliquiritigenin as an inhibitor of DSB may be a promising drug candidate for AIC.
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Affiliation(s)
- Xuechun Chen
- Department of Cardiology, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, 310006, China
- Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Changtong Liu
- Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Hong Zhao
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Yigang Zhong
- Department of Cardiology, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, 310006, China
| | - Yizhou Xu
- Department of Cardiology, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, 310006, China.
| | - Yi Wang
- Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China.
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Hangzhou, 310020, China.
- Future Health Laboratory, Innovation Center of Yangtze River Delta, Zhejiang University, Jiaxing, 314100, China.
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36
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Zhou M, Boulos JC, Omer EA, Rudbari HA, Schirmeister T, Micale N, Efferth T. Two palladium (II) complexes derived from halogen-substituted Schiff bases and 2-picolylamine induce parthanatos-type cell death in sensitive and multi-drug resistant CCRF-CEM leukemia cells. Eur J Pharmacol 2023; 956:175980. [PMID: 37567459 DOI: 10.1016/j.ejphar.2023.175980] [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: 05/26/2023] [Revised: 07/29/2023] [Accepted: 08/08/2023] [Indexed: 08/13/2023]
Abstract
The use of cisplatin and its derivatives in cancer treatment triggered the interest in metal-containing complexes as potential novel anticancer agents. Palladium (II)-based complexes have been synthesized in recent years with promising antitumor activity. Previously, we described the synthesis and cytotoxicity of palladium (II) complexes containing halogen-substituted Schiff bases and 2-picolylamine. Here, we selected two palladium (II) complexes with double chlorine-substitution or double iodine-substitution that displayed the best cytotoxicity in drug-sensitive CCRF-CEM and multidrug-resistant CEM/ADR5000 leukemia cells for further biological investigation. Surprisingly, these compounds did not significantly induce apoptotic cell death. This study aims to reveal the major mode of cell death of these two palladium (II) complexes. We performed annexin V-FITC/PI staining and flow cytometric mitochondrial membrane potential measurement followed by western blotting, immunofluorescence microscopy, and alkaline single cell electrophoresis (comet assay). J4 and J6 still induced neither apoptosis nor necrosis in both leukemia cell lines. They also insufficiently induced autophagy as evidenced by Beclin and p62 detection in western blotting. Interestingly, J4 and J6 induced a novel mode of cell death (parthanatos) as mainly demonstrated in CCRF-CEM cells by hyper-activation of poly(ADP-ribose) polymerase 1 (PARP) and poly(ADP-ribose) (PAR) using western blotting, flow cytometric measurement of mitochondrial membrane potential collapse, nuclear translocation of apoptosis-inducing factor (AIF) by immunofluorescence microscopy, and DNA damage by alkaline single cell electrophoresis (comet assay). AIF translocation was also observed in CEM/ADR5000 cells. Thus, parthanatos was the predominant mode of cell death induced by J4 and J6, which explains the high cytotoxicity in CCRF-CEM and CEM/ADR5000 cells. J4 and J6 may be interesting drug candidates and deserve further investigations to overcome resistance of tumors against apoptosis. This study will promote the design of further novel palladium (II)-based complexes as chemotherapeutic agents.
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Affiliation(s)
- Min Zhou
- Department of Pharmaceutical Biology, Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University-Mainz, Staudinger Weg 5, 55128, Mainz, Germany
| | - Joelle C Boulos
- Department of Pharmaceutical Biology, Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University-Mainz, Staudinger Weg 5, 55128, Mainz, Germany
| | - Ejlal A Omer
- Department of Pharmaceutical Biology, Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University-Mainz, Staudinger Weg 5, 55128, Mainz, Germany
| | - Hadi Amiri Rudbari
- Department of Chemistry, University of Isfahan, Isfahan, 81746-73441, Iran
| | - Tanja Schirmeister
- Department of Medicinal Chemistry, Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University-Mainz, Staudinger Weg 5, 55128, Mainz, Germany
| | - Nicola Micale
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale Ferdinando Stagno D'Alcontres 31, 1-98166, Messina, Italy
| | - Thomas Efferth
- Department of Pharmaceutical Biology, Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University-Mainz, Staudinger Weg 5, 55128, Mainz, Germany.
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37
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Aşcı Çelik D, Toğay VA. In vivo protective efficacy of astaxanthin against ionizing radiation-induced DNA damage. Chem Biol Drug Des 2023; 102:882-888. [PMID: 37545012 DOI: 10.1111/cbdd.14321] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 07/14/2023] [Accepted: 07/31/2023] [Indexed: 08/08/2023]
Abstract
Astaxanthin, a carotenoid pigment, is believed to be effective in the repair of DNA damage. Our study evaluates the effect of astaxanthin on DNA damage in rats exposed to whole-body radiotherapy using the comet assay. Thirty-two male rats were randomly divided into four groups (control, ionizing radiation, astaxanthin, and radiation+astaxanthin). The radiation and radiation+astaxanthin groups were exposed to X-rays at a dose of 8 gray (0.62 gray/min). Astaxanthin was administered at 4 mg/kg by gavage for 7 days starting from irradiation. The %TailDNA parameter was chosen as an indicator of DNA damage and the results were compared using one-way ANOVA. %TailDNA was 3.24 ± 3.12 in the control group, 2.85 ± 2.73 in the astaxanthin group, 4.11 ± 7.90 in the radiation group, and 3.59 ± 4.05 in the radiation+astaxanthin group. There was a significant increase in DNA damage in the radiation group, compared with the control and astaxanthin groups (p < .001). DNA damage was reduced in the radiation+astaxanthin group compared with the radiation group (p < .05). Although this decrease did not reduce damage to the level of the control group, it was significant. The decrease in radiation-induced DNA damage by astaxanthin administration in our study supports the hypothesis that astaxanthin is a promising agent for against/reducing DNA damage.
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Affiliation(s)
- Dilek Aşcı Çelik
- Süleyman Demirel University, Faculty of Medicine, Department of Medical Biology, Isparta, Turkey
| | - Vehbi Atahan Toğay
- Süleyman Demirel University, Faculty of Medicine, Department of Medical Biology, Isparta, Turkey
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38
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Fröhlich LM, Niessner H, Sauer B, Kämereit S, Chatziioannou E, Riel S, Sinnberg T, Schittek B. PARP Inhibitors Effectively Reduce MAPK Inhibitor Resistant Melanoma Cell Growth and Synergize with MAPK Inhibitors through a Synthetic Lethal Interaction In Vitro and In Vivo. CANCER RESEARCH COMMUNICATIONS 2023; 3:1743-1755. [PMID: 37674529 PMCID: PMC10478790 DOI: 10.1158/2767-9764.crc-23-0101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 05/03/2023] [Accepted: 07/27/2023] [Indexed: 09/08/2023]
Abstract
The efficacy of targeting the MAPK signaling pathway in patients with melanoma is limited by the rapid development of resistance mechanisms that result in disease relapse. In this article, we focus on targeting the DNA repair pathway as an antimelanoma therapy, especially in MAPK inhibitor resistant melanoma cells using PARP inhibitors. We found that MAPK inhibitor resistant melanoma cells are particularly sensitive to PARP inhibitor treatment due to a lower basal expression of the DNA damage sensor ataxia-telangiectasia mutated (ATM). As a consequence, MAPK inhibitor resistant melanoma cells have decreased homologous recombination repair activity leading to a reduced repair of double-strand breaks caused by the PARP inhibitors. We validated the clinical relevance of our findings by ATM expression analysis in biopsies from patients with melanoma before and after development of resistance to MAPK inhibitors. Furthermore, we show that inhibition of the MAPK pathway induces a homologous recombination repair deficient phenotype in melanoma cells irrespective of their MAPK inhibitor sensitivity status. MAPK inhibition results in a synthetic lethal interaction of a combinatorial treatment with PARP inhibitors, which significantly reduces melanoma cell growth in vitro and in vivo. In conclusion, this study shows that PARP inhibitor treatment is a valuable therapy option for patients with melanoma, either as a single treatment or as a combination with MAPK inhibitors depending on ATM expression. Significance We show that MAPK inhibitor resistant melanoma cells exhibit low ATM expression increasing their sensitivity toward PARP inhibitors and that a combination of MAPK/PARP inhibitors act synthetically lethal in melanoma cells. Our study shows that PARP inhibitor treatment is a valuable therapy option for patients with melanoma, either as a single treatment or as a combination with MAPK inhibitors depending on ATM expression, which could serve as a novel biomarker for treatment response.
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Affiliation(s)
- Lisa Marie Fröhlich
- Division of Dermatooncology, Department of Dermatology, University of Tübingen, Tübingen, Germany
| | - Heike Niessner
- Division of Dermatooncology, Department of Dermatology, University of Tübingen, Tübingen, Germany
| | - Birgit Sauer
- Division of Dermatooncology, Department of Dermatology, University of Tübingen, Tübingen, Germany
| | - Sofie Kämereit
- Division of Dermatooncology, Department of Dermatology, University of Tübingen, Tübingen, Germany
| | - Eftychia Chatziioannou
- Division of Dermatooncology, Department of Dermatology, University of Tübingen, Tübingen, Germany
| | - Simon Riel
- Department of Dermatology, University of Tübingen, Tübingen, Germany
| | - Tobias Sinnberg
- Division of Dermatooncology, Department of Dermatology, University of Tübingen, Tübingen, Germany
- Department of Dermatology, Venereology and Allergology, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Birgit Schittek
- Division of Dermatooncology, Department of Dermatology, University of Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC 2180) “Image-Guided and Functionally Instructed Tumor Therapies,” University of Tübingen, Tübingen, Germany
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39
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Dougherty MW, Valdés-Mas R, Wernke KM, Gharaibeh RZ, Yang Y, Brant JO, Riva A, Muehlbauer M, Elinav E, Puschhof J, Herzon SB, Jobin C. The microbial genotoxin colibactin exacerbates mismatch repair mutations in colorectal tumors. Neoplasia 2023; 43:100918. [PMID: 37499275 PMCID: PMC10413156 DOI: 10.1016/j.neo.2023.100918] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 07/14/2023] [Accepted: 07/19/2023] [Indexed: 07/29/2023]
Abstract
Certain Enterobacteriaceae strains contain a 54-kb biosynthetic gene cluster referred to as "pks" encoding the biosynthesis of a secondary metabolite, colibactin. Colibactin-producing E. coli promote colorectal cancer (CRC) in preclinical models, and in vitro induce a specific mutational signature that is also detected in human CRC genomes. Yet, how colibactin exposure affects the mutational landscape of CRC in vivo remains unclear. Here we show that colibactin-producing E. coli-driven colonic tumors in mice have a significantly higher SBS burden and a larger percentage of these mutations can be attributed to a signature associated with mismatch repair deficiency (MMRd; SBS15), compared to tumors developed in the presence of colibactin-deficient E. coli. We found that the synthetic colibactin 742 but not an inactive analog 746 causes DNA damage and induces transcriptional activation of p53 and senescence signaling pathways in non-transformed human colonic epithelial cells. In MMRd colon cancer cells (HCT 116), chronic exposure to 742 resulted in the upregulation of BRCA1, Fanconi anemia, and MMR signaling pathways as revealed by global transcriptomic analysis. This was accompanied by increased T>N single-base substitutions (SBS) attributed to the proposed pks+E. coli signature (SBS88), reactive oxygen species (SBS17), and mismatch-repair deficiency (SBS44). A significant co-occurrence between MMRd SBS44 and pks-associated SBS88 signature was observed in a large cohort of human CRC patients (n=2,945), and significantly more SBS44 mutations were found when SBS88 was also detected. Collectively, these findings reveal the host response mechanisms underlying colibactin genotoxic activity and suggest that colibactin may exacerbate MMRd-associated mutations.
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Affiliation(s)
- Michael W Dougherty
- Department of Medicine, University of Florida College of Medicine, Gainesville, FL, USA
| | - Rafael Valdés-Mas
- Systems Immunology Department, Weizmann Institute of Science, Rehovot, IL, Israel
| | - Kevin M Wernke
- Department of Chemistry, Yale University, New Haven, CT, USA
| | - Raad Z Gharaibeh
- Department of Medicine, University of Florida College of Medicine, Gainesville, FL, USA
| | - Ye Yang
- Department of Medicine, University of Florida College of Medicine, Gainesville, FL, USA
| | - Jason O Brant
- Department of Biostatistics, University of Florida College of Medicine, Gainesville, FL, USA
| | - Alberto Riva
- Bioinformatics Core, Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL, USA
| | - Marcus Muehlbauer
- Department of Medicine, University of Florida College of Medicine, Gainesville, FL, USA
| | - Eran Elinav
- Systems Immunology Department, Weizmann Institute of Science, Rehovot, IL, Israel; Microbiome and Cancer Division, German Cancer Research Center (DKFZ), Heidelberg, DE, Germany
| | - Jens Puschhof
- Microbiome and Cancer Division, German Cancer Research Center (DKFZ), Heidelberg, DE, Germany
| | - Seth B Herzon
- Department of Biostatistics, University of Florida College of Medicine, Gainesville, FL, USA; Departments of Pharmacology and Therapeutic Radiology, Yale University, New Haven, CT, USA
| | - Christian Jobin
- Department of Medicine, University of Florida College of Medicine, Gainesville, FL, USA; Department of Infectious Diseases and Immunology, University of Florida College of Medicine, Gainesville, FL, USA; Department of Anatomy and Cell Biology, University of Florida College of Medicine, Gainesville, FL, USA.
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40
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Jin B, Zhu J, Pan T, Yang Y, Liang L, Zhou Y, Zhang T, Teng Y, Wang Z, Wang X, Tian Q, Guo B, Li H, Chen T. MEN1 is a regulator of alternative splicing and prevents R-loop-induced genome instability through suppression of RNA polymerase II elongation. Nucleic Acids Res 2023; 51:7951-7971. [PMID: 37395406 PMCID: PMC10450199 DOI: 10.1093/nar/gkad548] [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: 10/02/2022] [Revised: 06/02/2023] [Accepted: 06/15/2023] [Indexed: 07/04/2023] Open
Abstract
The fidelity of alternative splicing (AS) patterns is essential for growth development and cell fate determination. However, the scope of the molecular switches that regulate AS remains largely unexplored. Here we show that MEN1 is a previously unknown splicing regulatory factor. MEN1 deletion resulted in reprogramming of AS patterns in mouse lung tissue and human lung cancer cells, suggesting that MEN1 has a general function in regulating alternative precursor mRNA splicing. MEN1 altered exon skipping and the abundance of mRNA splicing isoforms of certain genes with suboptimal splice sites. Chromatin immunoprecipitation and chromosome walking assays revealed that MEN1 favored the accumulation of RNA polymerase II (Pol II) in regions encoding variant exons. Our data suggest that MEN1 regulates AS by slowing the Pol II elongation rate and that defects in these processes trigger R-loop formation, DNA damage accumulation and genome instability. Furthermore, we identified 28 MEN1-regulated exon-skipping events in lung cancer cells that were closely correlated with survival in patients with lung adenocarcinoma, and MEN1 deficiency sensitized lung cancer cells to splicing inhibitors. Collectively, these findings led to the identification of a novel biological role for menin in maintaining AS homeostasis and link this role to the regulation of cancer cell behavior.
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Affiliation(s)
- Bangming Jin
- Department of Physiology, School of Basic Medical Sciences, Guizhou Medical University, 550025 Guiyang, China
- Department of Surgery, Affiliated Hospital of Guizhou Medical University, 550025 Guiyang, China
- Transformation Engineering Research Center of Chronic Disease Diagnosis and Treatment, Guizhou Medical University, Guiyang, China
- Guizhou Provincial Key Laboratory of Pathogenesis and Drug Research on Common Chronic Diseases, Guizhou Medical University, 550025 Guiyang, China
| | - Jiamei Zhu
- Department of Physiology, School of Basic Medical Sciences, Guizhou Medical University, 550025 Guiyang, China
- Transformation Engineering Research Center of Chronic Disease Diagnosis and Treatment, Guizhou Medical University, Guiyang, China
- Guizhou Provincial Key Laboratory of Pathogenesis and Drug Research on Common Chronic Diseases, Guizhou Medical University, 550025 Guiyang, China
| | - Ting Pan
- Department of Physiology, School of Basic Medical Sciences, Guizhou Medical University, 550025 Guiyang, China
- Transformation Engineering Research Center of Chronic Disease Diagnosis and Treatment, Guizhou Medical University, Guiyang, China
- Guizhou Provincial Key Laboratory of Pathogenesis and Drug Research on Common Chronic Diseases, Guizhou Medical University, 550025 Guiyang, China
| | - Yunqiao Yang
- Department of Physiology, School of Basic Medical Sciences, Guizhou Medical University, 550025 Guiyang, China
- Department of Surgery, Affiliated Hospital of Guizhou Medical University, 550025 Guiyang, China
- Transformation Engineering Research Center of Chronic Disease Diagnosis and Treatment, Guizhou Medical University, Guiyang, China
- Guizhou Provincial Key Laboratory of Pathogenesis and Drug Research on Common Chronic Diseases, Guizhou Medical University, 550025 Guiyang, China
| | - Li Liang
- Department of Physiology, School of Basic Medical Sciences, Guizhou Medical University, 550025 Guiyang, China
- Transformation Engineering Research Center of Chronic Disease Diagnosis and Treatment, Guizhou Medical University, Guiyang, China
- Guizhou Provincial Key Laboratory of Pathogenesis and Drug Research on Common Chronic Diseases, Guizhou Medical University, 550025 Guiyang, China
| | - Yuxia Zhou
- Department of Physiology, School of Basic Medical Sciences, Guizhou Medical University, 550025 Guiyang, China
- Transformation Engineering Research Center of Chronic Disease Diagnosis and Treatment, Guizhou Medical University, Guiyang, China
- Guizhou Provincial Key Laboratory of Pathogenesis and Drug Research on Common Chronic Diseases, Guizhou Medical University, 550025 Guiyang, China
| | - Tuo Zhang
- Department of Physiology, School of Basic Medical Sciences, Guizhou Medical University, 550025 Guiyang, China
- Transformation Engineering Research Center of Chronic Disease Diagnosis and Treatment, Guizhou Medical University, Guiyang, China
- Guizhou Provincial Key Laboratory of Pathogenesis and Drug Research on Common Chronic Diseases, Guizhou Medical University, 550025 Guiyang, China
| | - Yin Teng
- Department of Surgery, Affiliated Hospital of Guizhou Medical University, 550025 Guiyang, China
- Guizhou Institute of Precision Medicine, Affiliated Hospital of Guizhou Medical University, 550025 Guiyang, China
| | - Ziming Wang
- Department of Physiology, School of Basic Medical Sciences, Guizhou Medical University, 550025 Guiyang, China
- Transformation Engineering Research Center of Chronic Disease Diagnosis and Treatment, Guizhou Medical University, Guiyang, China
- Guizhou Provincial Key Laboratory of Pathogenesis and Drug Research on Common Chronic Diseases, Guizhou Medical University, 550025 Guiyang, China
| | - Xuyan Wang
- Department of Physiology, School of Basic Medical Sciences, Guizhou Medical University, 550025 Guiyang, China
- Transformation Engineering Research Center of Chronic Disease Diagnosis and Treatment, Guizhou Medical University, Guiyang, China
- Guizhou Provincial Key Laboratory of Pathogenesis and Drug Research on Common Chronic Diseases, Guizhou Medical University, 550025 Guiyang, China
| | - Qianting Tian
- Transformation Engineering Research Center of Chronic Disease Diagnosis and Treatment, Guizhou Medical University, Guiyang, China
- Guizhou Institute of Precision Medicine, Affiliated Hospital of Guizhou Medical University, 550025 Guiyang, China
| | - Bing Guo
- Department of Physiology, School of Basic Medical Sciences, Guizhou Medical University, 550025 Guiyang, China
- Transformation Engineering Research Center of Chronic Disease Diagnosis and Treatment, Guizhou Medical University, Guiyang, China
- Guizhou Provincial Key Laboratory of Pathogenesis and Drug Research on Common Chronic Diseases, Guizhou Medical University, 550025 Guiyang, China
| | - Haiyang Li
- Department of Surgery, Affiliated Hospital of Guizhou Medical University, 550025 Guiyang, China
- Guizhou Institute of Precision Medicine, Affiliated Hospital of Guizhou Medical University, 550025 Guiyang, China
| | - Tengxiang Chen
- Department of Physiology, School of Basic Medical Sciences, Guizhou Medical University, 550025 Guiyang, China
- Department of Surgery, Affiliated Hospital of Guizhou Medical University, 550025 Guiyang, China
- Transformation Engineering Research Center of Chronic Disease Diagnosis and Treatment, Guizhou Medical University, Guiyang, China
- Guizhou Provincial Key Laboratory of Pathogenesis and Drug Research on Common Chronic Diseases, Guizhou Medical University, 550025 Guiyang, China
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41
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Einig E, Jin C, Andrioletti V, Macek B, Popov N. RNAPII-dependent ATM signaling at collisions with replication forks. Nat Commun 2023; 14:5147. [PMID: 37620345 PMCID: PMC10449895 DOI: 10.1038/s41467-023-40924-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 08/16/2023] [Indexed: 08/26/2023] Open
Abstract
Deregulation of RNA Polymerase II (RNAPII) by oncogenic signaling leads to collisions of RNAPII with DNA synthesis machinery (transcription-replication conflicts, TRCs). TRCs can result in DNA damage and are thought to underlie genomic instability in tumor cells. Here we provide evidence that elongating RNAPII nucleates activation of the ATM kinase at TRCs to stimulate DNA repair. We show the ATPase WRNIP1 associates with RNAPII and limits ATM activation during unperturbed cell cycle. WRNIP1 binding to elongating RNAPII requires catalytic activity of the ubiquitin ligase HUWE1. Mutation of HUWE1 induces TRCs, promotes WRNIP1 dissociation from RNAPII and binding to the replisome, stimulating ATM recruitment and activation at RNAPII. TRCs and translocation of WRNIP1 are rapidly induced in response to hydroxyurea treatment to activate ATM and facilitate subsequent DNA repair. We propose that TRCs can provide a controlled mechanism for stalling of replication forks and ATM activation, instrumental in cellular response to replicative stress.
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Affiliation(s)
- Elias Einig
- Department of Medical Oncology and Pulmonology, University Hospital Tübingen, Otfried-Mueller-Str 14, 72076, Tübingen, Germany
| | - Chao Jin
- Department of Medical Oncology and Pulmonology, University Hospital Tübingen, Otfried-Mueller-Str 14, 72076, Tübingen, Germany
| | - Valentina Andrioletti
- Department of Medical Oncology and Pulmonology, University Hospital Tübingen, Otfried-Mueller-Str 14, 72076, Tübingen, Germany
- enGenome S.R.L., Via Fratelli Cuzio 42, 27100, Pavia, Italy
| | - Boris Macek
- Interfaculty Institute of Cell Biology, Eberhard Karls University of Tübingen, Auf d. Morgenstelle 15, 72076, Tübingen, Germany
| | - Nikita Popov
- Department of Medical Oncology and Pulmonology, University Hospital Tübingen, Otfried-Mueller-Str 14, 72076, Tübingen, Germany.
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42
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Hara T, Nakaoka H, Miyoshi T, Ishikawa F. The CST complex facilitates cell survival under oxidative genotoxic stress. PLoS One 2023; 18:e0289304. [PMID: 37590191 PMCID: PMC10434909 DOI: 10.1371/journal.pone.0289304] [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: 03/22/2023] [Accepted: 07/15/2023] [Indexed: 08/19/2023] Open
Abstract
Genomic DNA is constantly exposed to a variety of genotoxic stresses, and it is crucial for organisms to be equipped with mechanisms for repairing the damaged genome. Previously, it was demonstrated that the mammalian CST (CTC1-STN1-TEN1) complex, which was originally identified as a single-stranded DNA-binding trimeric protein complex essential for telomere maintenance, is required for survival in response to hydroxyurea (HU), which induces DNA replication fork stalling. It is still unclear, however, how the CST complex is involved in the repair of diverse types of DNA damage induced by oxidizing agents such as H2O2. STN1 knockdown (KD) sensitized HeLa cells to high doses of H2O2. While H2O2 induced DNA strand breaks throughout the cell cycle, STN1 KD cells were as resistant as control cells to H2O2 treatment when challenged in the G1 phase of the cell cycle, but they were sensitive when exposed to H2O2 in S/G2/M phase. STN1 KD cells showed a failure of DNA synthesis and RAD51 foci formation upon H2O2 treatment. Chemical inhibition of RAD51 in shSTN1 cells did not exacerbate the sensitivity to H2O2, implying that the CST complex and RAD51 act in the same pathway. Collectively, our results suggest that the CST complex is required for maintaining genomic stability in response to oxidative DNA damage, possibly through RAD51-dependent DNA repair/protection mechanisms.
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Affiliation(s)
- Tomohiko Hara
- Department of Gene Mechanisms, Graduate School of Biostudies, Kyoto University, Kyoto, Japan
- Radiation Biology Center, Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Hidenori Nakaoka
- Department of Gene Mechanisms, Graduate School of Biostudies, Kyoto University, Kyoto, Japan
- Radiation Biology Center, Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Tomoicihiro Miyoshi
- Department of Gene Mechanisms, Graduate School of Biostudies, Kyoto University, Kyoto, Japan
- Radiation Biology Center, Graduate School of Biostudies, Kyoto University, Kyoto, Japan
- Laboratory for Retrotransposon Dynamics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Fuyuki Ishikawa
- Department of Gene Mechanisms, Graduate School of Biostudies, Kyoto University, Kyoto, Japan
- Radiation Biology Center, Graduate School of Biostudies, Kyoto University, Kyoto, Japan
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Pinedo-Carpio E, Dessapt J, Beneyton A, Sacre L, Bérubé MA, Villot R, Lavoie EG, Coulombe Y, Blondeau A, Boulais J, Malina A, Luo VM, Lazaratos AM, Côté JF, Mallette FA, Guarné A, Masson JY, Fradet-Turcotte A, Orthwein A. FIRRM cooperates with FIGNL1 to promote RAD51 disassembly during DNA repair. SCIENCE ADVANCES 2023; 9:eadf4082. [PMID: 37556550 PMCID: PMC10411901 DOI: 10.1126/sciadv.adf4082] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 07/10/2023] [Indexed: 08/11/2023]
Abstract
Interstrand DNA cross-links (ICLs) represent complex lesions that compromise genomic stability. Several pathways have been involved in ICL repair, but the extent of factors involved in the resolution of ICL-induced DNA double-strand breaks (DSBs) remains poorly defined. Using CRISPR-based genomics, we identified FIGNL1 interacting regulator of recombination and mitosis (FIRRM) as a sensitizer of the ICL-inducing agent mafosfamide. Mechanistically, we showed that FIRRM, like its interactor Fidgetin like 1 (FIGNL1), contributes to the resolution of RAD51 foci at ICL-induced DSBs. While the stability of FIGNL1 and FIRRM is interdependent, expression of a mutant of FIRRM (∆WCF), which stabilizes the protein in the absence of FIGNL1, allows the resolution of RAD51 foci and cell survival, suggesting that FIRRM has FIGNL1-independent function during DNA repair. In line with this model, FIRRM binds preferentially single-stranded DNA in vitro, raising the possibility that it directly contributes to RAD51 disassembly by interacting with DNA. Together, our findings establish FIRRM as a promoting factor of ICL repair.
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Affiliation(s)
- Edgar Pinedo-Carpio
- Lady Davis Institute for Medical Research, Segal Cancer Centre, Jewish General Hospital, 3755 Chemin de la Côte-Sainte-Catherine, Montréal, QC H3T 1E2, Canada
- Division of Experimental Medicine, McGill University, Montréal, QC H4A 3J1, Canada
| | - Julien Dessapt
- CHU de Québec Research Center-Université Laval (L’Hôtel-Dieu de Québec), Laval University Cancer Research Center, Québec, QC G1R 3S3, Canada
- Department of Molecular Biology, Medical Biochemistry and Pathology, Université Laval, Québec, QC G1V 0A6, Canada
| | - Adèle Beneyton
- CHU de Québec Research Center-Université Laval (L’Hôtel-Dieu de Québec), Laval University Cancer Research Center, Québec, QC G1R 3S3, Canada
- Department of Molecular Biology, Medical Biochemistry and Pathology, Université Laval, Québec, QC G1V 0A6, Canada
| | - Lauralicia Sacre
- Department of Biochemistry, McGill University, Montréal, QC H3G 0B1, Canada
| | - Marie-Anne Bérubé
- CHU de Québec Research Center-Université Laval (L’Hôtel-Dieu de Québec), Laval University Cancer Research Center, Québec, QC G1R 3S3, Canada
- Department of Molecular Biology, Medical Biochemistry and Pathology, Université Laval, Québec, QC G1V 0A6, Canada
| | - Romain Villot
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montréal, QC H3C 3J7, Canada
- Maisonneuve-Rosemont Hospital Research Centre, Montréal, QC H1T 2M4 Canada
| | - Elise G. Lavoie
- CHU de Québec Research Center-Université Laval (L’Hôtel-Dieu de Québec), Laval University Cancer Research Center, Québec, QC G1R 3S3, Canada
- Department of Molecular Biology, Medical Biochemistry and Pathology, Université Laval, Québec, QC G1V 0A6, Canada
| | - Yan Coulombe
- CHU de Québec Research Center-Université Laval (L’Hôtel-Dieu de Québec), Laval University Cancer Research Center, Québec, QC G1R 3S3, Canada
- Department of Molecular Biology, Medical Biochemistry and Pathology, Université Laval, Québec, QC G1V 0A6, Canada
| | - Andréanne Blondeau
- CHU de Québec Research Center-Université Laval (L’Hôtel-Dieu de Québec), Laval University Cancer Research Center, Québec, QC G1R 3S3, Canada
- Department of Molecular Biology, Medical Biochemistry and Pathology, Université Laval, Québec, QC G1V 0A6, Canada
| | - Jonathan Boulais
- Montreal Clinical Research Institute (IRCM), Montreal, QC H2W 1R7, Canada
| | - Abba Malina
- Lady Davis Institute for Medical Research, Segal Cancer Centre, Jewish General Hospital, 3755 Chemin de la Côte-Sainte-Catherine, Montréal, QC H3T 1E2, Canada
- Maisonneuve-Rosemont Hospital Research Centre, Montréal, QC H1T 2M4 Canada
| | - Vincent M. Luo
- Lady Davis Institute for Medical Research, Segal Cancer Centre, Jewish General Hospital, 3755 Chemin de la Côte-Sainte-Catherine, Montréal, QC H3T 1E2, Canada
- Department of Microbiology and Immunology, McGill University, Montréal, QC H3A 2B4, Canada
| | - Anna-Maria Lazaratos
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montréal, QC H3C 3J7, Canada
- Montreal Clinical Research Institute (IRCM), Montreal, QC H2W 1R7, Canada
| | - Jean-François Côté
- Montreal Clinical Research Institute (IRCM), Montreal, QC H2W 1R7, Canada
- Département de Médecine, Université de Montréal, Montréal, QC H3C 3J7 Canada
| | - Frédérick A. Mallette
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montréal, QC H3C 3J7, Canada
- Maisonneuve-Rosemont Hospital Research Centre, Montréal, QC H1T 2M4 Canada
- Département de Médecine, Université de Montréal, Montréal, QC H3C 3J7 Canada
| | - Alba Guarné
- Department of Biochemistry, McGill University, Montréal, QC H3G 0B1, Canada
| | - Jean-Yves Masson
- CHU de Québec Research Center-Université Laval (L’Hôtel-Dieu de Québec), Laval University Cancer Research Center, Québec, QC G1R 3S3, Canada
- Department of Molecular Biology, Medical Biochemistry and Pathology, Université Laval, Québec, QC G1V 0A6, Canada
| | - Amélie Fradet-Turcotte
- CHU de Québec Research Center-Université Laval (L’Hôtel-Dieu de Québec), Laval University Cancer Research Center, Québec, QC G1R 3S3, Canada
- Department of Molecular Biology, Medical Biochemistry and Pathology, Université Laval, Québec, QC G1V 0A6, Canada
| | - Alexandre Orthwein
- Lady Davis Institute for Medical Research, Segal Cancer Centre, Jewish General Hospital, 3755 Chemin de la Côte-Sainte-Catherine, Montréal, QC H3T 1E2, Canada
- Division of Experimental Medicine, McGill University, Montréal, QC H4A 3J1, Canada
- Montreal Clinical Research Institute (IRCM), Montreal, QC H2W 1R7, Canada
- Department of Microbiology and Immunology, McGill University, Montréal, QC H3A 2B4, Canada
- Department of Radiation Oncology, Winship Cancer Institute, Emory University, Atlanta, GA 30322, USA
- Gerald Bronfman Department of Oncology, McGill University, Montréal, QC H4A 3T2, Canada
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Huang M, Yao F, Nie L, Wang C, Su D, Zhang H, Li S, Tang M, Feng X, Yu B, Chen Z, Wang S, Yin L, Mou L, Hart T, Chen J. FACS-based genome-wide CRISPR screens define key regulators of DNA damage signaling pathways. Mol Cell 2023; 83:2810-2828.e6. [PMID: 37541219 PMCID: PMC10421629 DOI: 10.1016/j.molcel.2023.07.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 02/17/2023] [Accepted: 07/05/2023] [Indexed: 08/06/2023]
Abstract
DNA damage-activated signaling pathways are critical for coordinating multiple cellular processes, which must be tightly regulated to maintain genome stability. To provide a comprehensive and unbiased perspective of DNA damage response (DDR) signaling pathways, we performed 30 fluorescence-activated cell sorting (FACS)-based genome-wide CRISPR screens in human cell lines with antibodies recognizing distinct endogenous DNA damage signaling proteins to identify critical regulators involved in DDR. We discovered that proteasome-mediated processing is an early and prerequisite event for cells to trigger camptothecin- and etoposide-induced DDR signaling. Furthermore, we identified PRMT1 and PRMT5 as modulators that regulate ATM protein level. Moreover, we discovered that GNB1L is a key regulator of DDR signaling via its role as a co-chaperone specifically regulating PIKK proteins. Collectively, these screens offer a rich resource for further investigation of DDR, which may provide insight into strategies of targeting these DDR pathways to improve therapeutic outcomes.
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Affiliation(s)
- Min Huang
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Fuwen Yao
- Department of Hepatopancreatobiliary Surgery, Shenzhen Institute of Translational Medicine, Health Science Center, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People's Hospital, Shenzhen, China
| | - Litong Nie
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Chao Wang
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Dan Su
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Huimin Zhang
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Siting Li
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Mengfan Tang
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Xu Feng
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Bin Yu
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Zhen Chen
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Shimin Wang
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Ling Yin
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Lisha Mou
- Department of Hepatopancreatobiliary Surgery, Shenzhen Institute of Translational Medicine, Health Science Center, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People's Hospital, Shenzhen, China
| | - Traver Hart
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Junjie Chen
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
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Murray A, Gough G, Cindrić A, Vučković F, Koschut D, Borelli V, Petrović DJ, Bekavac A, Plećaš A, Hribljan V, Brunmeir R, Jurić J, Pučić-Baković M, Slana A, Deriš H, Frkatović A, Groet J, O'Brien NL, Chen HY, Yeap YJ, Delom F, Havlicek S, Gammon L, Hamburg S, Startin C, D'Souza H, Mitrečić D, Kero M, Odak L, Krušlin B, Krsnik Ž, Kostović I, Foo JN, Loh YH, Dunn NR, de la Luna S, Spector T, Barišić I, Thomas MSC, Strydom A, Franceschi C, Lauc G, Krištić J, Alić I, Nižetić D. Dose imbalance of DYRK1A kinase causes systemic progeroid status in Down syndrome by increasing the un-repaired DNA damage and reducing LaminB1 levels. EBioMedicine 2023; 94:104692. [PMID: 37451904 PMCID: PMC10435767 DOI: 10.1016/j.ebiom.2023.104692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 06/15/2023] [Accepted: 06/20/2023] [Indexed: 07/18/2023] Open
Abstract
BACKGROUND People with Down syndrome (DS) show clinical signs of accelerated ageing. Causative mechanisms remain unknown and hypotheses range from the (essentially untreatable) amplified-chromosomal-instability explanation, to potential actions of individual supernumerary chromosome-21 genes. The latter explanation could open a route to therapeutic amelioration if the specific over-acting genes could be identified and their action toned-down. METHODS Biological age was estimated through patterns of sugar molecules attached to plasma immunoglobulin-G (IgG-glycans, an established "biological-ageing-clock") in n = 246 individuals with DS from three European populations, clinically characterised for the presence of co-morbidities, and compared to n = 256 age-, sex- and demography-matched healthy controls. Isogenic human induced pluripotent stem cell (hiPSCs) models of full and partial trisomy-21 with CRISPR-Cas9 gene editing and two kinase inhibitors were studied prior and after differentiation to cerebral organoids. FINDINGS Biological age in adults with DS is (on average) 18.4-19.1 years older than in chronological-age-matched controls independent of co-morbidities, and this shift remains constant throughout lifespan. Changes are detectable from early childhood, and do not require a supernumerary chromosome, but are seen in segmental duplication of only 31 genes, along with increased DNA damage and decreased levels of LaminB1 in nucleated blood cells. We demonstrate that these cell-autonomous phenotypes can be gene-dose-modelled and pharmacologically corrected in hiPSCs and derived cerebral organoids. Using isogenic hiPSC models we show that chromosome-21 gene DYRK1A overdose is sufficient and necessary to cause excess unrepaired DNA damage. INTERPRETATION Explanation of hitherto observed accelerated ageing in DS as a developmental progeroid syndrome driven by DYRK1A overdose provides a target for early pharmacological preventative intervention strategies. FUNDING Main funding came from the "Research Cooperability" Program of the Croatian Science Foundation funded by the European Union from the European Social Fund under the Operational Programme Efficient Human Resources 2014-2020, Project PZS-2019-02-4277, and the Wellcome Trust Grants 098330/Z/12/Z and 217199/Z/19/Z (UK). All other funding is described in details in the "Acknowledgements".
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Affiliation(s)
- Aoife Murray
- Faculty of Medicine and Dentistry, Blizard Institute, Queen Mary University of London, London, UK; The London Down Syndrome Consortium (LonDownS), London, UK.
| | - Gillian Gough
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
| | - Ana Cindrić
- Glycoscience Research Laboratory, Genos Ltd., Zagreb, Croatia
| | - Frano Vučković
- Glycoscience Research Laboratory, Genos Ltd., Zagreb, Croatia
| | - David Koschut
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore; Disease Intervention Technology Laboratory (DITL), Institute of Molecular and Cellular Biology (IMCB), Agency for Science, Technology and Research (A∗STAR), Singapore
| | - Vincenzo Borelli
- Department of Medical and Surgical Sciences, Alma Mater Studiorum University of Bologna, Italy
| | - Dražen J Petrović
- Glycoscience Research Laboratory, Genos Ltd., Zagreb, Croatia; Croatian Institute for Brain Research, School of Medicine, University of Zagreb, Zagreb, Croatia
| | - Ana Bekavac
- Croatian Institute for Brain Research, School of Medicine, University of Zagreb, Zagreb, Croatia
| | - Ante Plećaš
- Faculty of Veterinary Medicine, Department of Anatomy, Histology and Embryology, University of Zagreb, Zagreb, Croatia
| | - Valentina Hribljan
- Croatian Institute for Brain Research, School of Medicine, University of Zagreb, Zagreb, Croatia
| | - Reinhard Brunmeir
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
| | - Julija Jurić
- Glycoscience Research Laboratory, Genos Ltd., Zagreb, Croatia
| | | | - Anita Slana
- Glycoscience Research Laboratory, Genos Ltd., Zagreb, Croatia
| | - Helena Deriš
- Glycoscience Research Laboratory, Genos Ltd., Zagreb, Croatia
| | - Azra Frkatović
- Glycoscience Research Laboratory, Genos Ltd., Zagreb, Croatia
| | - Jűrgen Groet
- Faculty of Medicine and Dentistry, Blizard Institute, Queen Mary University of London, London, UK; The London Down Syndrome Consortium (LonDownS), London, UK
| | - Niamh L O'Brien
- Faculty of Medicine and Dentistry, Blizard Institute, Queen Mary University of London, London, UK; The London Down Syndrome Consortium (LonDownS), London, UK
| | - Hong Yu Chen
- Institute of Molecular and Cell Biology (IMCB), A∗STAR, Singapore
| | - Yee Jie Yeap
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
| | - Frederic Delom
- Faculty of Medicine and Dentistry, Blizard Institute, Queen Mary University of London, London, UK
| | - Steven Havlicek
- Laboratory of Neurogenetics, Genome Institute of Singapore, A∗STAR, Singapore
| | - Luke Gammon
- Faculty of Medicine and Dentistry, Blizard Institute, Queen Mary University of London, London, UK
| | - Sarah Hamburg
- The London Down Syndrome Consortium (LonDownS), London, UK
| | - Carla Startin
- The London Down Syndrome Consortium (LonDownS), London, UK; Department of Forensic and Neurodevelopmental Sciences, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK; Division of Psychiatry, University College London, London, UK; School of Psychology, University of Roehampton, London, UK
| | - Hana D'Souza
- The London Down Syndrome Consortium (LonDownS), London, UK; Centre for Brain and Cognitive Development, Birkbeck, University of London, London, UK
| | - Dinko Mitrečić
- Croatian Institute for Brain Research, School of Medicine, University of Zagreb, Zagreb, Croatia
| | - Mijana Kero
- Department of Medical Genetics, Children's Hospital Zagreb, Centre of Excellence for Reproductive and Regenerative Medicine, School of Medicine, University of Zagreb, Zagreb, Croatia
| | - Ljubica Odak
- Department of Medical Genetics, Children's Hospital Zagreb, Centre of Excellence for Reproductive and Regenerative Medicine, School of Medicine, University of Zagreb, Zagreb, Croatia
| | - Božo Krušlin
- Department of Pathology, School of Medicine, University of Zagreb, Zagreb, Croatia
| | - Željka Krsnik
- Croatian Institute for Brain Research, School of Medicine, University of Zagreb, Zagreb, Croatia
| | - Ivica Kostović
- Croatian Institute for Brain Research, School of Medicine, University of Zagreb, Zagreb, Croatia
| | - Jia Nee Foo
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore; Laboratory of Neurogenetics, Genome Institute of Singapore, A∗STAR, Singapore
| | - Yuin-Han Loh
- Institute of Molecular and Cell Biology (IMCB), A∗STAR, Singapore
| | - Norris Ray Dunn
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore; Institute of Molecular and Cell Biology (IMCB), A∗STAR, Singapore
| | - Susana de la Luna
- ICREA, Genome Biology Programme (CRG), Universitat Pompeu Fabra (UPF), CIBER of Rare Diseases, Barcelona, Spain
| | - Tim Spector
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Ingeborg Barišić
- Department of Medical Genetics, Children's Hospital Zagreb, Centre of Excellence for Reproductive and Regenerative Medicine, School of Medicine, University of Zagreb, Zagreb, Croatia
| | - Michael S C Thomas
- The London Down Syndrome Consortium (LonDownS), London, UK; Centre for Brain and Cognitive Development, Birkbeck, University of London, London, UK
| | - Andre Strydom
- The London Down Syndrome Consortium (LonDownS), London, UK; Department of Forensic and Neurodevelopmental Sciences, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK; Division of Psychiatry, University College London, London, UK
| | - Claudio Franceschi
- Department of Medical and Surgical Sciences, Alma Mater Studiorum University of Bologna, Italy; Institute of Information Technologies, Mathematics and Mechanics, Lobachevsky State University, Nizhny Novgorod 603022, Russia
| | - Gordan Lauc
- Glycoscience Research Laboratory, Genos Ltd., Zagreb, Croatia; Faculty of Pharmacy and Biochemistry, University of Zagreb, Zagreb, Croatia
| | | | - Ivan Alić
- Faculty of Medicine and Dentistry, Blizard Institute, Queen Mary University of London, London, UK; Faculty of Veterinary Medicine, Department of Anatomy, Histology and Embryology, University of Zagreb, Zagreb, Croatia.
| | - Dean Nižetić
- Faculty of Medicine and Dentistry, Blizard Institute, Queen Mary University of London, London, UK; The London Down Syndrome Consortium (LonDownS), London, UK; Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore.
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Isozaki H, Sakhtemani R, Abbasi A, Nikpour N, Stanzione M, Oh S, Langenbucher A, Monroe S, Su W, Cabanos HF, Siddiqui FM, Phan N, Jalili P, Timonina D, Bilton S, Gomez-Caraballo M, Archibald HL, Nangia V, Dionne K, Riley A, Lawlor M, Banwait MK, Cobb RG, Zou L, Dyson NJ, Ott CJ, Benes C, Getz G, Chan CS, Shaw AT, Gainor JF, Lin JJ, Sequist LV, Piotrowska Z, Yeap BY, Engelman JA, Lee JJK, Maruvka YE, Buisson R, Lawrence MS, Hata AN. Therapy-induced APOBEC3A drives evolution of persistent cancer cells. Nature 2023; 620:393-401. [PMID: 37407818 PMCID: PMC10804446 DOI: 10.1038/s41586-023-06303-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 06/08/2023] [Indexed: 07/07/2023]
Abstract
Acquired drug resistance to anticancer targeted therapies remains an unsolved clinical problem. Although many drivers of acquired drug resistance have been identified1-4, the underlying molecular mechanisms shaping tumour evolution during treatment are incompletely understood. Genomic profiling of patient tumours has implicated apolipoprotein B messenger RNA editing catalytic polypeptide-like (APOBEC) cytidine deaminases in tumour evolution; however, their role during therapy and the development of acquired drug resistance is undefined. Here we report that lung cancer targeted therapies commonly used in the clinic can induce cytidine deaminase APOBEC3A (A3A), leading to sustained mutagenesis in drug-tolerant cancer cells persisting during therapy. Therapy-induced A3A promotes the formation of double-strand DNA breaks, increasing genomic instability in drug-tolerant persisters. Deletion of A3A reduces APOBEC mutations and structural variations in persister cells and delays the development of drug resistance. APOBEC mutational signatures are enriched in tumours from patients with lung cancer who progressed after extended responses to targeted therapies. This study shows that induction of A3A in response to targeted therapies drives evolution of drug-tolerant persister cells, suggesting that suppression of A3A expression or activity may represent a potential therapeutic strategy in the prevention or delay of acquired resistance to lung cancer targeted therapy.
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Affiliation(s)
- Hideko Isozaki
- Massachusetts General Hospital Cancer Center, Boston, MA, USA.
- Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
| | - Ramin Sakhtemani
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ammal Abbasi
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
| | - Naveed Nikpour
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
| | | | - Sunwoo Oh
- Department of Biological Chemistry, Center for Epigenetics and Metabolism, Chao Family Comprehensive Cancer Center, School of Medicine, University of California Irvine, Irvine, CA, USA
| | | | - Susanna Monroe
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
| | - Wenjia Su
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
| | - Heidie Frisco Cabanos
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
- Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | | | - Nicole Phan
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
| | - Pégah Jalili
- Department of Biological Chemistry, Center for Epigenetics and Metabolism, Chao Family Comprehensive Cancer Center, School of Medicine, University of California Irvine, Irvine, CA, USA
| | - Daria Timonina
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
| | - Samantha Bilton
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
| | | | | | - Varuna Nangia
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
| | - Kristin Dionne
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
| | - Amanda Riley
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
| | - Matthew Lawlor
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
| | | | - Rosemary G Cobb
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
| | - Lee Zou
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
- Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC, USA
| | - Nicholas J Dyson
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
- Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Christopher J Ott
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
- Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Cyril Benes
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
- Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Gad Getz
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
- Department of Pathology, Harvard Medical School, Boston, MA, USA
| | - Chang S Chan
- Department of Medicine, Rutgers Robert Wood Johnson Medical School and Center for Systems and Computational Biology, Rutgers Cancer Institute, New Brunswick, NJ, USA
| | - Alice T Shaw
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
- Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Justin F Gainor
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
- Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Jessica J Lin
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
- Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Lecia V Sequist
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
- Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Zofia Piotrowska
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
- Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Beow Y Yeap
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
- Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Jeffrey A Engelman
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
- Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Jake June-Koo Lee
- Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Yosef E Maruvka
- Faculty of Biotechnology and Food Engineering, Lorey Loki Center for Life Science and Engineering, Technion, Haifa, Israel
| | - Rémi Buisson
- Department of Biological Chemistry, Center for Epigenetics and Metabolism, Chao Family Comprehensive Cancer Center, School of Medicine, University of California Irvine, Irvine, CA, USA
- Department of Pharmaceutical Sciences, School of Pharmacy & Pharmaceutical Sciences, University of California Irvine, Irvine, CA, USA
| | - Michael S Lawrence
- Massachusetts General Hospital Cancer Center, Boston, MA, USA.
- Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Aaron N Hata
- Massachusetts General Hospital Cancer Center, Boston, MA, USA.
- Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
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Shimizu N, Hamada Y, Morozumi R, Yamamoto J, Iwai S, Sugiyama KI, Ide H, Tsuda M. Repair of topoisomerase 1-induced DNA damage by tyrosyl-DNA phosphodiesterase 2 (TDP2) is dependent on its magnesium binding. J Biol Chem 2023; 299:104988. [PMID: 37392847 PMCID: PMC10407441 DOI: 10.1016/j.jbc.2023.104988] [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: 01/15/2023] [Revised: 06/12/2023] [Accepted: 06/13/2023] [Indexed: 07/03/2023] Open
Abstract
Topoisomerases are enzymes that relax DNA supercoiling during replication and transcription. Camptothecin, a topoisomerase 1 (TOP1) inhibitor, and its analogs trap TOP1 at the 3'-end of DNA as a DNA-bound intermediate, resulting in DNA damage that can kill cells. Drugs with this mechanism of action are widely used to treat cancers. It has previously been shown that tyrosyl-DNA phosphodiesterase 1 (TDP1) repairs TOP1-induced DNA damage generated by camptothecin. In addition, tyrosyl-DNA phosphodiesterase 2 (TDP2) plays critical roles in repairing topoisomerase 2 (TOP2)-induced DNA damage at the 5'-end of DNA and in promoting the repair of TOP1-induced DNA damage in the absence of TDP1. However, the catalytic mechanism by which TDP2 processes TOP1-induced DNA damage has not been elucidated. In this study, we found that a similar catalytic mechanism underlies the repair of TOP1- and TOP2-induced DNA damage by TDP2, with Mg2+-TDP2 binding playing a role in both repair mechanisms. We show chain-terminating nucleoside analogs are incorporated into DNA at the 3'-end and abort DNA replication to kill cells. Furthermore, we found that Mg2+-TDP2 binding also contributes to the repair of incorporated chain-terminating nucleoside analogs. Overall, these findings reveal the role played by Mg2+-TDP2 binding in the repair of both 3'- and 5'-blocking DNA damage.
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Affiliation(s)
- Naoto Shimizu
- Program of Mathematical and Life Sciences, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan
| | - Yusaku Hamada
- Program of Biomedical Science, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan
| | - Ryosuke Morozumi
- Program of Biomedical Science, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan
| | - Junpei Yamamoto
- Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka, Japan
| | - Shigenori Iwai
- Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka, Japan
| | - Kei-Ichi Sugiyama
- Division of Genetics and Mutagenesis, National Institute of Health Sciences, Kawasaki, Kanagawa, Japan
| | - Hiroshi Ide
- Program of Mathematical and Life Sciences, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan.
| | - Masataka Tsuda
- Program of Mathematical and Life Sciences, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan; Program of Biomedical Science, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan; Division of Genetics and Mutagenesis, National Institute of Health Sciences, Kawasaki, Kanagawa, Japan.
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Zhou M, Boulos JC, Omer EA, Klauck SM, Efferth T. Modes of Action of a Novel c-MYC Inhibiting 1,2,4-Oxadiazole Derivative in Leukemia and Breast Cancer Cells. Molecules 2023; 28:5658. [PMID: 37570631 PMCID: PMC10419799 DOI: 10.3390/molecules28155658] [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: 06/16/2023] [Revised: 07/19/2023] [Accepted: 07/24/2023] [Indexed: 08/13/2023] Open
Abstract
The c-MYC oncogene regulates multiple cellular activities and is a potent driver of many highly aggressive human cancers, such as leukemia and triple-negative breast cancer. The oxadiazole class of compounds has gained increasing interest for its anticancer activities. The aim of this study was to investigate the molecular modes of action of a 1,2,4-oxadiazole derivative (ZINC15675948) as a c-MYC inhibitor. ZINC15675948 displayed profound cytotoxicity at the nanomolar range in CCRF-CEM leukemia and MDA-MB-231-pcDNA3 breast cancer cells. Multidrug-resistant sublines thereof (i.e., CEM/ADR5000 and MDA-MB-231-BCRP) were moderately cross-resistant to this compound (<10-fold). Molecular docking and microscale thermophoresis revealed a strong binding of ZINC15675948 to c-MYC by interacting close to the c-MYC/MAX interface. A c-MYC reporter assay demonstrated that ZINC15675948 inhibited c-MYC activity. Western blotting and qRT-PCR showed that c-MYC expression was downregulated by ZINC15675948. Applying microarray hybridization and signaling pathway analyses, ZINC15675948 affected signaling routes downstream of c-MYC in both leukemia and breast cancer cells as demonstrated by the induction of DNA damage using single cell gel electrophoresis (alkaline comet assay) and induction of apoptosis using flow cytometry. ZINC15675948 also caused G2/M phase and S phase arrest in CCRF-CEM cells and MDA-MB-231-pcDNA3 cells, respectively, accompanied by the downregulation of CDK1 and p-CDK2 expression using western blotting. Autophagy induction was observed in CCRF-CEM cells but not MDA-MB-231-pcDNA3 cells. Furthermore, microarray-based mRNA expression profiling indicated that ZINC15675948 may target c-MYC-regulated ubiquitination, since the novel ubiquitin ligase (ELL2) was upregulated in the absence of c-MYC expression. We propose that ZINC15675948 is a promising natural product-derived compound targeting c-MYC in c-MYC-driven cancers through DNA damage, cell cycle arrest, and apoptosis.
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Affiliation(s)
- Min Zhou
- Department of Pharmaceutical Biology, Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University-Mainz, Staudinger Weg 5, 55128 Mainz, Germany
| | - Joelle C. Boulos
- Department of Pharmaceutical Biology, Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University-Mainz, Staudinger Weg 5, 55128 Mainz, Germany
| | - Ejlal A. Omer
- Department of Pharmaceutical Biology, Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University-Mainz, Staudinger Weg 5, 55128 Mainz, Germany
| | - Sabine M. Klauck
- Division of Cancer Genome Research, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), National Center for Tumor Disease (NCT), Im Neuenheimer Feld 460, 69120 Heidelberg, Germany
| | - Thomas Efferth
- Department of Pharmaceutical Biology, Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University-Mainz, Staudinger Weg 5, 55128 Mainz, Germany
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Wu T, Hou H, Dey A, Bachu M, Chen X, Wisniewski J, Kudoh F, Chen C, Chauhan S, Xiao H, Pan R, Ozato K. BRD4 directs mitotic cell division by inhibiting DNA damage. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.02.547436. [PMID: 37546888 PMCID: PMC10401944 DOI: 10.1101/2023.07.02.547436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
BRD4 binds to acetylated histones to regulate transcription and drive cancer cell proliferation. However, the role of BRD4 in normal cell growth remains to be elucidated. Here we investigated the question by using mouse embryonic fibroblasts with conditional Brd4 knockout (KO). We found that Brd4KO cells grow more slowly than wild type cells: they do not complete replication, fail to achieve mitosis, and exhibit extensive DNA damage throughout all cell cycle stages. BRD4 was required for expression of more than 450 cell cycle genes including genes encoding core histones and centromere/kinetochore proteins that are critical for genome replication and chromosomal segregation. Moreover, we show that many genes controlling R-loop formation and DNA damage response (DDR) require BRD4 for expression. Finally, BRD4 constitutively occupied genes controlling R-loop, DDR and cell cycle progression. We suggest that BRD4 epigenetically marks those genes and serves as a master regulator of normal cell growth.
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50
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Wörthmüller J, Disler S, Pradervand S, Richard F, Haerri L, Ruiz Buendía GA, Fournier N, Desmedt C, Rüegg C. MAGI1 Prevents Senescence and Promotes the DNA Damage Response in ER + Breast Cancer. Cells 2023; 12:1929. [PMID: 37566008 PMCID: PMC10417439 DOI: 10.3390/cells12151929] [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: 05/09/2023] [Revised: 06/30/2023] [Accepted: 07/18/2023] [Indexed: 08/12/2023] Open
Abstract
MAGI1 acts as a tumor suppressor in estrogen receptor-positive (ER+) breast cancer (BC), and its loss correlates with a more aggressive phenotype. To identify the pathways and events affected by MAGI1 loss, we deleted the MAGI1 gene in the ER+ MCF7 BC cell line and performed RNA sequencing and functional experiments in vitro. Transcriptome analyses revealed gene sets and biological processes related to estrogen signaling, the cell cycle, and DNA damage responses affected by MAGI1 loss. Upon exposure to TNF-α/IFN-γ, MCF7 MAGI1 KO cells entered a deeper level of quiescence/senescence compared with MCF7 control cells and activated the AKT and MAPK signaling pathways. MCF7 MAGI1 KO cells exposed to ionizing radiations or cisplatin had reduced expression of DNA repair proteins and showed increased sensitivity towards PARP1 inhibition using olaparib. Treatment with PI3K and AKT inhibitors (alpelisib and MK-2206) restored the expression of DNA repair proteins and sensitized cells to fulvestrant. An analysis of human BC patients' transcriptomic data revealed that patients with low MAGI1 levels had a higher tumor mutational burden and homologous recombination deficiency. Moreover, MAGI1 expression levels negatively correlated with PI3K/AKT and MAPK signaling, which confirmed our in vitro observations. Pharmacological and genomic evidence indicate HDACs as regulators of MAGI1 expression. Our findings provide a new view on MAGI1 function in cancer and identify potential treatment options to improve the management of ER+ BC patients with low MAGI1 levels.
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Affiliation(s)
- Janine Wörthmüller
- Laboratory of Experimental and Translational Oncology, Department of Oncology, Microbiology and Immunology (OMI), Faculty of Science and Medicine, University of Fribourg, 1700 Fribourg, Switzerland
| | - Simona Disler
- Laboratory of Experimental and Translational Oncology, Department of Oncology, Microbiology and Immunology (OMI), Faculty of Science and Medicine, University of Fribourg, 1700 Fribourg, Switzerland
| | - Sylvain Pradervand
- Lausanne Genomic Technologies Facility (LGTF), University of Lausanne, 1015 Lausanne, Switzerland
| | - François Richard
- Laboratory for Translational Breast Cancer Research, KU Leuven, 3000 Leuven, Belgium
| | - Lisa Haerri
- Laboratory of Experimental and Translational Oncology, Department of Oncology, Microbiology and Immunology (OMI), Faculty of Science and Medicine, University of Fribourg, 1700 Fribourg, Switzerland
| | - Gustavo A. Ruiz Buendía
- Translational Data Science-Facility, AGORA Cancer Research Center, Swiss Institute of Bioinformatics (SIB), Bugnon 25A, 1005 Lausanne, Switzerland
| | - Nadine Fournier
- Translational Data Science-Facility, AGORA Cancer Research Center, Swiss Institute of Bioinformatics (SIB), Bugnon 25A, 1005 Lausanne, Switzerland
| | - Christine Desmedt
- Laboratory for Translational Breast Cancer Research, KU Leuven, 3000 Leuven, Belgium
| | - Curzio Rüegg
- Laboratory of Experimental and Translational Oncology, Department of Oncology, Microbiology and Immunology (OMI), Faculty of Science and Medicine, University of Fribourg, 1700 Fribourg, Switzerland
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