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Lu C, Gao H, Li H, Luo N, Fan S, Li X, Deng R, He D, Zhao H. A novel LINC02321 promotes cell proliferation and decreases cisplatin sensitivity in bladder cancer by regulating RUVBL2. Transl Oncol 2024; 45:101962. [PMID: 38677015 PMCID: PMC11066559 DOI: 10.1016/j.tranon.2024.101962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2023] [Revised: 10/15/2023] [Accepted: 04/15/2024] [Indexed: 04/29/2024] Open
Abstract
Bladder cancer (BC) has a high incidence and is prone to recurrence. In most instances, the low 5-year survival rate of advanced BC patients results from postoperative recurrence and drug resistance. Long noncoding RNAs (lncRNAs) can participate in numerous biological functions by regulating the expression of genes to affect tumorigenesis. Our previous work had demonstrated that a novel lncRNA, LINC02321, was associated with BC prognosis. In this study, A high expression of LINC02321 was found in BC tissues, which was associated with poor prognosis in patients. LINC02321 promoted both proliferation and G1-G0 progression in BC cells, while also inhibited sensitivity to cisplatin. Mechanistically, LINC02321 can bind to RUVBL2 and regulate the expression levels of RUVBL2 protein by affecting its half-life. RUVBL2 is involved in the DNA damage response. The potential of DNA damage repair pathways to exert chemosensitization has been demonstrated in vivo. The rescue experiment demonstrated that RUVBL2 overexpression can markedly abolish the decreased cell proliferation and the increased sensitivity of BC cells to cisplatin caused by LINC02321 knockdown. The results indicate that LINC02321 functions as an oncogene in BC, and may serve as a novel potential target for controlling BC progression and addressing cisplatin resistance in BC therapy.
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Affiliation(s)
- Chuncheng Lu
- Department of Urology, The 1st Affiliated Hospital of Kunming Medical University, Kunming 650032, China; Yunnan Province Clinical Research Center for Chronic Kidney Disease, Kunming 650032, China
| | - Hongbin Gao
- Department of Urology, The 1st Affiliated Hospital of Kunming Medical University, Kunming 650032, China; Yunnan Province Clinical Research Center for Chronic Kidney Disease, Kunming 650032, China
| | - Haiyuan Li
- Department of Urology, The 1st Affiliated Hospital of Kunming Medical University, Kunming 650032, China; Yunnan Province Clinical Research Center for Chronic Kidney Disease, Kunming 650032, China
| | - Ning Luo
- Department of Urology, The 1st Affiliated Hospital of Kunming Medical University, Kunming 650032, China; Yunnan Province Clinical Research Center for Chronic Kidney Disease, Kunming 650032, China
| | - Shipeng Fan
- Department of Urology, The 1st Affiliated Hospital of Kunming Medical University, Kunming 650032, China; Yunnan Province Clinical Research Center for Chronic Kidney Disease, Kunming 650032, China
| | - Xi Li
- Department of Urology, The 1st Affiliated Hospital of Kunming Medical University, Kunming 650032, China; Yunnan Province Clinical Research Center for Chronic Kidney Disease, Kunming 650032, China
| | - Renbin Deng
- Department of Urology, The 1st Affiliated Hospital of Kunming Medical University, Kunming 650032, China; Yunnan Province Clinical Research Center for Chronic Kidney Disease, Kunming 650032, China
| | - Danpeng He
- Department of Urology, The 1st Affiliated Hospital of Kunming Medical University, Kunming 650032, China; Yunnan Province Clinical Research Center for Chronic Kidney Disease, Kunming 650032, China
| | - Hui Zhao
- Department of Urology, The 1st Affiliated Hospital of Kunming Medical University, Kunming 650032, China; Yunnan Province Clinical Research Center for Chronic Kidney Disease, Kunming 650032, China.
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Mao YQ, Seraphim TV, Wan Y, Wu R, Coyaud E, Bin Munim M, Mollica A, Laurent E, Babu M, Mennella V, Raught B, Houry WA. DPCD is a regulator of R2TP in ciliogenesis initiation through Akt signaling. Cell Rep 2024; 43:113713. [PMID: 38306274 DOI: 10.1016/j.celrep.2024.113713] [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] [Revised: 10/31/2023] [Accepted: 01/12/2024] [Indexed: 02/04/2024] Open
Abstract
R2TP is a chaperone complex consisting of the AAA+ ATPases RUVBL1 and RUVBL2, as well as RPAP3 and PIH1D1 proteins. R2TP is responsible for the assembly of macromolecular complexes mainly acting through different adaptors. Using proximity-labeling mass spectrometry, we identified deleted in primary ciliary dyskinesia (DPCD) as an adaptor of R2TP. Here, we demonstrate that R2TP-DPCD influences ciliogenesis initiation through a unique mechanism by interaction with Akt kinase to regulate its phosphorylation levels rather than its stability. We further show that DPCD is a heart-shaped monomeric protein with two domains. A highly conserved region in the cysteine- and histidine-rich domains-containing proteins and SGT1 (CS) domain of DPCD interacts with the RUVBL2 DII domain with high affinity to form a stable R2TP-DPCD complex both in cellulo and in vitro. Considering that DPCD is one among several CS-domain-containing proteins found to associate with RUVBL1/2, we propose that RUVBL1/2 are CS-domain-binding proteins that regulate complex assembly and downstream signaling.
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Affiliation(s)
- Yu-Qian Mao
- Department of Biochemistry, University of Toronto, Toronto, ON M5G 1M1, Canada
| | - Thiago V Seraphim
- Department of Biochemistry, University of Toronto, Toronto, ON M5G 1M1, Canada; Department of Chemistry and Biochemistry, University of Regina, Regina, SK S4S 0A2, Canada
| | - Yimei Wan
- Department of Biochemistry, University of Toronto, Toronto, ON M5G 1M1, Canada
| | - Ruikai Wu
- Department of Biochemistry, University of Toronto, Toronto, ON M5G 1M1, Canada
| | - Etienne Coyaud
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Muhammad Bin Munim
- Department of Biochemistry, University of Toronto, Toronto, ON M5G 1M1, Canada
| | - Antonio Mollica
- Department of Biochemistry, University of Toronto, Toronto, ON M5G 1M1, Canada
| | - Estelle Laurent
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Mohan Babu
- Department of Chemistry and Biochemistry, University of Regina, Regina, SK S4S 0A2, Canada
| | - Vito Mennella
- Department of Biochemistry, University of Toronto, Toronto, ON M5G 1M1, Canada; Cell Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; MRC Toxicology Unit, School of Biological Sciences, University of Cambridge, Cambridge CB2 1QR, UK; Department of Pathology, School of Biological Sciences, University of Cambridge, Cambridge CB2 1QP, UK
| | - Brian Raught
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Walid A Houry
- Department of Biochemistry, University of Toronto, Toronto, ON M5G 1M1, Canada; Department of Chemistry, University of Toronto, Toronto, ON M5S 3H6, Canada.
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Zemke NR, Hsu E, Barshop WD, Sha J, Wohlschlegel JA, Berk AJ. Adenovirus E1A binding to DCAF10 targets proteasomal degradation of RUVBL1/2 AAA+ ATPases required for quaternary assembly of multiprotein machines, innate immunity, and responses to metabolic stress. J Virol 2023; 97:e0099323. [PMID: 37962355 PMCID: PMC10734532 DOI: 10.1128/jvi.00993-23] [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: 07/08/2023] [Accepted: 10/16/2023] [Indexed: 11/15/2023] Open
Abstract
IMPORTANCE Inactivation of EP300/CREBB paralogous cellular lysine acetyltransferases (KATs) during the early phase of infection is a consistent feature of DNA viruses. The cell responds by stabilizing transcription factor IRF3 which activates transcription of scores of interferon-stimulated genes (ISGs), inhibiting viral replication. Human respiratory adenoviruses counter this by assembling a CUL4-based ubiquitin ligase complex that polyubiquitinylates RUVBL1 and 2 inducing their proteasomal degradation. This inhibits accumulation of active IRF3 and the expression of anti-viral ISGs, allowing replication of the respiratory HAdVs in the face of inhibition of EP300/CBEBBP KAT activity by the N-terminal region of E1A.
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Affiliation(s)
- Nathan R. Zemke
- Molecular Biology Institute, University of California, Los Angeles, California, USA
- Department of Cellular and Molecular Medicine, UCSD School of Medicine, La Jolla, California, USA
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, California, USA
| | - Emily Hsu
- Molecular Biology Institute, University of California, Los Angeles, California, USA
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, California, USA
- Department of Biological Chemistry, David Geffen School of Medicine at UCLA, Los Angeles, California, USA
| | - William D. Barshop
- Thermo Fisher Scientific, San Jose, California, USA
- Department of Biochemistry and Molecular Medicine and the Norris Comprehensive Cancer Center, Keck School of Medicine, USC, Los Angeles, California, USA
| | - Jihui Sha
- Thermo Fisher Scientific, San Jose, California, USA
| | - James A. Wohlschlegel
- Molecular Biology Institute, University of California, Los Angeles, California, USA
- Thermo Fisher Scientific, San Jose, California, USA
| | - Arnold J. Berk
- Molecular Biology Institute, University of California, Los Angeles, California, USA
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, California, USA
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4
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Li M, Yang L, Chan AKN, Pokharel SP, Liu Q, Mattson N, Xu X, Chang W, Miyashita K, Singh P, Zhang L, Li M, Wu J, Wang J, Chen B, Chan LN, Lee J, Zhang XH, Rosen ST, Müschen M, Qi J, Chen J, Hiom K, Bishop AJR, Chen C. Epigenetic Control of Translation Checkpoint and Tumor Progression via RUVBL1-EEF1A1 Axis. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2206584. [PMID: 37075745 PMCID: PMC10265057 DOI: 10.1002/advs.202206584] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 02/23/2023] [Indexed: 05/03/2023]
Abstract
Epigenetic dysregulation is reported in multiple cancers including Ewing sarcoma (EwS). However, the epigenetic networks underlying the maintenance of oncogenic signaling and therapeutic response remain unclear. Using a series of epigenetics- and complex-focused CRISPR screens, RUVBL1, the ATPase component of NuA4 histone acetyltransferase complex, is identified to be essential for EwS tumor progression. Suppression of RUVBL1 leads to attenuated tumor growth, loss of histone H4 acetylation, and ablated MYC signaling. Mechanistically, RUVBL1 controls MYC chromatin binding and modulates the MYC-driven EEF1A1 expression and thus protein synthesis. High-density CRISPR gene body scan pinpoints the critical MYC interacting residue in RUVBL1. Finally, this study reveals the synergism between RUVBL1 suppression and pharmacological inhibition of MYC in EwS xenografts and patient-derived samples. These results indicate that the dynamic interplay between chromatin remodelers, oncogenic transcription factors, and protein translation machinery can provide novel opportunities for combination cancer therapy.
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Affiliation(s)
- Mingli Li
- Department of Systems BiologyBeckman Research InstituteCity of Hope Comprehensive Cancer CenterDuarteCA91010USA
| | - Lu Yang
- Department of Systems BiologyBeckman Research InstituteCity of Hope Comprehensive Cancer CenterDuarteCA91010USA
- Division of Epigenetic and Transcriptional EngineeringBeckman Research InstituteCity of Hope Comprehensive Cancer CenterDuarteCA91010USA
| | - Anthony K. N. Chan
- Department of Systems BiologyBeckman Research InstituteCity of Hope Comprehensive Cancer CenterDuarteCA91010USA
- Division of Epigenetic and Transcriptional EngineeringBeckman Research InstituteCity of Hope Comprehensive Cancer CenterDuarteCA91010USA
| | - Sheela Pangeni Pokharel
- Department of Systems BiologyBeckman Research InstituteCity of Hope Comprehensive Cancer CenterDuarteCA91010USA
- Division of Epigenetic and Transcriptional EngineeringBeckman Research InstituteCity of Hope Comprehensive Cancer CenterDuarteCA91010USA
| | - Qiao Liu
- Department of Systems BiologyBeckman Research InstituteCity of Hope Comprehensive Cancer CenterDuarteCA91010USA
| | - Nicole Mattson
- Department of Systems BiologyBeckman Research InstituteCity of Hope Comprehensive Cancer CenterDuarteCA91010USA
| | - Xiaobao Xu
- Department of Systems BiologyBeckman Research InstituteCity of Hope Comprehensive Cancer CenterDuarteCA91010USA
| | - Wen‐Han Chang
- Department of Systems BiologyBeckman Research InstituteCity of Hope Comprehensive Cancer CenterDuarteCA91010USA
| | - Kazuya Miyashita
- Department of Systems BiologyBeckman Research InstituteCity of Hope Comprehensive Cancer CenterDuarteCA91010USA
| | - Priyanka Singh
- Department of Systems BiologyBeckman Research InstituteCity of Hope Comprehensive Cancer CenterDuarteCA91010USA
| | - Leisi Zhang
- Department of Systems BiologyBeckman Research InstituteCity of Hope Comprehensive Cancer CenterDuarteCA91010USA
| | - Maggie Li
- Department of Systems BiologyBeckman Research InstituteCity of Hope Comprehensive Cancer CenterDuarteCA91010USA
| | - Jun Wu
- City of Hope Comprehensive Cancer CenterDuarteCA91010USA
| | - Jinhui Wang
- City of Hope Comprehensive Cancer CenterDuarteCA91010USA
| | - Bryan Chen
- Department of Systems BiologyBeckman Research InstituteCity of Hope Comprehensive Cancer CenterDuarteCA91010USA
| | - Lai N. Chan
- Center of Molecular and Cellular OncologyYale Cancer CenterYale School of MedicineNew HavenCT06510USA
- Department of Cancer BiologyLerner Research InstituteCleveland ClinicClevelandOH44195USA
| | - Jaewoong Lee
- Center of Molecular and Cellular OncologyYale Cancer CenterYale School of MedicineNew HavenCT06510USA
- School of Biosystems and Biomedical SciencesCollege of Health ScienceKorea UniversitySeoul02841South Korea
- Interdisciplinary Program in Precision Public HealthKorea UniversitySeoul02841South Korea
| | | | | | - Markus Müschen
- Center of Molecular and Cellular OncologyYale Cancer CenterYale School of MedicineNew HavenCT06510USA
| | - Jun Qi
- Department of Cancer BiologyDana‐Farber Cancer InstituteHarvard Medical SchoolBostonMA02215USA
| | - Jianjun Chen
- Department of Systems BiologyBeckman Research InstituteCity of Hope Comprehensive Cancer CenterDuarteCA91010USA
- City of Hope Comprehensive Cancer CenterDuarteCA91010USA
| | - Kevin Hiom
- Division of Cellular MedicineSchool of MedicineUniversity of DundeeNethergateDundeeDD1 4HNUK
| | - Alexander J. R. Bishop
- Department of Cellular Systems and AnatomyUniversity of Texas Health Science Center at San AntonioSan AntonioTX78229USA
- Greehey Children's Cancer Research InstituteUniversity of Texas Health Science Center at San AntonioSan AntonioTX78229USA
| | - Chun‐Wei Chen
- Department of Systems BiologyBeckman Research InstituteCity of Hope Comprehensive Cancer CenterDuarteCA91010USA
- Division of Epigenetic and Transcriptional EngineeringBeckman Research InstituteCity of Hope Comprehensive Cancer CenterDuarteCA91010USA
- City of Hope Comprehensive Cancer CenterDuarteCA91010USA
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Dvořák Tomaštíková E, Yang F, Mlynárová K, Hafidh S, Schořová Š, Kusová A, Pernisová M, Přerovská T, Klodová B, Honys D, Fajkus J, Pecinka A, Schrumpfová PP. RUVBL proteins are involved in plant gametophyte development. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 114:325-337. [PMID: 36752686 DOI: 10.1111/tpj.16136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 01/25/2023] [Accepted: 02/01/2023] [Indexed: 05/10/2023]
Abstract
The proper development of male and female gametophytes is critical for successful sexual reproduction and requires a carefully regulated series of events orchestrated by a suite of various proteins. RUVBL1 and RUVBL2, plant orthologues of human Pontin and Reptin, respectively, belong to the evolutionarily highly conserved AAA+ family linked to a wide range of cellular processes. Previously, we found that RUVBL1 and RUVBL2A mutations are homozygous lethal in Arabidopsis. Here, we report that RUVBL1 and RUVBL2A play roles in reproductive development. We show that mutant plants produce embryo sacs with an abnormal structure or with various numbers of nuclei. Although pollen grains of heterozygous mutant plants exhibit reduced viability and reduced pollen tube growth in vitro, some of the ruvbl pollen tubes are capable of targeting ovules in vivo. Similarly, some ruvbl ovules retain the ability to attract wild-type pollen tubes but fail to develop further. The activity of the RUVBL1 and RUVBL2A promoters was observed in the embryo sac, pollen grains, and tapetum cells and, for RUVBL2A, also in developing ovules. In summary, we show that the RUVBL proteins are essential for the proper development of both male and particularly female gametophytes in Arabidopsis.
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Affiliation(s)
- Eva Dvořák Tomaštíková
- Centre of Plant Structural and Functional Genomics, Institute of Experimental Botany, Czech Academy of Sciences, Šlechtitelů 31, 77900, Olomouc, Czech Republic
| | - Fen Yang
- Centre of Plant Structural and Functional Genomics, Institute of Experimental Botany, Czech Academy of Sciences, Šlechtitelů 31, 77900, Olomouc, Czech Republic
- Department of Cell Biology and Genetics, Faculty of Science, Palacký University, Šlechtitelů 27, 77900, Olomouc, Czech Republic
| | - Kristína Mlynárová
- Laboratory of Functional Genomics and Proteomics, Faculty of Science, National Centre for Biomolecular Research, Masaryk University, Kamenice 5, CZ-62500, Brno, Czech Republic
| | - Said Hafidh
- Laboratory of Pollen Biology, Institute of Experimental Botany of the Czech Academy of Sciences, Rozvojová 263, CZ-165 02, Prague, Czech Republic
| | - Šárka Schořová
- Laboratory of Functional Genomics and Proteomics, Faculty of Science, National Centre for Biomolecular Research, Masaryk University, Kamenice 5, CZ-62500, Brno, Czech Republic
| | - Alžbeta Kusová
- Laboratory of Functional Genomics and Proteomics, Faculty of Science, National Centre for Biomolecular Research, Masaryk University, Kamenice 5, CZ-62500, Brno, Czech Republic
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Kamenice 5, CZ-62500, Brno, Czech Republic
| | - Markéta Pernisová
- Laboratory of Functional Genomics and Proteomics, Faculty of Science, National Centre for Biomolecular Research, Masaryk University, Kamenice 5, CZ-62500, Brno, Czech Republic
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Kamenice 5, CZ-62500, Brno, Czech Republic
| | - Tereza Přerovská
- Laboratory of Functional Genomics and Proteomics, Faculty of Science, National Centre for Biomolecular Research, Masaryk University, Kamenice 5, CZ-62500, Brno, Czech Republic
| | - Božena Klodová
- Laboratory of Pollen Biology, Institute of Experimental Botany of the Czech Academy of Sciences, Rozvojová 263, CZ-165 02, Prague, Czech Republic
- Department of Experimental Plant Biology, Faculty of Science, Charles University, Viničná 5, 128 00, Praha 2, Czech Republic
| | - David Honys
- Laboratory of Pollen Biology, Institute of Experimental Botany of the Czech Academy of Sciences, Rozvojová 263, CZ-165 02, Prague, Czech Republic
- Department of Experimental Plant Biology, Faculty of Science, Charles University, Viničná 5, 128 00, Praha 2, Czech Republic
| | - Jiří Fajkus
- Laboratory of Functional Genomics and Proteomics, Faculty of Science, National Centre for Biomolecular Research, Masaryk University, Kamenice 5, CZ-62500, Brno, Czech Republic
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Kamenice 5, CZ-62500, Brno, Czech Republic
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, CZ-61265, Brno, Czech Republic
| | - Ales Pecinka
- Centre of Plant Structural and Functional Genomics, Institute of Experimental Botany, Czech Academy of Sciences, Šlechtitelů 31, 77900, Olomouc, Czech Republic
- Department of Cell Biology and Genetics, Faculty of Science, Palacký University, Šlechtitelů 27, 77900, Olomouc, Czech Republic
| | - Petra Procházková Schrumpfová
- Laboratory of Functional Genomics and Proteomics, Faculty of Science, National Centre for Biomolecular Research, Masaryk University, Kamenice 5, CZ-62500, Brno, Czech Republic
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Kamenice 5, CZ-62500, Brno, Czech Republic
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Khurana J, Shrivastava A, Singh A, Gupta A. Exploring potential of Plasmodium RUVBL proteins as anti-malarial drug target. J Biomol Struct Dyn 2023; 41:736-752. [PMID: 34877896 DOI: 10.1080/07391102.2021.2011418] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Although malaria related cases and deaths have consistently declined over time, growing resistance to existing anti-malarial drugs in Plasmodium remains a matter of extreme concern. Since we rely so heavily on use of chemotherapy for malaria treatment and knowing that all the available anti-malarial drug will become virtually useless in the near future, we have to increase our understanding of basic biology of the parasite as well as characterize new molecular targets that can be exploited for anti-malarial therapy. In the present study, PfRUVBLs (AAA family member proteins) were evaluated for their potential as novel anti-malarial drug target candidates, using computational approaches. Virtual High-throughput screening of various pharmacophore libraries obtained from three different databases (which included, Asinex, ZINC15 & PubChem) followed by extra precision docking, resulted in identification of relevant hit compounds that showed binding affinity with the active region of PfRUVBL1 protein. Based on molecular docking data, MD simulations, and protein-ligand interaction studies, combined with toxicity assessment & ADME profiling data, at least three best hits were eventually identified that could be novel potent inhibitors of PfRUVBL1 protein and can be further tested for anti-malarial activity using in vitro protocols. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Juhi Khurana
- Epigenetics and Human Disease Laboratory, Department of Life Sciences, Shiv Nadar University, Greater Noida, India
| | - Ashish Shrivastava
- Bioinformatics Lab, Department of Life Sciences, Shiv Nadar University, Greater Noida, India
| | - Ashutosh Singh
- Bioinformatics Lab, Department of Life Sciences, Shiv Nadar University, Greater Noida, India
| | - Ashish Gupta
- Epigenetics and Human Disease Laboratory, Department of Life Sciences, Shiv Nadar University, Greater Noida, India
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Biological Functions of the DNA Glycosylase NEIL3 and Its Role in Disease Progression Including Cancer. Cancers (Basel) 2022; 14:cancers14235722. [PMID: 36497204 PMCID: PMC9737245 DOI: 10.3390/cancers14235722] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 11/16/2022] [Accepted: 11/16/2022] [Indexed: 11/24/2022] Open
Abstract
The accumulation of oxidative DNA base damage can severely disrupt the integrity of the genome and is strongly associated with the development of cancer. DNA glycosylase is the critical enzyme that initiates the base excision repair (BER) pathway, recognizing and excising damaged bases. The Nei endonuclease VIII-like 3 (NEIL3) is an emerging DNA glycosylase essential in maintaining genome stability. With an in-depth study of the structure and function of NEIL3, we found that it has properties related to the process of base damage repair. For example, it not only prefers the base damage of single-stranded DNA (ssDNA), G-quadruplex and DNA interstrand crosslinks (ICLs), but also participates in the maintenance of replication fork stability and telomere integrity. In addition, NEIL3 is strongly associated with the progression of cancers and cardiovascular and neurological diseases, is incredibly significantly overexpressed in cancers, and may become an independent prognostic marker for cancer patients. Interestingly, circNEIL3, a circular RNA of exon-encoded origin by NEIL3, also promotes the development of multiple cancers. In this review, we have summarized the structure and the characteristics of NEIL3 to repair base damage. We have focused on NEIL3 and circNEIL3 in cancer development, progression and prognosis.
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NEIL3 contributes to the Fanconi anemia/BRCA pathway by promoting the downstream double-strand break repair step. Cell Rep 2022; 41:111600. [PMID: 36351389 DOI: 10.1016/j.celrep.2022.111600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 08/30/2022] [Accepted: 10/13/2022] [Indexed: 11/09/2022] Open
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9
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Carraro C, Bonaguro L, Schulte-Schrepping J, Horne A, Oestreich M, Warnat-Herresthal S, Helbing T, De Franco M, Haendler K, Mukherjee S, Ulas T, Gandin V, Goettlich R, Aschenbrenner AC, Schultze JL, Gatto B. Decoding mechanism of action and sensitivity to drug candidates from integrated transcriptome and chromatin state. eLife 2022; 11:e78012. [PMID: 36043458 PMCID: PMC9433094 DOI: 10.7554/elife.78012] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 08/15/2022] [Indexed: 11/13/2022] Open
Abstract
Omics-based technologies are driving major advances in precision medicine, but efforts are still required to consolidate their use in drug discovery. In this work, we exemplify the use of multi-omics to support the development of 3-chloropiperidines, a new class of candidate anticancer agents. Combined analyses of transcriptome and chromatin accessibility elucidated the mechanisms underlying sensitivity to test agents. Furthermore, we implemented a new versatile strategy for the integration of RNA- and ATAC-seq (Assay for Transposase-Accessible Chromatin) data, able to accelerate and extend the standalone analyses of distinct omic layers. This platform guided the construction of a perturbation-informed basal signature predicting cancer cell lines' sensitivity and to further direct compound development against specific tumor types. Overall, this approach offers a scalable pipeline to support the early phases of drug discovery, understanding of mechanisms, and potentially inform the positioning of therapeutics in the clinic.
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Affiliation(s)
- Caterina Carraro
- Department of Pharmaceutical and Pharmacological Sciences, University of PadovaPadovaItaly
| | - Lorenzo Bonaguro
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V.BonnGermany
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of BonnBonnGermany
| | - Jonas Schulte-Schrepping
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V.BonnGermany
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of BonnBonnGermany
| | - Arik Horne
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V.BonnGermany
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of BonnBonnGermany
| | - Marie Oestreich
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V.BonnGermany
| | - Stefanie Warnat-Herresthal
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V.BonnGermany
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of BonnBonnGermany
| | - Tim Helbing
- Institute of Organic Chemistry, Justus Liebig University GiessenGiessenGermany
| | - Michele De Franco
- Department of Pharmaceutical and Pharmacological Sciences, University of PadovaPadovaItaly
| | - Kristian Haendler
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V.BonnGermany
- PRECISE Platform for Genomics and Epigenomics, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V. and University of BonnBonnGermany
- Institute of Human Genetics, University of LübeckLübeckGermany
| | - Sach Mukherjee
- Statistics and Machine Learning, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V.BonnGermany
- MRC Biostatistics Unit, University of CambridgeCambridgeUnited Kingdom
| | - Thomas Ulas
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V.BonnGermany
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of BonnBonnGermany
- PRECISE Platform for Genomics and Epigenomics, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V. and University of BonnBonnGermany
| | - Valentina Gandin
- Department of Pharmaceutical and Pharmacological Sciences, University of PadovaPadovaItaly
| | - Richard Goettlich
- Institute of Organic Chemistry, Justus Liebig University GiessenGiessenGermany
| | - Anna C Aschenbrenner
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V.BonnGermany
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of BonnBonnGermany
- PRECISE Platform for Genomics and Epigenomics, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V. and University of BonnBonnGermany
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical CenterNijmegenNetherlands
| | - Joachim L Schultze
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V.BonnGermany
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of BonnBonnGermany
- PRECISE Platform for Genomics and Epigenomics, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V. and University of BonnBonnGermany
| | - Barbara Gatto
- Department of Pharmaceutical and Pharmacological Sciences, University of PadovaPadovaItaly
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10
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Peake JD, Noguchi E. Fanconi anemia: current insights regarding epidemiology, cancer, and DNA repair. Hum Genet 2022; 141:1811-1836. [PMID: 35596788 DOI: 10.1007/s00439-022-02462-9] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 05/09/2022] [Indexed: 12/12/2022]
Abstract
Fanconi anemia is a genetic disorder that is characterized by bone marrow failure, as well as a predisposition to malignancies including leukemia and squamous cell carcinoma (SCC). At least 22 genes are associated with Fanconi anemia, constituting the Fanconi anemia DNA repair pathway. This pathway coordinates multiple processes and proteins to facilitate the repair of DNA adducts including interstrand crosslinks (ICLs) that are generated by environmental carcinogens, chemotherapeutic crosslinkers, and metabolic products of alcohol. ICLs can interfere with DNA transactions, including replication and transcription. If not properly removed and repaired, ICLs cause DNA breaks and lead to genomic instability, a hallmark of cancer. In this review, we will discuss the genetic and phenotypic characteristics of Fanconi anemia, the epidemiology of the disease, and associated cancer risk. The sources of ICLs and the role of ICL-inducing chemotherapeutic agents will also be discussed. Finally, we will review the detailed mechanisms of ICL repair via the Fanconi anemia DNA repair pathway, highlighting critical regulatory processes. Together, the information in this review will underscore important contributions to Fanconi anemia research in the past two decades.
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Affiliation(s)
- Jasmine D Peake
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, 245 N. 15th Street, Philadelphia, PA, 19102, USA
| | - Eishi Noguchi
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, 245 N. 15th Street, Philadelphia, PA, 19102, USA.
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11
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Reint G, Li Z, Labun K, Keskitalo S, Soppa I, Mamia K, Tolo E, Szymanska M, Meza-Zepeda LA, Lorenz S, Cieslar-Pobuda A, Hu X, Bordin DL, Staerk J, Valen E, Schmierer B, Varjosalo M, Taipale J, Haapaniemi E. Rapid genome editing by CRISPR-Cas9-POLD3 fusion. eLife 2021; 10:75415. [PMID: 34898428 PMCID: PMC8747517 DOI: 10.7554/elife.75415] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Accepted: 11/15/2021] [Indexed: 11/25/2022] Open
Abstract
Precision CRISPR gene editing relies on the cellular homology-directed DNA repair (HDR) to introduce custom DNA sequences to target sites. The HDR editing efficiency varies between cell types and genomic sites, and the sources of this variation are incompletely understood. Here, we have studied the effect of 450 DNA repair protein-Cas9 fusions on CRISPR genome editing outcomes. We find the majority of fusions to improve precision genome editing only modestly in a locus- and cell-type specific manner. We identify Cas9-POLD3 fusion that enhances editing by speeding up the initiation of DNA repair. We conclude that while DNA repair protein fusions to Cas9 can improve HDR CRISPR editing, most need to be optimized to the cell type and genomic site, highlighting the diversity of factors contributing to locus-specific genome editing outcomes.
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Affiliation(s)
- Ganna Reint
- Centre for Molecular Medicine, University of Oslo, Oslo, Norway
| | - Zhuokun Li
- Centre for Molecular Medicine, University of Oslo, Oslo, Norway
| | - Kornel Labun
- Department of Informatics, Computational Biology Unit, University of Bergen, Bergen, Norway
| | - Salla Keskitalo
- Centre for Biotechnology, University of Helsinki, Helsinki, Finland
| | - Inkeri Soppa
- Centre for Molecular Medicine, University of Oslo, Oslo, Finland
| | - Katariina Mamia
- Centre for Molecular Medicine, University of Oslo, Oslo, Norway
| | - Eero Tolo
- Faculty of Social Sciences, University of Helsinki, Oslo, Finland
| | | | - Leonardo A Meza-Zepeda
- Department of Core Facilities, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Susanne Lorenz
- Department of Core Facilities, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | | | - Xian Hu
- Centre for Molecular Medicine, University of Oslo, Oslo, Norway
| | - Diana L Bordin
- Department of Clinical Molecular Biology, Akershus University Hospital, Oslo, Norway
| | - Judith Staerk
- Centre for Molecular Medicine, University of Oslo, Oslo, Norway
| | - Eivind Valen
- Center for Biotechnology, University of Bergen, Bergen, Norway
| | - Bernhard Schmierer
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
| | - Markku Varjosalo
- Centre for Biotechnology, University of Helsinki, Helsinki, Finland
| | - Jussi Taipale
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Emma Haapaniemi
- Centre for Molecular Medicine, University of Oslo, Oslo, Norway
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12
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Zhang R, Cheung CY, Seo SU, Liu H, Pardeshi L, Wong KH, Chow LMC, Chau MP, Wang Y, Lee AR, Kwon WY, Chen S, Chan BKW, Wong K, Choy RKW, Ko BCB. RUVBL1/2 Complex Regulates Pro-Inflammatory Responses in Macrophages via Regulating Histone H3K4 Trimethylation. Front Immunol 2021; 12:679184. [PMID: 34276666 PMCID: PMC8282052 DOI: 10.3389/fimmu.2021.679184] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 05/14/2021] [Indexed: 12/13/2022] Open
Abstract
Macrophages play an important role in the host defense mechanism. In response to infection, macrophages activate a genetic program of pro-inflammatory response to kill any invading pathogen, and initiate an adaptive immune response. We have identified RUVBL2 - an ATP-binding protein belonging to the AAA+ (ATPase associated with diverse cellular activities) superfamily of ATPases - as a novel regulator in pro-inflammatory response of macrophages. Gene knockdown of Ruvbl2, or pharmacological inhibition of RUVBL1/2 activity, compromises type-2 nitric oxide synthase (Nos2) gene expression, nitric oxide production and anti-bacterial activity of mouse macrophages in response to lipopolysaccharides (LPS). RUVBL1/2 inhibitor similarly inhibits pro-inflammatory response in human monocytes, suggesting functional conservation of RUVBL1/2 in humans. Transcriptome analysis further revealed that major LPS-induced pro-inflammatory pathways in macrophages are regulated in a RUVBL1/2-dependent manner. Furthermore, RUVBL1/2 inhibition significantly reduced the level of histone H3K4me3 at the promoter region of Nos2 and Il6, two prototypical pro-inflammatory genes, and diminished the recruitment of NF-kappaB to the corresponding enhancers. Our study reveals RUVBL1/2 as an integral component of macrophage pro-inflammatory responses through epigenetic regulations, and the therapeutic potentials of RUVBL1/2 inhibitors in the treatment of diseases caused by aberrant activation of pro-inflammatory pathways.
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Affiliation(s)
- Rui Zhang
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hong Kong, China.,State Key Laboratory of Chemical Biology and Drug Discovery, The Hong Kong Polytechnic University, Hong Kong, China
| | - Chris Y Cheung
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hong Kong, China.,State Key Laboratory of Chemical Biology and Drug Discovery, The Hong Kong Polytechnic University, Hong Kong, China
| | - Sang-Uk Seo
- Department of Microbiology, Department of Biomedicine & Health Sciences, College of Medicine, The Catholic University of Korea, Seoul, South Korea
| | - Hang Liu
- The University Research Facility in Chemical and Environmental Analysis, The Hong Kong Polytechnic University, Hong Kong, China
| | - Lakhansing Pardeshi
- Faculty of Health Sciences, University of Macau, Avenida da Universidade, Taipa, Macau.,Genomics and Bioinformatics Core, Faculty of Health Sciences, University of Macau, Avenida da Universidade, Taipa, Macau
| | - Koon Ho Wong
- Faculty of Health Sciences, University of Macau, Avenida da Universidade, Taipa, Macau.,Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Avenida da Universidade, Taipa, Macau
| | - Larry M C Chow
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hong Kong, China.,State Key Laboratory of Chemical Biology and Drug Discovery, The Hong Kong Polytechnic University, Hong Kong, China
| | - Mary P Chau
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hong Kong, China.,State Key Laboratory of Chemical Biology and Drug Discovery, The Hong Kong Polytechnic University, Hong Kong, China
| | - Yixiang Wang
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hong Kong, China.,State Key Laboratory of Chemical Biology and Drug Discovery, The Hong Kong Polytechnic University, Hong Kong, China
| | - Ah Ra Lee
- Department of Microbiology, Department of Biomedicine & Health Sciences, College of Medicine, The Catholic University of Korea, Seoul, South Korea
| | - Woon Yong Kwon
- Department of Emergency Medicine, Seoul National University College of Medicine, Seoul, South Korea
| | - Sheng Chen
- Department of Infectious Diseases and Public Health, The City University of Hong Kong, Hong Kong, China
| | - Bill Kwan-Wai Chan
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hong Kong, China
| | - Kenneth Wong
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong, China
| | - Richard K W Choy
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong, China
| | - Ben C B Ko
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hong Kong, China.,State Key Laboratory of Chemical Biology and Drug Discovery, The Hong Kong Polytechnic University, Hong Kong, China
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13
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Ghosal K, Agatemor C, Han RI, Ku AT, Thomas S, Mukherjee S. Fanconi Anemia DNA Repair Pathway as a New Mechanism to Exploit Cancer Drug Resistance. Mini Rev Med Chem 2021; 20:779-787. [PMID: 31902358 DOI: 10.2174/1389557520666200103114556] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Revised: 10/17/2019] [Accepted: 12/02/2019] [Indexed: 12/27/2022]
Abstract
Chemotherapy employs anti-cancer drugs to stop the growth of cancerous cells, but one common obstacle to the success is the development of chemoresistance, which leads to failure of the previously effective anti-cancer drugs. Resistance arises from different mechanistic pathways, and in this critical review, we focus on the Fanconi Anemia (FA) pathway in chemoresistance. This pathway has yet to be intensively researched by mainstream cancer researchers. This review aims to inspire a new thrust toward the contribution of the FA pathway to drug resistance in cancer. We believe an indepth understanding of this pathway will open new frontiers to effectively treat drug-resistant cancer.
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Affiliation(s)
- Kajal Ghosal
- Dr. B.C. Roy College of Pharmacy and AHS, Durgapur 713206, India
| | - Christian Agatemor
- Department of Biomedical Engineering, School of Medicine, John Hopkins University, Baltimore MD, 21231, United States
| | - Richard I Han
- Department of Bioengineering, Rice University, Houston TX, 77030, United States
| | - Amy T Ku
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston TX, 77030, United States
| | - Sabu Thomas
- International and Inter University Center for Nanoscience and Nanotechnology (IIUCNN), Mahatma Gandhi University, Priyadarshini Hill, Kottayam 686560, Kerala, India
| | - Sudit Mukherjee
- Deparment of Biotechnology, National Institute of Technology, Durgapur, India
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14
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López-Perrote A, Hug N, González-Corpas A, Rodríguez CF, Serna M, García-Martín C, Boskovic J, Fernandez-Leiro R, Caceres JF, Llorca O. Regulation of RUVBL1-RUVBL2 AAA-ATPases by the nonsense-mediated mRNA decay factor DHX34, as evidenced by Cryo-EM. eLife 2020; 9:63042. [PMID: 33205750 PMCID: PMC7707835 DOI: 10.7554/elife.63042] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Accepted: 11/12/2020] [Indexed: 11/13/2022] Open
Abstract
Nonsense-mediated mRNA decay (NMD) is a surveillance pathway that degrades aberrant mRNAs and also regulates the expression of a wide range of physiological transcripts. RUVBL1 and RUVBL2 AAA-ATPases form an hetero-hexameric ring that is part of several macromolecular complexes such as INO80, SWR1, and R2TP. Interestingly, RUVBL1-RUVBL2 ATPase activity is required for NMD activation by an unknown mechanism. Here, we show that DHX34, an RNA helicase regulating NMD initiation, directly interacts with RUVBL1-RUVBL2 in vitro and in cells. Cryo-EM reveals that DHX34 induces extensive changes in the N-termini of every RUVBL2 subunit in the complex, stabilizing a conformation that does not bind nucleotide and thereby down-regulates ATP hydrolysis of the complex. Using ATPase-deficient mutants, we find that DHX34 acts exclusively on the RUVBL2 subunits. We propose a model, where DHX34 acts to couple RUVBL1-RUVBL2 ATPase activity to the assembly of factors required to initiate the NMD response.
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Affiliation(s)
- Andres López-Perrote
- Structural Biology Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Nele Hug
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburghx, Edinburgh, United Kingdom
| | - Ana González-Corpas
- Structural Biology Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Carlos F Rodríguez
- Structural Biology Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Marina Serna
- Structural Biology Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Carmen García-Martín
- Structural Biology Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Jasminka Boskovic
- Structural Biology Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Rafael Fernandez-Leiro
- Structural Biology Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Javier F Caceres
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburghx, Edinburgh, United Kingdom
| | - Oscar Llorca
- Structural Biology Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
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15
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Dauden MI, López-Perrote A, Llorca O. RUVBL1-RUVBL2 AAA-ATPase: a versatile scaffold for multiple complexes and functions. Curr Opin Struct Biol 2020; 67:78-85. [PMID: 33129013 DOI: 10.1016/j.sbi.2020.08.010] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 08/26/2020] [Accepted: 08/31/2020] [Indexed: 12/20/2022]
Abstract
RUVBL1 and RUVBL2 are two highly conserved AAA+ ATPases that form a hetero-hexameric complex that participates in a wide range of unrelated cellular processes, including chromatin remodeling, Fanconi Anemia (FA), nonsense-mediated mRNA decay (NMD), and assembly and maturation of several large macromolecular complexes such as RNA polymerases, the box C/D small nucleolar ribonucleoprotein (snoRNP) and mTOR complexes. How the RUVBL1-RUVBL2 complex works in such a variety of processes, sometimes antagonistic, has been obscure for a long time. Recent cryo-electron microscopy (cryo-EM) studies have started to reveal how RUVBL1-RUVBL2 forms a scaffold for complex protein-protein interactions and how the structure and ATPase activity of RUVBL1-RUVBL2 can be affected and regulated by the interaction with clients.
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Affiliation(s)
- Maria I Dauden
- Structural Biology Programme, Spanish National Cancer Research Centre (CNIO), Melchor Fernández Almagro 3, Madrid 28029, Spain
| | - Andrés López-Perrote
- Structural Biology Programme, Spanish National Cancer Research Centre (CNIO), Melchor Fernández Almagro 3, Madrid 28029, Spain
| | - Oscar Llorca
- Structural Biology Programme, Spanish National Cancer Research Centre (CNIO), Melchor Fernández Almagro 3, Madrid 28029, Spain.
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16
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Ha NT, Lee CH. Roles of Farnesyl-Diphosphate Farnesyltransferase 1 in Tumour and Tumour Microenvironments. Cells 2020; 9:cells9112352. [PMID: 33113804 PMCID: PMC7693003 DOI: 10.3390/cells9112352] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 10/23/2020] [Accepted: 10/24/2020] [Indexed: 12/14/2022] Open
Abstract
Farnesyl-diphosphate farnesyltransferase 1 (FDFT1, squalene synthase), a membrane-associated enzyme, synthesizes squalene via condensation of two molecules of farnesyl pyrophosphate. Accumulating evidence has noted that FDFT1 plays a critical role in cancer, particularly in metabolic reprogramming, cell proliferation, and invasion. Based on these advances in our knowledge, FDFT1 could be a potential target for cancer treatment. This review focuses on the contribution of FDFT1 to the hallmarks of cancer, and further, we discuss the applicability of FDFT1 as a cancer prognostic marker and target for anticancer therapy.
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17
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Park KC, Park JH, Baek SH, Kim KI. Pontin-deficiency causes senescence in fibroblast cells and epidermal keratinocytes but induces apoptosis in cancer cells. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2020; 1867:118740. [PMID: 32417257 DOI: 10.1016/j.bbamcr.2020.118740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 05/01/2020] [Accepted: 05/08/2020] [Indexed: 10/24/2022]
Abstract
Pontin, a member of the AAA+ ATPase family, plays important roles in a variety of cellular processes, including transcription regulation, DNA damage response, telomerase activity, and cellular transformation. In the previous studies, Pontin deletion in mice was lethal to embryos. Here, we demonstrate that the depletion of Pontin induced cellular senescence in mouse and human fibroblasts as well as in mouse epidermal keratinocytes. Fibroblast cells with Pontin depletion exhibited a defect in cell proliferation without showing apoptosis. Instead, they exhibited senescence-associated phenotypes including increased senescence-associated-β-galactosidase activity, elevated levels of p16INK4, and senescence-associated secretory phenotypes. Furthermore, conditional deletion of the Pontin gene in epidermal keratinocytes led to abnormal epidermal stratification, which was accompanied by the induction of senescence in Pontin-lacking cells. We found that Pontin depletion induced a spontaneous DNA damage response, which may be a cause of senescence. Contrary to the behavior of normal cells, Pontin depletion in several cancer cells caused apoptotic cell death without exhibiting senescence phenotypes.
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Affiliation(s)
- Koog Chan Park
- Department of Biological Sciences, Sookmyung Women's University, Seoul 04310, Republic of Korea; Research Institute of Women's Health, Sookmyung Women's University, Seoul 04310, Republic of Korea
| | - Joo Hyeon Park
- Department of Biological Sciences, Sookmyung Women's University, Seoul 04310, Republic of Korea; Research Institute of Women's Health, Sookmyung Women's University, Seoul 04310, Republic of Korea
| | - Sung Hee Baek
- Creative Research Initiatives Center for Epigenetic Code and Diseases, School of Biological Sciences, Seoul National University, Seoul 08826, South Korea
| | - Keun Il Kim
- Department of Biological Sciences, Sookmyung Women's University, Seoul 04310, Republic of Korea; Research Institute of Women's Health, Sookmyung Women's University, Seoul 04310, Republic of Korea.
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18
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Li N, Wang J, Wallace SS, Chen J, Zhou J, D’Andrea AD. Cooperation of the NEIL3 and Fanconi anemia/BRCA pathways in interstrand crosslink repair. Nucleic Acids Res 2020; 48:3014-3028. [PMID: 31980815 PMCID: PMC7102959 DOI: 10.1093/nar/gkaa038] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Revised: 12/12/2019] [Accepted: 01/22/2020] [Indexed: 12/19/2022] Open
Abstract
The NEIL3 DNA glycosylase is a base excision repair enzyme that excises bulky base lesions from DNA. Although NEIL3 has been shown to unhook interstrand crosslinks (ICL) in Xenopus extracts, how NEIL3 participants in ICL repair in human cells and its corporation with the canonical Fanconi anemia (FA)/BRCA pathway remain unclear. Here we show that the NEIL3 and the FA/BRCA pathways are non-epistatic in psoralen-ICL repair. The NEIL3 pathway is the major pathway for repairing psoralen-ICL, and the FA/BRCA pathway is only activated when NEIL3 is not present. Mechanistically, NEIL3 is recruited to psoralen-ICL in a rapid, PARP-dependent manner. Importantly, the NEIL3 pathway repairs psoralen-ICLs without generating double-strand breaks (DSBs), unlike the FA/BRCA pathway. In addition, we found that the RUVBL1/2 complex physically interact with NEIL3 and function within the NEIL3 pathway in psoralen-ICL repair. Moreover, TRAIP is important for the recruitment of NEIL3 but not FANCD2, and knockdown of TRAIP promotes FA/BRCA pathway activation. Interestingly, TRAIP is non-epistatic with both NEIL3 and FA pathways in psoralen-ICL repair, suggesting that TRAIP may function upstream of the two pathways. Taken together, the NEIL3 pathway is the major pathway to repair psoralen-ICL through a unique DSB-free mechanism in human cells.
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Affiliation(s)
- Niu Li
- Department of Medical Genetics and Molecular Diagnostic Laboratory, Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, China
- Key Laboratory of Pediatric Hematology and Oncology Ministry of Health, Department of Hematology and Oncology, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Jian Wang
- Department of Medical Genetics and Molecular Diagnostic Laboratory, Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Susan S Wallace
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, VT, USA
| | - Jing Chen
- Key Laboratory of Pediatric Hematology and Oncology Ministry of Health, Department of Hematology and Oncology, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jia Zhou
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Alan D D’Andrea
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Center for DNA Damage and Repair, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Susan F. Smith Center for Women's Cancers, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
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19
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Yenerall P, Das AK, Wang S, Kollipara RK, Li LS, Villalobos P, Flaming J, Lin YF, Huffman K, Timmons BC, Gilbreath C, Sonavane R, Kinch LN, Rodriguez-Canales J, Moran C, Behrens C, Hirasawa M, Takata T, Murakami R, Iwanaga K, Chen BPC, Grishin NV, Raj GV, Wistuba II, Minna JD, Kittler R. RUVBL1/RUVBL2 ATPase Activity Drives PAQosome Maturation, DNA Replication and Radioresistance in Lung Cancer. Cell Chem Biol 2019; 27:105-121.e14. [PMID: 31883965 DOI: 10.1016/j.chembiol.2019.12.005] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 11/07/2019] [Accepted: 12/06/2019] [Indexed: 02/03/2023]
Abstract
RUVBL1 and RUVBL2 (collectively RUVBL1/2) are essential AAA+ ATPases that function as co-chaperones and have been implicated in cancer. Here we investigated the molecular and phenotypic role of RUVBL1/2 ATPase activity in non-small cell lung cancer (NSCLC). We find that RUVBL1/2 are overexpressed in NSCLC patient tumors, with high expression associated with poor survival. Utilizing a specific inhibitor of RUVBL1/2 ATPase activity, we show that RUVBL1/2 ATPase activity is necessary for the maturation or dissociation of the PAQosome, a large RUVBL1/2-dependent multiprotein complex. We also show that RUVBL1/2 have roles in DNA replication, as inhibition of its ATPase activity can cause S-phase arrest, which culminates in cancer cell death via replication catastrophe. While in vivo pharmacological inhibition of RUVBL1/2 results in modest antitumor activity, it synergizes with radiation in NSCLC, but not normal cells, an attractive property for future preclinical development.
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Affiliation(s)
- Paul Yenerall
- Eugene McDermott Center for Human Growth and Development, UT Southwestern Medical Center, Dallas, TX 75390, USA; Hamon Center for Therapeutic Oncology Research, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Amit K Das
- Hamon Center for Therapeutic Oncology Research, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Shan Wang
- Eugene McDermott Center for Human Growth and Development, UT Southwestern Medical Center, Dallas, TX 75390, USA; Department of Urology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Rahul K Kollipara
- Eugene McDermott Center for Human Growth and Development, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Long Shan Li
- Hamon Center for Therapeutic Oncology Research, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Pamela Villalobos
- Department of Translational Molecular Pathology, UT M.D. Anderson Cancer Center, Houston, TX 77030, USA
| | - Josiah Flaming
- Hamon Center for Therapeutic Oncology Research, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Yu-Fen Lin
- Department of Radiation Oncology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Kenneth Huffman
- Hamon Center for Therapeutic Oncology Research, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Brenda C Timmons
- Hamon Center for Therapeutic Oncology Research, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Collin Gilbreath
- Department of Urology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Rajni Sonavane
- Department of Urology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Lisa N Kinch
- Howard Hughes Medical Institute and Departments of Biophysics and Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jaime Rodriguez-Canales
- Department of Translational Molecular Pathology, UT M.D. Anderson Cancer Center, Houston, TX 77030, USA
| | - Cesar Moran
- Department of Pathology, UT M.D. Anderson Cancer Center, Houston, TX 77030, USA
| | - Carmen Behrens
- Department of Thoracic/Head and Neck Medical Oncology, UT M.D. Anderson Cancer Center, Houston, TX 77030, USA
| | - Makoto Hirasawa
- Drug Metabolism & Pharmacokinetics Research Laboratories, Daiichi-Sankyo Co., Ltd., Tokyo 103-8426, Japan
| | - Takehiko Takata
- Oncology Medical Science Department, Medical Affairs, Daiichi-Sankyo Co., Ltd., Tokyo 103-8426, Japan
| | - Ryo Murakami
- Oncology Research Laboratories II, Daiichi-Sankyo Co., Ltd., Tokyo 103-8426, Japan
| | - Koichi Iwanaga
- Oncology Medical Science Department, Medical Affairs, Daiichi-Sankyo Co., Ltd., Tokyo 103-8426, Japan
| | - Benjamin P C Chen
- Department of Radiation Oncology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Nick V Grishin
- Howard Hughes Medical Institute and Departments of Biophysics and Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Ganesh V Raj
- Hamon Center for Therapeutic Oncology Research, UT Southwestern Medical Center, Dallas, TX 75390, USA; Department of Urology, UT Southwestern Medical Center, Dallas, TX 75390, USA; Department of Pharmacology, UT Southwestern Medical Center, Dallas, TX 75390, USA; Harold C. Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Ignacio I Wistuba
- Department of Translational Molecular Pathology, UT M.D. Anderson Cancer Center, Houston, TX 77030, USA; Department of Thoracic/Head and Neck Medical Oncology, UT M.D. Anderson Cancer Center, Houston, TX 77030, USA
| | - John D Minna
- Hamon Center for Therapeutic Oncology Research, UT Southwestern Medical Center, Dallas, TX 75390, USA; Department of Pharmacology, UT Southwestern Medical Center, Dallas, TX 75390, USA; Harold C. Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, TX 75390, USA; Department of Internal Medicine, UT Southwestern Medical Center, Dallas, TX 75390, USA.
| | - Ralf Kittler
- Eugene McDermott Center for Human Growth and Development, UT Southwestern Medical Center, Dallas, TX 75390, USA; Department of Pharmacology, UT Southwestern Medical Center, Dallas, TX 75390, USA; Harold C. Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, TX 75390, USA.
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20
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Andreev V, Hristova R, Asparuhova M, Danovski G, Stoynov S, Gospodinov A. Mammalian INO80 chromatin remodeler cooperates with FANCM to mediate DNA interstrand crosslink-induced checkpoint activation and repair. DNA Repair (Amst) 2019; 74:38-50. [DOI: 10.1016/j.dnarep.2018.12.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 11/30/2018] [Accepted: 12/27/2018] [Indexed: 11/30/2022]
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21
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Vangala JR, Radhakrishnan SK. Nrf1-mediated transcriptional regulation of the proteasome requires a functional TIP60 complex. J Biol Chem 2018; 294:2036-2045. [PMID: 30559296 DOI: 10.1074/jbc.ra118.006290] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 12/03/2018] [Indexed: 12/15/2022] Open
Abstract
Inhibition of the proteasome leads to proteotoxic stress, which is characterized by the buildup of ubiquitinated proteins that cannot be degraded properly. The transcription factor Nrf1 (also called NFE2L1) counteracts proteotoxic stress by inducing transcription of proteasome subunit genes, resulting in the restoration of proteasome activity. Further understanding of the Nrf1 pathway is therefore of interest in both neurodegeneration, where proteasome activity could be enhanced, and cancer, where suppression of this pathway could potentiate the cell-killing effect mediated by proteasome inhibitor drugs. Here, to identify novel regulators of Nrf1, we performed an RNAi screen in an engineered cell line, reporting on Nrf1 transcriptional activity. In addition to validating known regulators, we discovered that the AAA+ ATPase RUVBL1 is necessary for Nrf1's transcriptional activity. Given that RUVBL1 is part of different multisubunit complexes that play key roles in transcription, we dissected this phenomenon further and found that the TIP60 chromatin-regulatory complex is essential for Nrf1-dependent transcription of proteasome genes. Consistent with these observations, Nrf1, RUVBL1, and TIP60 proteins were co-recruited to the promoter regions of proteasome genes after proteasome inhibitor treatments. More importantly, depletion of RUVBL1 or TIP60 in various cancer cells sensitized them to cell death induced by proteasome inhibition. Overall, our study provides a framework for manipulating the TIP60-Nrf1 axis to alter proteasome function in various human diseases, including cancer.
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Affiliation(s)
- Janakiram R Vangala
- From the Department of Pathology and Massey Cancer Center, Virginia Commonwealth University, Richmond, Virginia 23298
| | - Senthil K Radhakrishnan
- From the Department of Pathology and Massey Cancer Center, Virginia Commonwealth University, Richmond, Virginia 23298
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22
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Lynham J, Houry WA. The Multiple Functions of the PAQosome: An R2TP- and URI1 Prefoldin-Based Chaperone Complex. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1106:37-72. [DOI: 10.1007/978-3-030-00737-9_4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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23
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Integrative gene network analysis identifies key signatures, intrinsic networks and host factors for influenza virus A infections. NPJ Syst Biol Appl 2017; 3:35. [PMID: 29214055 PMCID: PMC5712526 DOI: 10.1038/s41540-017-0036-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Revised: 10/17/2017] [Accepted: 11/07/2017] [Indexed: 12/13/2022] Open
Abstract
Influenza A virus, with the limited coding capacity of 10–14 proteins, requires the host cellular machinery for many aspects of its life cycle. Knowledge of these host cell requirements not only reveals molecular pathways exploited by the virus or triggered by the immune system, but also provides further targets for antiviral drug development. To uncover novel pathways and key targets of influenza infection, we assembled a large amount of data from 12 cell-based gene-expression studies of influenza infection for an integrative network analysis. We systematically identified differentially expressed genes and gene co-expression networks induced by influenza infection. We revealed the dedicator of cytokinesis 5 (DOCK5) played potentially an important role for influenza virus replication. CRISPR/Cas9 knockout of DOCK5 reduced influenza virus replication, indicating that DOCK5 is a key regulator for the viral life cycle. DOCK5’s targets determined by the DOCK5 knockout experiments strongly validated the predicted gene signatures and networks. This study systematically uncovered and validated fundamental patterns of molecular responses, intrinsic structures of gene co-regulation, and novel key targets in influenza virus infection. Molecular response to influenza infection involves a large number of interacting pathways in the form of complex molecular networks. Most studies on influenza infection have largely focused on testing specific molecules and hypotheses with limited data. Therefore, a global picture of molecular interactions in influenza infection is missing. In this study, we performed an integrative network analysis on a large amount of data from 12 cell-based gene expression studies of influenza infections. By combining differential expression, co-expression networks, and gene knockout experiments, we uncovered and validated fundamental patterns of molecular responses, intrinsic structures of gene co-regulation, and novel key targets in influenza infection. Our findings pave the way for other functional investigations into identifying novel therapeutic targets against influenza infection.
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24
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Baron BW, Baron RM, Baron JM. Reticulocytes Are an Enriched Source of the RUVBL1 Protein. Acta Haematol 2017; 138:162-165. [PMID: 28982102 DOI: 10.1159/000480449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Accepted: 08/19/2017] [Indexed: 11/19/2022]
Affiliation(s)
- Beverly W Baron
- Department of Pathology, The University of Chicago, Chicago, IL, USA
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25
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Mao YQ, Houry WA. The Role of Pontin and Reptin in Cellular Physiology and Cancer Etiology. Front Mol Biosci 2017; 4:58. [PMID: 28884116 PMCID: PMC5573869 DOI: 10.3389/fmolb.2017.00058] [Citation(s) in RCA: 82] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 08/03/2017] [Indexed: 12/29/2022] Open
Abstract
Pontin (RUVBL1, TIP49, TIP49a, Rvb1) and Reptin (RUVBL2, TIP48, TIP49b, Rvb2) are highly conserved ATPases of the AAA+ (ATPases Associated with various cellular Activities) superfamily and are involved in various cellular processes that are important for oncogenesis. First identified as being upregulated in hepatocellular carcinoma and colorectal cancer, their overexpression has since been shown in multiple cancer types such as breast, lung, gastric, esophageal, pancreatic, kidney, bladder as well as lymphatic, and leukemic cancers. However, their exact functions are still quite unknown as they interact with many molecular complexes with vastly different downstream effectors. Within the nucleus, Pontin and Reptin participate in the TIP60 and INO80 complexes important for chromatin remodeling. Although not transcription factors themselves, Pontin and Reptin modulate the transcriptional activities of bona fide proto-oncogenes such as MYC and β-catenin. They associate with proteins involved in DNA damage repair such as PIKK complexes as well as with the core complex of Fanconi anemia pathway. They have also been shown to be important for cell cycle progression, being involved in assembly of telomerase, mitotic spindle, RNA polymerase II, and snoRNPs. When the two ATPases localize to the cytoplasm, they were reported to promote cancer cell invasion and metastasis. Due to their various roles in carcinogenesis, it is not surprising that Pontin and Reptin are proving to be important biomarkers for diagnosis and prognosis of various cancers. They are also current targets for the development of new therapeutic anticancer drugs.
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Affiliation(s)
- Yu-Qian Mao
- Department of Biochemistry, University of TorontoToronto, ON, Canada
| | - Walid A Houry
- Department of Biochemistry, University of TorontoToronto, ON, Canada.,Department of Chemistry, University of TorontoToronto, ON, Canada
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26
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Clarke TL, Sanchez-Bailon MP, Chiang K, Reynolds JJ, Herrero-Ruiz J, Bandeiras TM, Matias PM, Maslen SL, Skehel JM, Stewart GS, Davies CC. PRMT5-Dependent Methylation of the TIP60 Coactivator RUVBL1 Is a Key Regulator of Homologous Recombination. Mol Cell 2017; 65:900-916.e7. [PMID: 28238654 PMCID: PMC5344794 DOI: 10.1016/j.molcel.2017.01.019] [Citation(s) in RCA: 101] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Revised: 09/20/2016] [Accepted: 01/17/2017] [Indexed: 11/29/2022]
Abstract
Protein post-translation modification plays an important role in regulating DNA repair; however, the role of arginine methylation in this process is poorly understood. Here we identify the arginine methyltransferase PRMT5 as a key regulator of homologous recombination (HR)-mediated double-strand break (DSB) repair, which is mediated through its ability to methylate RUVBL1, a cofactor of the TIP60 complex. We show that PRMT5 targets RUVBL1 for methylation at position R205, which facilitates TIP60-dependent mobilization of 53BP1 from DNA breaks, promoting HR. Mechanistically, we demonstrate that PRMT5-directed methylation of RUVBL1 is critically required for the acetyltransferase activity of TIP60, promoting histone H4K16 acetylation, which facilities 53BP1 displacement from DSBs. Interestingly, RUVBL1 methylation did not affect the ability of TIP60 to facilitate ATM activation. Taken together, our findings reveal the importance of PRMT5-mediated arginine methylation during DSB repair pathway choice through its ability to regulate acetylation-dependent control of 53BP1 localization.
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Affiliation(s)
- Thomas L Clarke
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Maria Pilar Sanchez-Bailon
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Kelly Chiang
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - John J Reynolds
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Joaquin Herrero-Ruiz
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Tiago M Bandeiras
- Instituto de Biologia Experimental e Tecnológica, 2780-157 Oeiras, Portugal
| | - Pedro M Matias
- Instituto de Biologia Experimental e Tecnológica, 2780-157 Oeiras, Portugal; Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, 2780-157 Oeiras, Portugal
| | - Sarah L Maslen
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
| | - J Mark Skehel
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
| | - Grant S Stewart
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Clare C Davies
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK.
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27
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Malik A, Domankevich V, Lijuan H, Xiaodong F, Korol A, Avivi A, Shams I. Genome maintenance and bioenergetics of the long-lived hypoxia-tolerant and cancer-resistant blind mole rat, Spalax: a cross-species analysis of brain transcriptome. Sci Rep 2016; 6:38624. [PMID: 27934892 PMCID: PMC5146665 DOI: 10.1038/srep38624] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 11/08/2016] [Indexed: 01/09/2023] Open
Abstract
The subterranean blind mole rat, Spalax, experiences acute hypoxia-reoxygenation cycles in its natural subterranean habitat. At the cellular level, these conditions are known to promote genomic instability, which underlies both cancer and aging. However, Spalax is a long-lived animal and is resistant to both spontaneous and induced cancers. To study this apparent paradox we utilized a computational procedure that allows detecting differences in transcript abundance between Spalax and the closely related above-ground Rattus norvegicus in individuals of different ages. Functional enrichment analysis showed that Spalax whole brain tissues maintain significantly higher normoxic mRNA levels of genes associated with DNA damage repair and DNA metabolism, yet keep significantly lower mRNA levels of genes involved in bioenergetics. Many of the genes that showed higher transcript abundance in Spalax are involved in DNA repair and metabolic pathways that, in other species, were shown to be downregulated under hypoxia, yet are required for overcoming replication- and oxidative-stress during the subsequent reoxygenation. We suggest that these differentially expressed genes may prevent the accumulation of DNA damage in mitotic and post-mitotic cells and defective resumption of replication in mitotic cells, thus maintaining genome integrity as an adaptation to acute hypoxia-reoxygenation cycles.
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Affiliation(s)
- Assaf Malik
- Institue of Evolution, University of Haifa, Haifa 3498838, Israel.,Bioinformatics Core Unit, University of Haifa, Haifa 3498838, Israel
| | - Vered Domankevich
- Institue of Evolution, University of Haifa, Haifa 3498838, Israel.,Deparment of Evolutionary and Environmental Biology, University of Haifa, Haifa 3498838, Israel
| | - Han Lijuan
- BGI-Tech, BGI-Shenzhen, Shenzhen 518083, China
| | | | - Abraham Korol
- Institue of Evolution, University of Haifa, Haifa 3498838, Israel.,Deparment of Evolutionary and Environmental Biology, University of Haifa, Haifa 3498838, Israel
| | - Aaron Avivi
- Institue of Evolution, University of Haifa, Haifa 3498838, Israel
| | - Imad Shams
- Institue of Evolution, University of Haifa, Haifa 3498838, Israel.,Deparment of Evolutionary and Environmental Biology, University of Haifa, Haifa 3498838, Israel
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28
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Runge JS, Raab JR, Magnuson T. Epigenetic Regulation by ATP-Dependent Chromatin-Remodeling Enzymes: SNF-ing Out Crosstalk. Curr Top Dev Biol 2016; 117:1-13. [PMID: 26969969 DOI: 10.1016/bs.ctdb.2015.10.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Cells utilize precise mechanisms to access genomic DNA with spatiotemporal accuracy. ATP-dependent chromatin-remodeling enzymes (also known simply as "remodelers") comprise a specialized class of enzymes that is intimately involved in genomic organization and accessibility. Remodelers selectively position nucleosomes to either alleviate chromatin compaction or achieve genomic condensation locally, based on a multitude of cellular signals. By dictating nucleosome position, remodelers control local euchromatic and heterochromatic states. These activities govern the accessibility of regulatory regions like promoters and enhancers to transcription factors, RNA polymerases, and coactivators or -repressors. As studies unravel the complexities of epigenetic topography, evidence points to a chromatin-based interactome where regulators interact competitively, cooperatively, and/or codependently through physical and functional means. These types of interactions, or crosstalk, between remodelers raise important questions for tissue development. Here, we briefly review the evidence for remodeler interactions and argue for additional studies examining crosstalk.
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Affiliation(s)
- John S Runge
- Curriculum for Genetics and Molecular Biology, University of North Carolina, Chapel Hill, North Carolina, USA; Department of Genetics, University of North Carolina, Chapel Hill, North Carolina, USA; Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Jesse R Raab
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina, USA; Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Terry Magnuson
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina, USA; Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina, USA.
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29
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A Novel Interaction of Ecdysoneless (ECD) Protein with R2TP Complex Component RUVBL1 Is Required for the Functional Role of ECD in Cell Cycle Progression. Mol Cell Biol 2015; 36:886-99. [PMID: 26711270 DOI: 10.1128/mcb.00594-15] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Accepted: 12/18/2015] [Indexed: 12/21/2022] Open
Abstract
Ecdysoneless (ECD) is an evolutionarily conserved protein whose germ line deletion is embryonic lethal. Deletion of Ecd in cells causes cell cycle arrest, which is rescued by exogenous ECD, demonstrating a requirement of ECD for normal mammalian cell cycle progression. However, the exact mechanism by which ECD regulates cell cycle is unknown. Here, we demonstrate that ECD protein levels and subcellular localization are invariant during cell cycle progression, suggesting a potential role of posttranslational modifications or protein-protein interactions. Since phosphorylated ECD was recently shown to interact with the PIH1D1 adaptor component of the R2TP cochaperone complex, we examined the requirement of ECD phosphorylation in cell cycle progression. Notably, phosphorylation-deficient ECD mutants that failed to bind to PIH1D1 in vitro fully retained the ability to interact with the R2TP complex and yet exhibited a reduced ability to rescue Ecd-deficient cells from cell cycle arrest. Biochemical analyses demonstrated an additional phosphorylation-independent interaction of ECD with the RUVBL1 component of the R2TP complex, and this interaction is essential for ECD's cell cycle progression function. These studies demonstrate that interaction of ECD with RUVBL1, and its CK2-mediated phosphorylation, independent of its interaction with PIH1D1, are important for its cell cycle regulatory function.
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30
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Gentili C, Castor D, Kaden S, Lauterbach D, Gysi M, Steigemann P, Gerlich DW, Jiricny J, Ferrari S. Chromosome Missegregation Associated with RUVBL1 Deficiency. PLoS One 2015; 10:e0133576. [PMID: 26201077 PMCID: PMC4511761 DOI: 10.1371/journal.pone.0133576] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2014] [Accepted: 06/30/2015] [Indexed: 12/31/2022] Open
Abstract
RUVBL1 (RuvB-like1) and RUVBL2 (RuvB-like 2) are integral components of multisubunit protein complexes involved in processes ranging from cellular metabolism, transcription and chromatin remodeling to DNA repair. Here, we show that although RUVBL1 and RUVBL2 are known to form heterodimeric complexes in which they stabilize each other, the subunits separate during cytokinesis. In anaphase-to-telophase transition, RUVBL1 localizes to structures of the mitotic spindle apparatus, where it partially co-localizes with polo-like kinase 1 (PLK1). The ability of PLK1 to phosphorylate RUVBL1-but not RUVBL2-in vitro and their physical association in vivo suggest that this kinase differentially regulates the function of the RuvB-like proteins during mitosis. We further show that siRNA-mediated knock-down of RuvB-like proteins causes severe defects in chromosome alignment and segregation. In addition, we show that the ATPase activity of RUVBL1 is indispensable for cell proliferation. Our data thus demonstrate that RUVBL1 is essential for efficient mitosis and proliferation.
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Affiliation(s)
- Christian Gentili
- Institute of Molecular Cancer Research of the University of Zurich and the ETH Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland
| | - Dennis Castor
- Institute of Molecular Cancer Research of the University of Zurich and the ETH Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland
| | - Svenja Kaden
- Institute of Molecular Cancer Research of the University of Zurich and the ETH Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland
| | - David Lauterbach
- Institute of Molecular Cancer Research of the University of Zurich and the ETH Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland
| | - Mario Gysi
- Institute of Molecular Cancer Research of the University of Zurich and the ETH Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland
| | - Patrick Steigemann
- Institute of Biochemistry, Schafmattstrasse 18, HPM E17.2, Swiss Institute of Technology Zurich (ETHZ), CH-8093, Zurich, Switzerland
| | - Daniel W. Gerlich
- Institute of Biochemistry, Schafmattstrasse 18, HPM E17.2, Swiss Institute of Technology Zurich (ETHZ), CH-8093, Zurich, Switzerland
| | - Josef Jiricny
- Institute of Molecular Cancer Research of the University of Zurich and the ETH Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland
| | - Stefano Ferrari
- Institute of Molecular Cancer Research of the University of Zurich and the ETH Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland
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31
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von Morgen P, Hořejší Z, Macurek L. Substrate recognition and function of the R2TP complex in response to cellular stress. Front Genet 2015; 6:69. [PMID: 25767478 PMCID: PMC4341119 DOI: 10.3389/fgene.2015.00069] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Accepted: 02/10/2015] [Indexed: 11/18/2022] Open
Abstract
The R2TP complex is a HSP90 co-chaperone, which consists of four subunits: PIH1D1, RPAP3, RUVBL1, and RUVBL2. It is involved in the assembly of large protein or protein–RNA complexes such as RNA polymerase, small nucleolar ribonucleoproteins (snoRNPs), phosphatidylinositol 3 kinase-related kinases (PIKKs), and their complexes. While RPAP3 has a HSP90 binding domain and the RUVBLs comprise ATPase activities important for R2TP functions, PIH1D1 contains a PIH-N domain that specifically recognizes phosphorylated substrates of the R2TP complex. In this review we provide an overview of the current knowledge of the R2TP complex with the focus on the recently identified structural and mechanistic features of the R2TP complex functions. We also discuss the way R2TP regulates cellular response to stress caused by low levels of nutrients or by DNA damage and its possible exploitation as a target for anti-cancer therapy.
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Affiliation(s)
- Patrick von Morgen
- Department of Cancer Cell Biology, Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Prague Czech Republic
| | - Zuzana Hořejší
- Department of Cancer Cell Biology, Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Prague Czech Republic ; DNA Damage Response Laboratory, London Research Institute, London UK
| | - Libor Macurek
- Department of Cancer Cell Biology, Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Prague Czech Republic
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32
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Abstract
In developing a new quantitative AP-MS method for exploring interactomes in the chicken B-cell line DT40, we also surveyed the most abundant proteins in this organism and explored the likely contaminants that bind to a variety of affinity resins that would later be confirmed quantitatively [1]. We present the ‘Top 150 abundant DT40 proteins list’, the DT40 beadomes as well as protein interaction lists for the Phosphatidyl inositol 5-phosphate 4-kinase 2β and Fanconi anaemia protein complexes.
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Affiliation(s)
- Johanna S. Rees
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, UK
- Cambridge Centre for Proteomics, University of Cambridge, Cambridge CB2 1QR, UK
- Corresponding author.
| | - Kathryn S. Lilley
- Cambridge Centre for Proteomics, University of Cambridge, Cambridge CB2 1QR, UK
| | - Antony P. Jackson
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, UK
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33
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Rees JS, Lilley KS, Jackson AP. SILAC-iPAC: a quantitative method for distinguishing genuine from non-specific components of protein complexes by parallel affinity capture. J Proteomics 2014; 115:143-56. [PMID: 25534881 PMCID: PMC4329988 DOI: 10.1016/j.jprot.2014.12.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Revised: 11/28/2014] [Accepted: 12/11/2014] [Indexed: 01/17/2023]
Abstract
Pull-down assays can identify members of protein complexes but suffer from co-isolation of contaminants. The problem is particularly acute when the specifically interacting partners are of low-abundance and/or bind transiently with low affinity. To differentiate true interacting partners from contaminants, we have combined SILAC labelling with a proteomic method called “Interactomes by Parallel Affinity Capture” (iPAC). In our method, a cell-line stably expressing a doubly tagged target endogenous protein and its tag-less control cell-line are differentially SILAC labelled. Lysates from the two cell-lines are mixed and the tagged protein is independently purified for MS analysis using multiple affinity resins in parallel. This allows the quantitative identification of tagged proteins and their binding partners. SILAC–iPAC provides a rigorous and sensitive approach that can discriminate between genuine binding partners and contaminants, even when the contaminants in the pull-down are in large excess. We employed our method to examine the interacting partners of phosphatidyl inositol 5-phosphate 4-kinase 2β subunit (PI5P4K2β) and the Fanconi anaemia core complex in the chicken pre-B cell-line DT40. We confirmed known components of these two complexes, and we have identified new potential binding partners. Combining the iPAC approach with SILAC labelling provides a sensitive and fully quantitative method for the discrimination of specific interactions under conditions where low signal to noise ratios are unavoidable. In addition, our work provides the first characterisation of the most abundant proteins within the DT40 proteome and the non-specific DT40 ‘beadomes’ (non-specific proteins binding to beads) for common epitope tags. Given the importance and widespread use of the DT40 cell-line, these will be important resources for the cell biology and immunology communities. Biological significance SILAC–iPAC provides an improved method for the analysis of low-affinity and/or low abundance protein-protein interactions. We use it to clarify two examples where the nature of the protein complexes are known, or are currently unclear. The method is simple and quantitative and will be applicable to many problems in cell and molecular biology. We also report the first chicken beadomes. SILAC–iPAC; an improved AP-MS method to quantitatively detect low abundance proteins RUVBL1 and its partner RUVBL2 are novel interactors of the Fanconi anaemia complex. First characterisation of chicken DT40 beadomes using four common epitope tags
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Affiliation(s)
- Johanna S Rees
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, UK; Cambridge Centre for Proteomics, University of Cambridge, Cambridge CB2 1QR, UK.
| | - Kathryn S Lilley
- Cambridge Centre for Proteomics, University of Cambridge, Cambridge CB2 1QR, UK
| | - Antony P Jackson
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, UK.
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