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Wallach I, Bernard D, Nguyen K, Ho G, Morrison A, Stecula A, Rosnik A, O’Sullivan AM, Davtyan A, Samudio B, Thomas B, Worley B, Butler B, Laggner C, Thayer D, Moharreri E, Friedland G, Truong H, van den Bedem H, Ng HL, Stafford K, Sarangapani K, Giesler K, Ngo L, Mysinger M, Ahmed M, Anthis NJ, Henriksen N, Gniewek P, Eckert S, de Oliveira S, Suterwala S, PrasadPrasad SVK, Shek S, Contreras S, Hare S, Palazzo T, O’Brien TE, Van Grack T, Williams T, Chern TR, Kenyon V, Lee AH, Cann AB, Bergman B, Anderson BM, Cox BD, Warrington JM, Sorenson JM, Goldenberg JM, Young MA, DeHaan N, Pemberton RP, Schroedl S, Abramyan TM, Gupta T, Mysore V, Presser AG, Ferrando AA, Andricopulo AD, Ghosh A, Ayachi AG, Mushtaq A, Shaqra AM, Toh AKL, Smrcka AV, Ciccia A, de Oliveira AS, Sverzhinsky A, de Sousa AM, Agoulnik AI, Kushnir A, Freiberg AN, Statsyuk AV, Gingras AR, Degterev A, Tomilov A, Vrielink A, Garaeva AA, Bryant-Friedrich A, Caflisch A, Patel AK, Rangarajan AV, Matheeussen A, Battistoni A, Caporali A, Chini A, Ilari A, Mattevi A, Foote AT, Trabocchi A, Stahl A, Herr AB, Berti A, Freywald A, Reidenbach AG, Lam A, Cuddihy AR, White A, Taglialatela A, Ojha AK, Cathcart AM, Motyl AAL, Borowska A, D’Antuono A, Hirsch AKH, Porcelli AM, Minakova A, Montanaro A, Müller A, Fiorillo A, Virtanen A, O’Donoghue AJ, Del Rio Flores A, Garmendia AE, Pineda-Lucena A, Panganiban AT, Samantha A, Chatterjee AK, Haas AL, Paparella AS, John ALS, Prince A, ElSheikh A, Apfel AM, Colomba A, O’Dea A, Diallo BN, Ribeiro BMRM, Bailey-Elkin BA, Edelman BL, Liou B, Perry B, Chua BSK, Kováts B, Englinger B, Balakrishnan B, Gong B, Agianian B, Pressly B, Salas BPM, Duggan BM, Geisbrecht BV, Dymock BW, Morten BC, Hammock BD, Mota BEF, Dickinson BC, Fraser C, Lempicki C, Novina CD, Torner C, Ballatore C, Bon C, Chapman CJ, Partch CL, Chaton CT, Huang C, Yang CY, Kahler CM, Karan C, Keller C, Dieck CL, Huimei C, Liu C, Peltier C, Mantri CK, Kemet CM, Müller CE, Weber C, Zeina CM, Muli CS, Morisseau C, Alkan C, Reglero C, Loy CA, Wilson CM, Myhr C, Arrigoni C, Paulino C, Santiago C, Luo D, Tumes DJ, Keedy DA, Lawrence DA, Chen D, Manor D, Trader DJ, Hildeman DA, Drewry DH, Dowling DJ, Hosfield DJ, Smith DM, Moreira D, Siderovski DP, Shum D, Krist DT, Riches DWH, Ferraris DM, Anderson DH, Coombe DR, Welsbie DS, Hu D, Ortiz D, Alramadhani D, Zhang D, Chaudhuri D, Slotboom DJ, Ronning DR, Lee D, Dirksen D, Shoue DA, Zochodne DW, Krishnamurthy D, Duncan D, Glubb DM, Gelardi ELM, Hsiao EC, Lynn EG, Silva EB, Aguilera E, Lenci E, Abraham ET, Lama E, Mameli E, Leung E, Christensen EM, Mason ER, Petretto E, Trakhtenberg EF, Rubin EJ, Strauss E, Thompson EW, Cione E, Lisabeth EM, Fan E, Kroon EG, Jo E, García-Cuesta EM, Glukhov E, Gavathiotis E, Yu F, Xiang F, Leng F, Wang F, Ingoglia F, van den Akker F, Borriello F, Vizeacoumar FJ, Luh F, Buckner FS, Vizeacoumar FS, Bdira FB, Svensson F, Rodriguez GM, Bognár G, Lembo G, Zhang G, Dempsey G, Eitzen G, Mayer G, Greene GL, Garcia GA, Lukacs GL, Prikler G, Parico GCG, Colotti G, De Keulenaer G, Cortopassi G, Roti G, Girolimetti G, Fiermonte G, Gasparre G, Leuzzi G, Dahal G, Michlewski G, Conn GL, Stuchbury GD, Bowman GR, Popowicz GM, Veit G, de Souza GE, Akk G, Caljon G, Alvarez G, Rucinski G, Lee G, Cildir G, Li H, Breton HE, Jafar-Nejad H, Zhou H, Moore HP, Tilford H, Yuan H, Shim H, Wulff H, Hoppe H, Chaytow H, Tam HK, Van Remmen H, Xu H, Debonsi HM, Lieberman HB, Jung H, Fan HY, Feng H, Zhou H, Kim HJ, Greig IR, Caliandro I, Corvo I, Arozarena I, Mungrue IN, Verhamme IM, Qureshi IA, Lotsaris I, Cakir I, Perry JJP, Kwiatkowski J, Boorman J, Ferreira J, Fries J, Kratz JM, Miner J, Siqueira-Neto JL, Granneman JG, Ng J, Shorter J, Voss JH, Gebauer JM, Chuah J, Mousa JJ, Maynes JT, Evans JD, Dickhout J, MacKeigan JP, Jossart JN, Zhou J, Lin J, Xu J, Wang J, Zhu J, Liao J, Xu J, Zhao J, Lin J, Lee J, Reis J, Stetefeld J, Bruning JB, Bruning JB, Coles JG, Tanner JJ, Pascal JM, So J, Pederick JL, Costoya JA, Rayman JB, Maciag JJ, Nasburg JA, Gruber JJ, Finkelstein JM, Watkins J, Rodríguez-Frade JM, Arias JAS, Lasarte JJ, Oyarzabal J, Milosavljevic J, Cools J, Lescar J, Bogomolovas J, Wang J, Kee JM, Kee JM, Liao J, Sistla JC, Abrahão JS, Sishtla K, Francisco KR, Hansen KB, Molyneaux KA, Cunningham KA, Martin KR, Gadar K, Ojo KK, Wong KS, Wentworth KL, Lai K, Lobb KA, Hopkins KM, Parang K, Machaca K, Pham K, Ghilarducci K, Sugamori KS, McManus KJ, Musta K, Faller KME, Nagamori K, Mostert KJ, Korotkov KV, Liu K, Smith KS, Sarosiek K, Rohde KH, Kim KK, Lee KH, Pusztai L, Lehtiö L, Haupt LM, Cowen LE, Byrne LJ, Su L, Wert-Lamas L, Puchades-Carrasco L, Chen L, Malkas LH, Zhuo L, Hedstrom L, Hedstrom L, Walensky LD, Antonelli L, Iommarini L, Whitesell L, Randall LM, Fathallah MD, Nagai MH, Kilkenny ML, Ben-Johny M, Lussier MP, Windisch MP, Lolicato M, Lolli ML, Vleminckx M, Caroleo MC, Macias MJ, Valli M, Barghash MM, Mellado M, Tye MA, Wilson MA, Hannink M, Ashton MR, Cerna MVC, Giorgis M, Safo MK, Maurice MS, McDowell MA, Pasquali M, Mehedi M, Serafim MSM, Soellner MB, Alteen MG, Champion MM, Skorodinsky M, O’Mara ML, Bedi M, Rizzi M, Levin M, Mowat M, Jackson MR, Paige M, Al-Yozbaki M, Giardini MA, Maksimainen MM, De Luise M, Hussain MS, Christodoulides M, Stec N, Zelinskaya N, Van Pelt N, Merrill NM, Singh N, Kootstra NA, Singh N, Gandhi NS, Chan NL, Trinh NM, Schneider NO, Matovic N, Horstmann N, Longo N, Bharambe N, Rouzbeh N, Mahmoodi N, Gumede NJ, Anastasio NC, Khalaf NB, Rabal O, Kandror O, Escaffre O, Silvennoinen O, Bishop OT, Iglesias P, Sobrado P, Chuong P, O’Connell P, Martin-Malpartida P, Mellor P, Fish PV, Moreira POL, Zhou P, Liu P, Liu P, Wu P, Agogo-Mawuli P, Jones PL, Ngoi P, Toogood P, Ip P, von Hundelshausen P, Lee PH, Rowswell-Turner RB, Balaña-Fouce R, Rocha REO, Guido RVC, Ferreira RS, Agrawal RK, Harijan RK, Ramachandran R, Verma R, Singh RK, Tiwari RK, Mazitschek R, Koppisetti RK, Dame RT, Douville RN, Austin RC, Taylor RE, Moore RG, Ebright RH, Angell RM, Yan R, Kejriwal R, Batey RA, Blelloch R, Vandenberg RJ, Hickey RJ, Kelm RJ, Lake RJ, Bradley RK, Blumenthal RM, Solano R, Gierse RM, Viola RE, McCarthy RR, Reguera RM, Uribe RV, do Monte-Neto RL, Gorgoglione R, Cullinane RT, Katyal S, Hossain S, Phadke S, Shelburne SA, Geden SE, Johannsen S, Wazir S, Legare S, Landfear SM, Radhakrishnan SK, Ammendola S, Dzhumaev S, Seo SY, Li S, Zhou S, Chu S, Chauhan S, Maruta S, Ashkar SR, Shyng SL, Conticello SG, Buroni S, Garavaglia S, White SJ, Zhu S, Tsimbalyuk S, Chadni SH, Byun SY, Park S, Xu SQ, Banerjee S, Zahler S, Espinoza S, Gustincich S, Sainas S, Celano SL, Capuzzi SJ, Waggoner SN, Poirier S, Olson SH, Marx SO, Van Doren SR, Sarilla S, Brady-Kalnay SM, Dallman S, Azeem SM, Teramoto T, Mehlman T, Swart T, Abaffy T, Akopian T, Haikarainen T, Moreda TL, Ikegami T, Teixeira TR, Jayasinghe TD, Gillingwater TH, Kampourakis T, Richardson TI, Herdendorf TJ, Kotzé TJ, O’Meara TR, Corson TW, Hermle T, Ogunwa TH, Lan T, Su T, Banjo T, O’Mara TA, Chou T, Chou TF, Baumann U, Desai UR, Pai VP, Thai VC, Tandon V, Banerji V, Robinson VL, Gunasekharan V, Namasivayam V, Segers VFM, Maranda V, Dolce V, Maltarollo VG, Scoffone VC, Woods VA, Ronchi VP, Van Hung Le V, Clayton WB, Lowther WT, Houry WA, Li W, Tang W, Zhang W, Van Voorhis WC, Donaldson WA, Hahn WC, Kerr WG, Gerwick WH, Bradshaw WJ, Foong WE, Blanchet X, Wu X, Lu X, Qi X, Xu X, Yu X, Qin X, Wang X, Yuan X, Zhang X, Zhang YJ, Hu Y, Aldhamen YA, Chen Y, Li Y, Sun Y, Zhu Y, Gupta YK, Pérez-Pertejo Y, Li Y, Tang Y, He Y, Tse-Dinh YC, Sidorova YA, Yen Y, Li Y, Frangos ZJ, Chung Z, Su Z, Wang Z, Zhang Z, Liu Z, Inde Z, Artía Z, Heifets A. AI is a viable alternative to high throughput screening: a 318-target study. Sci Rep 2024; 14:7526. [PMID: 38565852 PMCID: PMC10987645 DOI: 10.1038/s41598-024-54655-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 02/15/2024] [Indexed: 04/04/2024] Open
Abstract
High throughput screening (HTS) is routinely used to identify bioactive small molecules. This requires physical compounds, which limits coverage of accessible chemical space. Computational approaches combined with vast on-demand chemical libraries can access far greater chemical space, provided that the predictive accuracy is sufficient to identify useful molecules. Through the largest and most diverse virtual HTS campaign reported to date, comprising 318 individual projects, we demonstrate that our AtomNet® convolutional neural network successfully finds novel hits across every major therapeutic area and protein class. We address historical limitations of computational screening by demonstrating success for target proteins without known binders, high-quality X-ray crystal structures, or manual cherry-picking of compounds. We show that the molecules selected by the AtomNet® model are novel drug-like scaffolds rather than minor modifications to known bioactive compounds. Our empirical results suggest that computational methods can substantially replace HTS as the first step of small-molecule drug discovery.
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Zhu A, Hopkins KM, Friedman RA, Bernstock JD, Broustas CG, Lieberman HB. DNMT1 and DNMT3B regulate tumorigenicity of human prostate cancer cells by controlling RAD9 expression through targeted methylation. Carcinogenesis 2021; 42:220-231. [PMID: 32780107 PMCID: PMC7905840 DOI: 10.1093/carcin/bgaa088] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Revised: 07/15/2020] [Accepted: 08/05/2020] [Indexed: 12/18/2022] Open
Abstract
Prostate cancer is the second most common type of cancer and the second leading cause of cancer death in American men. RAD9 stabilizes the genome, but prostate cancer cells and tumors often have high quantities of the protein. Reduction of RAD9 level within prostate cancer cells decreases tumorigenicity of nude mouse xenographs and metastasis phenotypes in culture, indicating that RAD9 overproduction is essential for the disease. In prostate cancer DU145 cells, CpG hypermethylation in a transcription suppressor site of RAD9 intron 2 causes high-level gene expression. Herein, we demonstrate that DNA methyltransferases DNMT1 and DNMT3B are highly abundant in prostate cancer cells DU145, CWR22, LNCaP and PC-3; yet, these DNMTs bind primarily to the transcription suppressor in DU145, the only cells where methylation is critical for RAD9 regulation. For DU145 cells, DNMT1 or DNMT3B shRNA reduced RAD9 level and tumorigenicity, and RAD9 ectopic expression restored this latter activity in the DNMT knockdown cells. High levels of RAD9, DNMT1, DNMT3B and RAD9 transcription suppressor hypermethylation were significantly correlated in prostate tumors, and not in normal prostate tissues. Based on these results, we propose a novel model where RAD9 is regulated epigenetically by DNMT1 and DNMT3B, via targeted hypermethylation, and that consequent RAD9 overproduction promotes prostate tumorigenesis.
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Affiliation(s)
- Aiping Zhu
- Center for Radiological Research, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Kevin M Hopkins
- Center for Radiological Research, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Richard A Friedman
- Biomedical Informatics Shared Resource, Herbert Irving Comprehensive Cancer Center, New York, NY, USA
- Department of Biomedical Informatics, Columbia University, New York, NY, USA
| | - Joshua D Bernstock
- Center for Radiological Research, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Constantinos G Broustas
- Center for Radiological Research, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Howard B Lieberman
- Center for Radiological Research, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Department of Environmental Health Sciences, Columbia University Mailman School of Public Health, New York, NY, USA
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Broustas CG, Hopkins KM, Panigrahi SK, Wang L, Virk RK, Lieberman HB. RAD9A promotes metastatic phenotypes through transcriptional regulation of anterior gradient 2 (AGR2). Carcinogenesis 2019; 40:164-172. [PMID: 30295739 DOI: 10.1093/carcin/bgy131] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Revised: 09/17/2018] [Accepted: 10/04/2018] [Indexed: 01/01/2023] Open
Abstract
RAD9A plays an important role in prostate tumorigenesis and metastasis-related phenotypes. The protein classically functions as part of the RAD9A-HUS1-RAD1 complex but can also act independently. RAD9A can selectively transactivate multiple genes, including CDKN1A and NEIL1 by binding p53-consensus sequences in or near promoters. RAD9A is overexpressed in human prostate cancer specimens and cell lines; its expression correlates with tumor progression. Silencing RAD9A in prostate cancer cells impairs their ability to form tumors in vivo and migrate as well as grow anchorage independently in vitro. We demonstrate herein that RAD9A transcriptionally controls AGR2, a gene aberrantly overexpressed in patients with metastatic prostate cancer. Transient or stable knockdown of RAD9A in PC-3 cells caused downregulation of AGR2 protein abundance. Reduced AGR2 protein levels were due to lower abundance of AGR2 mRNA. The AGR2 genomic region upstream of the coding initiation site contains several p53 consensus sequences. RAD9A bound specifically to the 5'-untranslated region of AGR2 in PC-3 cells at a partial p53 consensus sequence at position +3136 downstream from the transcription start site, determined by chromatin immunoprecipitation, followed by PCR amplification. Binding of RAD9A to the p53 consensus sequence was sufficient to drive AGR2 gene transcription, shown by a luciferase reporter assay. In contrast, when the RAD9A-binding sequence on the AGR2 was mutated, no luciferase activity was detected. Knockdown of RAD9A in PC-3 cells impaired cell migration and anchorage-independent growth. However, ectopically expressed AGR2 in RAD9A-depleted PC-3 cells restored these phenotypes. Our results suggest RAD9A drives metastasis by controlling AGR2 abundance.
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Affiliation(s)
- Constantinos G Broustas
- Center for Radiological Research, Columbia University Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, USA
| | - Kevin M Hopkins
- Center for Radiological Research, Columbia University Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, USA
| | - Sunil K Panigrahi
- Center for Radiological Research, Columbia University Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, USA
| | - Li Wang
- Center for Radiological Research, Columbia University Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, USA
| | - Renu K Virk
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Howard B Lieberman
- Center for Radiological Research, Columbia University Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, USA.,Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University Irving Medical Center, New York, NY, USA
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Lieberman HB, Rai AJ, Friedman RA, Hopkins KM, Broustas CG. Prostate cancer: unmet clinical needs and RAD9 as a candidate biomarker for patient management. Transl Cancer Res 2018; 7:S651-S661. [PMID: 30079300 PMCID: PMC6071673 DOI: 10.21037/tcr.2018.01.21] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Prostate cancer is a complex disease, with multiple subtypes and clinical presentations. Much progress has been made in recent years to understand the underlying genetic basis that drives prostate cancer. Such mechanistic information is useful for development of novel therapeutic targets, to identify biomarkers for early detection or to distinguish between aggressive and indolent disease, and to predict treatment outcome. Multiple tests have become available in recent years to address these clinical needs for prostate cancer. We describe several of these assays, summarizing test details, performance characteristics, and acknowledging their limitations. There is a pressing unmet need for novel biomarkers that can demonstrate improvement in these areas. We introduce one such candidate biomarker, RAD9, describe its functions in the DNA damage response, and detail why it can potentially fill this void. RAD9 has multiple roles in prostate carcinogenesis, making it potentially useful as a clinical tool for men with prostate cancer. RAD9 was originally identified as a radioresistance gene, and subsequent investigations revealed several key functions in the response of cells to DNA damage, including involvement in cell cycle checkpoint control, at least five DNA repair pathways, and apoptosis. Further studies indicated aberrant overexpression in approximately 45% of prostate tumors, with a strong correlation between RAD9 abundance and cancer stage. A causal relationship between RAD9 and prostate cancer was first demonstrated using a mouse model, where tumorigenicity of human prostate cancer cells after subcutaneous injection into nude mice was diminished when RNA interference was used to reduce the normally high levels of the protein. In addition to activity needed for the initial development of tumors, cell culture studies indicated roles for RAD9 in promoting prostate cancer progression by controlling cell migration and invasion through regulation of ITGB1 protein levels, and anoikis resistance by modulating AKT activation. Furthermore, RAD9 enhances the resistance of human prostate cancer cells to radiation in part by regulating ITGB1 protein abundance. RAD9 binds androgen receptor and inhibits androgen-induced androgen receptor's activity as a transcription factor. Moreover, RAD9 also acts as a gene-specific transcription factor, through binding p53 consensus sequences at target gene promoters, and this likely contributes to its oncogenic activity. Given these diverse and extensive activities, RAD9 plays important roles in the initiation and progression of prostate cancer and can potentially serve as a valuable biomarker useful in the management of patients with this disease.
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Affiliation(s)
- Howard B. Lieberman
- Center for Radiological Research, Columbia University College of Physicians and Surgeons, New York, NY, USA
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Alex J. Rai
- Department of Pathology and Cell Biology and Special Chemistry Laboratories, Columbia University Medical Center and New York Presbyterian Hospital, New York, NY, USA
| | - Richard A. Friedman
- Biomedical Informatics Shared Resource, Herbert Irving Comprehensive Cancer Center and Department of Biomedical Informatics, Columbia University, New York, NY, USA
| | - Kevin M. Hopkins
- Center for Radiological Research, Columbia University College of Physicians and Surgeons, New York, NY, USA
| | - Constantinos G. Broustas
- Center for Radiological Research, Columbia University College of Physicians and Surgeons, New York, NY, USA
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Lieberman HB, Panigrahi SK, Hopkins KM, Wang L, Broustas CG. p53 and RAD9, the DNA Damage Response, and Regulation of Transcription Networks. Radiat Res 2017; 187:424-432. [PMID: 28140789 DOI: 10.1667/rr003cc.1] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The way cells respond to DNA damage is important since inefficient repair or misrepair of lesions can have deleterious consequences, including mutation, genomic instability, neurodegenerative disorders, premature aging, cancer or death. Whether damage occurs spontaneously as a byproduct of normal metabolic processes, or after exposure to exogenous agents, cells muster a coordinated, complex DNA damage response (DDR) to mitigate potential harmful effects. A variety of activities are involved to promote cell survival, and include DNA repair, DNA damage tolerance, as well as transient cell cycle arrest to provide time for repair before entry into critical cell cycle phases, an event that could be lethal if traversal occurs while damage is present. When such damage is prolonged or not repairable, senescence, apoptosis or autophagy is induced. One major level of DDR regulation occurs via the orchestrated transcriptional control of select sets of genes encoding proteins that mediate the response. p53 is a transcription factor that transactivates specific DDR downstream genes through binding DNA consensus sequences usually in or near target gene promoter regions. The profile of p53-regulated genes activated at any given time varies, and is dependent upon type of DNA damage or stress experienced, exact composition of the consensus DNA binding sequence, presence of other DNA binding proteins, as well as cell context. RAD9 is another protein critical for the response of cells to DNA damage, and can also selectively regulate gene transcription. The limited studies addressing the role of RAD9 in transcription regulation indicate that the protein transactivates at least one of its target genes, p21/waf1/cip1, by binding to DNA sequences demonstrated to be a p53 response element. NEIL1 is also regulated by RAD9 through a similar DNA sequence, though not yet directly verified as a bonafide p53 response element. These findings suggest a novel pathway whereby p53 and RAD9 control the DDR through a shared mechanism involving an overlapping network of downstream target genes. Details and unresolved questions about how these proteins coordinate or compete to execute the DDR through transcriptional reprogramming, as well as biological implications, are discussed.
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Affiliation(s)
- Howard B Lieberman
- a Center for Radiological Research, Columbia University College of Physicians and Surgeons, New York, New York 10032; and.,b Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, New York 10032
| | - Sunil K Panigrahi
- a Center for Radiological Research, Columbia University College of Physicians and Surgeons, New York, New York 10032; and
| | - Kevin M Hopkins
- a Center for Radiological Research, Columbia University College of Physicians and Surgeons, New York, New York 10032; and
| | - Li Wang
- a Center for Radiological Research, Columbia University College of Physicians and Surgeons, New York, New York 10032; and
| | - Constantinos G Broustas
- a Center for Radiological Research, Columbia University College of Physicians and Surgeons, New York, New York 10032; and
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Panigrahi SK, Hopkins KM, Lieberman HB. Regulation of NEIL1 protein abundance by RAD9 is important for efficient base excision repair. Nucleic Acids Res 2015; 43:4531-46. [PMID: 25873625 PMCID: PMC4482081 DOI: 10.1093/nar/gkv327] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Accepted: 03/31/2015] [Indexed: 11/21/2022] Open
Abstract
RAD9 participates in DNA damage-induced cell cycle checkpoints and DNA repair. As a member of the RAD9-HUS1-RAD1 (9-1-1) complex, it can sense DNA damage and recruit ATR to damage sites. RAD9 binding can enhance activities of members of different DNA repair pathways, including NEIL1 DNA glycosylase, which initiates base excision repair (BER) by removing damaged DNA bases. Moreover, RAD9 can act independently of 9-1-1 as a gene-specific transcription factor. Herein, we show that mouse Rad9−/− relative to Rad9+/+ embryonic stem (ES) cells have reduced levels of Neil1 protein. Also, human prostate cancer cells, DU145 and PC-3, knocked down for RAD9 demonstrate reduced NEIL1 abundance relative to controls. We found that Rad9 is required for Neil1 protein stability in mouse ES cells, whereas it regulates NEIL1 transcription in the human cells. RAD9 depletion enhances sensitivity to UV, gamma rays and menadione, but ectopic expression of RAD9 or NEIL1 restores resistance. Glycosylase/apurinic lyase activity was reduced in Rad9−/− mouse ES and RAD9 knocked-down human prostate cancer whole cell extracts, relative to controls. Neil1 or Rad9 addition restored this incision activity. Thus, we demonstrate that RAD9 regulates BER by controlling NEIL1 protein levels, albeit by different mechanisms in human prostate cancer versus mouse ES cells.
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Affiliation(s)
- Sunil K Panigrahi
- Center for Radiological Research, College of Physicians and Surgeons, Columbia University Medical Center, New York, NY 10032, USA
| | - Kevin M Hopkins
- Center for Radiological Research, College of Physicians and Surgeons, Columbia University Medical Center, New York, NY 10032, USA
| | - Howard B Lieberman
- Center for Radiological Research, College of Physicians and Surgeons, Columbia University Medical Center, New York, NY 10032, USA Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University Medical Center, New York, NY 10032, USA
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Ghandhi SA, Ponnaiya B, Panigrahi SK, Hopkins KM, Cui Q, Hei TK, Amundson SA, Lieberman HB. RAD9 deficiency enhances radiation induced bystander DNA damage and transcriptomal response. Radiat Oncol 2014; 9:206. [PMID: 25234738 PMCID: PMC4261775 DOI: 10.1186/1748-717x-9-206] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2014] [Accepted: 09/12/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Radiation induced bystander effects are an important component of the overall response of cells to irradiation and are associated with human health risks. The mechanism responsible includes intra-cellular and inter-cellular signaling by which the bystander response is propagated. However, details of the signaling mechanism are not well defined. METHODS We measured the bystander response of Mrad9+/+ and Mrad9-/- mouse embryonic stem cells, as well as human H1299 cells with inherent or RNA interference-mediated reduced RAD9 levels after exposure to 1 Gy α particles, by scoring chromosomal aberrations and micronuclei formation, respectively. In addition, we used microarray gene expression analyses to profile the transcriptome of directly irradiated and bystander H1299 cells. RESULTS We demonstrated that Mrad9 null enhances chromatid aberration frequency induced by radiation in bystander mouse embryonic stem cells. In addition, we found that H1299 cells with reduced RAD9 protein levels showed a higher frequency of radiation induced bystander micronuclei formation, compared with parental cells containing inherent levels of RAD9. The enhanced bystander response in human cells was associated with a unique transcriptomic profile. In unirradiated cells, RAD9 reduction broadly affected stress response pathways at the mRNA level; there was reduction in transcript levels corresponding to genes encoding multiple members of the UVA-MAPK and p38MAPK families, such as STAT1 and PARP1, suggesting that these signaling mechanisms may not function optimally when RAD9 is reduced. Using network analysis, we found that differential activation of the SP1 and NUPR1 transcriptional regulators was predicted in directly irradiated and bystander H1299 cells. Transcription factor prediction analysis also implied that HIF1α (Hypoxia induced factor 1 alpha) activation by protein stabilization in irradiated cells could be a negative predictor of the bystander response, suggesting that local hypoxic stress experienced by cells directly exposed to radiation may influence whether or not they will elicit a bystander response in neighboring cells.
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Affiliation(s)
| | | | | | | | | | | | | | - Howard B Lieberman
- Center for Radiological Research, Columbia University College of Physicians and Surgeons, New York, NY 10032, USA.
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Vasileva A, Hopkins KM, Wang X, Weisbach MM, Friedman RA, Wolgemuth DJ, Lieberman HB. The DNA damage checkpoint protein RAD9A is essential for male meiosis in the mouse. Development 2013. [DOI: 10.1242/dev.103317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Vasileva A, Hopkins KM, Wang X, Weisbach MM, Friedman RA, Wolgemuth DJ, Lieberman HB. The DNA damage checkpoint protein RAD9A is essential for male meiosis in the mouse. J Cell Sci 2013; 126:3927-38. [PMID: 23788429 PMCID: PMC3757332 DOI: 10.1242/jcs.126763] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/28/2013] [Indexed: 01/01/2023] Open
Abstract
In mitotic cells, RAD9A functions in repairing DNA double-strand breaks (DSBs) by homologous recombination and facilitates the process by cell cycle checkpoint control in response to DNA damage. DSBs occur naturally in the germline during meiosis but whether RAD9A participates in repairing such breaks is not known. In this study, we determined that RAD9A is indeed expressed in the male germ line with a peak of expression in late pachytene and diplotene stages, and the protein was found associated with the XY body. As complete loss of RAD9A is embryonic lethal, we constructed and characterized a mouse strain with Stra8-Cre driven germ cell-specific ablation of Rad9a beginning in undifferentiated spermatogonia in order to assess its role in spermatogenesis. Adult mutant male mice were infertile or sub-fertile due to massive loss of spermatogenic cells. The onset of this loss occurs during meiotic prophase, and there was an increase in the numbers of apoptotic spermatocytes as determined by TUNEL. Spermatocytes lacking RAD9A usually arrested in meiotic prophase, specifically in pachytene. The incidence of unrepaired DNA breaks increased, as detected by accumulation of γH2AX and DMC1 foci on the axes of autosomal chromosomes in pachytene spermatocytes. The DNA topoisomerase IIβ-binding protein 1 (TOPBP1) was still localized to the sex body, albeit with lower intensity, suggesting that RAD9A may be dispensable for sex body formation. We therefore show for the first time that RAD9A is essential for male fertility and for repair of DNA DSBs during meiotic prophase I.
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Affiliation(s)
- Ana Vasileva
- Center for Radiological Research, College of Physicians and Surgeons, Columbia University Medical Center, 630 West 168th St., VC 11-219/220, New York, NY 10032, USA
- Genetics & Development and Obstetrics and Gynecology, The Institute of Human Nutrition, Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, Russ Berrie 608, 1150 St. Nicholas Avenue, New York, NY 10032, USA
| | - Kevin M. Hopkins
- Center for Radiological Research, College of Physicians and Surgeons, Columbia University Medical Center, 630 West 168th St., VC 11-219/220, New York, NY 10032, USA
| | - Xiangyuan Wang
- Genetics & Development and Obstetrics and Gynecology, The Institute of Human Nutrition, Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, Russ Berrie 608, 1150 St. Nicholas Avenue, New York, NY 10032, USA
| | - Melissa M. Weisbach
- Genetics & Development and Obstetrics and Gynecology, The Institute of Human Nutrition, Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, Russ Berrie 608, 1150 St. Nicholas Avenue, New York, NY 10032, USA
| | - Richard A. Friedman
- Biomedical Informatics Shared Resource of the Herbert Irving Comprehensive Cancer Center and Department of Biomedical Informatics, Columbia University Medical Center, 1130 St. Nicholas Avenue, Room 824, New York, NY 10032, USA
| | - Debra J. Wolgemuth
- Genetics & Development and Obstetrics and Gynecology, The Institute of Human Nutrition, Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, Russ Berrie 608, 1150 St. Nicholas Avenue, New York, NY 10032, USA
| | - Howard B. Lieberman
- Center for Radiological Research, College of Physicians and Surgeons, Columbia University Medical Center, 630 West 168th St., VC 11-219/220, New York, NY 10032, USA
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University Medical Center, New York, NY 10032, USA
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Abstract
RAD9 regulates multiple cellular processes that influence genomic integrity, and for at least some of its functions the protein acts as part of a heterotrimeric complex bound to HUS1 and RAD1 proteins. RAD9 participates in DNA repair, including base excision repair, homologous recombination repair and mismatch repair, multiple cell cycle phase checkpoints and apoptosis. In addition, functions including the transactivation of downstream target genes, immunoglobulin class switch recombination, as well as 3'-5' exonuclease activity have been reported. Aberrant RAD9 expression has been linked to breast, lung, thyroid, skin and prostate tumorigenesis, and a cause-effect relationship has been demonstrated for the latter two. Interestingly, human RAD9 overproduction correlates with prostate cancer whereas deletion of Mrad9, the corresponding mouse gene, in keratinocytes leads to skin cancer. These results reveal that RAD9 protein can function as an oncogene or tumor suppressor, and aberrantly high or low levels can have deleterious health consequences. It is not clear which of the many functions of RAD9 is critical for carcinogenesis, but several alternatives are considered herein and implications for the development of novel cancer therapies based on these findings are examined.
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Affiliation(s)
- Howard B Lieberman
- Center for Radiological Research, Columbia University College of Physicians and Surgeons, 630 W 168th St, New York, NY 10032, USA.
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Leloup C, Hopkins KM, Wang X, Zhu A, Wolgemuth DJ, Lieberman HB. Mouse Rad9b is essential for embryonic development and promotes resistance to DNA damage. Dev Dyn 2011; 239:2837-50. [PMID: 20842695 DOI: 10.1002/dvdy.22415] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
RAD9 participates in promoting resistance to DNA damage, cell cycle checkpoint control, DNA repair, apoptosis, embryogenesis, and regulation of transcription. A paralogue of RAD9 (named RAD9B) has been identified. To define the function of mouse Rad9b (Mrad9b), embryonic stem (ES) cells with a targeted gene deletion were constructed and used to generate Mrad9b mutant mice. Mrad9b(-/-) embryos are resorbed after E7.5 while some of the heterozygotes die between E12.5 and a few days after birth. Mrad9b is expressed in embryonic brain and Mrad9b(+/-) embryos exhibit abnormal neural tube closure. Mrad9b(-/-) mouse embryonic fibroblasts are not viable. Mrad9b(-/-) ES cells are more sensitive to gamma rays and mitomycin C than Mrad9b(+/+) controls, but show normal gamma-ray-induced G2/M checkpoint control. There is no evidence of spontaneous genomic instability in Mrad9b(-/-) cells. Our findings thus indicate that Mrad9b is essential for embryonic development and mediates resistance to certain DNA damaging agents.
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Affiliation(s)
- Corinne Leloup
- Center for Radiological Research, College of Physicians and Surgeons, Columbia University, New York, New York 10032, USA
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Han L, Hu Z, Liu Y, Wang X, Hopkins KM, Lieberman HB, Hang H. Mouse Rad1 deletion enhances susceptibility for skin tumor development. Mol Cancer 2010; 9:67. [PMID: 20334655 PMCID: PMC2864214 DOI: 10.1186/1476-4598-9-67] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2009] [Accepted: 03/24/2010] [Indexed: 01/19/2023] Open
Abstract
Background Cells are constantly exposed to stresses from cellular metabolites as well as environmental genotoxins. DNA damage caused by these genotoxins can be efficiently fixed by DNA repair in cooperation with cell cycle checkpoints. Unrepaired DNA lesions can lead to cell death, gene mutation and cancer. The Rad1 protein, evolutionarily conserved from yeast to humans, exists in cells as monomer as well as a component in the 9-1-1 protein complex. Rad1 plays crucial roles in DNA repair and cell cycle checkpoint control, but its contribution to carcinogenesis is unknown. Results To address this question, we constructed mice with a deletion of Mrad1. Matings between heterozygous Mrad1 mutant mice produced Mrad1+/+ and Mrad1+/- but no Mrad1-/- progeny, suggesting the Mrad1 null is embryonic lethal. Mrad1+/- mice demonstrated no overt abnormalities up to one and half years of age. DMBA-TPA combinational treatment was used to induce tumors on mouse skin. Tumors were larger, more numerous, and appeared earlier on the skin of Mrad1+/- mice compared to Mrad1+/+ animals. Keratinocytes isolated from Mrad1+/- mice had significantly more spontaneous DNA double strand breaks, proliferated slower and had slightly enhanced spontaneous apoptosis than Mrad1+/+ control cells. Conclusion These data suggest that Mrad1 is important for preventing tumor development, probably through maintaining genomic integrity. The effects of heterozygous deletion of Mrad1 on proliferation and apoptosis of keratinocytes is different from those resulted from Mrad9 heterozygous deletion (from our previous study), suggesting that Mrad1 also functions independent of Mrad9 besides its role in the Mrad9-Mrad1-Mhus1 complex in mouse cells.
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Affiliation(s)
- Lu Han
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Road Datun, Beijing 100101, China
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Hu Z, Liu Y, Zhang C, Zhao Y, He W, Han L, Yang L, Hopkins KM, Yang X, Lieberman HB, Hang H. Targeted deletion of Rad9 in mouse skin keratinocytes enhances genotoxin-induced tumor development. Cancer Res 2008; 68:5552-61. [PMID: 18632607 DOI: 10.1158/0008-5472.can-07-5670] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The Rad9 gene is evolutionarily conserved from yeast to humans and plays crucial roles in genomic maintenance, DNA repair, and cell cycle checkpoint controls. However, the function of this gene with respect to tumorigenesis is not well-understood. A Rad9-null mutation in mice causes embryonic lethality. In this study, we created mice in which mouse Rad9, Mrad9, was deleted only in keratinocytes to permit examination of the potential function of the gene in tumor development. Mice with Mrad9(+/-) or Mrad9(-/-) keratinocytes showed no overt, spontaneous morphologic defects and seemed similar to wild-type controls. Painting the carcinogen 7,12-dimethylbenzanthracene (DMBA) onto the skin of the animals caused earlier onset and more frequent formation of tumors and senile skin plaques in Mrad9(-/-) mice, compared with Mrad9(+/-) and Mrad9(+/+) littermates. DNA damage response genes p21, p53, and Mrad9B were expressed at higher levels in Mrad9(-/-) relative to Mrad9(+/+) skin. Keratinocytes isolated from Mrad9(-/-) skin had more spontaneous and DMBA-induced DNA double strand breaks than Mrad9(+/+) keratinocytes, and the levels were reduced by incubation with the antioxidant epigallocatechin gallate. These data suggest that Mrad9 plays an important role in maintaining genomic stability and preventing tumor development in keratinocytes.
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Affiliation(s)
- Zhishang Hu
- National Laboratory of Biomacromolecules, Chinese Academy of Sciences, Beijing, China
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Kleiman NJ, David J, Elliston CD, Hopkins KM, Smilenov LB, Brenner DJ, Worgul BV, Hall EJ, Lieberman HB. Mrad9 and Atm Haploinsufficiency Enhance Spontaneous and X-Ray-Induced Cataractogenesis in Mice. Radiat Res 2007; 168:567-73. [PMID: 17973559 DOI: 10.1667/rr1122.1] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2007] [Accepted: 07/02/2007] [Indexed: 11/03/2022]
Affiliation(s)
- Norman J Kleiman
- Center for Radiological Research, Columbia University College of Physicians and Surgeons, New York, NY 10032, USA
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Pandita RK, Sharma GG, Laszlo A, Hopkins KM, Davey S, Chakhparonian M, Gupta A, Wellinger RJ, Zhang J, Powell SN, Roti Roti JL, Lieberman HB, Pandita TK. Mammalian Rad9 plays a role in telomere stability, S- and G2-phase-specific cell survival, and homologous recombinational repair. Mol Cell Biol 2006; 26:1850-64. [PMID: 16479004 PMCID: PMC1430264 DOI: 10.1128/mcb.26.5.1850-1864.2006] [Citation(s) in RCA: 115] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
The protein products of several rad checkpoint genes of Schizosaccharomyces pombe (rad1+, rad3+, rad9+, rad17+, rad26+, and hus1+) play crucial roles in sensing changes in DNA structure, and several function in the maintenance of telomeres. When the mammalian homologue of S. pombe Rad9 was inactivated, increases in chromosome end-to-end associations and frequency of telomere loss were observed. This telomere instability correlated with enhanced S- and G2-phase-specific cell killing, delayed kinetics of gamma-H2AX focus appearance and disappearance, and reduced chromosomal repair after ionizing radiation (IR) exposure, suggesting that Rad9 plays a role in cell cycle phase-specific DNA damage repair. Furthermore, mammalian Rad9 interacted with Rad51, and inactivation of mammalian Rad9 also resulted in decreased homologous recombinational (HR) repair, which occurs predominantly in the S and G2 phases of the cell cycle. Together, these findings provide evidence of roles for mammalian Rad9 in telomere stability and HR repair as a mechanism for promoting cell survival after IR exposure.
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Affiliation(s)
- Raj K Pandita
- Department of Radiation Oncology, Washington University School of Medicine, 4511 Forest Park Ave., St. Louis, MO 63108, USA.
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Karnitz LM, Flatten KS, Wagner JM, Loegering D, Hackbarth JS, Arlander SJH, Vroman BT, Thomas MB, Baek YU, Hopkins KM, Lieberman HB, Chen J, Cliby WA, Kaufmann SH. Gemcitabine-induced activation of checkpoint signaling pathways that affect tumor cell survival. Mol Pharmacol 2005; 68:1636-44. [PMID: 16126823 DOI: 10.1124/mol.105.012716] [Citation(s) in RCA: 103] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Two signaling pathways are activated by antineoplastic therapies that damage DNA and stall replication. In one pathway, double-strand breaks activate ataxia-telangiectasia mutated kinase (ATM) and checkpoint kinase 2 (Chk2), two protein kinases that regulate apoptosis, cell-cycle arrest, and DNA repair. In the second pathway, other types of DNA lesions and replication stress activate the Rad9-Hus1-Rad1 complex and the protein kinases ataxia-telangiectasia mutated and Rad3-related kinase (ATR) and checkpoint kinase 1 (Chk1), leading to changes that block cell-cycle progression, stabilize stalled replication forks, and influence DNA repair. Gemcitabine and cytarabine are two highly active chemotherapeutic agents that disrupt DNA replication. Here, we examine the roles these pathways play in tumor cell survival after treatment with these agents. Cells lacking Rad9, Chk1, or ATR were more sensitive to gemcitabine and cytarabine, consistent with the fact that these agents stall replication forks, and this sensitization was independent of p53 status. Interestingly, ATM depletion sensitized cells to gemcitabine and ionizing radiation but not cytarabine. Together, these results demonstrate that 1) gemcitabine triggers both checkpoint signaling pathways, 2) both pathways contribute to cell survival after gemcitabine-induced replication stress, and 3) although gemcitabine and cytarabine both stall replication forks, ATM plays differential roles in cell survival after treatment with these agents.
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Affiliation(s)
- Larry M Karnitz
- Division of Oncology Research, Guggenheim 13, Mayo Clinic College of Medicine, 200 First Street, S.W., Rochester, Minnesota 55905, USA.
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Smilenov LB, Lieberman HB, Mitchell SA, Baker RA, Hopkins KM, Hall EJ. Combined haploinsufficiency for ATM and RAD9 as a factor in cell transformation, apoptosis, and DNA lesion repair dynamics. Cancer Res 2005; 65:933-8. [PMID: 15705893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/01/2023]
Abstract
Loss of function of oncogenes, tumor suppressor genes and DNA damage processing genes has been implicated in the development of many types of cancer, but for the vast majority of cases, there is no link to specific germ line mutations. In the last several years, heterozygosity leading to haploinsufficiency for proteins involved in DNA repair pathways was shown to play a role in genomic instability and carcinogenesis after DNA damage is induced. Because the effect of haploinsufficiency for one protein is relatively small, we hypothesize that predisposition to cancer could be a result of the additive effect of heterozygosity for two or more genes, critical for pathways that control DNA damage signaling, repair or apoptosis. To address this issue, primary mouse cells, haploinsufficient for one or two proteins, ATM and RAD9, related to the cellular response to DNA damage were examined. The results show that cells having low levels of both ATM and RAD9 proteins are more sensitive to transformation by radiation, have different DNA double-strand break repair dynamics and are less apoptotic when compared with wild-type controls or those cells haploinsufficient for only one of these proteins. Our conclusions are that under stress conditions, the efficiency and capacity for DNA repair mediated by the ATM/RAD9 cell signaling network depend on the abundance of both proteins and that, in general, DNA repair network efficiencies are genotype-dependent and can vary within a specific range.
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Affiliation(s)
- Lubomir B Smilenov
- Center for Radiological Research, College of Physicians and Surgeons, Columbia University, 630 West 168th Street, New York, NY 10032, USA.
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Smilenov LB, Lieberman HB, Mitchell SA, Baker RA, Hopkins KM, Hall EJ. Combined Haploinsufficiency for ATM and RAD9 as a Factor in Cell Transformation, Apoptosis, and DNA Lesion Repair Dynamics. Cancer Res 2005. [DOI: 10.1158/0008-5472.933.65.3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Loss of function of oncogenes, tumor suppressor genes and DNA damage processing genes has been implicated in the development of many types of cancer, but for the vast majority of cases, there is no link to specific germ line mutations. In the last several years, heterozygosity leading to haploinsufficiency for proteins involved in DNA repair pathways was shown to play a role in genomic instability and carcinogenesis after DNA damage is induced. Because the effect of haploinsufficiency for one protein is relatively small, we hypothesize that predisposition to cancer could be a result of the additive effect of heterozygosity for two or more genes, critical for pathways that control DNA damage signaling, repair or apoptosis. To address this issue, primary mouse cells, haploinsufficient for one or two proteins, ATM and RAD9, related to the cellular response to DNA damage were examined. The results show that cells having low levels of both ATM and RAD9 proteins are more sensitive to transformation by radiation, have different DNA double-strand break repair dynamics and are less apoptotic when compared with wild-type controls or those cells haploinsufficient for only one of these proteins. Our conclusions are that under stress conditions, the efficiency and capacity for DNA repair mediated by the ATM/RAD9 cell signaling network depend on the abundance of both proteins and that, in general, DNA repair network efficiencies are genotype-dependent and can vary within a specific range.
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Affiliation(s)
- Lubomir B. Smilenov
- Center for Radiological Research, College of Physicians and Surgeons, Columbia University, New York, New York
| | - Howard B. Lieberman
- Center for Radiological Research, College of Physicians and Surgeons, Columbia University, New York, New York
| | - Stephen A. Mitchell
- Center for Radiological Research, College of Physicians and Surgeons, Columbia University, New York, New York
| | - Ronald A. Baker
- Center for Radiological Research, College of Physicians and Surgeons, Columbia University, New York, New York
| | - Kevin M. Hopkins
- Center for Radiological Research, College of Physicians and Surgeons, Columbia University, New York, New York
| | - Eric J. Hall
- Center for Radiological Research, College of Physicians and Surgeons, Columbia University, New York, New York
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Hopkins KM, Auerbach W, Wang XY, Hande MP, Hang H, Wolgemuth DJ, Joyner AL, Lieberman HB. Deletion of mouse rad9 causes abnormal cellular responses to DNA damage, genomic instability, and embryonic lethality. Mol Cell Biol 2004; 24:7235-48. [PMID: 15282322 PMCID: PMC479733 DOI: 10.1128/mcb.24.16.7235-7248.2004] [Citation(s) in RCA: 98] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The fission yeast Schizosaccharomyces pombe rad9 gene promotes cell survival through activation of cell cycle checkpoints induced by DNA damage. Mouse embryonic stem cells with a targeted deletion of Mrad9, the mouse ortholog of this gene, were created to evaluate its function in mammals. Mrad9(-/-) cells demonstrated a marked increase in spontaneous chromosome aberrations and HPRT mutations, indicating a role in the maintenance of genomic integrity. These cells were also extremely sensitive to UV light, gamma rays, and hydroxyurea, and heterozygotes were somewhat sensitive to the last two agents relative to Mrad9(+/+) controls. Mrad9(-/-) cells could initiate but not maintain gamma-ray-induced G(2) delay and retained the ability to delay DNA synthesis rapidly after UV irradiation, suggesting that checkpoint abnormalities contribute little to the radiosensitivity observed. Ectopic expression of Mrad9 or human HRAD9 complemented Mrad9(-/-) cell defects, indicating that the gene has radioresponse and genomic maintenance functions that are evolutionarily conserved. Mrad9(+/-) mice were generated, but heterozygous intercrosses failed to yield Mrad9(-/-) pups, since embryos died at midgestation. Furthermore, Mrad9(-/-) mouse embryo fibroblasts were not viable. These investigations establish Mrad9 as a key mammalian genetic element of pathways that regulate the cellular response to DNA damage, maintenance of genomic integrity, and proper embryonic development.
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Affiliation(s)
- Kevin M Hopkins
- Center for Radiological Research, College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
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Yin Y, Zhu A, Jin YJ, Liu YX, Zhang X, Hopkins KM, Lieberman HB. Human RAD9 checkpoint control/proapoptotic protein can activate transcription of p21. Proc Natl Acad Sci U S A 2004; 101:8864-9. [PMID: 15184659 PMCID: PMC428438 DOI: 10.1073/pnas.0403130101] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
When human cells incur DNA damage, two fundamental responses can follow, cell cycle arrest or apoptosis. Human RAD9 (hRAD9) and p53 function in both processes, but the mechanistic relationship between their activities is unknown. p53 mediates checkpoint control at G(1) by transcriptional regulation of p21. In this report, we show that hRAD9, like p53, can also regulate p21 at the transcriptional level. We demonstrate that overexpression of hRAD9 leads to increased p21 RNA and encoded protein levels. The promoter region of p21 fused to a luciferase reporter can be transactivated by either hRAD9 or p53, indicating that hRAD9 regulates the p21 promoter for transcriptional control of expression. Using an electrophoretic mobility-shift assay, we show that hRAD9 specifically binds to a p53-consensus DNA-binding sequence in the p21 promoter. Microarray screening coupled with Northern analysis reveals that hRAD9 regulates the abundance of other messages in addition to p21. Our data reveal a previously undescribed mechanism for regulation of p21 and demonstrate that hRAD9 can control gene transcription. We suggest that hRAD9 and p53 co-regulate p21 to direct cell cycle progression by similar molecular mechanisms. Furthermore, hRAD9 might regulate other cellular processes as well by modulating transcription of multiple down-stream target genes.
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Affiliation(s)
- Yuxin Yin
- Center for Radiological Research, Department of Radiation Oncology, College of Physicians and Surgeons, Columbia University, 630 West 168th Street, New York, NY 10032, USA
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21
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Loegering D, Arlander SJH, Hackbarth J, Vroman BT, Roos-Mattjus P, Hopkins KM, Lieberman HB, Karnitz LM, Kaufmann SH. Rad9 protects cells from topoisomerase poison-induced cell death. J Biol Chem 2004; 279:18641-7. [PMID: 14988409 DOI: 10.1074/jbc.m313536200] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Previous studies have suggested two possible roles for Rad9 in mammalian cells subjected to replication stress or DNA damage. One model suggests that a Rad9-containing clamp is loaded onto damaged DNA, where it participates in Chk1 activation and subsequent events that contribute to cell survival. The other model suggests that Rad9 translocates to mitochondria, where it triggers apoptosis by binding to and inhibiting Bcl-2 and Bcl-x(L). To further study the role of Rad9, parental and Rad9(-/-) murine embryonic stem (ES) cells were treated with camptothecin, etoposide, or cytarabine, all prototypic examples of three classes of widely used anticancer agents. All three agents induced Rad9 chromatin binding. Each of these agents also triggered S-phase checkpoint activation in parental ES cells, as indicated by a caffeine-inhibitable decrease in [3H]thymidine incorporation into DNA and Cdc25A down-regulation. Interestingly, the ability of cytarabine to activate the S-phase checkpoint was severely compromised in Rad9(-/-) cells, whereas activation of this checkpoint by camptothecin and etoposide was unaltered, suggesting that the action of cytarabine is readily distinguished from that of classical topoisomerase poisons. Nonetheless, Rad9 deletion sensitized ES cells to the cytotoxic effects of all three agents, as evidenced by enhanced apoptosis and diminished colony formation. Collectively, these results suggest that the predominant role of Rad9 in ES cells is to promote survival after replicative stress and topoisomerase-mediated DNA damage.
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Affiliation(s)
- David Loegering
- Division of Oncology Research, Mayo Clinic, Rochester, Minnesota 55905, USA
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Affiliation(s)
- Howard B Lieberman
- Department of Radiation Oncology, Columbia University College of Physicians and Surgeons, New York, NY, USA
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Hopkins KM, Wang X, Berlin A, Hang H, Thaker HM, Lieberman HB. Expression of mammalian paralogues of HRAD9 and Mrad9 checkpoint control genes in normal and cancerous testicular tissue. Cancer Res 2003; 63:5291-8. [PMID: 14500360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/27/2023]
Abstract
Human and mouse paralogues of the evolutionarily conserved mammalian HRAD9 and Mrad9 cell cycle checkpoint control genes have been isolated and called HRAD9B and Mrad9B, respectively. HRAD9B encodes a protein that is 414 amino acids long and is 55% similar and 35% identical to the HRAD9 gene product. The Mrad9B protein is 398 amino acids long and is 50% similar and 35% identical to its paralogue. We demonstrate that the encoded human protein is nuclear and can physically interact with checkpoint proteins HRAD1, HRAD9, HHUS1, and HHUS1B, much like HRAD9. Northern blot analysis to detect tissue specificity indicates that the human and mouse genes are expressed predominantly in the testis. The abundance of HRAD9B RNA, as judged by quantitative reverse transcription-PCR, is very low in most testicular tumors, particularly those of germ cell origin, i.e., seminomas, relative to normal testis control, nonseminomas, or Leydig tumor cells. RNA levels corresponding to HRAD17, another checkpoint control gene, demonstrated a similar pattern, but in general, higher quantities of this message were detected in samples. Furthermore, normal/tumor tissue differences were not as dramatic or consistent from sample to sample, especially for the seminomas. Our results demonstrate for the first time that HRAD9 and Mrad9 are part of a gene family and reveal a new genetic element encoding a product that interacts with multiple, known cell cycle checkpoint control proteins. The findings also indicate that HRAD9B can serve as a biomarker in particular for testicular seminomas and might be causally related to the disease.
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Affiliation(s)
- Kevin M Hopkins
- Center for Radiological Research, Columbia University College of Physicians and Surgeons, New York, New York 10032, USA
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Roos-Mattjus P, Hopkins KM, Oestreich AJ, Vroman BT, Johnson KL, Naylor S, Lieberman HB, Karnitz LM. Phosphorylation of human Rad9 is required for genotoxin-activated checkpoint signaling. J Biol Chem 2003; 278:24428-37. [PMID: 12709442 DOI: 10.1074/jbc.m301544200] [Citation(s) in RCA: 96] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Rad9, a key component of genotoxin-activated checkpoint signaling pathways, associates with Hus1 and Rad1 in a heterotrimeric complex (the 9-1-1 complex). Rad9 is inducibly and constitutively phosphorylated. However, the role of Rad9 phosphorylation is unknown. Here we identified nine phosphorylation sites, all of which lie in the carboxyl-terminal 119-amino acid Rad9 tail and examined the role of phosphorylation in genotoxin-triggered checkpoint activation. Rad9 mutants lacking a Ser-272 phosphorylation site, which is phosphorylated in response to genotoxins, had no effect on survival or checkpoint activation in Mrad9-/- mouse ES cells treated with hydroxyurea (HU), ionizing radiation (IR), or ultraviolet radiation (UV). In contrast, additional Rad9 tail phosphorylation sites were essential for Chk1 activation following HU, IR, and UV treatment. Consistent with a role for Chk1 in S-phase arrest, HU- and UV-induced S-phase arrest was abrogated in the Rad9 phosphorylation mutants. In contrast, however, Rad9 did not play a role in IR-induced S-phase arrest. Clonogenic assays revealed that cells expressing a Rad9 mutant lacking phosphorylation sites were as sensitive as Rad9-/- cells to UV and HU. Although Rad9 contributed to survival of IR-treated cells, the identified phosphorylation sites only minimally contributed to survival following IR treatment. Collectively, these results demonstrate that the Rad9 phospho-tail is a key participant in the Chk1 activation pathway and point to additional roles for Rad9 in cellular responses to IR.
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Affiliation(s)
- Pia Roos-Mattjus
- Department of Biochemistry and Molecular Biology, Mayo Clinic and Foundation, Rochester, Minnesota 55905, USA
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Abstract
It has long been accepted that the radiation-induced heritable effects in mammalian cells are the result of direct DNA damage. Recent evidence, however, suggests that when a cell population is exposed to a low dose of alpha particles, biological effects occur in a larger proportion of cells than are estimated to have been traversed by alpha particles. Experiments involving the Columbia University microbeam, which allows a known fraction of cells to be traversed by a defined number of alpha particles, have demonstrated a bystander effect for clonogenic survival and oncogenic transformation in C3H 10T(1/2) cells. When 1 to 16 alpha particles were passed through the nuclei of 10% of a C3H 10T(1/2) cell population, more cells were unable to form colonies than were actually traversed by alpha particles. Both hit and non-hit cells contributed to the outcome of the experiments. The present work was undertaken to assess the bystander effect of radiation in only non-hit cells. For this purpose, Chinese hamster V79 cells transfected with hygromycin- or neomycin-resistance genes were used. V79 cells stably transfected with a hygromycin resistance gene and stained with a nuclear dye were irradiated with the charged-particle microbeam in the presence of neomycin-resistant cells. The biological effect was studied in the neomycin-resistant V79 cells after selective removal of the hit cells with geneticin treatment.
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Affiliation(s)
- S G Sawant
- Center for Radiological Research, Columbia University, New York, New York 10032, USA
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Elder RT, Song XQ, Chen M, Hopkins KM, Lieberman HB, Zhao Y. Involvement of rhp23, a Schizosaccharomyces pombe homolog of the human HHR23A and Saccharomyces cerevisiae RAD23 nucleotide excision repair genes, in cell cycle control and protein ubiquitination. Nucleic Acids Res 2002; 30:581-91. [PMID: 11788722 PMCID: PMC99819 DOI: 10.1093/nar/30.2.581] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
A functional homolog (rhp23) of human HHR23A and Saccharomyces cerevisiae RAD23 was cloned from the fission yeast Schizosaccharomyces pombe and characterized. Consistent with the role of Rad23 homologs in nucleotide excision repair, rhp23 mutant cells are moderately sensitive to UV light but demonstrate wild-type resistance to gamma-rays and hydroxyurea. Expression of the rhp23, RAD23 or HHR23A cDNA restores UV resistance to the mutant, indicating that rhp23 is a functional homolog of the human and S.cerevisiae genes. The rhp23::ura4 mutation also causes a delay in the G2 phase of the cell cycle which is corrected when rhp23, RAD23 or HHR23A cDNA is expressed. Rhp23 is present throughout the cell but is located predominantly in the nucleus, and the nuclear levels of Rhp23 decrease around the time of S phase in the cell cycle. Rhp23 is ubiquitinated at low levels, but overexpression of the rhp23 cDNA induces a large increase in ubiquitination of other proteins. Consistent with a role in protein ubiquitination, Rhp23 binds ubiquitin, as determined by two-hybrid analysis. Thus, the rhp23 gene plays a role not only in nucleotide excision repair but also in cell cycle regulation and the ubiquitination pathways.
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Affiliation(s)
- Robert T Elder
- Children's Memorial Institute for Education and Research, Departments of Pediatrics and Microbiology-Immunology, Northwestern University Medical School, 2430 North Halstead Street, 218, Chicago, IL 60614, USA
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Hang H, Rauth SJ, Hopkins KM, Lieberman HB. Mutant alleles of Schizosaccharomyces pombe rad9(+) alter hydroxyurea resistance, radioresistance and checkpoint control. Nucleic Acids Res 2000; 28:4340-9. [PMID: 11058134 PMCID: PMC113140 DOI: 10.1093/nar/28.21.4340] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2000] [Revised: 09/08/2000] [Accepted: 09/08/2000] [Indexed: 11/13/2022] Open
Abstract
Schizosaccharomyces pombe rad9 mutations can render cells sensitive to hydroxyurea (HU), gamma-rays and UV light and eliminate associated checkpoint controls. In vitro mutagenesis was performed on S.pombe rad9 and altered alleles were transplaced into the genome to ascertain the functional significance of five groups of evolutionarily conserved amino acids. Most targeted regions were changed to alanines, whereas rad9-S3 encodes a protein devoid of 22 amino acids normally present in yeast but absent from mammalian Rad9 proteins. We examined whether these rad9 alleles confer radiation and HU sensitivity and whether the sensitivities correlate with checkpoint control deficiencies. One rad9 mutant allele was fully active, whereas four others demonstrated partial loss of function. rad9-S1, which contains alterations in a BH3-like domain, conferred HU resistance but increased sensitivity to gamma-rays and UV light, without affecting checkpoint controls. rad9-S2 reduced gamma-ray sensitivity marginally, without altering other phenotypes. Two alleles, rad9-S4 and rad9-S5, reduced HU sensitivity, radiosensitivity and caused aberrant checkpoint function. HU-induced checkpoint control could not be uncoupled from drug resistance. These results establish unique as well as overlapping functional domains within Rad9p and provide evidence that requirements of the protein for promoting resistance to radiation and HU are not identical.
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Affiliation(s)
- H Hang
- Center for Radiological Research, Columbia University, 630 West 168th Street, New York, NY 10032, USA
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28
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Abstract
Here we report that the Schizosaccharomyces pombe Rad9 (SpRad9) protein contains a group of amino acids with similarity to the Bcl-2 homology 3 death domain, which is required for SpRad9 interaction with human Bcl-2 and apoptosis induction in human cells. Overexpression of Bcl-2 in S. pombe inhibits cell growth independently of rad9, but enhances resistance of rad9-null cells to methyl methanesulfonate, ultraviolet and ionizing radiation. These observations suggest that SpRad9 may represent the first member of the Bcl-2 protein family identified in yeast, though the cell death pathways in S. pombe may differ from those found in mammals.
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Affiliation(s)
- K Komatsu
- Drug Discovery Program, H. Lee Moffitt Cancer Center, 12902 Magnolia Drive, Tampa, FL 33612, USA
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Komatsu K, Miyashita T, Hang H, Hopkins KM, Zheng W, Cuddeback S, Yamada M, Lieberman HB, Wang HG. Human homologue of S. pombe Rad9 interacts with BCL-2/BCL-xL and promotes apoptosis. Nat Cell Biol 2000; 2:1-6. [PMID: 10620799 DOI: 10.1038/71316] [Citation(s) in RCA: 112] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
DNA damage induces apoptosis through a signalling pathway that can be suppressed by the BCL-2 protein, but the mechanism by which DNA damage does this is unknown. Here, using yeast two-hybrid and co-immunoprecipitation studies, we show that RAD9, a human protein involved in the control of a cell-cycle checkpoint, interacts with the anti-apoptotic Bcl-2-family proteins BCL-2 and BCL-x L, but not with the pro-apoptotic BAX and BAD. When overexpressed in mammalian cells, RAD9 induces apoptosis that can be blocked by BCL-2 or BCL-x L. Conversely, antisense RAD9 RNA suppresses cell death induced by methyl methanesulphonate. These findings indicate that RAD9 may have a new role in regulating apoptosis after DNA damage, in addition to its previously described checkpoint-control and other radioresistance-promoting functions.
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Affiliation(s)
- K Komatsu
- Drug Discovery Program, H. Lee Moffitt Cancer Center and Research Institute, Department of Pharmacology and Therapeutics, University of South Florida College of Medicine, 12902 Magnolia Drive, Tampa, Florida 33612, USA
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30
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Hang H, Rauth SJ, Hopkins KM, Davey SK, Lieberman HB. Molecular cloning and tissue-specific expression of Mrad9, a murine orthologue of the Schizosaccharomyces pombe rad9+ checkpoint control gene. J Cell Physiol 1998; 177:241-7. [PMID: 9766521 DOI: 10.1002/(sici)1097-4652(199811)177:2<241::aid-jcp6>3.0.co;2-n] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
We have isolated a murine cDNA, Mrad9, that is orthologous to the fission yeast rad9+ and human HRAD9 genes. Mrad9 encodes a 389 amino acid long, 42,032 Dalton protein that is 27% identical and 56% similar to Rad9p, and 82% identical and 88% similar to HRAD9, at the amino acid level. Expression of the Mrad9 cDNA in Schizosaccharomyces pombe rad9::ura4+ cells restores nearly wild-type levels of hydroxyurea resistance and early S phase checkpoint control to mutant fission yeast cell populations. However, UV resistance is only minimally restored, and mutant cells remain sensitive to gamma radiation. Mrad9 genomic DNA was isolated from a mouse 129/SvEv library. The Mrad9 gene was local ized to a 15-kbp genomic DNA fragment, and contains 10 exons separated by 9 introns. Northern blot analysis indicates that the gene is expressed in many different tissues of the adult mouse, but the mRNA is most abundant in the heart and present at very low levels in the liver. These studies demonstrate the existence of a murine orthologue of the fission yeast rad9+ gene and underscore at least the partial evolutionary conservation of rad9+-dependent checkpoint control mechanisms.
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Affiliation(s)
- H Hang
- Center for Radiological Research, Columbia University, New York, New York 10032, USA
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31
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Davey S, Han CS, Ramer SA, Klassen JC, Jacobson A, Eisenberger A, Hopkins KM, Lieberman HB, Freyer GA. Fission yeast rad12+ regulates cell cycle checkpoint control and is homologous to the Bloom's syndrome disease gene. Mol Cell Biol 1998; 18:2721-8. [PMID: 9566891 PMCID: PMC110651 DOI: 10.1128/mcb.18.5.2721] [Citation(s) in RCA: 77] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/1997] [Accepted: 02/10/1998] [Indexed: 02/07/2023] Open
Abstract
The human BLM gene is a member of the Escherichia coli recQ helicase family, which includes the Saccharomyces cerevisiae SGS1 and human WRN genes. Defects in BLM are responsible for the human disease Bloom's syndrome, which is characterized in part by genomic instability and a high incidence of cancer. Here we describe the cloning of rad12+, which is the fission yeast homolog of BLM and is identical to the recently reported rhq1+ gene. We showed that rad12 null cells are sensitive to DNA damage induced by UV light and gamma radiation, as well as to the DNA synthesis inhibitor hydroxyurea. Overexpression of the wild-type rad12+ gene also leads to sensitivity to these agents and to defects associated with the loss of the S-phase and G2-phase checkpoint control. We showed genetically and biochemically that rad12+ acts upstream from rad9+, one of the fission yeast G2 checkpoint control genes, in regulating exit from the S-phase checkpoint. The physical chromosome segregation defects seen in rad12 null cells combined with the checkpoint regulation defect seen in the rad12+ overproducer implicate rad12+ as a key coupler of chromosomal integrity with cell cycle progression.
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Affiliation(s)
- S Davey
- Department of Oncology, Queen's University, Kingston, Ontario, Canada.
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Lieberman HB, Hopkins KM, Nass M, Demetrick D, Davey S. A human homolog of the Schizosaccharomyces pombe rad9+ checkpoint control gene. Proc Natl Acad Sci U S A 1996; 93:13890-5. [PMID: 8943031 PMCID: PMC19459 DOI: 10.1073/pnas.93.24.13890] [Citation(s) in RCA: 93] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/1996] [Accepted: 09/12/1996] [Indexed: 02/03/2023] Open
Abstract
The product of the Schizosaccharomyces pombe rad9+ gene is required for cell cycle arrest at the G2 checkpoints in response to incompletely replicated or damaged DNA. We have identified a human cDNA from an infant brain library that is a structural homolog of S. pombe rad9+, by searching the dBest data base for sequences similar to the fission yeast gene. The human gene encodes a 391-amino acid long, 42,520-Da protein that is approximately 25% identical and 52% similar to the yeast protein. The human and yeast gene products demonstrate partial conservation of function, as the human cDNA can rescue to different degrees the sensitivity of S. pombe rad9::ura4+ cells to the DNA synthesis inhibitor hydroxyurea and gamma rays, as well as the associated checkpoint controls. These results suggest an underlying conservation of the molecular mechanisms of S and G2 checkpoint control pathways in most if not all eukaryotes. Fluorescence in situ hybridization using a fragment of the corresponding human genome as a probe, in conjunction with PCR reactions employing DNA from human X rodent somatic cell hybrids, has localized the gene to human chromosome 11q13.1-13.2. This region contains a number of tumor suppressor loci, and based on the biology of checkpoint control genes, HRAD9 should be considered a strong candidate for one of them.
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Affiliation(s)
- H B Lieberman
- Center for Radiological Research, Columbia University, New York, NY 10032, USA.
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Affiliation(s)
- K M Hopkins
- Department of Oral and Maxillofacial Surgery, University of Tennessee, Memphis College of Dentistry 38163, USA
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Hang H, Hager DN, Goriparthi L, Hopkins KM, Shih H, Lieberman HB. Schizosaccharomyces pombe rad23 is allelic with swi10, a mating-type switching/radioresistance gene that shares sequence homology with human and mouse ERCC1. Gene 1996; 170:113-7. [PMID: 8621070 DOI: 10.1016/0378-1119(95)00872-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Schizosaccharomyces pombe (Sp) rad23-1 mutant cells are extremely sensitive to UV light and ionizing radiation. A genomic DNA fragment that contains wild-type (wt) rad23 has been cloned. The DNA sequence of this cloned gene has been determined and was found to be identical to the previously characterized mating-type switching/radioresistance gene, swi10. Complementation tests between rad23-1 and swi10-154 mutant cells exclusively produce UV-sensitive progeny and confirm that these two genes are allelic. The DNA sequences of rad23-1 and swi10-154 reveal that each contains a single, unique point mutation. In rad23-1, Glu231 changes to a stop codon, resulting in the production of a truncated protein. In swi10-154, a G to A transition mutation is within a splice consensus sequence for intron 1. Therefore, the corresponding mRNA is incapable of being processed appropriately.
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Affiliation(s)
- H Hang
- Center for Radiological Research, Columbia University, New York, NY 10032, USA
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Lieberman HB, Hopkins KM. Schizosaccharomyces malidevorans and Sz. octosporus homologues of Sz. pombe rad9, a gene that mediates radioresistance and cell-cycle progression. Gene 1994; 150:281-6. [PMID: 7821792 DOI: 10.1016/0378-1119(94)90438-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The rad9 gene of Schizosaccharomyces pombe is involved in promoting resistance to ionizing radiation and UV light, as well as regulating cell cycle progression after irradiation. We have isolated functional rad9 cognates from two other fission yeasts, Sz. malidevorans and Sz. octosporus, that can restore radioresistance and the radiation-induced G2 delay response to Sz. pombe rad9::ura4 cells. The Sz. pombe and Sz. malidevorans genes are identical at the nucleotide sequence level, which reflects their close evolutionary relationship. Each bears three introns and codes for a 47 464-Da protein that contain 426 amino acids (aa). In contrast, Sz. octosporus rad9 contains five introns and codes for a 48 210-Da protein that is 432-aa long. The Sz. pombe rad9 product is only 65% identical and 80% similar to the corresponding Sz. octosporus gene product. All of the strains synthesize a rad9 RNA of approx. 1.6 kb. The presence of a rad9-like gene in these yeasts suggests that the cellular process(es) mediated by rad9, and used by these organisms to increase survival and transiently delay cycling in G2 after irradiation, are conserved. The isolation, analyses and comparison of rad9 genes from different organisms should aid in elucidating the specific biological role of the corresponding protein and especially help pinpoint regions important for function.
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Affiliation(s)
- H B Lieberman
- Center for Radiological Research, Columbia University, New York, NY 10032
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36
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Hopkins KM. Then and now ... human resources management. J Healthc Educ Train 1994; 9:7-10. [PMID: 10156679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
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37
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Zhao Y, Hopkins KM, Lieberman HB. A method for the preparation and storage of frozen, competent Schizosaccharomyces pombe spheroplasts. Biotechniques 1993; 15:238. [PMID: 8373587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Affiliation(s)
- Y Zhao
- Center for Radiological Research, Columbia University, New York, NY 10032
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Lieberman HB, Hopkins KM, Laverty M, Chu HM. Molecular cloning and analysis of Schizosaccharomyces pombe rad9, a gene involved in DNA repair and mutagenesis. Mol Gen Genet 1992; 232:367-76. [PMID: 1588907 DOI: 10.1007/bf00266239] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The mutant allele rad9-192 renders Schizosaccharomyces pombe cells sensitive to ionizing radiation and UV light. We have isolated from a S. pombe genomic DNA library a unique recombinant plasmid that is capable of restoring wild-type levels of radioresistance to a rad9-192-containing cell population. Plasmid integration studies using the cloned DNA, coupled with mating and tetrad analyses, indicate that this isolated DNA contains the wild-type rad9 gene. We inactivated the repair function of the cloned fragment by a single insertion of the S. pombe ura4 gene. This nonfunctional fragment was used to create a viable disruption mutant, thus demonstrating that the rad9 gene does not encode an essential cellular function. In addition, the rad9-192 mutant population is as radiosensitive as the disruption mutant, indicating that rad9 gene function is severely if not totally inhibited by the molecular defect responsible for the rad9-192 phenotype. DNA sequence analysis of rad9 reveals an open reading frame of 1,278 bp, interrupted by three introns 53 bp, 57 bp, and 56 bp long, respectively, and ending in the termination codon TAG. This gene is capable of encoding a protein of 426 amino acids, with a corresponding calculated molecular weight of 47,464 daltons. No significant homology was detected between the rad9 gene or its deduced protein sequence and sequences previously entered into DNA and protein sequence data banks.
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Affiliation(s)
- H B Lieberman
- Department of Radiation Oncology, Columbia University College of Physicians and Surgeons, New York, NY 10032
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Temeyer KB, Hopkins KM, Chapman LF. A molecular model for illegitimate recombination in Bacillus subtilis. SAAS Bull Biochem Biotechnol 1991; 4:52-5. [PMID: 1369322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 03/25/2023]
Abstract
The recombinant DNA junctions at which pUB110 and Bacillus subtilis chromosomal DNA were joined to form the plasmid pKBT1 were cloned and sequenced. From the sequencing data we conclude that the pUB110 sequence is intact in the pair of cloned pKBT1 fragments and pTL12 sequences are not present. A molecular model for the formation of pKBT1 based on structural motifs characteristic of the joint sites is presented.
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Affiliation(s)
- K B Temeyer
- Agricultural Research Service, US Department of Agriculture, Kerrville, TX 78028
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40
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Hopkins KM. Emerging patterns of services and case finding for children with HIV infection. Ment Retard 1989; 27:219-22. [PMID: 2479809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
A population of young children is appearing with HIV infection of perinatal origin whose personal and family problems are complex. Most of their mothers are involved with intravenous drug abuse. The infants are in reasonable health for the first half year and then present with increasing medical and developmental problems. Eventually, the majority require foster care. Some are integrated in intervention or preschool services, with confidentiality protected; others are in segregated educational programs. Family supports and specialized services are often inadequate.
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Hopkins KM, Grosz J, Cohen H, Diamond G, Nozyce M. The Developmental and Family Services Unit--a model AIDS project serving developmentally disabled children and their families. AIDS Care 1989; 1:281-5. [PMID: 2484930 DOI: 10.1080/09540128908253033] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
This paper describes a model program that uses a multidisciplinary team to assess the developmental and psychosocial needs of HIV-infected children and their families. The objective of the program is to assess the needs of the children, in order to provide rehabilitative and psychosocial services; and to improve the quality of life by optimizing developmental functioning. The team includes developmental pediatricians, social workers, psychologists, a medical ethicist, physiatrist, psycho-educational specialist, and occupational, physical, and language therapists, each of whom perform complete evaluations. A weekly conference results in the formation of an individual Family Service Plan for each child and family. Forty children have been evaluated and are in program. Family compositions were varied and non-traditional. The disabilities and rehabilitative needs differed as well. The most frequently required services were occupational therapy and psychosocial intervention, to increase parental coping skills in handling disabled, chronically ill children. Children with HIV infection are living longer and will have serious deficits. The need to develop services to address the unique developmental and psychosocial needs of the children and families iS paramount.
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Affiliation(s)
- K M Hopkins
- Albert Einstein College of Medicine, Bronx, New York
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