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Dolgova N, Uhlemann EME, Boniecki MT, Vizeacoumar FS, Ara A, Nouri P, Ralle M, Tonelli M, Abbas SA, Patry J, Elhasasna H, Freywald A, Vizeacoumar F, Dmitriev OY. MEMO1 binds iron and modulates iron homeostasis in cancer cells. eLife 2024; 13:e86354. [PMID: 38640016 DOI: 10.7554/elife.86354] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Accepted: 04/15/2024] [Indexed: 04/20/2024] Open
Abstract
Mediator of ERBB2-driven Cell Motility 1 (MEMO1) is an evolutionary conserved protein implicated in many biological processes; however, its primary molecular function remains unknown. Importantly, MEMO1 is overexpressed in many types of cancer and was shown to modulate breast cancer metastasis through altered cell motility. To better understand the function of MEMO1 in cancer cells, we analyzed genetic interactions of MEMO1 using gene essentiality data from 1028 cancer cell lines and found multiple iron-related genes exhibiting genetic relationships with MEMO1. We experimentally confirmed several interactions between MEMO1 and iron-related proteins in living cells, most notably, transferrin receptor 2 (TFR2), mitoferrin-2 (SLC25A28), and the global iron response regulator IRP1 (ACO1). These interactions indicate that cells with high MEMO1 expression levels are hypersensitive to the disruptions in iron distribution. Our data also indicate that MEMO1 is involved in ferroptosis and is linked to iron supply to mitochondria. We have found that purified MEMO1 binds iron with high affinity under redox conditions mimicking intracellular environment and solved MEMO1 structures in complex with iron and copper. Our work reveals that the iron coordination mode in MEMO1 is very similar to that of iron-containing extradiol dioxygenases, which also display a similar structural fold. We conclude that MEMO1 is an iron-binding protein that modulates iron homeostasis in cancer cells.
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Affiliation(s)
- Natalia Dolgova
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, Canada
| | - Eva-Maria E Uhlemann
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, Canada
| | - Michal T Boniecki
- Protein Characterization and Crystallization Facility, University of Saskatchewan, Saskatoon, Canada
| | - Frederick S Vizeacoumar
- Department of Pathology and Laboratory Medicine, University of Saskatchewan, Saskatoon, Canada
| | - Anjuman Ara
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, Canada
| | - Paria Nouri
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, Canada
| | - Martina Ralle
- Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, United States
| | - Marco Tonelli
- National Magnetic Resonance Facility at Madison, University of Wisconsin-Madison, Madison, United States
| | - Syed A Abbas
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, Canada
| | - Jaala Patry
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, Canada
| | - Hussain Elhasasna
- Department of Pathology and Laboratory Medicine, University of Saskatchewan, Saskatoon, Canada
| | - Andrew Freywald
- Department of Pathology and Laboratory Medicine, University of Saskatchewan, Saskatoon, Canada
| | - Franco Vizeacoumar
- Cancer Research Department, University of Saskatchewan, Saskatoon, Canada
| | - Oleg Y Dmitriev
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, Canada
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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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Salapa HE, Thibault PA, Libner CD, Ding Y, Clarke JPWE, Denomy C, Hutchinson C, Abidullah HM, Austin Hammond S, Pastushok L, Vizeacoumar FS, Levin MC. hnRNP A1 dysfunction alters RNA splicing and drives neurodegeneration in multiple sclerosis (MS). Nat Commun 2024; 15:356. [PMID: 38191621 PMCID: PMC10774274 DOI: 10.1038/s41467-023-44658-1] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 12/22/2023] [Indexed: 01/10/2024] Open
Abstract
Neurodegeneration is the primary driver of disease progression in multiple sclerosis (MS) resulting in permanent disability, creating an urgent need to discover its underlying mechanisms. Herein, we establish that dysfunction of the RNA binding protein heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1) results in differential of binding to RNA targets causing alternative RNA splicing, which contributes to neurodegeneration in MS and its models. Using RNAseq of MS brains, we discovered differential expression and aberrant splicing of hnRNP A1 target RNAs involved in neuronal function and RNA homeostasis. We confirmed this in vivo in experimental autoimmune encephalomyelitis employing CLIPseq specific for hnRNP A1, where hnRNP A1 differentially binds and regulates RNA, including aberrantly spliced targets identified in human samples. Additionally, dysfunctional hnRNP A1 expression in neurons caused neurite loss and identical changes in splicing, corroborating hnRNP A1 dysfunction as a cause of neurodegeneration. Collectively, these data indicate hnRNP A1 dysfunction causes altered neuronal RNA splicing, resulting in neurodegeneration in MS.
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Affiliation(s)
- Hannah E Salapa
- Office of the Saskatchewan Multiple Sclerosis Clinical Research Chair, University of Saskatchewan, Saskatoon, SK, S7K 0M7, Canada
- Cameco MS Neuroscience Research Centre, College of Medicine, University of Saskatchewan, Saskatoon, SK, S7K 0M7, Canada
- Neurology Division, Department of Medicine, University of Saskatchewan, Saskatoon, SK, S7N 0X8, Canada
| | - Patricia A Thibault
- Office of the Saskatchewan Multiple Sclerosis Clinical Research Chair, University of Saskatchewan, Saskatoon, SK, S7K 0M7, Canada
- Cameco MS Neuroscience Research Centre, College of Medicine, University of Saskatchewan, Saskatoon, SK, S7K 0M7, Canada
- Neurology Division, Department of Medicine, University of Saskatchewan, Saskatoon, SK, S7N 0X8, Canada
| | - Cole D Libner
- Office of the Saskatchewan Multiple Sclerosis Clinical Research Chair, University of Saskatchewan, Saskatoon, SK, S7K 0M7, Canada
- Cameco MS Neuroscience Research Centre, College of Medicine, University of Saskatchewan, Saskatoon, SK, S7K 0M7, Canada
- Department of Health Sciences, College of Medicine, University of Saskatchewan, Saskatoon, SK, S7N 5E5, Canada
| | - Yulian Ding
- Division of Oncology, College of Medicine, University of Saskatchewan, Saskatoon, SK, S7N 5E5, Canada
- Division of Biomedical Engineering, College of Medicine, University of Saskatchewan, Saskatoon, SK, S7N 5A9, Canada
| | - Joseph-Patrick W E Clarke
- Office of the Saskatchewan Multiple Sclerosis Clinical Research Chair, University of Saskatchewan, Saskatoon, SK, S7K 0M7, Canada
- Cameco MS Neuroscience Research Centre, College of Medicine, University of Saskatchewan, Saskatoon, SK, S7K 0M7, Canada
- Neurology Division, Department of Medicine, University of Saskatchewan, Saskatoon, SK, S7N 0X8, Canada
| | - Connor Denomy
- Division of Oncology, College of Medicine, University of Saskatchewan, Saskatoon, SK, S7N 5E5, Canada
| | - Catherine Hutchinson
- Office of the Saskatchewan Multiple Sclerosis Clinical Research Chair, University of Saskatchewan, Saskatoon, SK, S7K 0M7, Canada
- Cameco MS Neuroscience Research Centre, College of Medicine, University of Saskatchewan, Saskatoon, SK, S7K 0M7, Canada
- Neurology Division, Department of Medicine, University of Saskatchewan, Saskatoon, SK, S7N 0X8, Canada
| | - Hashim M Abidullah
- Office of the Saskatchewan Multiple Sclerosis Clinical Research Chair, University of Saskatchewan, Saskatoon, SK, S7K 0M7, Canada
- Cameco MS Neuroscience Research Centre, College of Medicine, University of Saskatchewan, Saskatoon, SK, S7K 0M7, Canada
- Department of Anatomy, Physiology and Pharmacology, College of Medicine, University of Saskatchewan, Saskatoon, SK, S7N 5E5, Canada
| | - S Austin Hammond
- Next-Generation Sequencing Facility, University of Saskatchewan, Saskatoon, SK, S7N 5E5, Canada
| | - Landon Pastushok
- Advanced Diagnostics Research Laboratory, Department of Pathology and Lab Medicine, College of Medicine, University of Saskatchewan, Saskatoon, SK, S7N 5E5, Canada
| | - Frederick S Vizeacoumar
- Department of Pathology and Laboratory Medicine, University of Saskatchewan, Saskatoon, SK, S7N 5E5, Canada
| | - Michael C Levin
- Office of the Saskatchewan Multiple Sclerosis Clinical Research Chair, University of Saskatchewan, Saskatoon, SK, S7K 0M7, Canada.
- Cameco MS Neuroscience Research Centre, College of Medicine, University of Saskatchewan, Saskatoon, SK, S7K 0M7, Canada.
- Neurology Division, Department of Medicine, University of Saskatchewan, Saskatoon, SK, S7N 0X8, Canada.
- Department of Anatomy, Physiology and Pharmacology, College of Medicine, University of Saskatchewan, Saskatoon, SK, S7N 5E5, Canada.
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Köbel M, Yang RZ, Kang EY, Al-Shamma Z, Cook LS, Kinloch M, Carey MS, Hopkins L, Nelson GS, McManus KJ, Vizeacoumar FS, Vizeacoumar FJ, Freywald A, Fu Y, Reuss DE, Lee CH. Survey of NF1 inactivation by surrogate immunohistochemistry in ovarian carcinomas. Gynecol Oncol 2023; 178:80-88. [PMID: 37820398 DOI: 10.1016/j.ygyno.2023.09.016] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 09/26/2023] [Accepted: 09/29/2023] [Indexed: 10/13/2023]
Abstract
OBJECTIVE Inhibition of the MAPK pathway by MEK inhibitors (MEKi) is currently a therapeutic standard in several cancer types, including ovarian low-grade serous carcinoma (LGSC). A common MAPK pathway alteration in tubo-ovarian high-grade serous carcinoma (HGSC) is the genomic inactivation of neurofibromin 1 (NF1). The primary objectives of our study were to survey the prevalence of NF1 inactivation in the principal ovarian carcinoma histotype as well as to evaluate its associations with clinico-pathological parameters and key biomarkers including BRCA1/2 status in HGSC. METHODS A recently commercialized NF1 antibody (clone NFC) was orthogonally validated on an automated immunohistochemistry (IHC) platform and IHC was performed on tissue microarrays containing 2140 ovarian carcinoma cases. Expression was interpreted as loss/inactivated (complete or subclonal) versus normal/retained. RESULTS Loss of NF1 expression was detected in 250/1429 (17.4%) HGSC including 11% with subclonal loss. Survival of NF1-inactivated HGSC patients was intermediate between favorable BRCA1/2 mutated HGSC and unfavorable CCNE1 high-level amplified HGSC. NF1 inactivation was mutually exclusive with CCNE1 high-level amplifications, co-occurred with RB1 loss and occurred at similar frequencies in BRCA1/2 mutated versus wild-type HGSC. NF1 loss was found in 21/286 (7.3%) endometrioid carcinomas with a favorable prognostic association (p = 0.048), and in 4/64 (5.9%) LGSC, mutually exclusive with other driver events. CONCLUSIONS NF1 inactivation occurs in a significant subset of BRCA1/2 wild-type HGSC and a subset of LGSC. While the functional effects of NF1 inactivation need to be further characterized, this signifies a potential therapeutic opportunity to explore targeting NF1 inactivation in these tumors.
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Affiliation(s)
- Martin Köbel
- Department of Pathology, University of Calgary, Calgary, Alberta, Canada.
| | - Rui Zhe Yang
- Department of Oncology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Eun Young Kang
- Department of Pathology, University of Calgary, Calgary, Alberta, Canada
| | - Zainab Al-Shamma
- Department of Pathology, University of Calgary, Calgary, Alberta, Canada
| | - Linda S Cook
- Department of CSPH-Epidemiology, University of Colorado-Anschutz, Aurora, CO, USA
| | - Mary Kinloch
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Mark S Carey
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Laura Hopkins
- Division of Oncology, College of Medicine, University of Saskatchewan, Saskatchewan, Canada; Saskatchewan Cancer Agency, Saskatoon, Saskatchewan, Canada
| | - Gregg S Nelson
- Department of Oncology, Division of Gynecologic Oncology, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Kirk J McManus
- Department of Biochemistry & Medical Genetics, University of Manitoba, Winnipeg, Manitoba, Canada; Paul Albrechtsen Research Institute CancerCare, CancerCare Manitoba, Winnipeg, Manitoba, Canada
| | - Frederick S Vizeacoumar
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Franco J Vizeacoumar
- Division of Oncology, College of Medicine, University of Saskatchewan, Saskatchewan, Canada; Saskatchewan Cancer Agency, Saskatoon, Saskatchewan, Canada
| | - Andrew Freywald
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - YangXin Fu
- Department of Oncology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - David E Reuss
- Department of Neuropathology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany; Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), German Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany
| | - Cheng-Han Lee
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada
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5
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El Zawily A, Vizeacoumar FS, Dahiya R, Banerjee SL, Bhanumathy KK, Elhasasna H, Hanover G, Sharpe JC, Sanchez MG, Greidanus P, Stacey RG, Moon KM, Alexandrov I, Himanen JP, Nikolov DB, Fonge H, White AP, Foster LJ, Wang B, Toosi BM, Bisson N, Mirzabekov TA, Vizeacoumar FJ, Freywald A. A Multipronged Unbiased Strategy Guides the Development of an Anti-EGFR/EPHA2-Bispecific Antibody for Combination Cancer Therapy. Clin Cancer Res 2023; 29:2686-2701. [PMID: 36976175 PMCID: PMC10345963 DOI: 10.1158/1078-0432.ccr-22-2535] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 12/26/2022] [Accepted: 03/01/2023] [Indexed: 03/29/2023]
Abstract
PURPOSE Accumulating analyses of pro-oncogenic molecular mechanisms triggered a rapid development of targeted cancer therapies. Although many of these treatments produce impressive initial responses, eventual resistance onset is practically unavoidable. One of the main approaches for preventing this refractory condition relies on the implementation of combination therapies. This includes dual-specificity reagents that affect both of their targets with a high level of selectivity. Unfortunately, selection of target combinations for these treatments is often confounded by limitations in our understanding of tumor biology. Here, we describe and validate a multipronged unbiased strategy for predicting optimal co-targets for bispecific therapeutics. EXPERIMENTAL DESIGN Our strategy integrates ex vivo genome-wide loss-of-function screening, BioID interactome profiling, and gene expression analysis of patient data to identify the best fit co-targets. Final validation of selected target combinations is done in tumorsphere cultures and xenograft models. RESULTS Integration of our experimental approaches unambiguously pointed toward EGFR and EPHA2 tyrosine kinase receptors as molecules of choice for co-targeting in multiple tumor types. Following this lead, we generated a human bispecific anti-EGFR/EPHA2 antibody that, as predicted, very effectively suppresses tumor growth compared with its prototype anti-EGFR therapeutic antibody, cetuximab. CONCLUSIONS Our work not only presents a new bispecific antibody with a high potential for being developed into clinically relevant biologics, but more importantly, successfully validates a novel unbiased strategy for selecting biologically optimal target combinations. This is of a significant translational relevance, as such multifaceted unbiased approaches are likely to augment the development of effective combination therapies for cancer treatment. See related commentary by Kumar, p. 2570.
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Affiliation(s)
- Amr El Zawily
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Saskatchewan, Royal University Hospital, Saskatoon, Saskatchewan, Canada
- Department of Biology, College of Liberal Arts and Sciences, University of Iowa, Iowa City, Iowa
| | - Frederick S. Vizeacoumar
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Saskatchewan, Royal University Hospital, Saskatoon, Saskatchewan, Canada
| | - Renuka Dahiya
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Saskatchewan, Royal University Hospital, Saskatoon, Saskatchewan, Canada
| | - Sara L. Banerjee
- Department of Molecular Biology, Medical Biochemistry and Pathology, PROTEO and Centre de recherche du Centre Hospitalier Universitaire (CHU) de Quebec-Université Laval, Division Oncologie, Québec, Canada
| | - Kalpana K. Bhanumathy
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Saskatchewan, Royal University Hospital, Saskatoon, Saskatchewan, Canada
| | - Hussain Elhasasna
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Saskatchewan, Royal University Hospital, Saskatoon, Saskatchewan, Canada
| | - Glinton Hanover
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Saskatchewan, Royal University Hospital, Saskatoon, Saskatchewan, Canada
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Health Sciences, Saskatoon, Saskatchewan, Canada
| | - Jessica C. Sharpe
- Department of Small Animal Clinical Sciences, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, Canada
| | - Malkon G. Sanchez
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Saskatchewan, Royal University Hospital, Saskatoon, Saskatchewan, Canada
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Health Sciences, Saskatoon, Saskatchewan, Canada
| | - Paul Greidanus
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Saskatchewan, Royal University Hospital, Saskatoon, Saskatchewan, Canada
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Health Sciences, Saskatoon, Saskatchewan, Canada
| | - R. Greg Stacey
- Michael Smith Laboratories and Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Kyung-Mee Moon
- Michael Smith Laboratories and Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
| | | | - Juha P. Himanen
- Department of Biochemistry, University of Turku, Turku, Finland
| | - Dimitar B. Nikolov
- Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, New York
| | - Humphrey Fonge
- Department of Medical Imaging, College of Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
- Department of Medical Imaging, Royal University Hospital, Saskatoon, Saskatchewan, Canada
| | - Aaron P. White
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Health Sciences, Saskatoon, Saskatchewan, Canada
- Vaccine and Infectious Disease Organization-International Vaccine Centre, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Leonard J. Foster
- Michael Smith Laboratories and Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Bingcheng Wang
- Division of Cancer Biology, Department of Medicine, MetroHealth Medical Center, and Case Western Reserve University School of Medicine, Case Comprehensive Cancer Center, Cleveland, Ohio
| | - Behzad M. Toosi
- Department of Small Animal Clinical Sciences, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, Canada
| | - Nicolas Bisson
- Department of Molecular Biology, Medical Biochemistry and Pathology, PROTEO and Centre de recherche du Centre Hospitalier Universitaire (CHU) de Quebec-Université Laval, Division Oncologie, Québec, Canada
| | | | - Franco J. Vizeacoumar
- Cancer Research, Saskatchewan Cancer Agency and Division of Oncology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Andrew Freywald
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Saskatchewan, Royal University Hospital, Saskatoon, Saskatchewan, Canada
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6
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Hanover G, Vizeacoumar FS, Banerjee SL, Nair R, Dahiya R, Osornio-Hernandez AI, Morales AM, Freywald T, Himanen JP, Toosi BM, Bisson N, Vizeacoumar FJ, Freywald A. Integration of cancer-related genetic landscape of Eph receptors and ephrins with proteomics identifies a crosstalk between EPHB6 and EGFR. Cell Rep 2023; 42:112670. [PMID: 37392382 DOI: 10.1016/j.celrep.2023.112670] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 05/05/2023] [Accepted: 06/05/2023] [Indexed: 07/03/2023] Open
Abstract
Eph receptors and their ephrin ligands are viewed as promising targets for cancer treatment; however, targeting them is hindered by their context-dependent functionalities. To circumvent this, we explore molecular landscapes underlying their pro- and anti-malignant activities. Using unbiased bioinformatics approaches, we construct a cancer-related network of genetic interactions (GIs) of all Ephs and ephrins to assist in their therapeutic manipulation. We also apply genetic screening and BioID proteomics and integrate them with machine learning approaches to select the most relevant GIs of one Eph receptor, EPHB6. This identifies a crosstalk between EPHB6 and EGFR, and further experiments confirm the ability of EPHB6 to modulate EGFR signaling, enhancing the proliferation of cancer cells and tumor development. Taken together, our observations show EPHB6 involvement in EGFR action, suggesting its targeting might be beneficial in EGFR-dependent tumors, and confirm that the Eph family genetic interactome presented here can be effectively exploited in developing cancer treatment approaches.
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Affiliation(s)
- Glinton Hanover
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Saskatchewan, Royal University Hospital, Room 2841, 103 Hospital Drive, Saskatoon, SK S7N 0W8, Canada; Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, GA20 Health Sciences, 107 Wiggins Road, Saskatoon, SK S7N 5E5, Canada
| | - Frederick S Vizeacoumar
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Saskatchewan, Royal University Hospital, Room 2841, 103 Hospital Drive, Saskatoon, SK S7N 0W8, Canada
| | - Sara L Banerjee
- Department of Molecular Biology, Medical Biochemistry and Pathology, PROTEO and Centre de Recherche du Centre Hospitalier Universitaire (CHU) de Quebec-Université Laval, Division Oncologie, 9 Rue McMahon, Québec, QC G1R 3S3, Canada
| | - Raveena Nair
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Saskatchewan, Royal University Hospital, Room 2841, 103 Hospital Drive, Saskatoon, SK S7N 0W8, Canada; Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, GA20 Health Sciences, 107 Wiggins Road, Saskatoon, SK S7N 5E5, Canada
| | - Renuka Dahiya
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Saskatchewan, Royal University Hospital, Room 2841, 103 Hospital Drive, Saskatoon, SK S7N 0W8, Canada
| | - Ana I Osornio-Hernandez
- Department of Molecular Biology, Medical Biochemistry and Pathology, PROTEO and Centre de Recherche du Centre Hospitalier Universitaire (CHU) de Quebec-Université Laval, Division Oncologie, 9 Rue McMahon, Québec, QC G1R 3S3, Canada
| | - Alain Morejon Morales
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Saskatchewan, Royal University Hospital, Room 2841, 103 Hospital Drive, Saskatoon, SK S7N 0W8, Canada; Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, GA20 Health Sciences, 107 Wiggins Road, Saskatoon, SK S7N 5E5, Canada
| | - Tanya Freywald
- Cancer Research, Saskatchewan Cancer Agency and Division of Oncology, University of Saskatchewan, 4D30.2 Health Sciences Building, 107 Wiggins Road, Saskatoon, SK S7N 5E5, Canada
| | - Juha P Himanen
- Department of Biochemistry, University of Turku, 20500 Turku, Finland
| | - Behzad M Toosi
- Department of Small Animal Clinical Sciences, Western College of Veterinary Medicine, University of Saskatchewan, 52 Campus Drive, Saskatoon, SK S7N 5B4, Canada
| | - Nicolas Bisson
- Department of Molecular Biology, Medical Biochemistry and Pathology, PROTEO and Centre de Recherche du Centre Hospitalier Universitaire (CHU) de Quebec-Université Laval, Division Oncologie, 9 Rue McMahon, Québec, QC G1R 3S3, Canada.
| | - Franco J Vizeacoumar
- Cancer Research, Saskatchewan Cancer Agency and Division of Oncology, University of Saskatchewan, 4D30.2 Health Sciences Building, 107 Wiggins Road, Saskatoon, SK S7N 5E5, Canada.
| | - Andrew Freywald
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Saskatchewan, Royal University Hospital, Room 2841, 103 Hospital Drive, Saskatoon, SK S7N 0W8, Canada.
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7
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Arna AB, Patel H, Singh RS, Vizeacoumar FS, Kusalik A, Freywald A, Vizeacoumar FJ, Wu Y. Synthetic lethal interactions of DEAD/H-box helicases as targets for cancer therapy. Front Oncol 2023; 12:1087989. [PMID: 36761420 PMCID: PMC9905851 DOI: 10.3389/fonc.2022.1087989] [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] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 12/28/2022] [Indexed: 01/26/2023] Open
Abstract
DEAD/H-box helicases are implicated in virtually every aspect of RNA metabolism, including transcription, pre-mRNA splicing, ribosomes biogenesis, nuclear export, translation initiation, RNA degradation, and mRNA editing. Most of these helicases are upregulated in various cancers and mutations in some of them are associated with several malignancies. Lately, synthetic lethality (SL) and synthetic dosage lethality (SDL) approaches, where genetic interactions of cancer-related genes are exploited as therapeutic targets, are emerging as a leading area of cancer research. Several DEAD/H-box helicases, including DDX3, DDX9 (Dbp9), DDX10 (Dbp4), DDX11 (ChlR1), and DDX41 (Sacy-1), have been subjected to SL analyses in humans and different model organisms. It remains to be explored whether SDL can be utilized to identity druggable targets in DEAD/H-box helicase overexpressing cancers. In this review, we analyze gene expression data of a subset of DEAD/H-box helicases in multiple cancer types and discuss how their SL/SDL interactions can be used for therapeutic purposes. We also summarize the latest developments in clinical applications, apart from discussing some of the challenges in drug discovery in the context of targeting DEAD/H-box helicases.
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Affiliation(s)
- Ananna Bhadra Arna
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK, Canada
| | - Hardikkumar Patel
- Department of Pathology and Laboratory Medicine, University of Saskatchewan, Saskatoon, SK, Canada
| | - Ravi Shankar Singh
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK, Canada
| | - Frederick S. Vizeacoumar
- Department of Pathology and Laboratory Medicine, University of Saskatchewan, Saskatoon, SK, Canada
| | - Anthony Kusalik
- Department of Computer Science, University of Saskatchewan, Saskatoon, SK, Canada
| | - Andrew Freywald
- Department of Pathology and Laboratory Medicine, University of Saskatchewan, Saskatoon, SK, Canada
| | - Franco J. Vizeacoumar
- Division of Oncology, College of Medicine, University of Saskatchewan and Saskatchewan Cancer Agency, Saskatoon, SK, Canada,*Correspondence: Yuliang Wu, ; Franco J. Vizeacoumar,
| | - Yuliang Wu
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK, Canada,*Correspondence: Yuliang Wu, ; Franco J. Vizeacoumar,
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8
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Maranda V, Zhang Y, Vizeacoumar FS, Freywald A, Vizeacoumar FJ. A CRISPR Platform for Targeted In Vivo Screens. Methods Mol Biol 2023; 2614:397-409. [PMID: 36587138 DOI: 10.1007/978-1-0716-2914-7_24] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Large-scale genetic screens are becoming increasingly used as powerful tools to query the genome to identify therapeutic targets in cancer. The advent of the CRISPR technology has revolutionized the effectiveness of these screens and has made it possible to carry out loss-of-function screens to identify cancer-specific genetic interactions. Such loss-of-function screens can be performed in silico, in vitro, and in vivo, depending on the scale of the screen, as well as research questions to be answered. Performing screens in vivo has its challenges but also advantages, providing opportunities to study the tumor microenvironment and cancer immunity. In this chapter, we present a procedural framework and associated notes for conducting in vivo CRISPR knockout screens in cancer models to study cancer biology, anti-tumor immune responses, tumor microenvironment, and predicting treatment responses.
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Affiliation(s)
- Vincent Maranda
- Division of Oncology, College of Medicine, University of Saskatchewan, Saskatoon, Canada
| | - Yue Zhang
- Division of Oncology, College of Medicine, University of Saskatchewan, Saskatoon, Canada
| | | | - Andrew Freywald
- Department of Pathology, College of Medicine, University of Saskatchewan, Saskatoon, Canada.
| | - Franco J Vizeacoumar
- Division of Oncology, College of Medicine, University of Saskatchewan, Saskatoon, Canada.
- Cancer Research Department, Saskatchewan Cancer Agency, Saskatoon, Canada.
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9
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Arnason TG, MacDonald-Dickinson V, Gaunt MC, Davies GF, Lobanova L, Trost B, Gillespie ZE, Waldner M, Baldwin P, Borrowman D, Marwood H, Vizeacoumar FS, Vizeacoumar FJ, Eskiw CH, Kusalik A, Harkness TAA. Activation of the Anaphase Promoting Complex Reverses Multiple Drug Resistant Cancer in a Canine Model of Multiple Drug Resistant Lymphoma. Cancers (Basel) 2022; 14:cancers14174215. [PMID: 36077749 PMCID: PMC9454423 DOI: 10.3390/cancers14174215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 08/03/2022] [Revised: 08/25/2022] [Accepted: 08/27/2022] [Indexed: 11/16/2022] Open
Abstract
Simple Summary Multiple drug resistant cancers develop all too soon in patients who received successful cancer treatment. A lack of treatment options often leaves palliative care as the last resort. We tested whether the insulin sensitizer, metformin, known to have anti-cancer activity, could impact canines with drug resistant lymphoma when added to chemotherapy. All canines in the study expressed protein markers of drug resistance and within weeks of receiving metformin, the markers were decreased. A microarray was performed, and from four canines assessed, a common set of 290 elevated genes were discovered in tumor cells compared to control cells. This cluster was enriched with genes that stall the cell cycle, with a large component representing substrates of the Anaphase Promoting Complex (APC), which degrades proteins. One canine entered partial remission. RNAs from this canine showed that APC substrates were decreased during remission and elevated again during relapse, suggesting that the APC was impaired in drug resistant canines and restored when remission occurred. We validated our results in cell lines using APC inhibitors and activators. We conclude that the APC may be a vital guardian of the genome and could delay the onset of multiple drug resistance when activated. Abstract Like humans, canine lymphomas are treated by chemotherapy cocktails and frequently develop multiple drug resistance (MDR). Their shortened clinical timelines and tumor accessibility make canines excellent models to study MDR mechanisms. Insulin-sensitizers have been shown to reduce the incidence of cancer in humans prescribed them, and we previously demonstrated that they also reverse and delay MDR development in vitro. Here, we treated canines with MDR lymphoma with metformin to assess clinical and tumoral responses, including changes in MDR biomarkers, and used mRNA microarrays to determine differential gene expression. Metformin reduced MDR protein markers in all canines in the study. Microarrays performed on mRNAs gathered through longitudinal tumor sampling identified a 290 gene set that was enriched in Anaphase Promoting Complex (APC) substrates and additional mRNAs associated with slowed mitotic progression in MDR samples compared to skin controls. mRNAs from a canine that went into remission showed that APC substrate mRNAs were decreased, indicating that the APC was activated during remission. In vitro validation using canine lymphoma cells selected for resistance to chemotherapeutic drugs confirmed that APC activation restored MDR chemosensitivity, and that APC activity was reduced in MDR cells. This supports the idea that rapidly pushing MDR cells that harbor high loads of chromosome instability through mitosis, by activating the APC, contributes to improved survival and disease-free duration.
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Affiliation(s)
- Terra G. Arnason
- Division of Endocrinology and Metabolism, Department of Medicine, Saskatoon, SK S7N 0W8, Canada
- Department of Anatomy and Cell Biology, Saskatoon, SK S7N 5E5, Canada
- Department of Anatomy, Physiology and Pharmacology, Saskatoon, SK S7N 5E5, Canada
- Correspondence: (T.G.A.); (T.A.A.H.)
| | - Valerie MacDonald-Dickinson
- Department of Small Animal Clinical Sciences, Western College of Veterinary Medicine, Saskatoon, SK S7N 5B4, Canada
| | - Matthew Casey Gaunt
- Department of Small Animal Clinical Sciences, Western College of Veterinary Medicine, Saskatoon, SK S7N 5B4, Canada
| | - Gerald F. Davies
- Department of Anatomy and Cell Biology, Saskatoon, SK S7N 5E5, Canada
- Department of Biochemistry, Microbiology and Immunology, Saskatoon, SK S7N 5E5, Canada
| | - Liubov Lobanova
- Division of Endocrinology and Metabolism, Department of Medicine, Saskatoon, SK S7N 0W8, Canada
| | - Brett Trost
- Department of Computer Science, Saskatoon, SK S7N 5C9, Canada
| | - Zoe E. Gillespie
- Department of Food and Bioproduct Sciences, Saskatoon, SK S7N 5A8, Canada
| | - Matthew Waldner
- Department of Computer Science, Saskatoon, SK S7N 5C9, Canada
| | - Paige Baldwin
- Department of Anatomy and Cell Biology, Saskatoon, SK S7N 5E5, Canada
| | - Devon Borrowman
- Department of Anatomy and Cell Biology, Saskatoon, SK S7N 5E5, Canada
| | - Hailey Marwood
- Department of Anatomy and Cell Biology, Saskatoon, SK S7N 5E5, Canada
| | - Frederick S. Vizeacoumar
- Department of Pathology and Laboratory Medicine, University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada
| | - Franco J. Vizeacoumar
- Department of Pathology and Laboratory Medicine, University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada
| | | | - Anthony Kusalik
- Department of Computer Science, Saskatoon, SK S7N 5C9, Canada
| | - Troy A. A. Harkness
- Department of Anatomy and Cell Biology, Saskatoon, SK S7N 5E5, Canada
- Department of Biochemistry, Microbiology and Immunology, Saskatoon, SK S7N 5E5, Canada
- Correspondence: (T.G.A.); (T.A.A.H.)
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10
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Sepehri Z, Banerjee A, Vizeacoumar FS, Freywald A, Vizeacoumar FJ, Dolinsky VW, Davie JR. Differential expression of
HNF1A
and
HNF1A‐AS1
in colon cancer cells. IUBMB Life 2022; 74:496-507. [DOI: 10.1002/iub.2609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 02/06/2022] [Accepted: 02/09/2022] [Indexed: 11/10/2022]
Affiliation(s)
- Zahra Sepehri
- Department of Biochemistry and Medical Genetics University of Manitoba Winnipeg Manitoba Canada
- Department of Internal Medicine Zabol University of Medical Sciences Zabol Iran
| | - Archana Banerjee
- Division of Oncology, College of Medicine University of Saskatchewan Saskatoon SK Canada
- Cancer Research Department, Saskatchewan Cancer Agency, 107 Wiggins Road Saskatoon SK Canada
| | - Frederick S. Vizeacoumar
- Department of Pathology and Laboratory Medicine College of Medicine, University of Saskatchewan, Room 2841, Royal University Hospital, 103 Hospital Drive Saskatoon SK Canada
| | - Andrew Freywald
- Department of Pathology and Laboratory Medicine College of Medicine, University of Saskatchewan, Room 2841, Royal University Hospital, 103 Hospital Drive Saskatoon SK Canada
| | - Franco J. Vizeacoumar
- Division of Oncology, College of Medicine University of Saskatchewan Saskatoon SK Canada
- Cancer Research Department, Saskatchewan Cancer Agency, 107 Wiggins Road Saskatoon SK Canada
| | - Vernon W. Dolinsky
- Diabetes Research Envisioned and Accomplished in Manitoba (DREAM) Theme of the Children's Hospital Research Institute of Manitoba Winnipeg MB Canada
- Department of Pharmacology and Therapeutics University of Manitoba Winnipeg MB Canada
| | - James R. Davie
- Department of Biochemistry and Medical Genetics University of Manitoba Winnipeg Manitoba Canada
- Research Institute in Oncology and Hematology, CancerCare Manitoba Winnipeg Manitoba Canada
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11
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Chafe SC, Vizeacoumar FS, Venkateswaran G, Nemirovsky O, Awrey S, Brown WS, McDonald PC, Carta F, Metcalfe A, Karasinska JM, Huang L, Muthuswamy SK, Schaeffer DF, Renouf DJ, Supuran CT, Vizeacoumar FJ, Dedhar S. Genome-wide synthetic lethal screen unveils novel CAIX-NFS1/xCT axis as a targetable vulnerability in hypoxic solid tumors. Sci Adv 2021; 7:7/35/eabj0364. [PMID: 34452919 PMCID: PMC8397268 DOI: 10.1126/sciadv.abj0364] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 07/06/2021] [Indexed: 05/23/2023]
Abstract
The metabolic mechanisms involved in the survival of tumor cells within the hypoxic niche remain unclear. We carried out a synthetic lethal CRISPR screen to identify survival mechanisms governed by the tumor hypoxia-induced pH regulator carbonic anhydrase IX (CAIX). We identified a redox homeostasis network containing the iron-sulfur cluster enzyme, NFS1. Depletion of NFS1 or blocking cyst(e)ine availability by inhibiting xCT, while targeting CAIX, enhanced ferroptosis and significantly inhibited tumor growth. Suppression of CAIX activity acidified intracellular pH, increased cellular reactive oxygen species accumulation, and induced susceptibility to alterations in iron homeostasis. Mechanistically, inhibiting bicarbonate production by CAIX or sodium-driven bicarbonate transport, while targeting xCT, decreased adenosine 5'-monophosphate-activated protein kinase activation and increased acetyl-coenzyme A carboxylase 1 activation. Thus, an alkaline intracellular pH plays a critical role in suppressing ferroptosis, a finding that may lead to the development of innovative therapeutic strategies for solid tumors to overcome hypoxia- and acidosis-mediated tumor progression and therapeutic resistance.
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Affiliation(s)
- Shawn C Chafe
- Department of Integrative Oncology, BC Cancer Research Institute, Vancouver, BC V5Z 1L3, Canada
| | - Frederick S Vizeacoumar
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Saskatchewan, Saskatoon, SK S7N 0W8, Canada
| | - Geetha Venkateswaran
- Department of Integrative Oncology, BC Cancer Research Institute, Vancouver, BC V5Z 1L3, Canada
| | - Oksana Nemirovsky
- Department of Integrative Oncology, BC Cancer Research Institute, Vancouver, BC V5Z 1L3, Canada
| | - Shannon Awrey
- Department of Integrative Oncology, BC Cancer Research Institute, Vancouver, BC V5Z 1L3, Canada
| | - Wells S Brown
- Department of Integrative Oncology, BC Cancer Research Institute, Vancouver, BC V5Z 1L3, Canada
| | - Paul C McDonald
- Department of Integrative Oncology, BC Cancer Research Institute, Vancouver, BC V5Z 1L3, Canada
| | - Fabrizio Carta
- NEUROFARBA Department, University of Florence, Via U. Schiff 6, Florence 50019, Italy
| | | | | | - Ling Huang
- Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Senthil K Muthuswamy
- Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - David F Schaeffer
- Pancreas Centre BC, Vancouver, BC V3Z 1M9, Canada
- Department of Pathology and Laboratory Medicine, Vancouver General Hospital, Vancouver, BC V5Z 1M9, Canada
| | - Daniel J Renouf
- Pancreas Centre BC, Vancouver, BC V3Z 1M9, Canada
- Medical Oncology, BC Cancer, Vancouver, BC V5Z 4E67, Canada
| | - Claudiu T Supuran
- NEUROFARBA Department, University of Florence, Via U. Schiff 6, Florence 50019, Italy
| | - Franco J Vizeacoumar
- Division of Oncology, College of Medicine, University of Saskatchewan, Saskatoon, SK S7N 0W8, Canada
- Cancer Research Department, Saskatchewan Cancer Agency, Saskatoon, SK S7N 4E5, Canada
| | - Shoukat Dedhar
- Department of Integrative Oncology, BC Cancer Research Institute, Vancouver, BC V5Z 1L3, Canada.
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
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12
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Dong SXM, Vizeacoumar FS, Bhanumathy KK, Alli N, Gonzalez-Lopez C, Gajanayaka N, Caballero R, Ali H, Freywald A, Cassol E, Angel JB, Vizeacoumar FJ, Kumar A. Identification of novel genes involved in apoptosis of HIV-infected macrophages using unbiased genome-wide screening. BMC Infect Dis 2021; 21:655. [PMID: 34233649 PMCID: PMC8261936 DOI: 10.1186/s12879-021-06346-7] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Accepted: 06/15/2021] [Indexed: 12/01/2022] Open
Abstract
Background Macrophages, besides resting latently infected CD4+ T cells, constitute the predominant stable, major non-T cell HIV reservoirs. Therefore, it is essential to eliminate both latently infected CD4+ T cells and tissue macrophages to completely eradicate HIV in patients. Until now, most of the research focus is directed towards eliminating latently infected CD4+ T cells. However, few approaches have been directed at killing of HIV-infected macrophages either in vitro or in vivo. HIV infection dysregulates the expression of many host genes essential for the survival of infected cells. We postulated that exploiting this alteration may yield novel targets for the selective killing of infected macrophages. Methods We applied a pooled shRNA-based genome-wide approach by employing a lentivirus-based library of shRNAs to screen novel gene targets whose inhibition should selectively induce apoptosis in HIV-infected macrophages. Primary human MDMs were infected with HIV-eGFP and HIV-HSA viruses. Infected MDMs were transfected with siRNAs specific for the promising genes followed by analysis of apoptosis by flow cytometry using labelled Annexin-V in HIV-infected, HIV-exposed but uninfected bystander MDMs and uninfected MDMs. The results were analyzed using student’s t-test from at least four independent experiments. Results We validated 28 top hits in two independent HIV infection models. This culminated in the identification of four target genes, Cox7a2, Znf484, Cstf2t, and Cdk2, whose loss-of-function induced apoptosis preferentially in HIV-infected macrophages. Silencing these single genes killed significantly higher number of HIV-HSA-infected MDMs compared to the HIV-HSA-exposed, uninfected bystander macrophages, indicating the specificity in the killing of HIV-infected macrophages. The mechanism governing Cox7a2-mediated apoptosis of HIV-infected macrophages revealed that targeting respiratory chain complex II and IV genes also selectively induced apoptosis of HIV-infected macrophages possibly through enhanced ROS production. Conclusions We have identified above-mentioned novel genes and specifically the respiratory chain complex II and IV genes whose silencing may cause selective elimination of HIV-infected macrophages and eventually the HIV-macrophage reservoirs. The results highlight the potential of the identified genes as targets for eliminating HIV-infected macrophages in physiological environment as part of an HIV cure strategy. Supplementary Information The online version contains supplementary material available at 10.1186/s12879-021-06346-7.
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Affiliation(s)
- Simon X M Dong
- Apoptosis Research Center, Children's Hospital of Eastern Ontario, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada.,Department of Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Frederick S Vizeacoumar
- Department of Pathology, College of Medicine, University of Saskatchewan, Saskatoon, SK, Canada
| | - Kalpana K Bhanumathy
- Department of Pathology, College of Medicine, University of Saskatchewan, Saskatoon, SK, Canada
| | - Nezeka Alli
- Department of Pathology, College of Medicine, University of Saskatchewan, Saskatoon, SK, Canada
| | | | - Niranjala Gajanayaka
- Apoptosis Research Center, Children's Hospital of Eastern Ontario, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Ramon Caballero
- Apoptosis Research Center, Children's Hospital of Eastern Ontario, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada.,Department of Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Hamza Ali
- Apoptosis Research Center, Children's Hospital of Eastern Ontario, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada.,Department of Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Andrew Freywald
- Department of Pathology, College of Medicine, University of Saskatchewan, Saskatoon, SK, Canada
| | - Edana Cassol
- Department of Health Sciences, Carleton University, Ottawa, ON, Canada
| | - Jonathan B Angel
- Department of Medicine, the Ottawa Health Research Institute, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Franco J Vizeacoumar
- Department of Pathology, College of Medicine, University of Saskatchewan, Saskatoon, SK, Canada. .,Cancer Research, Saskatchewan Cancer Agency, 107 Wiggins Road, Saskatoon, SK, Canada.
| | - Ashok Kumar
- Apoptosis Research Center, Children's Hospital of Eastern Ontario, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada. .,Department of Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada. .,Department of Pathology and Laboratory Medicine, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada.
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13
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Wong L, Vizeacoumar FS, Vizeacoumar FJ, Chelico L. APOBEC1 cytosine deaminase activity on single-stranded DNA is suppressed by replication protein A. Nucleic Acids Res 2021; 49:322-339. [PMID: 33330905 PMCID: PMC7797036 DOI: 10.1093/nar/gkaa1201] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 11/23/2020] [Accepted: 11/25/2020] [Indexed: 12/22/2022] Open
Abstract
Many APOBEC cytidine deaminase members are known to induce ‘off-target’ cytidine deaminations in 5′TC motifs in genomic DNA that contribute to cancer evolution. In this report, we characterized APOBEC1, which is a possible cancer related APOBEC since APOBEC1 mRNA is highly expressed in certain types of tumors, such as lung adenocarcinoma. We found a low level of APOBEC1-induced DNA damage, as measured by γH2AX foci, in genomic DNA of a lung cancer cell line that correlated to its inability to compete in vitro with replication protein A (RPA) for ssDNA. This suggests that RPA can act as a defense against off-target deamination for some APOBEC enzymes. Overall, the data support the model that the ability of an APOBEC to compete with RPA can better predict genomic damage than combined analysis of mRNA expression levels in tumors and analysis of mutation signatures.
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Affiliation(s)
- Lai Wong
- Department of Biochemistry, Microbiology, and Immunology, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5E5, Canada
| | - Frederick S Vizeacoumar
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Saskatchewan, Saskatoon S7N 5E5, Canada
| | - Franco J Vizeacoumar
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Saskatchewan, Saskatoon S7N 5E5, Canada.,Cancer Research, Saskatchewan Cancer Agency, Saskatoon, Saskatchewan S7S 0A6, Canada
| | - Linda Chelico
- Department of Biochemistry, Microbiology, and Immunology, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5E5, Canada
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14
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K. Bhanumathy K, Balagopal A, Vizeacoumar FS, Vizeacoumar FJ, Freywald A, Giambra V. Protein Tyrosine Kinases: Their Roles and Their Targeting in Leukemia. Cancers (Basel) 2021; 13:cancers13020184. [PMID: 33430292 PMCID: PMC7825731 DOI: 10.3390/cancers13020184] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 12/30/2020] [Accepted: 01/04/2021] [Indexed: 12/16/2022] Open
Abstract
Simple Summary Protein phosphorylation is a key regulatory mechanism that controls a wide variety of cellular responses. This process is catalysed by the members of the protein kinase superfamily that are classified into two main families based on their ability to phosphorylate either tyrosine or serine and threonine residues in their substrates. Massive research efforts have been invested in dissecting the functions of tyrosine kinases, revealing their importance in the initiation and progression of human malignancies. Based on these investigations, numerous tyrosine kinase inhibitors have been included in clinical protocols and proved to be effective in targeted therapies for various haematological malignancies. In this review, we provide insights into the role of tyrosine kinases in leukaemia and discuss their targeting for therapeutic purposes with the currently available inhibitory compounds. Abstract Protein kinases constitute a large group of enzymes catalysing protein phosphorylation and controlling multiple signalling events. The human protein kinase superfamily consists of 518 members and represents a complicated system with intricate internal and external interactions. Protein kinases are classified into two main families based on the ability to phosphorylate either tyrosine or serine and threonine residues. Among the 90 tyrosine kinase genes, 58 are receptor types classified into 20 groups and 32 are of the nonreceptor types distributed into 10 groups. Tyrosine kinases execute their biological functions by controlling a variety of cellular responses, such as cell division, metabolism, migration, cell–cell and cell matrix adhesion, cell survival and apoptosis. Over the last 30 years, a major focus of research has been directed towards cancer-associated tyrosine kinases owing to their critical contributions to the development and aggressiveness of human malignancies through the pathological effects on cell behaviour. Leukaemia represents a heterogeneous group of haematological malignancies, characterised by an uncontrolled proliferation of undifferentiated hematopoietic cells or leukaemia blasts, mostly derived from bone marrow. They are usually classified as chronic or acute, depending on the rates of their progression, as well as myeloid or lymphoblastic, according to the type of blood cells involved. Overall, these malignancies are relatively common amongst both children and adults. In malignant haematopoiesis, multiple tyrosine kinases of both receptor and nonreceptor types, including AXL receptor tyrosine kinase (AXL), Discoidin domain receptor 1 (DDR1), Vascular endothelial growth factor receptor (VEGFR), Fibroblast growth factor receptor (FGFR), Mesenchymal–epithelial transition factor (MET), proto-oncogene c-Src (SRC), Spleen tyrosine kinase (SYK) and pro-oncogenic Abelson tyrosine-protein kinase 1 (ABL1) mutants, are implicated in the pathogenesis and drug resistance of practically all types of leukaemia. The role of ABL1 kinase mutants and their therapeutic inhibitors have been extensively analysed in scientific literature, and therefore, in this review, we provide insights into the impact and mechanism of action of other tyrosine kinases involved in the development and progression of human leukaemia and discuss the currently available and emerging treatment options based on targeting these molecules.
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Affiliation(s)
- Kalpana K. Bhanumathy
- Division of Oncology, College of Medicine, University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada; (A.B.); (F.J.V.)
- Correspondence: (K.K.B.); (V.G.); Tel.: +1-(306)-716-7456 (K.K.B.); +39-0882-416574 (V.G.)
| | - Amrutha Balagopal
- Division of Oncology, College of Medicine, University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada; (A.B.); (F.J.V.)
| | - Frederick S. Vizeacoumar
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada; (F.S.V.); (A.F.)
| | - Franco J. Vizeacoumar
- Division of Oncology, College of Medicine, University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada; (A.B.); (F.J.V.)
- Cancer Research Department, Saskatchewan Cancer Agency, 107 Wiggins Road, Saskatoon, SK S7N 5E5, Canada
| | - Andrew Freywald
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada; (F.S.V.); (A.F.)
| | - Vincenzo Giambra
- Institute for Stem Cell Biology, Regenerative Medicine and Innovative Therapies (ISBReMIT), Fondazione IRCCS Casa Sollievo della Sofferenza, 71013 San Giovanni Rotondo, FG, Italy
- Correspondence: (K.K.B.); (V.G.); Tel.: +1-(306)-716-7456 (K.K.B.); +39-0882-416574 (V.G.)
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15
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MacAuley MJ, Abuhussein O, Vizeacoumar FS. Identification of Synthetic Lethal Interactions Using High-Throughput, Arrayed CRISPR/Cas9-Based Platforms. Methods Mol Biol 2021; 2381:135-149. [PMID: 34590274 DOI: 10.1007/978-1-0716-1740-3_7] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Over the past two decades, the concept of synthetic lethality (SL) that queries genetic relationships between gene pairs has gradually emerged as one of the best strategies to selectively eliminate cancer cells. Some of the most successful approaches to identify synthetic lethal interactions (SLIs) were largely dependent on pooled screening formats that require heavy validation in order to mitigate false positives. Here, we describe a high-throughput method to identify SLIs using CRISPR-based strategy that covers, high-throughput production of plasmid DNA preparations, lentiviral production, and subsequent cellular transduction using single guide RNAs (sgRNAs). This method could be adopted to query hundreds of SLIs. As an example, we describe the methods associated with building an interaction map for DNA damage and repair (DDR) genes. The use of multiwell plates and image-based quantification allows a comparative measurement of SLIs at a high-resolution on a one-by-one basis. Furthermore, this scalable, arrayed CRISPR screening method can be applied to multiple cancer cell types, and genes of interest, resulting in new functional discoveries that can be exploited therapeutically.
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Affiliation(s)
- MacKenzie J MacAuley
- Department of Health Sciences, Cancer Cluster, College of Medicine, University of Saskatchewan, Saskatoon, SK, Canada.
| | - Omar Abuhussein
- College of Pharmacy and Nutrition, University of Saskatchewan, Saskatoon, SK, Canada
| | - Frederick S Vizeacoumar
- Department of Health Sciences, Cancer Cluster, College of Medicine, University of Saskatchewan, Saskatoon, SK, Canada.
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Saskatchewan, Saskatoon, SK, Canada.
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16
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Cunningham CE, MacAuley MJ, Vizeacoumar FS, Abuhussein O, Freywald A, Vizeacoumar FJ. The CINs of Polo-Like Kinase 1 in Cancer. Cancers (Basel) 2020; 12:cancers12102953. [PMID: 33066048 PMCID: PMC7599805 DOI: 10.3390/cancers12102953] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Revised: 10/08/2020] [Accepted: 10/09/2020] [Indexed: 02/07/2023] Open
Abstract
Simple Summary Many alterations specific to cancer cells have been investigated as targets for targeted therapies. Chromosomal instability is a characteristic of nearly all cancers that can limit response to targeted therapies by ensuring the tumor population is not genetically homogenous. Polo-like Kinase 1 (PLK1) is often up regulated in cancers and it regulates chromosomal instability extensively. PLK1 has been the subject of much pre-clinical and clinical studies, but thus far, PLK1 inhibitors have not shown significant improvement in cancer patients. We discuss the numerous roles and interactions of PLK1 in regulating chromosomal instability, and how these may provide an avenue for identifying targets for targeted therapies. As selective inhibitors of PLK1 showed limited clinical success, we also highlight how genetic interactions of PLK1 may be exploited to tackle these challenges. Abstract Polo-like kinase 1 (PLK1) is overexpressed near ubiquitously across all cancer types and dysregulation of this enzyme is closely tied to increased chromosomal instability and tumor heterogeneity. PLK1 is a mitotic kinase with a critical role in maintaining chromosomal integrity through its function in processes ranging from the mitotic checkpoint, centrosome biogenesis, bipolar spindle formation, chromosome segregation, DNA replication licensing, DNA damage repair, and cytokinesis. The relation between dysregulated PLK1 and chromosomal instability (CIN) makes it an attractive target for cancer therapy. However, clinical trials with PLK1 inhibitors as cancer drugs have generally displayed poor responses or adverse side-effects. This is in part because targeting CIN regulators, including PLK1, can elevate CIN to lethal levels in normal cells, affecting normal physiology. Nevertheless, aiming at related genetic interactions, such as synthetic dosage lethal (SDL) interactions of PLK1 instead of PLK1 itself, can help to avoid the detrimental side effects associated with increased levels of CIN. Since PLK1 overexpression contributes to tumor heterogeneity, targeting SDL interactions may also provide an effective strategy to suppressing this malignant phenotype in a personalized fashion.
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Affiliation(s)
- Chelsea E. Cunningham
- Department of Pathology, College of Medicine, University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada; (M.J.M.); (F.S.V.)
- Correspondence: (C.E.C.); (A.F.); (F.J.V.); Tel.: +1-(306)-327-7864 (C.E.C.); +1-(306)-966-5248 (A.F.); +1-(306)-966-7010 (F.J.V.)
| | - Mackenzie J. MacAuley
- Department of Pathology, College of Medicine, University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada; (M.J.M.); (F.S.V.)
| | - Frederick S. Vizeacoumar
- Department of Pathology, College of Medicine, University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada; (M.J.M.); (F.S.V.)
| | - Omar Abuhussein
- College of Pharmacy, University of Saskatchewan, 104 Clinic Place, Saskatoon, SK S7N 2Z4, Canada;
| | - Andrew Freywald
- Department of Pathology, College of Medicine, University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada; (M.J.M.); (F.S.V.)
- Correspondence: (C.E.C.); (A.F.); (F.J.V.); Tel.: +1-(306)-327-7864 (C.E.C.); +1-(306)-966-5248 (A.F.); +1-(306)-966-7010 (F.J.V.)
| | - Franco J. Vizeacoumar
- Department of Pathology, College of Medicine, University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada; (M.J.M.); (F.S.V.)
- College of Pharmacy, University of Saskatchewan, 104 Clinic Place, Saskatoon, SK S7N 2Z4, Canada;
- Cancer Research, Saskatchewan Cancer Agency, 107 Wiggins Road, Saskatoon, SK S7N 5E5, Canada
- Correspondence: (C.E.C.); (A.F.); (F.J.V.); Tel.: +1-(306)-327-7864 (C.E.C.); +1-(306)-966-5248 (A.F.); +1-(306)-966-7010 (F.J.V.)
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17
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Denomy C, Germain S, Haave B, Vizeacoumar FS, Freywald A, Weaver BA, Vizeacoumar FJ. Banding Together: A Systematic Comparison of The Cancer Genome Atlas and the Mitelman Databases. Cancer Res 2019; 79:5181-5190. [PMID: 31416843 DOI: 10.1158/0008-5472.can-19-0585] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 05/22/2019] [Accepted: 08/09/2019] [Indexed: 11/16/2022]
Abstract
Cytogenetic aberrations at the single-cell level represent an important characteristic of cancer cells relevant to tumor evolution and prognosis. However, with the advent of The Cancer Genome Atlas (TCGA), there has been a major shift in cancer research to the use of data from aggregate cell populations. Given that tumor cells harbor hundreds to thousands of biologically relevant genetic alterations that manifest as intratumor heterogeneity, these aggregate analyses may miss alterations readily observable at single-cell resolution. Using the Mitelman Database of Chromosome Aberrations and Gene Fusions in Cancer, we developed an algorithm to parse International System for Cytogenetic Nomenclature notation for quantitative abnormalities. Comparison of the Mitelman database and TCGA demonstrated that the Mitelman database is a powerful resource, and that cytogenetic aberrations captured by traditional approaches used in Mitelman database are on par with population-based genomic analyses used in TCGA. This algorithm will help nonspecialists to overcome the challenges associated with the format and syntax of the Mitelman database. SIGNIFICANCE: A novel in silico approach compares cytogenetic data between the Mitelman database and TCGA, highlighting the advantages and limitations of both datasets.
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Affiliation(s)
- Connor Denomy
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Saskatchewan, Saskatoon, Canada
| | - Samuel Germain
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Saskatchewan, Saskatoon, Canada
| | - Bjorn Haave
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Saskatchewan, Saskatoon, Canada
| | - Frederick S Vizeacoumar
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Saskatchewan, Saskatoon, Canada
| | - Andrew Freywald
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Saskatchewan, Saskatoon, Canada
| | - Beth A Weaver
- Department of Cell and Regenerative Biology, Department of Oncology/McArdle Laboratory for Cancer Research and Carbone Cancer Center, University of Wisconsin-Madison, Madison, Wisconsin
| | - Franco J Vizeacoumar
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Saskatchewan, Saskatoon, Canada. .,Cancer Research, Saskatchewan Cancer Agency, Saskatoon, Canada
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18
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Kirzinger MWB, Vizeacoumar FS, Haave B, Gonzalez-Lopez C, Bonham K, Kusalik A, Vizeacoumar FJ. Humanized yeast genetic interaction mapping predicts synthetic lethal interactions of FBXW7 in breast cancer. BMC Med Genomics 2019; 12:112. [PMID: 31351478 PMCID: PMC6660958 DOI: 10.1186/s12920-019-0554-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 06/27/2019] [Indexed: 02/08/2023] Open
Abstract
Background Synthetic lethal interactions (SLIs) that occur between gene pairs are exploited for cancer therapeutics. Studies in the model eukaryote yeast have identified ~ 550,000 negative genetic interactions that have been extensively studied, leading to characterization of novel pathways and gene functions. This resource can be used to predict SLIs that can be relevant to cancer therapeutics. Methods We used patient data to identify genes that are down-regulated in breast cancer. InParanoid orthology mapping was performed to identify yeast orthologs of the down-regulated genes and predict their corresponding SLIs in humans. The predicted network graphs were drawn with Cytoscape. CancerRXgene database was used to predict drug response. Results Harnessing the vast available knowledge of yeast genetics, we generated a Humanized Yeast Genetic Interaction Network (HYGIN) for 1009 human genes with 10,419 interactions. Through the addition of patient-data from The Cancer Genome Atlas (TCGA), we generated a breast cancer specific subnetwork. Specifically, by comparing 1009 genes in HYGIN to genes that were down-regulated in breast cancer, we identified 15 breast cancer genes with 130 potential SLIs. Interestingly, 32 of the 130 predicted SLIs occurred with FBXW7, a well-known tumor suppressor that functions as a substrate-recognition protein within a SKP/CUL1/F-Box ubiquitin ligase complex for proteasome degradation. Efforts to validate these SLIs using chemical genetic data predicted that patients with loss of FBXW7 may respond to treatment with drugs like Selumitinib or Cabozantinib. Conclusions This study provides a patient-data driven interpretation of yeast SLI data. HYGIN represents a novel strategy to uncover therapeutically relevant cancer drug targets and the yeast SLI data offers a major opportunity to mine these interactions. Electronic supplementary material The online version of this article (10.1186/s12920-019-0554-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Morgan W B Kirzinger
- Department of Computer Science, College of Arts and Science, University of Saskatchewan, 176 Thorvaldson Bldg, 110 Science Place, Saskatoon, Saskatchewan, S7N 5C9, Canada
| | - Frederick S Vizeacoumar
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Saskatchewan, 107 Wiggins Road, Saskatoon, Saskatchewan, S7N 5E5, Canada
| | - Bjorn Haave
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Saskatchewan, 107 Wiggins Road, Saskatoon, Saskatchewan, S7N 5E5, Canada
| | - Cristina Gonzalez-Lopez
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Saskatchewan, 107 Wiggins Road, Saskatoon, Saskatchewan, S7N 5E5, Canada
| | - Keith Bonham
- Cancer Research, Saskatchewan Cancer Agency, 107 Wiggins Road, Saskatoon, Saskatchewan, S7N 5E5, Canada.,Division of Oncology, College of Medicine, University of Saskatchewan, 107 Wiggins Road, Saskatoon, Saskatchewan, S7N 5E5, Canada
| | - Anthony Kusalik
- Department of Computer Science, College of Arts and Science, University of Saskatchewan, 176 Thorvaldson Bldg, 110 Science Place, Saskatoon, Saskatchewan, S7N 5C9, Canada.
| | - Franco J Vizeacoumar
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Saskatchewan, 107 Wiggins Road, Saskatoon, Saskatchewan, S7N 5E5, Canada. .,Cancer Research, Saskatchewan Cancer Agency, 107 Wiggins Road, Saskatoon, Saskatchewan, S7N 5E5, Canada. .,Division of Oncology, College of Medicine, University of Saskatchewan, 107 Wiggins Road, Saskatoon, Saskatchewan, S7N 5E5, Canada. .,Cancer Cluster, Rm 4D01.5 Health Science Bldg, University of Saskatchewan, 107 Wiggins Road, Saskatoon, SK, S7N 5E5, Canada.
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19
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Cunningham CE, MacAuley MJ, Yadav G, Vizeacoumar FS, Freywald A, Vizeacoumar FJ. Targeting the CINful genome: Strategies to overcome tumor heterogeneity. Prog Biophys Mol Biol 2019; 147:77-91. [PMID: 30817936 DOI: 10.1016/j.pbiomolbio.2019.02.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Revised: 02/14/2019] [Accepted: 02/17/2019] [Indexed: 01/21/2023]
Abstract
Genomic instability, and more specifically chromosomal instability (CIN), arises from a number of processes that are defective in cancer, such as aberrant mitotic cell division, replication stress, defective DNA damage repair, and ineffective telomere maintenance. CIN is an emerging hallmark of cancer that contributes to tumor heterogeneity through increased rates of genetic alterations. As genetic heterogeneity within a single tumor and between tumors is a key challenge leading to treatment failures, this brings to question, whether therapeutic approaches should aim at the genetic diversity or a specific mutation present within these tumors. Answering this question will determine the future of personalized targeted therapies. Here we discuss, how the genetic diversity associated with CIN in tumor cells can be used as a therapeutic advantage and targeted by exploiting the genetic concepts of synthetic lethality and synthetic dosage lethality. Given that a number of CIN-related pathways work together to fix the DNA damage within our genome and ensure proper segregation of chromosomes, we specifically focus on the genetic interactions amongst these pathways and their potential therapeutic applicability in cancer. We also discuss, how tumor genetic heterogeneity can be targeted in emerging immunotherapeutic approaches.
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Affiliation(s)
- Chelsea E Cunningham
- Department of Pathology, Cancer Cluster, College of Medicine, University of Saskatchewan, Saskatoon, S7N 5E5 Canada
| | - Mackenzie J MacAuley
- Department of Pathology, Cancer Cluster, College of Medicine, University of Saskatchewan, Saskatoon, S7N 5E5 Canada
| | - Garima Yadav
- Department of Pathology, Cancer Cluster, College of Medicine, University of Saskatchewan, Saskatoon, S7N 5E5 Canada
| | - Frederick S Vizeacoumar
- Department of Pathology, Cancer Cluster, College of Medicine, University of Saskatchewan, Saskatoon, S7N 5E5 Canada
| | - Andrew Freywald
- Department of Pathology, Cancer Cluster, College of Medicine, University of Saskatchewan, Saskatoon, S7N 5E5 Canada.
| | - Franco J Vizeacoumar
- Department of Pathology, Cancer Cluster, College of Medicine, University of Saskatchewan, Saskatoon, S7N 5E5 Canada; Cancer Research, Saskatchewan Cancer Agency, 107 Wiggins Road, Saskatoon, S7N 5E5, Canada.
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20
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Miah S, Bagu E, Goel R, Ogunbolude Y, Dai C, Ward A, Vizeacoumar FS, Davies G, Vizeacoumar FJ, Anderson D, Lukong KE. Estrogen receptor signaling regulates the expression of the breast tumor kinase in breast cancer cells. BMC Cancer 2019; 19:78. [PMID: 30651078 PMCID: PMC6335685 DOI: 10.1186/s12885-018-5186-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 12/05/2018] [Indexed: 02/07/2023] Open
Abstract
Background BRK is, a non-receptor tyrosine kinase, overexpressed in approximately 85% of human invasive ductal breast tumors. It is not clear whether BRK expression correlates with breast cancer subtypes, or the expression has prognostic or diagnostic significance. Herein, we investigated the correlation of BRK with any breast cancer subtypes and clinicopathological significance of BRK expression in breast cancer. Methods In this study, we examined BRK expression in 120 breast tumor samples and 29 breast cancer cell lines to explore the positive correlation between BRK and the expression of ERα. We used immunohistochemistry, RT-PCR, and immunoblotting to analyse our experimental samples. Result We demonstrate that estrogen induces BRK gene and protein expression in ER+ breast cancer cells. Over-expression of ERα in the ER-negative breast cancer cell line increased BRK expression, and knock-down of ESR1 in MCF7 cells reduced BRK levels. Further, we provide evidence that BRK is regulated by ERα signaling and the presence of ER antagonists (tamoxifen and fulvestrant) reduce the expression of BRK in ER-positive breast cancer cells. Finally, we demonstrate that the overall survival of ER-positive breast cancer patients is poor when their cancers express high levels of BRK. Conclusion Our data indicate that BRK is a prognostic marker for ER+ breast cancers and provide a strong rationale for targeting BRK to improve patients’ survival. Electronic supplementary material The online version of this article (10.1186/s12885-018-5186-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sayem Miah
- Department of Biochemistry, Microbiology & Immunology, College of Medicine, University of Saskatchewan, 107 Wiggins Road, Saskatoon, SK, S7N 5E5, Canada
| | - Edward Bagu
- Department of Biochemistry, Microbiology & Immunology, College of Medicine, University of Saskatchewan, 107 Wiggins Road, Saskatoon, SK, S7N 5E5, Canada
| | - Raghuveera Goel
- Department of Biochemistry, Microbiology & Immunology, College of Medicine, University of Saskatchewan, 107 Wiggins Road, Saskatoon, SK, S7N 5E5, Canada
| | - Yetunde Ogunbolude
- Department of Biochemistry, Microbiology & Immunology, College of Medicine, University of Saskatchewan, 107 Wiggins Road, Saskatoon, SK, S7N 5E5, Canada
| | - Chenlu Dai
- Department of Biochemistry, Microbiology & Immunology, College of Medicine, University of Saskatchewan, 107 Wiggins Road, Saskatoon, SK, S7N 5E5, Canada
| | - Alison Ward
- Cancer Research, Saskatchewan Cancer Agency, and Division of Oncology, College of Medicine, University of Saskatchewan, Saskatoon, SK, S7N 5E5, Canada
| | | | - Gerald Davies
- Department of Anatomy and Cell Biology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Franco J Vizeacoumar
- Cancer Research, Saskatchewan Cancer Agency, and Division of Oncology, College of Medicine, University of Saskatchewan, Saskatoon, SK, S7N 5E5, Canada.,Department of Pathology, University of Saskatchewan, Saskatoon, S7N 0W8, Canada.,College of Pharmacy and Nutrition, University of Saskatchewan, Saskatoon, S7N 5C9, Canada
| | - Deborah Anderson
- Department of Biochemistry, Microbiology & Immunology, College of Medicine, University of Saskatchewan, 107 Wiggins Road, Saskatoon, SK, S7N 5E5, Canada.,Cancer Research, Saskatchewan Cancer Agency, and Division of Oncology, College of Medicine, University of Saskatchewan, Saskatoon, SK, S7N 5E5, Canada
| | - Kiven Erique Lukong
- Department of Biochemistry, Microbiology & Immunology, College of Medicine, University of Saskatchewan, 107 Wiggins Road, Saskatoon, SK, S7N 5E5, Canada.
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21
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Parameswaran S, Vizeacoumar FS, Kalyanasundaram Bhanumathy K, Qin F, Islam MF, Toosi BM, Cunningham CE, Mousseau DD, Uppalapati MC, Stirling PC, Wu Y, Bonham K, Freywald A, Li H, Vizeacoumar FJ. Molecular characterization of an MLL1 fusion and its role in chromosomal instability. Mol Oncol 2018; 13:422-440. [PMID: 30548174 PMCID: PMC6360371 DOI: 10.1002/1878-0261.12423] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 11/06/2018] [Accepted: 11/26/2018] [Indexed: 01/02/2023] Open
Abstract
Chromosomal rearrangements involving the mixed‐lineage leukemia (MLL1) gene are common in a unique group of acute leukemias, with more than 100 fusion partners in this malignancy alone. However, do these fusions occur or have a role in solid tumors? We performed extensive network analyses of MLL1‐fusion partners in patient datasets, revealing that multiple MLL1‐fusion partners exhibited significant interactions with the androgen‐receptor signaling pathway. Further exploration of tumor sequence data from TCGA predicts the presence of MLL1 fusions with truncated SET domain in prostate tumors. To investigate the physiological relevance of MLL1 fusions in solid tumors, we engineered a truncated version of MLL1 by fusing it with one of its known fusion partners, ZC3H13, to use as a model system. Functional characterization with cell‐based assays revealed that MLL1‐ZC3H13 fusion induced chromosomal instability, affected mitotic progression, and enhanced tumorsphere formation. The MLL1‐ZC3H13 chimera consistently increased the expression of a cancer stem cell marker (CD44); in addition, we detected potential collateral lethality between DOT1L and MLL1 fusions. Our work reveals that MLL1 fusions are likely prevalent in solid tumors and exhibit a potential pro‐tumorigenic role.
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Affiliation(s)
- Sreejit Parameswaran
- Department of Pathology and Laboratory Medicine, Cancer Cluster, College of Medicine, University of Saskatchewan, Saskatoon, Canada
| | - Frederick S Vizeacoumar
- Department of Pathology and Laboratory Medicine, Cancer Cluster, College of Medicine, University of Saskatchewan, Saskatoon, Canada
| | | | - Fujun Qin
- Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA, USA
| | - Md Fahmid Islam
- Department of Pathology and Laboratory Medicine, Cancer Cluster, College of Medicine, University of Saskatchewan, Saskatoon, Canada
| | - Behzad M Toosi
- Department of Pathology and Laboratory Medicine, Cancer Cluster, College of Medicine, University of Saskatchewan, Saskatoon, Canada
| | - Chelsea E Cunningham
- Department of Pathology and Laboratory Medicine, Cancer Cluster, College of Medicine, University of Saskatchewan, Saskatoon, Canada
| | - Darrell D Mousseau
- Cell Signaling Laboratory, Departments of Psychiatry and Physiology, University of Saskatchewan, Saskatoon, Canada
| | - Maruti C Uppalapati
- Department of Pathology and Laboratory Medicine, Cancer Cluster, College of Medicine, University of Saskatchewan, Saskatoon, Canada
| | - Peter C Stirling
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, Canada
| | - Yuliang Wu
- Department of Biochemistry, Cancer Cluster, College of Medicine, University of Saskatchewan, Saskatoon, Canada
| | - Keith Bonham
- Cancer Research, Saskatchewan Cancer Agency, Saskatoon, Canada
| | - Andrew Freywald
- Department of Pathology and Laboratory Medicine, Cancer Cluster, College of Medicine, University of Saskatchewan, Saskatoon, Canada
| | - Hui Li
- Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA, USA
| | - Franco J Vizeacoumar
- Department of Pathology and Laboratory Medicine, Cancer Cluster, College of Medicine, University of Saskatchewan, Saskatoon, Canada.,Cancer Research, Saskatchewan Cancer Agency, Saskatoon, Canada
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22
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Hui KKW, Dojo Soeandy C, Chang S, Vizeacoumar FS, Sun T, Datti A, Henderson JT. Cell-based high-throughput screen for small molecule inhibitors of Bax translocation. J Cell Mol Med 2018; 23:1784-1797. [PMID: 30548903 PMCID: PMC6378228 DOI: 10.1111/jcmm.14076] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Revised: 11/09/2018] [Accepted: 11/13/2018] [Indexed: 12/22/2022] Open
Abstract
Aberrant regulation of programmed cell death (PCD) has been tied to an array of human pathologies ranging from cancers to autoimmune disorders to diverse forms of neurodegeneration. Pharmacologic modulation of PCD signalling is therefore of central interest to a number of clinical and biomedical applications. A key component of PCD signalling involves the modulation of pro‐ and anti‐apoptotic Bcl‐2 family members. Among these, Bax translocation represents a critical regulatory phase in PCD. In the present study, we have employed a high‐content high‐throughput screen to identify small molecules which inhibit the cellular process of Bax re‐distribution to the mitochondria following commitment of the cell to die. Screening of 6246 Generally Recognized As Safe compounds from four chemical libraries post‐induction of cisplatin‐mediated PCD resulted in the identification of 18 compounds which significantly reduced levels of Bax translocation. Further examination revealed protective effects via reduction of executioner caspase activity and enhanced mitochondrial function. Consistent with their effects on Bax translocation, these compounds exhibited significant rescue against in vitro and in vivo cisplatin‐induced apoptosis. Altogether, our findings identify a new set of clinically useful small molecules PCD inhibitors and highlight the role which cAMP plays in regulating Bax‐mediated PCD.
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Affiliation(s)
- Kelvin Kai-Wan Hui
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON, Canada.,RIKEN Center for Brain Science, Wako, Japan
| | - Chesarahmia Dojo Soeandy
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON, Canada
| | - Stephano Chang
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON, Canada
| | - Frederick S Vizeacoumar
- Department of Pathology and Laboratory Medicine, Royal University Hospital, College of Medicine, University of Saskatchewan, Saskatoon, SK, Canada
| | - Thomas Sun
- Mount Sinai Hospital, Lunenfeld-Tanenbaum Research Institute, Toronto, ON, Canada
| | - Alessandro Datti
- SMART Laboratory for High-Throughput Screening Programs, Mount Sinai Hospital, Network Biology Collaborative Centre, Toronto, ON, Canada.,Department of Agriculture, Food, and Environmental Sciences, University of Perugia, Perugia, Italy
| | - Jeffrey T Henderson
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON, Canada
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23
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Parameswaran S, Kundapur D, Vizeacoumar FS, Freywald A, Uppalapati M, Vizeacoumar FJ. A Road Map to Personalizing Targeted Cancer Therapies Using Synthetic Lethality. Trends Cancer 2018; 5:11-29. [PMID: 30616753 DOI: 10.1016/j.trecan.2018.11.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Revised: 10/28/2018] [Accepted: 11/08/2018] [Indexed: 12/12/2022]
Abstract
Targeted therapies rely on the genetic and epigenetic status of the tumor cells and are seen as the most promising approach to treat cancer today. However, current targeted therapies focus on directly inhibiting those molecules that are altered in tumor cells. Unfortunately, targeting these molecules, even with specific inhibitors, is challenging as tumor cells rewire their genetic circuitry to eliminate genetic dependency on these targets. Here, we describe how synthetic lethality approaches can be used to identify genetic dependencies and develop personalized targeted therapies. We also discuss strategies to specifically target these genetic dependencies, using small molecule and biologic drugs.
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Affiliation(s)
- Sreejit Parameswaran
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Saskatchewan, Saskatoon, S7N 5E5, Canada; These authors contributed equally
| | - Deeksha Kundapur
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Saskatchewan, Saskatoon, S7N 5E5, Canada; These authors contributed equally
| | - Frederick S Vizeacoumar
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Saskatchewan, Saskatoon, S7N 5E5, Canada
| | - Andrew Freywald
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Saskatchewan, Saskatoon, S7N 5E5, Canada.
| | - Maruti Uppalapati
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Saskatchewan, Saskatoon, S7N 5E5, Canada.
| | - Franco J Vizeacoumar
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Saskatchewan, Saskatoon, S7N 5E5, Canada; Cancer Research, Saskatchewan Cancer Agency, 107 Wiggins Road, Saskatoon, S7N 5E5, Canada.
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24
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Jing A, Vizeacoumar FS, Parameswaran S, Haave B, Cunningham CE, Wu Y, Arnold R, Bonham K, Freywald A, Han J, Vizeacoumar FJ. Expression-based analyses indicate a central role for hypoxia in driving tumor plasticity through microenvironment remodeling and chromosomal instability. NPJ Syst Biol Appl 2018; 4:38. [PMID: 30374409 PMCID: PMC6200725 DOI: 10.1038/s41540-018-0074-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Revised: 09/25/2018] [Accepted: 09/27/2018] [Indexed: 12/27/2022] Open
Abstract
Can transcriptomic alterations drive the evolution of tumors? We asked if changes in gene expression found in all patients arise earlier in tumor development and can be relevant to tumor progression. Our analyses of non-mutated genes from the non-amplified regions of the genome of 158 triple-negative breast cancer (TNBC) cases identified 219 exclusively expression-altered (EEA) genes that may play important role in TNBC. Phylogenetic analyses of these genes predict a "punctuated burst" of multiple gene upregulation events occurring at early stages of tumor development, followed by minimal subsequent changes later in tumor progression. Remarkably, this punctuated burst of expressional changes is instigated by hypoxia-related molecular events, predominantly in two groups of genes that control chromosomal instability (CIN) and those that remodel tumor microenvironment (TME). We conclude that alterations in the transcriptome are not stochastic and that early-stage hypoxia induces CIN and TME remodeling to permit further tumor evolution.
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Affiliation(s)
- Anqi Jing
- Department of Electrical and Computer Engineering, University of Alberta, Edmonton, AB T6G2R3 Canada
| | - Frederick S. Vizeacoumar
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Saskatchewan, Saskatoon, SK S7N 5E5 Canada
| | - Sreejit Parameswaran
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Saskatchewan, Saskatoon, SK S7N 5E5 Canada
| | - Bjorn Haave
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Saskatchewan, Saskatoon, SK S7N 5E5 Canada
| | - Chelsea E. Cunningham
- Department of Biochemistry, Cancer Cluster, College of Medicine, University of Saskatchewan, Saskatoon, SK S7N 5E5 Canada
| | - Yuliang Wu
- Department of Biochemistry, Cancer Cluster, College of Medicine, University of Saskatchewan, Saskatoon, SK S7N 5E5 Canada
| | - Roland Arnold
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Keith Bonham
- Department of Biochemistry, Cancer Cluster, College of Medicine, University of Saskatchewan, Saskatoon, SK S7N 5E5 Canada
- Cancer Research, Saskatchewan Cancer Agency, Saskatoon, SK S7N 5E5 Canada
| | - Andrew Freywald
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Saskatchewan, Saskatoon, SK S7N 5E5 Canada
- Department of Biochemistry, Cancer Cluster, College of Medicine, University of Saskatchewan, Saskatoon, SK S7N 5E5 Canada
| | - Jie Han
- Department of Electrical and Computer Engineering, University of Alberta, Edmonton, AB T6G2R3 Canada
| | - Franco J. Vizeacoumar
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Saskatchewan, Saskatoon, SK S7N 5E5 Canada
- Department of Biochemistry, Cancer Cluster, College of Medicine, University of Saskatchewan, Saskatoon, SK S7N 5E5 Canada
- Cancer Research, Saskatchewan Cancer Agency, Saskatoon, SK S7N 5E5 Canada
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25
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Reis JM, Xu X, McDonald S, Woloschuk RM, Jaikaran ASI, Vizeacoumar FS, Woolley GA, Uppalapati M. Discovering Selective Binders for Photoswitchable Proteins Using Phage Display. ACS Synth Biol 2018; 7:2355-2364. [PMID: 30203962 DOI: 10.1021/acssynbio.8b00123] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Nature provides an array of proteins that change conformation in response to light. The discovery of a complementary array of proteins that bind only the light-state or dark-state conformation of their photoactive partner proteins would allow each light-switchable protein to be used as an optogenetic tool to control protein-protein interactions. However, as many photoactive proteins have no known binding partner, the advantages of optogenetic control-precise spatial and temporal resolution-are currently restricted to a few well-defined natural systems. In addition, the affinities and kinetics of native interactions are often suboptimal and are difficult to engineer in the absence of any structural information. We report a phage display strategy using a small scaffold protein that can be used to discover new binding partners for both light and dark states of a given light-switchable protein. We used our approach to generate binding partners that interact specifically with the light state or the dark state conformation of two light-switchable proteins: PYP, a test case for a protein with no known partners, and AsLOV2, a well-characterized protein. We show that these novel light-switchable protein-protein interactions can function in living cells to control subcellular localization processes.
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Affiliation(s)
- Jakeb M. Reis
- Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H7, Canada
| | - Xiuling Xu
- Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H7, Canada
| | - Sherin McDonald
- Department of Pathology and Laboratory Medicine, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5A2, Canada
| | - Ryan M. Woloschuk
- Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H7, Canada
| | - Anna S. I. Jaikaran
- Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H7, Canada
| | - Frederick S. Vizeacoumar
- Department of Pathology and Laboratory Medicine, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5A2, Canada
| | - G. Andrew Woolley
- Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H7, Canada
| | - Maruti Uppalapati
- Department of Pathology and Laboratory Medicine, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5A2, Canada
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26
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Toosi BM, El Zawily A, Truitt L, Shannon M, Allonby O, Babu M, DeCoteau J, Mousseau D, Ali M, Freywald T, Gall A, Vizeacoumar FS, Kirzinger MW, Geyer CR, Anderson DH, Kim T, Welm AL, Siegel P, Vizeacoumar FJ, Kusalik A, Freywald A. EPHB6 augments both development and drug sensitivity of triple-negative breast cancer tumours. Oncogene 2018; 37:4073-4093. [PMID: 29700392 PMCID: PMC6062499 DOI: 10.1038/s41388-018-0228-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [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: 05/17/2017] [Revised: 01/30/2018] [Accepted: 02/27/2018] [Indexed: 12/20/2022]
Abstract
Triple-negative breast cancer (TNBC) tumours that lack expression of oestrogen, and progesterone receptors, and do not overexpress the HER2 receptor represent the most aggressive breast cancer subtype, which is characterised by the resistance to therapy in frequently relapsing tumours and a high rate of patient mortality. This is likely due to the resistance of slowly proliferating tumour-initiating cells (TICs), and understanding molecular mechanisms that control TICs behaviour is crucial for the development of effective therapeutic approaches. Here, we present our novel findings, indicating that an intrinsically catalytically inactive member of the Eph group of receptor tyrosine kinases, EPHB6, partially suppresses the epithelial–mesenchymal transition in TNBC cells, while also promoting expansion of TICs. Our work reveals that EPHB6 interacts with the GRB2 adapter protein and that its effect on enhancing cell proliferation is mediated by the activation of the RAS-ERK pathway, which allows it to elevate the expression of the TIC-related transcription factor, OCT4. Consistent with this, suppression of either ERK or OCT4 activities blocks EPHB6-induced pro-proliferative responses. In line with its ability to trigger propagation of TICs, EPHB6 accelerates tumour growth, potentiates tumour initiation and increases TIC populations in xenograft models of TNBC. Remarkably, EPHB6 also suppresses tumour drug resistance to DNA-damaging therapy, probably by forcing TICs into a more proliferative, drug-sensitive state. In agreement, patients with higher EPHB6 expression in their tumours have a better chance for recurrence-free survival. These observations describe an entirely new mechanism that governs TNBC and suggest that it may be beneficial to enhance EPHB6 action concurrent with applying a conventional DNA-damaging treatment, as it would decrease drug resistance and improve tumour elimination.
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Affiliation(s)
- Behzad M Toosi
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Saskatchewan, Room 2841, Royal University Hospital, 103 Hospital Drive, Saskatoon, SK, S7N 0W8, Canada
| | - Amr El Zawily
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Saskatchewan, Room 2841, Royal University Hospital, 103 Hospital Drive, Saskatoon, SK, S7N 0W8, Canada.,Faculty of Science, Damanhour University, Damanhour, 22516, Egypt
| | - Luke Truitt
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Saskatchewan, Room 2841, Royal University Hospital, 103 Hospital Drive, Saskatoon, SK, S7N 0W8, Canada
| | - Matthew Shannon
- Department of Computer Science, University of Saskatchewan, 176 Thorvaldsen Bldg., 110 Science Place, Saskatoon, SK, S7N 5C9, Canada
| | - Odette Allonby
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Saskatchewan, Room 2841, Royal University Hospital, 103 Hospital Drive, Saskatoon, SK, S7N 0W8, Canada
| | - Mohan Babu
- Department of Chemistry and Biochemistry, Faculty of Science, University of Regina, Room 232, Research and Innovation Centre, Regina, SK, S4S 0A2, Canada
| | - John DeCoteau
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Saskatchewan, Room 2841, Royal University Hospital, 103 Hospital Drive, Saskatoon, SK, S7N 0W8, Canada
| | - Darrell Mousseau
- Cell Signaling Laboratory, Department of Psychiatry, College of Medicine, University of Saskatchewan, GB41 Health Sciences Building, 107 Wiggins Road, Saskatoon, SK, S7N 5E5, Canada
| | - Mohsin Ali
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Saskatchewan, Room 2841, Royal University Hospital, 103 Hospital Drive, Saskatoon, SK, S7N 0W8, Canada
| | - Tanya Freywald
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Saskatchewan, Room 2841, Royal University Hospital, 103 Hospital Drive, Saskatoon, SK, S7N 0W8, Canada
| | - Amanda Gall
- Department of Biochemistry, College of Medicine, University of Saskatchewan, Room 2D01 Health Science Building, 107 Wiggins Road, Saskatoon, SK, S7N 5E5, Canada
| | - Frederick S Vizeacoumar
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Saskatchewan, Room 2841, Royal University Hospital, 103 Hospital Drive, Saskatoon, SK, S7N 0W8, Canada
| | - Morgan W Kirzinger
- Department of Computer Science, University of Saskatchewan, 176 Thorvaldsen Bldg., 110 Science Place, Saskatoon, SK, S7N 5C9, Canada
| | - C Ronald Geyer
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Saskatchewan, Room 2841, Royal University Hospital, 103 Hospital Drive, Saskatoon, SK, S7N 0W8, Canada
| | - Deborah H Anderson
- Saskatchewan Cancer Agency, University of Saskatchewan, 4D30.2 Health Sciences Building, 107 Wiggins Road, Saskatoon, SK, S7N 5E5, Canada
| | - TaeHyung Kim
- Donnelly Centre for Cellular and Biomolecular Research and Department of Computer Science, University of Toronto, Toronto, ON, M5S 3E1, Canada
| | - Alana L Welm
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, 2000 Circle of Hope, Salt Lake City, UT, 84112, USA
| | - Peter Siegel
- Goodman Cancer Research Centre, McGill University, 1160 Pine Avenue West, Montreal, QC, H3A 1A3, Canada
| | - Franco J Vizeacoumar
- Saskatchewan Cancer Agency, University of Saskatchewan, 4D30.2 Health Sciences Building, 107 Wiggins Road, Saskatoon, SK, S7N 5E5, Canada
| | - Anthony Kusalik
- Department of Computer Science, University of Saskatchewan, 176 Thorvaldsen Bldg., 110 Science Place, Saskatoon, SK, S7N 5C9, Canada.
| | - Andrew Freywald
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Saskatchewan, Room 2841, Royal University Hospital, 103 Hospital Drive, Saskatoon, SK, S7N 0W8, Canada.
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27
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Paul JM, Toosi B, Vizeacoumar FS, Bhanumathy KK, Li Y, Gerger C, El Zawily A, Freywald T, Anderson DH, Mousseau D, Kanthan R, Zhang Z, Vizeacoumar FJ, Freywald A. Targeting synthetic lethality between the SRC kinase and the EPHB6 receptor may benefit cancer treatment. Oncotarget 2018; 7:50027-50042. [PMID: 27418135 PMCID: PMC5226566 DOI: 10.18632/oncotarget.10569] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Accepted: 06/17/2016] [Indexed: 12/11/2022] Open
Abstract
Application of tumor genome sequencing has identified numerous loss-of-function alterations in cancer cells. While these alterations are difficult to target using direct interventions, they may be attacked with the help of the synthetic lethality (SL) approach. In this approach, inhibition of one gene causes lethality only when another gene is also completely or partially inactivated. The EPHB6 receptor tyrosine kinase has been shown to have anti-malignant properties and to be downregulated in multiple cancers, which makes it a very attractive target for SL applications. In our work, we used a genome-wide SL screen combined with expression and interaction network analyses, and identified the SRC kinase as a SL partner of EPHB6 in triple-negative breast cancer (TNBC) cells. Our experiments also reveal that this SL interaction can be targeted by small molecule SRC inhibitors, SU6656 and KX2-391, and can be used to improve elimination of human TNBC tumors in a xenograft model. Our observations are of potential practical importance, since TNBC is an aggressive heterogeneous malignancy with a very high rate of patient mortality due to the lack of targeted therapies, and our work indicates that FDA-approved SRC inhibitors may potentially be used in a personalized manner for treating patients with EPHB6-deficient TNBC. Our findings are also of a general interest, as EPHB6 is downregulated in multiple malignancies and our data serve as a proof of principle that EPHB6 deficiency may be targeted by small molecule inhibitors in the SL approach.
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Affiliation(s)
- James M Paul
- Department of Biochemistry, University of Saskatchewan, Saskatoon, SK, S7N 5E5, Canada
| | - Behzad Toosi
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Saskatchewan, Royal University Hospital, Saskatoon, SK, S7N 0W8, Canada
| | - Frederick S Vizeacoumar
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Saskatchewan, Royal University Hospital, Saskatoon, SK, S7N 0W8, Canada
| | - Kalpana Kalyanasundaram Bhanumathy
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Saskatchewan, Royal University Hospital, Saskatoon, SK, S7N 0W8, Canada
| | - Yue Li
- Department of Computer Science, University of Toronto, Toronto, ON, M5S 3G4, Canada.,The Donnelly Centre, University of Toronto, Toronto, ON, M5S 3E1, Canada.,Present address: Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Courtney Gerger
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Saskatchewan, Royal University Hospital, Saskatoon, SK, S7N 0W8, Canada
| | - Amr El Zawily
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Saskatchewan, Royal University Hospital, Saskatoon, SK, S7N 0W8, Canada.,Faculty of Science, Damanhour University, Damanhour, 22516, Egypt
| | - Tanya Freywald
- Cancer Research, Saskatchewan Cancer Agency, Saskatoon, SK, S7N 5E5, Canada
| | - Deborah H Anderson
- Cancer Research, Saskatchewan Cancer Agency, Saskatoon, SK, S7N 5E5, Canada
| | - Darrell Mousseau
- Cell Signaling Laboratory, Neuroscience Cluster, University of Saskatchewan, Saskatoon, SK, S7N 5E5, Canada
| | - Rani Kanthan
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Saskatchewan, Royal University Hospital, Saskatoon, SK, S7N 0W8, Canada
| | - Zhaolei Zhang
- Department of Computer Science, University of Toronto, Toronto, ON, M5S 3G4, Canada.,The Donnelly Centre, University of Toronto, Toronto, ON, M5S 3E1, Canada
| | - Franco J Vizeacoumar
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Saskatchewan, Royal University Hospital, Saskatoon, SK, S7N 0W8, Canada.,Cancer Research, Saskatchewan Cancer Agency, Saskatoon, SK, S7N 5E5, Canada
| | - Andrew Freywald
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Saskatchewan, Royal University Hospital, Saskatoon, SK, S7N 0W8, Canada
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28
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Auslander N, Cunningham CE, Toosi BM, McEwen EJ, Yizhak K, Vizeacoumar FS, Parameswaran S, Gonen N, Freywald T, Bhanumathy KK, Freywald A, Vizeacoumar FJ, Ruppin E. An integrated computational and experimental study uncovers FUT9 as a metabolic driver of colorectal cancer. Mol Syst Biol 2017; 13:956. [PMID: 29196508 PMCID: PMC5740504 DOI: 10.15252/msb.20177739] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Metabolic alterations play an important role in cancer and yet, few metabolic cancer driver genes are known. Here we perform a combined genomic and metabolic modeling analysis searching for metabolic drivers of colorectal cancer. Our analysis predicts FUT9, which catalyzes the biosynthesis of Ley glycolipids, as a driver of advanced-stage colon cancer. Experimental testing reveals FUT9's complex dual role; while its knockdown enhances proliferation and migration in monolayers, it suppresses colon cancer cells expansion in tumorspheres and inhibits tumor development in a mouse xenograft models. These results suggest that FUT9's inhibition may attenuate tumor-initiating cells (TICs) that are known to dominate tumorspheres and early tumor growth, but promote bulk tumor cells. In agreement, we find that FUT9 silencing decreases the expression of the colorectal cancer TIC marker CD44 and the level of the OCT4 transcription factor, which is known to support cancer stemness. Beyond its current application, this work presents a novel genomic and metabolic modeling computational approach that can facilitate the systematic discovery of metabolic driver genes in other types of cancer.
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Affiliation(s)
- Noam Auslander
- Department of Computer Science, Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD, USA
| | - Chelsea E Cunningham
- Department of Pathology, Cancer Cluster, College of Medicine, University of Saskatchewan, Saskatoon, SK, Canada
| | - Behzad M Toosi
- Department of Pathology, Cancer Cluster, College of Medicine, University of Saskatchewan, Saskatoon, SK, Canada
| | - Emily J McEwen
- Department of Pathology, Cancer Cluster, College of Medicine, University of Saskatchewan, Saskatoon, SK, Canada
| | - Keren Yizhak
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Frederick S Vizeacoumar
- Department of Pathology, Cancer Cluster, College of Medicine, University of Saskatchewan, Saskatoon, SK, Canada
| | - Sreejit Parameswaran
- Department of Pathology, Cancer Cluster, College of Medicine, University of Saskatchewan, Saskatoon, SK, Canada
| | - Nir Gonen
- Sagol School of Neuroscience, Tel-Aviv University, Tel-Aviv, Israel
| | - Tanya Freywald
- Department of Pathology, Cancer Cluster, College of Medicine, University of Saskatchewan, Saskatoon, SK, Canada
| | - Kalpana K Bhanumathy
- Department of Pathology, Cancer Cluster, College of Medicine, University of Saskatchewan, Saskatoon, SK, Canada
| | - Andrew Freywald
- Department of Pathology, Cancer Cluster, College of Medicine, University of Saskatchewan, Saskatoon, SK, Canada
| | - Franco J Vizeacoumar
- Department of Pathology, Cancer Cluster, College of Medicine, University of Saskatchewan, Saskatoon, SK, Canada .,Cancer Research, Saskatchewan Cancer Agency, Saskatoon, SK, Canada
| | - Eytan Ruppin
- Department of Computer Science, Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD, USA
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29
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El Zawily A, McEwen E, Toosi B, Vizeacoumar FS, Freywald T, Vizeacoumar FJ, Freywald A. The EphB6 receptor is overexpressed in pediatric T cell acute lymphoblastic leukemia and increases its sensitivity to doxorubicin treatment. Sci Rep 2017; 7:14767. [PMID: 29116180 PMCID: PMC5676711 DOI: 10.1038/s41598-017-15200-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [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: 07/19/2017] [Accepted: 10/23/2017] [Indexed: 11/17/2022] Open
Abstract
While impressive improvements have been achieved in T-ALL therapy, current treatment approaches fail in approximately 25% of patients and these patients have limited treatment options. Another significant group of patients is being overtreated, which causes long-lasting side effects. Identification of molecules controlling drug resistance in T-ALL is crucial for treatment optimisation in both scenarios. We report here the EphB6 receptor is frequently overexpressed in T-ALL. Remarkably, our observations indicate that EphB6 acts in T-ALL cells to enhance sensitivity to a DNA-damaging drug, doxorubicin, as interruption of EphB6 activity interferes with the efficiency of doxorubicin-induced eradication of T-ALL cells in cell culture and in xenograft animals. This effect relies on the protection of Akt kinase signaling, while Akt inhibition combined with doxorubicin application produces synergistic effects on the elimination of EphB6-deficient T-ALL cells. These data imply that EphB6 suppresses T-ALL resistance by interfering with Akt activity. Our observations highlight a novel role for EphB6 in reducing drug resistance of T-ALL and suggest that doxorubicin treatment should produce better results if personalised based on EphB6 levels. If successfully verified in clinical studies, this approach should improve outcomes for T-ALL patients resistant to current therapies and for patients, who are being overtreated.
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Affiliation(s)
- Amr El Zawily
- Department of Pathology and Laboratory Medicine, University of Saskatchewan, Royal University Hospital, 103 Hospital Drive, Saskatoon, SK, S7N 0W8, Canada.,Faculty of Science, Damanhour University, Damanhour, 22516, Egypt
| | - Emily McEwen
- Department of Biochemistry, University of Saskatchewan, 107 Wiggins Road, Saskatoon, SK, S7N 5E5, Canada
| | - Behzad Toosi
- Department of Pathology and Laboratory Medicine, University of Saskatchewan, Royal University Hospital, 103 Hospital Drive, Saskatoon, SK, S7N 0W8, Canada
| | - Frederick S Vizeacoumar
- Department of Oncology, University of Saskatchewan,107 Wiggins Road, Saskatoon, SK, S7N 5E5, Canada
| | - Tanya Freywald
- Department of Pathology and Laboratory Medicine, University of Saskatchewan, Royal University Hospital, 103 Hospital Drive, Saskatoon, SK, S7N 0W8, Canada
| | - Franco J Vizeacoumar
- Department of Pathology and Laboratory Medicine, University of Saskatchewan, Royal University Hospital, 103 Hospital Drive, Saskatoon, SK, S7N 0W8, Canada.
| | - Andrew Freywald
- Department of Pathology and Laboratory Medicine, University of Saskatchewan, Royal University Hospital, 103 Hospital Drive, Saskatoon, SK, S7N 0W8, Canada.
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Smith SE, Mellor P, Ward AK, Kendall S, McDonald M, Vizeacoumar FS, Vizeacoumar FJ, Napper S, Anderson DH. Molecular characterization of breast cancer cell lines through multiple omic approaches. Breast Cancer Res 2017; 19:65. [PMID: 28583138 PMCID: PMC5460504 DOI: 10.1186/s13058-017-0855-0] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Accepted: 05/09/2017] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Breast cancer cell lines are frequently used as model systems to study the cellular properties and biology of breast cancer. Our objective was to characterize a large, commonly employed panel of breast cancer cell lines obtained from the American Type Culture Collection (ATCC 30-4500 K) to enable researchers to make more informed decisions in selecting cell lines for specific studies. Information about these cell lines was obtained from a wide variety of sources. In addition, new information about cellular pathways that are activated within each cell line was generated. METHODS We determined key protein expression data using immunoblot analyses. In addition, two analyses on serum-starved cells were carried out to identify cellular proteins and pathways that are activated in these cells. These analyses were performed using a commercial PathScan array and a novel and more extensive phosphopeptide-based kinome analysis that queries 1290 phosphorylation events in major signaling pathways. Data about this panel of breast cancer cell lines was also accessed from several online sources, compiled and summarized for the following areas: molecular classification, mRNA expression, mutational status of key proteins and other possible cancer-associated mutations, and the tumorigenic and metastatic capacity in mouse xenograft models of breast cancer. RESULTS The cell lines that were characterized included 10 estrogen receptor (ER)-positive, 12 human epidermal growth factor receptor 2 (HER2)-amplified and 18 triple negative breast cancer cell lines, in addition to 4 non-tumorigenic breast cell lines. Within each subtype, there was significant genetic heterogeneity that could impact both the selection of model cell lines and the interpretation of the results obtained. To capture the net activation of key signaling pathways as a result of these mutational combinations, profiled pathway activation status was examined. This provided further clarity for which cell lines were particularly deregulated in common or unique ways. CONCLUSIONS These two new kinase or "Kin-OMIC" analyses add another dimension of important data about these frequently used breast cancer cell lines. This will assist researchers in selecting the most appropriate cell lines to use for breast cancer studies and provide context for the interpretation of the emerging results.
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Affiliation(s)
- Shari E Smith
- Cancer Cluster, University of Saskatchewan, 107 Wiggins Road, Saskatoon, SK, S7N 5E5, Canada
| | - Paul Mellor
- Cancer Cluster, University of Saskatchewan, 107 Wiggins Road, Saskatoon, SK, S7N 5E5, Canada
| | - Alison K Ward
- Cancer Cluster, University of Saskatchewan, 107 Wiggins Road, Saskatoon, SK, S7N 5E5, Canada
| | - Stephanie Kendall
- Cancer Cluster, University of Saskatchewan, 107 Wiggins Road, Saskatoon, SK, S7N 5E5, Canada
| | - Megan McDonald
- Vaccine Infectious Disease Organization - International Vaccine Centre (VIDO-InterVac), University of Saskatchewan, 120 Veterinary Road, Saskatoon, SK, S7N 5E3, Canada
| | - Frederick S Vizeacoumar
- Cancer Cluster, University of Saskatchewan, 107 Wiggins Road, Saskatoon, SK, S7N 5E5, Canada
| | - Franco J Vizeacoumar
- Cancer Cluster, University of Saskatchewan, 107 Wiggins Road, Saskatoon, SK, S7N 5E5, Canada.,Cancer Research, Saskatchewan Cancer Agency, 107 Wiggins Road, Saskatoon, SK, S7N 5E5, Canada
| | - Scott Napper
- Vaccine Infectious Disease Organization - International Vaccine Centre (VIDO-InterVac), University of Saskatchewan, 120 Veterinary Road, Saskatoon, SK, S7N 5E3, Canada
| | - Deborah H Anderson
- Cancer Cluster, University of Saskatchewan, 107 Wiggins Road, Saskatoon, SK, S7N 5E5, Canada. .,Cancer Research, Saskatchewan Cancer Agency, 107 Wiggins Road, Saskatoon, SK, S7N 5E5, Canada.
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31
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Islam MF, Watanabe A, Wong L, Lazarou C, Vizeacoumar FS, Abuhussein O, Hill W, Uppalapati M, Geyer CR, Vizeacoumar FJ. Enhancing the throughput and multiplexing capabilities of next generation sequencing for efficient implementation of pooled shRNA and CRISPR screens. Sci Rep 2017; 7:1040. [PMID: 28432350 PMCID: PMC5430825 DOI: 10.1038/s41598-017-01170-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [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: 11/24/2016] [Accepted: 03/20/2017] [Indexed: 11/11/2022] Open
Abstract
Next generation sequencing is becoming the method of choice for functional genomic studies that use pooled shRNA or CRISPR libraries. A key challenge in sequencing these mixed-oligo libraries is that they are highly susceptible to hairpin and/or heteroduplex formation. This results in polyclonal, low quality, and incomplete reads and reduces sequencing throughput. Unfortunately, this challenge is significantly magnified in low-to-medium throughput bench-top sequencers as failed reads significantly perturb the maximization of sequence coverage and multiplexing capabilities. Here, we report a methodology that can be adapted to maximize the coverage on a bench-top, Ion PGM System for smaller shRNA libraries with high efficiency. This ligation-based, half-shRNA sequencing strategy minimizes failed sequences and is also equally amenable to high-throughput sequencers for increased multiplexing. Towards this, we also demonstrate that our strategy to reduce heteroduplex formation improves multiplexing capabilities of pooled CRISPR screens using Illumina NextSeq 500. Overall, our method will facilitate sequencing of pooled shRNA or CRISPR libraries from genomic DNA and maximize sequence coverage.
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Affiliation(s)
- Md Fahmid Islam
- Department of Biochemistry, University of Saskatchewan, Saskatoon, S7N 5E5, Canada
| | - Atsushi Watanabe
- Department of Pathology, University of Saskatchewan, Saskatoon, S7N 0W8, Canada.,Department of Hematology, Nephrology and Rheumatology, Graduate School of Medicine, Akita University, Akita, Japan
| | - Lai Wong
- Department of Biochemistry, University of Saskatchewan, Saskatoon, S7N 5E5, Canada
| | - Conor Lazarou
- Department of Pathology, University of Saskatchewan, Saskatoon, S7N 0W8, Canada
| | | | - Omar Abuhussein
- College of Pharmacy and Nutrition, University of Saskatchewan, Saskatoon, S7N 5C9, Canada
| | - Wayne Hill
- Department of Pathology, University of Saskatchewan, Saskatoon, S7N 0W8, Canada
| | - Maruti Uppalapati
- Department of Pathology, University of Saskatchewan, Saskatoon, S7N 0W8, Canada
| | - C Ronald Geyer
- Department of Pathology, University of Saskatchewan, Saskatoon, S7N 0W8, Canada.
| | - Franco J Vizeacoumar
- Department of Pathology, University of Saskatchewan, Saskatoon, S7N 0W8, Canada. .,College of Pharmacy and Nutrition, University of Saskatchewan, Saskatoon, S7N 5C9, Canada. .,Cancer Research, Saskatchewan Cancer Agency, 107 Wiggins Road, Saskatoon, S7N 5E5, Canada.
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32
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Cunningham CE, Li S, Vizeacoumar FS, Bhanumathy KK, Lee JS, Parameswaran S, Furber L, Abuhussein O, Paul JM, McDonald M, Templeton SD, Shukla H, El Zawily AM, Boyd F, Alli N, Mousseau DD, Geyer R, Bonham K, Anderson DH, Yan J, Yu-Lee LY, Weaver BA, Uppalapati M, Ruppin E, Sablina A, Freywald A, Vizeacoumar FJ. Therapeutic relevance of the protein phosphatase 2A in cancer. Oncotarget 2016; 7:61544-61561. [PMID: 27557495 PMCID: PMC5308671 DOI: 10.18632/oncotarget.11399] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Accepted: 08/10/2016] [Indexed: 11/25/2022] Open
Abstract
Chromosomal Instability (CIN) is regarded as a unifying feature of heterogeneous tumor populations, driving intratumoral heterogeneity. Polo-Like Kinase 1 (PLK1), a serine-threonine kinase that is often overexpressed across multiple tumor types, is one of the key regulators of CIN and is considered as a potential therapeutic target. However, targeting PLK1 has remained a challenge due to the off-target effects caused by the inhibition of other members of the polo-like family. Here we use synthetic dosage lethality (SDL), where the overexpression of PLK1 is lethal only when another, normally non-lethal, mutation or deletion is present. Rather than directly inhibiting PLK1, we found that inhibition of PP2A causes selective lethality to PLK1-overexpressing breast, pancreatic, ovarian, glioblastoma, and prostate cancer cells. As PP2A is widely regarded as a tumor suppressor, we resorted to gene expression datasets from cancer patients to functionally dissect its therapeutic relevance. We identified two major classes of PP2A subunits that negatively correlated with each other. Interestingly, most mitotic regulators, including PLK1, exhibited SDL interactions with only one class of PP2A subunits (PPP2R1A, PPP2R2D, PPP2R3B, PPP2R5B and PPP2R5D). Validation studies and other functional cell-based assays showed that inhibition of PPP2R5D affects both levels of phospho-Rb as well as sister chromatid cohesion in PLK1-overexpressing cells. Finally, analysis of clinical data revealed that patients with high expression of mitotic regulators and low expression of Class I subunits of PP2A improved survival. Overall, these observations point to a context-dependent role of PP2A that warrants further exploration for therapeutic benefits.
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Affiliation(s)
- Chelsea E. Cunningham
- Department of Pathology, Cancer Cluster, College of Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, S7N 5E5 Canada
| | - Shuangshuang Li
- Department of Pathology, Cancer Cluster, College of Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, S7N 5E5 Canada
| | - Frederick S. Vizeacoumar
- Department of Pathology, Cancer Cluster, College of Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, S7N 5E5 Canada
| | | | - Joo Sang Lee
- Center for Bioinformatics and Computational Biology, Department of Computer Science, University of Maryland, Maryland, MD 20742, USA
| | - Sreejit Parameswaran
- Department of Pathology, Cancer Cluster, College of Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, S7N 5E5 Canada
| | - Levi Furber
- Department of Pathology, Cancer Cluster, College of Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, S7N 5E5 Canada
| | - Omar Abuhussein
- College of Pharmacy, University of Saskatchewan, Saskatoon, Saskatchewan, S7N 2Z4, Canada
| | - James M. Paul
- Department of Pathology, Cancer Cluster, College of Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, S7N 5E5 Canada
| | - Megan McDonald
- Department of Pathology, Cancer Cluster, College of Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, S7N 5E5 Canada
| | - Shaina D. Templeton
- Department of Pathology, Cancer Cluster, College of Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, S7N 5E5 Canada
| | - Hersh Shukla
- Department of Pathology, Cancer Cluster, College of Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, S7N 5E5 Canada
| | - Amr M. El Zawily
- Department of Pathology, Cancer Cluster, College of Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, S7N 5E5 Canada
| | - Frederick Boyd
- Department of Pathology, Cancer Cluster, College of Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, S7N 5E5 Canada
| | - Nezeka Alli
- Department of Pathology, Cancer Cluster, College of Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, S7N 5E5 Canada
| | - Darrell D. Mousseau
- Cell Signaling Laboratory, University of Saskatchewan, Saskatoon, Saskatchewan, S7N 5E5 Canada
| | - Ron Geyer
- Department of Pathology, Cancer Cluster, College of Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, S7N 5E5 Canada
| | - Keith Bonham
- Cancer Research, Saskatchewan Cancer Agency, Saskatoon, Saskatchewan, S7N 5E5, Canada
| | - Deborah H. Anderson
- Cancer Research, Saskatchewan Cancer Agency, Saskatoon, Saskatchewan, S7N 5E5, Canada
| | - Jiong Yan
- Department of Pathology, Cancer Cluster, College of Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, S7N 5E5 Canada
| | - Li-Yuan Yu-Lee
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Beth A. Weaver
- Department of Cell and Regenerative Biology and Carbone Cancer Center, University of Wisconsin-Madison, Madison, WI 53705-2275, USA
| | - Maruti Uppalapati
- Department of Pathology, Cancer Cluster, College of Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, S7N 5E5 Canada
| | - Eytan Ruppin
- Center for Bioinformatics and Computational Biology, Department of Computer Science, University of Maryland, Maryland, MD 20742, USA
| | - Anna Sablina
- VIB Center for the Biology of Disease, VIB, 3000 Leuven, Belgium
| | - Andrew Freywald
- Department of Pathology, Cancer Cluster, College of Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, S7N 5E5 Canada
| | - Franco J. Vizeacoumar
- Department of Pathology, Cancer Cluster, College of Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, S7N 5E5 Canada
- College of Pharmacy, University of Saskatchewan, Saskatoon, Saskatchewan, S7N 2Z4, Canada
- Cancer Research, Saskatchewan Cancer Agency, Saskatoon, Saskatchewan, S7N 5E5, Canada
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Ward AK, Mellor P, Smith SE, Kendall S, Just NA, Vizeacoumar FS, Sarker S, Phillips Z, Alvi R, Saxena A, Vizeacoumar FJ, Carlsen SA, Anderson DH. Epigenetic silencing of CREB3L1 by DNA methylation is associated with high-grade metastatic breast cancers with poor prognosis and is prevalent in triple negative breast cancers. Breast Cancer Res 2016; 18:12. [PMID: 26810754 PMCID: PMC4727399 DOI: 10.1186/s13058-016-0672-x] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Accepted: 01/12/2016] [Indexed: 12/12/2022] Open
Abstract
Background CREB3L1 (cAMP-responsive element-binding protein 3-like protein 1), a member of the unfolded protein response, has recently been identified as a metastasis suppressor in both breast and bladder cancer. Methods Quantitative real time PCR (qPCR) and immunoblotting were used to determine the impact of histone deacetylation and DNA methylation inhibitors on CREB3L1 expression in breast cancer cell lines. Breast cancer cell lines and tumor samples were analyzed similarly, and CREB3L1 gene methylation was determined using sodium bisulfite conversion and DNA sequencing. Immunohistochemistry was used to determine nuclear versus cytoplasmic CREB3L1 protein. Large breast cancer database analyses were carried out to examine relationships between CREB3L1 gene methylation and mRNA expression in addition to CREB3L1 mRNA expression and prognosis. Results This study demonstrates that the low CREB3L1 expression previously seen in highly metastatic breast cancer cell lines is caused in part by epigenetic silencing. Treatment of several highly metastatic breast cancer cell lines that had low CREB3L1 expression with DNA methyltransferase and histone deacetylase inhibitors induced expression of CREB3L1, both mRNA and protein. In human breast tumors, CREB3L1 mRNA expression was upregulated in low and medium-grade tumors, most frequently of the luminal and HER2 amplified subtypes. In contrast, CREB3L1 expression was repressed in high-grade tumors, and its loss was most frequently associated with triple negative breast cancers (TNBCs). Importantly, bioinformatics analyses of tumor databases support these findings, with methylation of the CREB3L1 gene associated with TNBCs, and strongly negatively correlated with CREB3L1 mRNA expression. Decreased CREB3L1 mRNA expression was associated with increased tumor grade and reduced progression-free survival. An immunohistochemistry analysis revealed that low-grade breast tumors frequently had nuclear CREB3L1 protein, in contrast to the high-grade breast tumors in which CREB3L1 was cytoplasmic, suggesting that differential localization may also regulate CREB3L1 effectiveness in metastasis suppression. Conclusions Our data further strengthens the role for CREB3L1 as a metastasis suppressor in breast cancer and demonstrates that epigenetic silencing is a major regulator of the loss of CREB3L1 expression. We also highlight that CREB3L1 expression is frequently altered in many cancer types suggesting that it could have a broader role in cancer progression and metastasis. Electronic supplementary material The online version of this article (doi:10.1186/s13058-016-0672-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Alison K Ward
- Cancer Research Group, University of Saskatchewan, 107 Wiggins Road, Saskatoon, SK, S7N 5E5, Canada.
| | - Paul Mellor
- Cancer Research Group, University of Saskatchewan, 107 Wiggins Road, Saskatoon, SK, S7N 5E5, Canada.
| | - Shari E Smith
- Cancer Research Group, University of Saskatchewan, 107 Wiggins Road, Saskatoon, SK, S7N 5E5, Canada.
| | - Stephanie Kendall
- Cancer Research Group, University of Saskatchewan, 107 Wiggins Road, Saskatoon, SK, S7N 5E5, Canada.
| | - Natasha A Just
- Cancer Research Group, University of Saskatchewan, 107 Wiggins Road, Saskatoon, SK, S7N 5E5, Canada.
| | - Frederick S Vizeacoumar
- Cancer Research Group, University of Saskatchewan, 107 Wiggins Road, Saskatoon, SK, S7N 5E5, Canada.
| | - Sabuj Sarker
- Epidemiology and Performance Measurement, Saskatchewan Cancer Agency, 4-2105 8th Street, Saskatoon, SK, S7H 0T8, Canada.
| | - Zoe Phillips
- Epidemiology and Performance Measurement, Saskatchewan Cancer Agency, 4-2105 8th Street, Saskatoon, SK, S7H 0T8, Canada.
| | - Riaz Alvi
- Epidemiology and Performance Measurement, Saskatchewan Cancer Agency, 4-2105 8th Street, Saskatoon, SK, S7H 0T8, Canada.
| | - Anurag Saxena
- Department of Pathology and Lab Medicine, Royal University Hospital, 2841 - 103 Hospital Drive, Saskatoon, SK, S7N 0W8, Canada.
| | - Franco J Vizeacoumar
- Cancer Research Group, University of Saskatchewan, 107 Wiggins Road, Saskatoon, SK, S7N 5E5, Canada. .,Cancer Research, Saskatchewan Cancer Agency, 107 Wiggins Road, Saskatoon, SK, S7N 5E5, Canada.
| | - Svein A Carlsen
- Cancer Research, Saskatchewan Cancer Agency, 107 Wiggins Road, Saskatoon, SK, S7N 5E5, Canada.
| | - Deborah H Anderson
- Cancer Research Group, University of Saskatchewan, 107 Wiggins Road, Saskatoon, SK, S7N 5E5, Canada. .,Cancer Research, Saskatchewan Cancer Agency, 107 Wiggins Road, Saskatoon, SK, S7N 5E5, Canada.
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Marcotte R, Brown KR, Suarez F, Sayad A, Karamboulas K, Krzyzanowski PM, Sircoulomb F, Medrano M, Fedyshyn Y, Koh JL, van Dyk D, Fedyshyn B, Luhova M, Brito GC, Vizeacoumar FJ, Vizeacoumar FS, Datti A, Kasimer D, Buzina A, Mero P, Misquitta C, Normand J, Haider M, Ketela T, Wrana JL, Rottapel R, Neel BG, Moffat J. Essential gene profiles in breast, pancreatic, and ovarian cancer cells. Cancer Discov 2012; 2:172-189. [PMID: 22585861 PMCID: PMC5057396 DOI: 10.1158/2159-8290.cd-11-0224] [Citation(s) in RCA: 234] [Impact Index Per Article: 19.5] [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] [Indexed: 12/16/2022]
Abstract
UNLABELLED Genomic analyses are yielding a host of new information on the multiple genetic abnormalities associated with specific types of cancer. A comprehensive description of cancer-associated genetic abnormalities can improve our ability to classify tumors into clinically relevant subgroups and, on occasion, identify mutant genes that drive the cancer phenotype ("drivers"). More often, though, the functional significance of cancer-associated mutations is difficult to discern. Genome-wide pooled short hairpin RNA (shRNA) screens enable global identification of the genes essential for cancer cell survival and proliferation, providing a "functional genomic" map of human cancer to complement genomic studies. Using a lentiviral shRNA library targeting ~16,000 genes and a newly developed, dynamic scoring approach, we identified essential gene profiles in 72 breast, pancreatic, and ovarian cancer cell lines. Integrating our results with current and future genomic data should facilitate the systematic identification of drivers, unanticipated synthetic lethal relationships, and functional vulnerabilities of these tumor types. SIGNIFICANCE This study presents a resource of genome-scale, pooled shRNA screens for 72 breast, pancreatic, and ovarian cancer cell lines that will serve as a functional complement to genomics data, facilitate construction of essential gene profiles, help uncover synthetic lethal relationships, and identify uncharacterized genetic vulnerabilities in these tumor types. SIGNIFICANCE This study presents a resource of genome-scale, pooled shRNA screens for 72 breast, pancreatic, and ovarian cancer cell lines that will serve as a functional complement to genomics data, facilitate construction of essential gene profiles, help uncover synthetic lethal relationships, and identify uncharacterized genetic vulnerabilities in these tumor types.
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Affiliation(s)
- Richard Marcotte
- Campbell Family Cancer Research Institute, Ontario Cancer Institute, Princess Margaret Hospital University Health Network, Toronto, Canada
| | - Kevin R. Brown
- Donnelly Centre and Banting & Best Department of Medical Research, University of Toronto, Toronto, Canada
- Ontario Institute for Cancer Research, Toronto, Canada
| | - Fernando Suarez
- Campbell Family Cancer Research Institute, Ontario Cancer Institute, Princess Margaret Hospital University Health Network, Toronto, Canada
| | - Azin Sayad
- Donnelly Centre and Banting & Best Department of Medical Research, University of Toronto, Toronto, Canada
| | - Konstantina Karamboulas
- Donnelly Centre and Banting & Best Department of Medical Research, University of Toronto, Toronto, Canada
| | - Paul M. Krzyzanowski
- Campbell Family Cancer Research Institute, Ontario Cancer Institute, Princess Margaret Hospital University Health Network, Toronto, Canada
| | - Fabrice Sircoulomb
- Campbell Family Cancer Research Institute, Ontario Cancer Institute, Princess Margaret Hospital University Health Network, Toronto, Canada
| | - Mauricio Medrano
- Department of Medical Biophysics, University of Toronto, Toronto, Canada
- Campbell Family Cancer Research Institute, Ontario Cancer Institute, Princess Margaret Hospital University Health Network, Toronto, Canada
| | - Yaroslav Fedyshyn
- Donnelly Centre and Banting & Best Department of Medical Research, University of Toronto, Toronto, Canada
| | - Judice L.Y. Koh
- Donnelly Centre and Banting & Best Department of Medical Research, University of Toronto, Toronto, Canada
- Ontario Institute for Cancer Research, Toronto, Canada
| | - Dewald van Dyk
- Donnelly Centre and Banting & Best Department of Medical Research, University of Toronto, Toronto, Canada
| | - Bodhana Fedyshyn
- Donnelly Centre and Banting & Best Department of Medical Research, University of Toronto, Toronto, Canada
| | - Marianna Luhova
- Donnelly Centre and Banting & Best Department of Medical Research, University of Toronto, Toronto, Canada
| | | | - Franco J. Vizeacoumar
- Donnelly Centre and Banting & Best Department of Medical Research, University of Toronto, Toronto, Canada
| | | | - Alessandro Datti
- Samuel Lunenfeld Research Institute, Toronto, Canada
- Department of Experimental Medicine and Biochemical Sciences, University of Perugia, Perugia, Italy
| | - Dahlia Kasimer
- Donnelly Centre and Banting & Best Department of Medical Research, University of Toronto, Toronto, Canada
| | - Alla Buzina
- Donnelly Centre and Banting & Best Department of Medical Research, University of Toronto, Toronto, Canada
| | - Patricia Mero
- Donnelly Centre and Banting & Best Department of Medical Research, University of Toronto, Toronto, Canada
| | - Christine Misquitta
- Donnelly Centre and Banting & Best Department of Medical Research, University of Toronto, Toronto, Canada
| | - Josee Normand
- Campbell Family Cancer Research Institute, Ontario Cancer Institute, Princess Margaret Hospital University Health Network, Toronto, Canada
| | - Maliha Haider
- Campbell Family Cancer Research Institute, Ontario Cancer Institute, Princess Margaret Hospital University Health Network, Toronto, Canada
| | - Troy Ketela
- Donnelly Centre and Banting & Best Department of Medical Research, University of Toronto, Toronto, Canada
- Ontario Institute for Cancer Research, Toronto, Canada
| | - Jeffrey L. Wrana
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
- Samuel Lunenfeld Research Institute, Toronto, Canada
| | - Robert Rottapel
- Department of Medical Biophysics, University of Toronto, Toronto, Canada
- Campbell Family Cancer Research Institute, Ontario Cancer Institute, Princess Margaret Hospital University Health Network, Toronto, Canada
- Ontario Institute for Cancer Research, Toronto, Canada
| | - Benjamin G. Neel
- Department of Medical Biophysics, University of Toronto, Toronto, Canada
- Campbell Family Cancer Research Institute, Ontario Cancer Institute, Princess Margaret Hospital University Health Network, Toronto, Canada
| | - Jason Moffat
- Donnelly Centre and Banting & Best Department of Medical Research, University of Toronto, Toronto, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
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Jin K, Li J, Vizeacoumar FS, Li Z, Min R, Zamparo L, Vizeacoumar FJ, Datti A, Andrews B, Boone C, Zhang Z. PhenoM: a database of morphological phenotypes caused by mutation of essential genes in Saccharomyces cerevisiae. Nucleic Acids Res 2011; 40:D687-94. [PMID: 22009677 PMCID: PMC3245137 DOI: 10.1093/nar/gkr827] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [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] [Indexed: 12/19/2022] Open
Abstract
About one-fifth of the genes in the budding yeast are essential for haploid viability and cannot be functionally assessed using standard genetic approaches such as gene deletion. To facilitate genetic analysis of essential genes, we and others have assembled collections of yeast strains expressing temperature-sensitive (ts) alleles of essential genes. To explore the phenotypes caused by essential gene mutation we used a panel of genetically engineered fluorescent markers to explore the morphology of cells in the ts strain collection using high-throughput microscopy. Here, we describe the design and implementation of an online database, PhenoM (Phenomics of yeast Mutants), for storing, retrieving, visualizing and data mining the quantitative single-cell measurements extracted from micrographs of the ts mutant cells. PhenoM allows users to rapidly search and retrieve raw images and their quantified morphological data for genes of interest. The database also provides several data-mining tools, including a PhenoBlast module for phenotypic comparison between mutant strains and a Gene Ontology module for functional enrichment analysis of gene sets showing similar morphological alterations. The current PhenoM version 1.0 contains 78 194 morphological images and 1 909 914 cells covering six subcellular compartments or structures for 775 ts alleles spanning 491 essential genes. PhenoM is freely available at http://phenom.ccbr.utoronto.ca/.
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Affiliation(s)
- Ke Jin
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
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Li Z, Vizeacoumar FJ, Bahr S, Li J, Warringer J, Vizeacoumar FS, Min R, Vandersluis B, Bellay J, Devit M, Fleming JA, Stephens A, Haase J, Lin ZY, Baryshnikova A, Lu H, Yan Z, Jin K, Barker S, Datti A, Giaever G, Nislow C, Bulawa C, Myers CL, Costanzo M, Gingras AC, Zhang Z, Blomberg A, Bloom K, Andrews B, Boone C. Systematic exploration of essential yeast gene function with temperature-sensitive mutants. Nat Biotechnol 2011; 29:361-7. [PMID: 21441928 DOI: 10.1038/nbt.1832] [Citation(s) in RCA: 296] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2011] [Accepted: 03/01/2011] [Indexed: 11/09/2022]
Abstract
Conditional temperature-sensitive (ts) mutations are valuable reagents for studying essential genes in the yeast Saccharomyces cerevisiae. We constructed 787 ts strains, covering 497 (∼45%) of the 1,101 essential yeast genes, with ∼30% of the genes represented by multiple alleles. All of the alleles are integrated into their native genomic locus in the S288C common reference strain and are linked to a kanMX selectable marker, allowing further genetic manipulation by synthetic genetic array (SGA)-based, high-throughput methods. We show two such manipulations: barcoding of 440 strains, which enables chemical-genetic suppression analysis, and the construction of arrays of strains carrying different fluorescent markers of subcellular structure, which enables quantitative analysis of phenotypes using high-content screening. Quantitative analysis of a GFP-tubulin marker identified roles for cohesin and condensin genes in spindle disassembly. This mutant collection should facilitate a wide range of systematic studies aimed at understanding the functions of essential genes.
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Affiliation(s)
- Zhijian Li
- Banting and Best Department of Medical Research, The Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
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Vizeacoumar FJ, van Dyk N, S Vizeacoumar F, Cheung V, Li J, Sydorskyy Y, Case N, Li Z, Datti A, Nislow C, Raught B, Zhang Z, Frey B, Bloom K, Boone C, Andrews BJ. Integrating high-throughput genetic interaction mapping and high-content screening to explore yeast spindle morphogenesis. ACTA ACUST UNITED AC 2010; 188:69-81. [PMID: 20065090 PMCID: PMC2812844 DOI: 10.1083/jcb.200909013] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.8] [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] [Indexed: 11/22/2022]
Abstract
A combination of yeast genetics, synthetic genetic array analysis, and high-throughput screening reveals that sumoylation of Mcm21p promotes disassembly of the mitotic spindle. We describe the application of a novel screening approach that combines automated yeast genetics, synthetic genetic array (SGA) analysis, and a high-content screening (HCS) system to examine mitotic spindle morphogenesis. We measured numerous spindle and cellular morphological parameters in thousands of single mutants and corresponding sensitized double mutants lacking genes known to be involved in spindle function. We focused on a subset of genes that appear to define a highly conserved mitotic spindle disassembly pathway, which is known to involve Ipl1p, the yeast aurora B kinase, as well as the cell cycle regulatory networks mitotic exit network (MEN) and fourteen early anaphase release (FEAR). We also dissected the function of the kinetochore protein Mcm21p, showing that sumoylation of Mcm21p regulates the enrichment of Ipl1p and other chromosomal passenger proteins to the spindle midzone to mediate spindle disassembly. Although we focused on spindle disassembly in a proof-of-principle study, our integrated HCS-SGA method can be applied to virtually any pathway, making it a powerful means for identifying specific cellular functions.
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Affiliation(s)
- Franco J Vizeacoumar
- Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada
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