Publications

2024

• Systematic comparison of CRISPR and shRNA screens to identify essential genes using graph-based unsupervised learning model. Ding Y, Denomy C, Freywald A, Pan Y, Vizeacoumar FJ, Vizeacoumar FS†, Wu F†. Cells 2024. Oct4; 13(19):1653. († Corresponding authors)
• Preclinical 3D model screening reveals digoxin as an effective therapy for a rare and aggressive type of endometrial cancer. Kumar PP, Smith D, Key J, Dong H, Ganapathysamy A, Maranda V, Wong NKY, Fernandez ML, Kim H, Zhang G, Ewanowich C, Hopkins L, Freywald A, Postovit LM, Köbel M, Fu Y, Vizeacoumar FS, Vizeacoumar FJ, Carey MS, Lee C-H. Gynecologic Oncology. 2024; 188,162-168.
• MEMO1 binds iron and modulates iron homeostasis in cancer cells. Dolgova N, Uhlemann EE, Boniecki MT, Vizeacoumar FS, Ara A, Nouri P, Ralle M, Tonelli M, Abbas SA, Patry J, Elhasasna H, Freywald A, Vizeacoumar FJ†, Dmitriev OY†. Elife. 2024 Apr 19;13:e86354. doi: 10.7554/eLife.86354. Epub ahead of print. († Corresponding authors)
• AI is a viable alternative to high throughput screening: a 318-target study. The Atomwise AIMS Program. Sci Rep 2024 Apr 2;14(1):7526.
• hnRNP A1 dysfunction alters RNA splicing and drives neurodegeneration in multiple sclerosis (MS). Salapa HE, Thibault PA, Libner CD, Ding Y, Clarke JWE, Denomy C, Hutchinson C, Abidullah HM, Hammond SA, Pastushok L, Vizeacoumar FS, Levin MC. Nat Commun. 2024 Jan 8;15(1):356.

2023

• Survey of NF1 inactivation by surrogae immunohistochemistry in ovarian carcinomas. Köbel M, Yong 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. Gynecol Oncol. 2023 Oct 9;178:80-88. doi: 10.1016/j.ygyno.2023.09.016. Online ahead of print.
• Integration of cancer-related genetic landscape of Eph receptors and ephrins with proteomics identifies a crosstalk between EPHB6 and EGFR. 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†. Cell Rep. 2023 Jun 30;42(7):112670. doi: 10.1016/j.celrep.2023.112670. Online ahead of print. († Corresponding authors).
• Generation of a SARS-CoV-2 Reverse Genetics System and Novel Human Lung Cell Lines That Exhibit High Virus-Induced Cytopathology. Khan JQ, Rohamare M, Rajamanickam K, Bhanumathy KK, Lew J, Kumar A, Falzarano D, Vizeacoumar FJ, Wilson JA. Viruses. 2023 May 30;15(6):1281. doi: 10.3390/v15061281.
• A multipronged unbiased strategy guides the development of an anti-EGFR/EPHA2-bispecific antibody for combination cancer therayp. 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†. Clin Cancer Res. 2023 Mar 28;OF1-OF16. doi: 10.1158/1078-0432.CCR-22-2535. Online ahead of print. († Corresponding authors).
• Synthetic lethal interactions of DEAD/H-box helicases as targets for cancer therapy. Arna AB, Patel H, Singh RS, Vizeacoumar FS, Kusalik A, Freywald A, Vizeacoumar FJ†, Wu Y†.  Front. Oncol. 2023 Jan 26;12:1087989. († Corresponding authors).
  
• A CRISPR Platform for Targeted In Vivo Screens. Maranda V, Zhang Y, Vizeacoumar FS, Freywald A†, Vizeacoumar FJ†. Methods Mol Biol. 2023;2614:397-409. doi: 10.1007/978-1-0716-2914-7_24. († Corresponding authors).

2022

• Homoharringtonine demonstrates a cytotoxic effect against triple-negative breast cancer cell lines and acts synergistically with paclitaxel. Plett R, Mellor P, Kendall S, Hammond SA, Boulet A, Plaza K, Vizeacoumar FS, Vizeacoumar FJ†, Anderson DH†. Sci Rep. 2022 Sep 19;12(1):15663. doi: 10.1038/s41598-022-19621-7. († Corresponding authors).
• Activation of the Anaphase Promoting Complex Reverses Multiple Drug Resistant Cancer in a Canine Model of Multiple Drug Resistant Lymphoma. 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. Cancers. 2022; 14(17):4215. https://doi.org/10.3390/cancers14174215.
• A Drug Repurposing Screen Identifies Fludarabine Phosphate as a Potential Therapeutic Agent for N-MYC Overexpressing Neuroendocrine Prostate Cancers. Elhasasna H, Khan R, Bhanumathy KK, Vizeacoumar FS, Walke P, Bautista M, Dahiya DK, Maranda V, Patel H, Balagopal A, Alli N, Krishnan A, Freywald A†, Vizeacoumar FJ†. Cells 2022, 11(14), 2246; doi.org/10.3390/cells11142246 († Corresponding authors).
• Differential expression of HNF1A and HNF1A-AS1 in colon cancer cells. Sepehri Z, Banerjee A, Vizeacoumar FS, Freywald A, Vizeacoumar FJ, Dolinsky VW, Davie JR. IUBMB Life. 2022 Jun;74(6):496-507. doi: 10.1002/iub.2609. Epub 2022 Mar 2.

2021

• Sympathetic signaling facilitates progression of neuroendocrine prostate cancer. Dwivedi S, Bautista M, Shrestha S, Elhasasna H, Chaphekar T, Vizeacoumar FS, Krishnan A. Cell Death Discov. 2021 Nov 22;7(1):364. doi: 10.1038/s41420-021-00752-1.
• Computational Prediction of Chemical Tools for Identification and Validation of Synthetic Lethal Interaction Networks. Bhanumathy KK, Abuhussein O, Vizeacoumar FS, Freywald A, Vizeacoumar FJ, Phenix CP, Price EW, Cao R. Methods Mol Biol. 2021;2381:333-358. doi: 10.1007/978-1-0716-1740-3_18.
• Identification of Synthetic Lethal Interactions Using High-Throughput, Arrayed CRISPR/Cas9-Based Platforms. MacAuley MJ, Abuhussein O, Vizeacoumar FS. Methods Mol Biol. 2021;2381:135-149. doi: 10.1007/978-1-0716-1740-3_7.
• INCISOR: An Algorithm to Identify Synthetic Rescue Mediators of Resistance to Targeted and Immunotherapy. Wang X, Vizeacoumar FS, Sahu AD. Methods Mol Biol. 2021;2381:203-215. doi: 10.1007/978-1-0716-1740-3_11.
• Genome-wide synthetic lethal screen unveils novel CAIX – NFS1/xCT axis as a targetable vulnerability in hypoxic solid tumors. 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.  Science Advances 2021 Aug 27;7(35):eabj0364. doi: 10.1126/sciadv.abj0364. Print 2021 Aug.
  
• Identification of novel genes involved in apoptosis of HIV-infected macrophages using unbiased genome-wide screening. 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†.  BMC Infectious Diseases. 2021 Jul 7;21(1):655.2021 († Corresponding authors).
• Mining the plasma-proteome associated genes in patients with gastro-esophageal cancers for biomarker discovery. Vizeacoumar FS, Guo H, Dwernychuk L, Zaidi A, Freywald A, Wu F, Vizeacoumar FJ†, Ahmed S†. Sci Rep. 2021 Apr 7;11(1):7590. († Corresponding authors).
• Protein Tyrosine Kinases: Their Roles and Their Targeting in Leukemia. Bhanumathy KK, Balagopal A, Vizeacoumar FS, Vizeacoumar FJ, Freywald A, Giambra V. Cancers 2021, 13(2), 184.
• APOBEC1 cytosine deaminase activity on single-stranded DNA is suppressed by replication protein A. Wong L, Vizeacoumar FS, Vizeacoumar FJ, Chelico L. Nucleic Acids Res. 2021 Jan 11;49(1):322-339.

2020

• The CINs of Polo-Like Kinase 1 in Cancer. Cunningham CE†, MacAuley MJ, Vizeacoumar FS, Abuhussein O, Freywald A†, Vizeacoumar FJ†. Cancers 2020, 12(10), 2953. († Corresponding authors).

2019

• Banding Together: A Systematic Comparison of The Cancer Genome Atlas and the Mitelman Database. Denomy C, Germain S, Haave B, Vizeacoumar FS, Freywald A, Weaver B, Vizeacoumar FJ†. Cancer Research. 2019 Aug 15 DOI: 10.1158/0008-5472.CAN-19-0585 († Corresponding author).
• Humanized yeast genetic interaction mapping predicts synthetic lethal interactions of FBXW7 in breast cancer. Kirzinger MWB, Vizeacoumar FS, Haave B, Gonzalez-Lopez C, Bonham K, Kusalik A†, Vizeacoumar FJ†. BMC Med Genomics. 2019 Jul 27;12(1):112. doi: 10.1186/s12920-019-0554-z († Corresponding authors).
• Targeting the CINful genome: Strategies to overcome tumor heterogeneity. Cunningham CE, MacAuley MJ, Yadav G, Vizeacoumar FS, Freywald A†, Vizeacoumar FJ†. Prog Biophys Mol Biol. 2019 Feb 25. pii: S0079-6107(18)30284-0. doi: 10.1016/j.pbiomolbio.2019.02.006. [Epub ahead of print] († Corresponding authors).
• Estrogen receptor signaling regulates the expression of breast tumor kinase in breast cancer cells. Miah S, Bagu E, Goel R, Yetunde O, Dai C, Ward A, Vizeacoumar FS, Davies G, Vizeacoumar FJ, Anderson D and Lukng KE. BMC Cancer (2019) 19:78. DOI: https://doi.org/10.1186/s12885-018-5186-8.
• A Road map to personalizing targeted cancer therapies using synthetic lethality. Parameswaran S, Kundapur D, Vizeacoumar FS, Freywald A†, Uppalapati MC†, Vizeacoumar FJ†. Trends in Cancer 2019 Jan;5(1):11-29. doi: 10.1016/j.trecan.2018.11.001. Epub 2018 Dec 7. Review († Corresponding authors).
• Molecular characterization of a MLL1 fusion and its role in chromosomal instability. 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†. Mol Oncol. 2019 Feb;13(2):422-440. doi: 10.1002/1878-0261.12423. Epub 2018 Dec 31(† Corresponding author).

2018

• Expression-based analyses indicate a central role for hypoxia in driving tumor plasticity through microenvironment remodeling and chromosomal instability. Jing A, Vizeacoumar FS, Parameswaran S, Haave B, Cunningham CE, Wu Y, Arnold R, Bonham K, Freywald A, Han J†, Vizeacoumar FJ†. NPJ Syst Biol Appl. 2018 Oct 24;4:38. doi: 10.1038/s41540-018-0074-z. eCollection 2018. († Corresponding authors).
• Discovering Selective Binders for Photoswitchable Proteins Using Phage Display. Reis JM, Xu X, McDonald S, Woloschuk RM, Jaikaran ASI, Vizeacoumar FS, Woolley GA, Uppalapati M. ACS Synth Biol. 2018 Oct 19;7(10):2355-2364. doi: 10.1021/acssynbio.8b00123. Epub 2018 Sep 27.
• Global phosphoproteomic analysis identifies SRMS-regulated secondary signaling intermediates. Goel RK, Meyer M, Paczkowska M, Reimand J, Vizeacoumar FS, Vizeacoumar FJ, Lam TT, Lukong KE. Proteome Sci. 2018 Aug 18;16:16. doi: 10.1186/s12953-018-0143-7.

2017

• FRK inhibits breast cancer cell migration and invasion by suppressing epithelial-mesenchymal transition. Ogunbolude Y, Dai C, Bagu ET, Goel RK, Miah S, MacAusland-Berg J, Ng CY, Chibbar R, Napper S, Raptis L, Vizeacoumar FS, Vizeacoumar FJ, Bonham K, Lukong KE. Oncotarget. 2017 Dec 6;8(68):113034-113065. doi: 10.18632/oncotarget.22958. eCollection 2017 Dec 22.
• An integrated computational and experimental study uncovers FUT9 as a metabolic driver of colorectal cancer. 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†. Mol Syst Biol. 2017 Dec 1;13(12):956. doi: 10.15252/msb.20177739. († Corresponding authors).
• The EphB6 receptor is overexpressed in pediatric T cell acute lymphoblastic leukemia and increases its sensitivity to doxorubicin treatment. El Zawily A, McEwen E, Toosi B, Vizeacoumar FS, Freywald T, Vizeacoumar FJ†, Freywald A†. Sci Rep. 2017 Nov 7;7(1):14767. doi: 10.1038/s41598-017-15200-3. († Corresponding authors).
• Molecular characterization of breast cancer cell lines through multiple omic approaches. Smith SE, Mellor P, Ward AK, Kendall S, McDonald M, Vizeacoumar FS, Vizeacoumar FJ, Napper S, Anderson DH. Breast Cancer Research 2017 Jun 5; 19(1):65. Doi:10.1186/s13058-017-0855-0.
• Enhancing the throughput and multiplexing capabilities of next generation sequencing for efficient implementation of pooled shRNA and CRISPR screens. Islam MF, Watanabe A, Wong L, Lazarou C, Vizeacoumar FS, Abuhussein O, Hill W, Uppalapati M, Geyer CR, Vizeacoumar FJ†.  Sci Rep. 2017 Apr 21;7(1):1040. doi: 10.1038/s41598-017-01170-z. († Corresponding author).

2016

• Therapeutic relevance of the protein phosphatase 2A in cancer. Cunningham CE, Li S, Vizeacoumar FS, Bhanumathy KK, Lee JS, Parameswaran S, Furber L, Abuhussain O, Paul JM, McDonald M, Templeton SD, Shukla H, Boyd F, Alli N, Mousseau D, Geyer R, Bonham K, Anderson DH, Yan J, Yu-Lee L, Weaver BA, Uppalapati1 M, Ruppin E, Sablina A, Freywald A, Vizeacoumar FJ†. Oncotarget. 2016 Sep 20;7(38):61544-61561. doi: 10.18632/oncotarget.11399. († Corresponding author).
• Targeting synthetic lethality between the SRC kinase and the EPHB6 receptor may benefit cancer treatment. 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†. Oncotarget. 2016 Aug 2;7(31):50027-50042. doi: 10.18632/oncotarget.10569. († Corresponding authors).
• 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. 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. Breast Cancer Research 2016 Jan 25;18(1):12. doi: 10.1186/s13058-016-0672-x.