Skip to main content

Illinois IGB

Research Areas

Anticancer Discovery from Pets to People: Publications

Winter, J., Luu, A., Gapinske, M., Manandhar, S., Shirguppe, S., Woods, W. S., ... Perez-Pinera, P. (2019). Author Correction: Targeted exon skipping with AAV-mediated split adenine base editors (Cell Discovery, (2019), 5, 1, (41), 10.1038/s41421-019-0109-7). Cell Discovery, 5(1), [56]. https://doi.org/10.1038/s41421-019-0125-7

Janin, M., Ortiz-Barahona, V., de Moura, M. C., Martínez-Cardús, A., Llinàs-Arias, P., Soler, M., ... Esteller, M. (2019). Epigenetic loss of RNA-methyltransferase NSUN5 in glioma targets ribosomes to drive a stress adaptive translational program. Acta Neuropathologica, 138(6), 1053-1074. https://doi.org/10.1007/s00401-019-02062-4

Thirawatananond, P., McPherson, R. L., Malhi, J., Nathan, S., Lambrecht, M. J., Brichacek, M., ... Gabelli, S. B. (2019). Structural analyses of NudT16–ADP-ribose complexes direct rational design of mutants with improved processing of poly(ADP-ribosyl)ated proteins. Scientific reports, 9(1), [5940]. https://doi.org/10.1038/s41598-019-39491-w

Winter, J., Luu, A., Gapinske, M., Manandhar, S., Shirguppe, S., Woods, W. S., ... Perez-Pinera, P. (2019). Targeted exon skipping with AAV-mediated split adenine base editors. Cell Discovery, 5(1), [41]. https://doi.org/10.1038/s41421-019-0109-7

Parker, E. N., Drown, B. S., Geddes, E. J., Lee, H. Y., Ismail, N., Lau, G. W., & Hergenrother, P. J. (2019). Implementation of permeation rules leads to a FabI inhibitor with activity against Gram-negative pathogens. Nature Microbiology. https://doi.org/10.1038/s41564-019-0604-5

Boudreau, M. W., Peh, J., & Hergenrother, P. J. (2019). Procaspase-3 Overexpression in Cancer: A Paradoxical Observation with Therapeutic Potential. ACS chemical biology, 14(11), 2335-2348. https://doi.org/10.1021/acschembio.9b00338

Winter, J., & Perez-Pinera, P. (2019). Directed Evolution of CRISPR-Cas9 Base Editors. Trends in Biotechnology, 37(11), 1151-1153. https://doi.org/10.1016/j.tibtech.2019.09.005

Roberts, R. D., Lizardo, M. M., Reed, D. R., Hingorani, P., Glover, J., Allen-Rhoades, W., ... Crompton, B. D. (2019). Provocative questions in osteosarcoma basic and translational biology: A report from the Children's Oncology Group. Cancer, 125(20), 3514-3525. https://doi.org/10.1002/cncr.32351

Brown, A., Winter, J., Gapinske, M., Tague, N., Woods, W. S., & Perez-Pinera, P. (2019). Multiplexed and tunable transcriptional activation by promoter insertion using nuclease-assisted vector integration. Nucleic acids research, 47(12), e67. https://doi.org/10.1093/nar/gkz210

Hejna, M., Moon, W. M., Cheng, J., Kawakami, A., Fisher, D. E., & Song, J. (2019). Local genomic features predict the distinct and overlapping binding patterns of the bHLH-Zip family oncoproteins MITF and MYC-MAX. Pigment Cell and Melanoma Research, 32(4), 500-509. https://doi.org/10.1111/pcmr.12762

Llabani, E., Hicklin, R. W., Lee, H. Y., Motika, S. E., Crawford, L. A., Weerapana, E., & Hergenrother, P. (2019). Diverse compounds from pleuromutilin lead to a thioredoxin inhibitor and inducer of ferroptosis. Nature Chemistry, 11(6), 521-532. https://doi.org/10.1038/s41557-019-0261-6

Aye, Y., & Hergenrother, P. (2019). Editorial overview: From the iceman to modern medicine. Current Opinion in Chemical Biology, 50, A1-A2. https://doi.org/10.1016/j.cbpa.2019.04.021

Parks, C. A., Henning, K. R., Pavelko, K. D., Hansen, M. J., Van Keulen, V. P., Reed, B. K., ... Pease, L. R. (2019). Breaking tolerance with engineered class I antigen-presenting molecules. Proceedings of the National Academy of Sciences of the United States of America, 116(8), 3136-3145. https://doi.org/10.1073/pnas.1807465116

Bingham, T. W., Hernandez, L. W., Olson, D. G., Svec, R. L., Hergenrother, P., & Sarlah, D. (2019). Enantioselective Synthesis of Isocarbostyril Alkaloids and Analogs Using Catalytic Dearomative Functionalization of Benzene. Journal of the American Chemical Society, 141(1), 657-670. https://doi.org/10.1021/jacs.8b12123

Roy, J., Dibaeinia, P., Fan, T. M., Sinha, S., & Das, A. (2019). Global analysis of osteosarcoma lipidomes reveal altered lipid profiles in metastatic versus nonmetastatic cells. Journal of Lipid Research, 60(2), 375-387. https://doi.org/10.1194/jlr.M088559

Schlein, L. J., Fadl-Alla, B., Pondenis, H. C., Lezmi, S., Eberhart, C. G., LeBlanc, A. K., ... Fan, T. M. (2019). Immunohistochemical characterization of procaspase-3 overexpression as a druggable target with PAC-1, a procaspase-3 activator, in canine and human brain cancers. Frontiers in Oncology, 9(FEB), [96]. https://doi.org/10.3389/fonc.2019.00096

Denisov, I. G., Schuler, M. A., & Sligar, S. (2019). Nanodiscs as a New Tool to Examine Lipid–Protein Interactions. In Methods in Molecular Biology (pp. 645-671). (Methods in Molecular Biology; Vol. 2003). Humana Press Inc.. https://doi.org/10.1007/978-1-4939-9512-7_25

Zhang, Y., Manjunath, M., Kim, Y., Heintz, J., & Song, J. (2019). Sequenceng: An interactive knowledge base of sequencing techniques. Bioinformatics, 35(8), 1438-1440. https://doi.org/10.1093/bioinformatics/bty794

Finnegan, A., Cho, R. J., Luu, A., Harirchian, P., Lee, J., Cheng, J. B., & Song, J. S. (2019). Single-cell transcriptomics reveals spatial and temporal turnover of keratinocyte differentiation regulators. Frontiers in Genetics, 10(JUL), [775]. https://doi.org/10.3389/fgene.2019.00775

Sharma, P., Harris, D. T., Stone, J. D., & Kranz, D. M. (2019). T-cell receptors engineered de novo for peptide specificity can mediate optimal t-cell activity without self cross-reactivity. Cancer Immunology Research, 7(12), 2025-2035. https://doi.org/10.1158/2326-6066.CIR-19-0035

Sharma, P., & Kranz, D. M. (2019). T cell receptors for gene transfer in adoptive T cell therapy. Critical Reviews in Immunology, 39(2), 105-122. https://doi.org/10.1615/CritRevImmunol.2019030788

Zhang, Y., Manjunath, M., Yan, J., Baur, B. A., Zhang, S., Roy, S., & Song, J. (2019). The cancer-associated genetic variant rs3903072 modulates immune cells in the tumor microenvironment. Frontiers in Genetics, 10(JUL), [754]. https://doi.org/10.3389/fgene.2019.00754

Richter, M. F., & Hergenrother, P. J. (2019). The challenge of converting gram-positive-only compounds into broad-spectrum antibiotics. Annals of the New York Academy of Sciences, 1435(1), 18-38. https://doi.org/10.1111/nyas.13598

Watson, M. K., Mitchell, M. A., Stern, A. W., Labelle, A. L., Joslyn, S., Fan, T. M., ... Marshall, K. (2019). EVALUATING THE CLINICAL AND PHYSIOLOGICAL EFFECTS OF LONG-TERM ULTRAVIOLET B RADIATION ON RABBITS (ORYCTOLAGUS CUNICULUS). Journal of Exotic Pet Medicine, 28, 43-55. https://doi.org/10.1053/j.jepm.2018.04.016

Blaha, D. T., Anderson, S. D., Yoakum, D. M., Hager, M. V., Zha, Y., Gajewski, T. F., & Kranz, D. M. (2019). High-throughput stability screening of neoantigen/HLA complexes improves immunogenicity predictions. Cancer Immunology Research, 7(1), 50-61. https://doi.org/10.1158/2326-6066.CIR-18-0395

Dowling, M., Samuelson, J., Fadl-Alla, B., Pondenis, H. C., Byrum, M., Barger, A. M., & Fan, T. M. (2019). Overexpression of prostate specific membrane antigen by canine hemangiosarcoma cells provides opportunity for the molecular detection of disease burdens within hemorrhagic body cavity effusions. PloS one, 14(1), [e0210297]. https://doi.org/10.1371/journal.pone.0210297

1.2. 2018

Overgaard, N. H., Fan, T. M., Schachtschneider, K. M., Principe, D. R., Schook, L. B., & Jungersen, G. (2018). Of Mice, Dogs, Pigs, and Men: Choosing the Appropriate Model for Immuno-Oncology Research. ILAR Journal, 59(3), 247-262. https://doi.org/10.1093/ilar/ily014

Rack, J. G. M., Ariza, A., Drown, B. S., Henfrey, C., Bartlett, E., Shirai, T., ... Ahel, I. (2018). (ADP-ribosyl)hydrolases: Structural Basis for Differential Substrate Recognition and Inhibition. Cell chemical biology, 25(12), 1533-1546.e12. https://doi.org/10.1016/j.chembiol.2018.11.001

Drown, B. S., Shirai, T., Rack, J. G. M., Ahel, I., & Hergenrother, P. (2018). Monitoring Poly(ADP-ribosyl)glycohydrolase Activity with a Continuous Fluorescent Substrate. Cell chemical biology, 25(12), 1562-1570.e19. https://doi.org/10.1016/j.chembiol.2018.09.008

Burton, J. H., Mazcko, C., LeBlanc, A., Covey, J. M., Ji, J., Kinders, R. J., ... Pommier, Y. (2018). NCI comparative oncology program testing of non-camptothecin indenoisoquinoline topoisomerase I inhibitors in naturally occurring canine lymphoma. Clinical Cancer Research, 24(23), 5830-5840. https://doi.org/10.1158/1078-0432.CCR-18-1498

Cao, J., Perez-Pinera, P., Lowenhaupt, K., Wu, M. R., Purcell, O., De La Fuente-Nunez, C., & Lu, T. K. (2018). Versatile and on-demand biologics co-production in yeast. Nature communications, 9(1), [77]. https://doi.org/10.1038/s41467-017-02587-w

Svec, R. L., Furiassi, L., Skibinski, C. G., Fan, T. M., Riggins, G. J., & Hergenrother, P. J. (2018). Tunable Stability of Imidazotetrazines Leads to a Potent Compound for Glioblastoma. ACS chemical biology, 13(11), 3206-3216. https://doi.org/10.1021/acschembio.8b00864

Svec, R. L., & Hergenrother, P. (2018). Oxygen Starvation Unmasks a Killer. Cell chemical biology, 25(11), 1313-1314. https://doi.org/10.1016/j.chembiol.2018.10.028

Cheng, J. B., Sedgewick, A. J., Finnegan, A. I., Harirchian, P., Lee, J., Kwon, S., ... Cho, R. J. (2018). Transcriptional Programming of Normal and Inflamed Human Epidermis at Single-Cell Resolution. Cell Reports, 25(4), 871-883. https://doi.org/10.1016/j.celrep.2018.09.006

Livezey, M., Huang, R., Hergenrother, P., & Shapiro, D. J. (2018). Strong and sustained activation of the anticipatory unfolded protein response induces necrotic cell death. Cell Death and Differentiation, 25(10), 1796-1807. https://doi.org/10.1038/s41418-018-0143-2

Gaj, T., & Perez Pinera, P. (2018). The continuously evolving CRISPR barcoding toolbox Jin-Soo Kim. Genome biology, 19(1), [143]. https://doi.org/10.1186/s13059-018-1541-y

Tasker, S. Z., Cowfer, A. E., & Hergenrother, P. (2018). Preparation of Structurally Diverse Compounds from the Natural Product Lycorine. Organic Letters, 20(18), 5894-5898. https://doi.org/10.1021/acs.orglett.8b02562

Jin, H., Finnegan, A. I., & Song, J. S. (2018). A unified computational framework for modeling genome-wide nucleosome landscape. Physical Biology, 15(6), [066011]. https://doi.org/10.1088/1478-3975/aadad2

Mancini, A., Xavier-Magalhães, A., Woods, W. S., Nguyen, K. T., Amen, A. M., Hayes, J. L., ... Costello, J. F. (2018). Disruption of the β1L Isoform of GABP Reverses Glioblastoma Replicative Immortality in a TERT Promoter Mutation-Dependent Manner. Cancer Cell, 34(3), 513-528.e8. https://doi.org/10.1016/j.ccell.2018.08.003

Gurumurthy, C. B., & Perez-Pinera, P. (2018). Technological advances in integrating multi-kilobase DNA sequences into genomes. Current Opinion in Biomedical Engineering, 7, 16-23. https://doi.org/10.1016/j.cobme.2018.08.004

Anorma, C., Hedhli, J., Bearrood, T. E., Pino, N. W., Gardner, S. H., Inaba, H., ... Chan, J. K. F. (2018). Surveillance of Cancer Stem Cell Plasticity Using an Isoform-Selective Fluorescent Probe for Aldehyde Dehydrogenase 1A1. ACS Central Science, 4(8), 1045-1055. https://doi.org/10.1021/acscentsci.8b00313

Peh, J., Boudreau, M. W., Smith, H. M., & Hergenrother, P. (2018). Overcoming Resistance to Targeted Anticancer Therapies through Small-Molecule-Mediated MEK Degradation. Cell chemical biology, 25(8), 996-1005.e4. https://doi.org/10.1016/j.chembiol.2018.05.008

Gapinske, M., Luu, A., Winter, J., Woods, W. S., Kostan, K. A., Shiva, N., ... Perez Pinera, P. (2018). CRISPR-SKIP: Programmable gene splicing with single base editors. Genome biology, 19(1), [107]. https://doi.org/10.1186/s13059-018-1482-5

Zhao, C., & Song, J. S. (2018). Quantum transport senses community structure in networks. Physical Review E, 98(2), [022301]. https://doi.org/10.1103/PhysRevE.98.022301

Roy, J., Watson, J. E., Hong, I. S., Fan, T. M., & Das, A. (2018). Antitumorigenic Properties of Omega-3 Endocannabinoid Epoxides. Journal of Medicinal Chemistry, 61(13), 5569-5579. https://doi.org/10.1021/acs.jmedchem.8b00243

Drown, B. S., & Hergenrother, P. (2018). Going on offense against the gram-negative defense. Proceedings of the National Academy of Sciences of the United States of America, 115(26), 6530-6532. https://doi.org/10.1073/pnas.1807278115

Phillips, H., Maxwell, E. A., Schaeffer, D. J., & Fan, T. M. (2018). Simulation of spatial diffusion of platinum from carboplatin-impregnated calcium sulfate hemihydrate beads by use of an agarose gelatin tissue phantom. American journal of veterinary research, 79(6), 592-599. https://doi.org/10.2460/ajvr.79.6.592

Yin, Q., Tang, L., Cai, K., Yang, X., Yin, L., Zhang, Y., ... Cheng, J. (2018). Albumin as a "trojan Horse" for polymeric nanoconjugate transendothelial transport across tumor vasculatures for improved cancer targeting. Biomaterials Science, 6(5), 1189-1200. https://doi.org/10.1039/c8bm00149a

Zhang, Y., Manjunath, M., Zhang, S., Chasman, D., Roy, S., & Song, J. S. (2018). Integrative genomic analysis predicts causative cis-regulatory mechanisms of the breast cancer–associated genetic variant rs4415084. Cancer Research, 78(7), 1579-1591. https://doi.org/10.1158/0008-5472.CAN-17-3486

Saba, C. F., Vickery, K. R., Clifford, C. A., Burgess, K. E., Phillips, B., Vail, D. M., ... Thamm, D. H. (2018). Rabacfosadine for relapsed canine B-cell lymphoma: Efficacy and adverse event profiles of 2 different doses. Veterinary and comparative oncology, 16(1), E76-E82. https://doi.org/10.1111/vco.12337

Aebersold, R., Agar, J. N., Amster, I. J., Baker, M. S., Bertozzi, C. R., Boja, E. S., ... Zhang, B. (2018). How many human proteoforms are there? Nature chemical biology, 14(3), 206-214. https://doi.org/10.1038/nchembio.2576

Denisov, I. G., Baylon, J. L., Grinkova, Y. V., Tajkhorshid, E., & Sligar, S. G. (2018). Drug-Drug Interactions between Atorvastatin and Dronedarone Mediated by Monomeric CYP3A4. Biochemistry, 57(5), 805-816. https://doi.org/10.1021/acs.biochem.7b01012

Harris, D. T., Hager, M. V., Smith, S. N., Cai, Q., Stone, J. D., Kruger, P., ... Kranz, D. M. (2018). Comparison of t cell activities mediated by human TCRs and CARs that use the same recognition domains. Journal of Immunology, 200(3), 1088-1100. https://doi.org/10.4049/jimmunol.1700236

Maxwell, E. A., Phillips, H., Schaeffer, D. J., & Fan, T. M. (2018). In vitro chemosensitivity of feline injection site-associated sarcoma cell lines to carboplatin. Veterinary Surgery, 47(2), 219-226. https://doi.org/10.1111/vsu.12709

Manjunath, M., Zhang, Y., Kim, Y., Yeo, S. H., Sobh, O., Russell, N., ... Song, J. S. (2018). ClusterEnG: An interactive educational web resource for clustering and visualizing high-dimensional data. PeerJ Computer Science, 2018(5), [e155]. https://doi.org/10.7717/peerj-cs.155

Hejna, M., Jorapur, A., Zhang, Y., Song, J., & Judson, R. L. (2018). Quantification of mammalian tumor cell state plasticity with digital holographic cytometry. In Quantitative Phase Imaging IV (Vol. 10503). [1050312] SPIE. https://doi.org/10.1117/12.2290462

Sharma, P., & Kranz, D. M. (2018). Subtle changes at the variable domain interface of the T-cell receptor can strongly increase affinity. Journal of Biological Chemistry, 293(5), 1820-1834. https://doi.org/10.1074/jbc.M117.814152

Gapinske, M., Tague, N., Winter, J., Underhill, G. H., & Perez Pinera, P. (2018). Targeted gene knock out using nuclease-assisted vector integration: Hemi- and Homozygous deletion of JAG1. In Methods in Molecular Biology (pp. 233-248). (Methods in Molecular Biology; Vol. 1772). Humana Press Inc.. https://doi.org/10.1007/978-1-4939-7795-6_13

Zheng, X., Andruska, N., Lambrecht, M. J., He, S., Parissenti, A., Hergenrother, P. J., ... Shapiro, D. J. (2018). Targeting multidrug-resistant ovarian cancer through estrogen receptor a dependent ATP depletion caused by hyperactivation of the unfolded protein response. Oncotarget, 9(19), 14741-14753. https://doi.org/10.18632/oncotarget.10819