Publications

Publications:

Uttam S, Stern AM, Sevinsky C, Furman S, Pullara F, Spagnolo D, Nguyen L, Gough A, Ginty F, Taylor DL., Chennubhotla CS Spatial domain analysis predicts risk of colorectal cancer recurrence and infers associated tumor microenvironment networks. Nature Communications. 2020; doi: 10.1038/s41467-020-17083-x. In Press

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Jane EP, Premkumar DR, Thambireddy S, Golbourn B, Agnihotri S, Bertrand KC, Mack SC, Myers MI, Chattopadhyay A, Taylor DL, Schurdak ME, Stern AM, Pollack IF. Targeting NAD+ Biosynthesis Overcomes Panobinostat and Bortezomib-Induced Malignant Glioma Resistance. Mol Cancer Res. 2020 Apr 1;. doi: 10.1158/1541-7786.MCR-19-0669. [Epub ahead of print] PubMed PMID: 32238439.

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Albert Gough, Alejandro Soto-Gutierrez, Lawrence Vernetti, Mo R. Ebrahimkhani, Andrew M. Stern, D. Lansing Taylor. Human Liver Biomimetic Microphysiology Systems in Therapeutic Discovery, Development and Precision Medicine. Nature Reviews, Accepted, 2020

Argemi J, Latasa MU, Atkinson SR, Blokhin IO, Massey V, Gue JP, Cabezas J, Lozano JJ, Van Booven D, Bell A, Cao S, Vernetti LA, Arab JP, Ventura-Cots M, Edmunds LR, Fondevilla C, Stärkel P, Dubuquoy L, Louvet A, Odena G, Gomez JL, Aragon T, Altamirano J, Caballeria J, Jurczak MJ, Taylor DL, Berasain C, Wahlestedt C, Monga SP, Morgan MY, Sancho-Bru P, Mathurin P, Furuya S, Lackner C, Rusyn I, Shah VH, Thursz MR, Mann J, Avila MA, Bataller R. Defective HNF4alpha-dependent gene expression as a driver of hepatocellular failure in alcoholic hepatitis. Nat Commun. 2019 Jul 16;10(1):3126. PubMed PMID: 31311938; PubMed Central PMCID: PMC6635373.

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Abecassis I, Sedgewick AJ, Romkes M, Buch S, Nukui T, Kapetanaki MG, Vogt A, Kirkwood JM, Benos PV, Tawbi H. PARP1 rs1805407 Increases Sensitivity to PARP1 Inhibitors in Cancer Cells Suggesting an Improved Therapeutic Strategy. Sci Rep. 2019;9(1):3309. PubMed PMID: 30824778; PMCID: PMC6397203.

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Kho DH, Uddin MH, Chatterjee M, Vogt A, Raz A, Wu GS. GP78 Cooperates with Dual-Specificity Phosphatase 1 To Stimulate Epidermal Growth Factor Receptor-Mediated Extracellular Signal-Regulated Kinase Signaling. Mol Cell Biol. 2019;39(11). PubMed PMID: 31061093; PMCID: PMC6517599.

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Nmezi B, Vollmer LL, Shun TY, Gough A, Rolyan H, Liu F, Jia Y, Padiath QS, Vogt A. Development and Optimization of a High-Content Analysis Platform to Identify Suppressors of Lamin B1 Overexpression as a Therapeutic Strategy for Autosomal Dominant Leukodystrophy. SLAS Discov. 2020:2472555220915821. PubMed PMID: 32349647.

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Mutant huntingtin disrupts mitochondrial proteostasis by interacting with TIM23. Yablonska S, Ganesan V, Ferrando LM, Kim J, Pyzel A, Baranova OV, Khattar NK, Larkin TM, Baranov SV, Chen N, Strohlein CE, Stevens DA, Wang X, Chang YF, Schurdak ME, Carlisle DL, Minden JS and Friedlander RM (2019) Proceedings of the National Academy of Sciences of the United States of America;116(33):16593-602. Epub 2019/07/28. doi: 10.1073/pnas.1904101116. PubMed PMID: 31346086.

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Harnessing Human Microphysiology Systems as Key Experimental Models for Quantitative Systems Pharmacology. Taylor DL, Gough A, Schurdak ME, Vernetti L, Chennubhotla CS, Lefever D, Pei F, Faeder JR, Lezon TR, Stern AM and Bahar I (2019) Handbook of experimental pharmacology. Epub 2019/06/16. doi: 10.1007/164_2019_239. PubMed PMID: 31201557.

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Applications of the Microphysiology Systems Database for Experimental ADME-Tox and Disease Models. Schurdak M, Vernetti L, Bergenthal L, Wolter QK, Shun TY, Karcher S, Taylor DL and Gough A (2019) bioRxiv:776500. doi: 10.1101/776500.

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A High-Throughput Assay for DNA Replication Inhibitors Based upon Multivariate Analysis of Yeast Growth Kinetics. Ngo M, Wechter N, Tsai E, Shun TY, Gough A, Schurdak ME, Schwacha A and Vogt A (2019) SLAS Discov;24(6):669-81. Epub 2019/02/26. doi: 10.1177/2472555219829740. PubMed PMID: 30802412.

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Modeling the Effect of the Metastatic Microenvironment on Phenotypes Conferred by Estrogen Receptor Mutations Using a Human Liver Microphysiological System. Miedel MT, Gavlock DC, Jia S, Gough A, Taylor DL and Stern AM (2019) Scientific reports;9(1):8341. Epub 2019/06/07. doi: 10.1038/s41598-019-44756-5. PubMed PMID: 31171849.

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Paths to Successful Translation of New Therapies for Severe Traumatic Brain Injury in the Golden Age of Traumatic Brain Injury Research: A Pittsburgh Vision. Kochanek PM, Jackson TC, Jha RM, Clark RSB, Okonkwo DO, Bayir H, Poloyac SM, Wagner AK, Empey PE, Conley YP, Bell MJ, Kline AE, Bondi CO, Simon DW, Carlson SW, Puccio AM, Horvat CM, Au AK, Elmer J, Treble-Barna A, Ikonomovic MD, Shutter LA, Taylor DL, Stern AM, Graham SH, Kagan VE, Jackson EK, Wisniewski SR and Dixon CE (2019) J Neurotrauma. Epub 2018/12/07. doi: 10.1089/neu.2018.6203. PubMed PMID: 30520681.

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GP78 Cooperates with Dual-Specificity Phosphatase 1 To Stimulate Epidermal Growth Factor Receptor-Mediated Extracellular Signal-Regulated Kinase Signaling. Kho DH, Uddin MH, Chatterjee M, Vogt A, Raz A and Wu GS (2019) Mol Cell Biol;39(11). Epub 2019/05/08. doi: 10.1128/mcb.00485-18. PubMed PMID: 31061093.

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Defective HNF4alpha-dependent gene expression as a driver of hepatocellular failure in alcoholic hepatitis. Argemi J, Latasa MU, Atkinson SR, Blokhin IO, Massey V, Gue JP, Cabezas J, Lozano JJ, Van Booven D, Bell A, Cao S, Vernetti LA, Arab JP, Ventura-Cots M, Edmunds LR, Fondevilla C, Starkel P, Dubuquoy L, Louvet A, Odena G, Gomez JL, Aragon T, Altamirano J, Caballeria J, Jurczak MJ, Taylor DL, Berasain C, Wahlestedt C, Monga SP, Morgan MY, Sancho-Bru P, Mathurin P, Furuya S, Lackner C, Rusyn I, Shah VH, Thursz MR, Mann J, Avila MA and Bataller R (2019) Nature communications;10(1):3126. Epub 2019/07/18. doi: 10.1038/s41467-019-11004-3. PubMed PMID: 31311938.

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PARP1 rs1805407 Increases Sensitivity to PARP1 Inhibitors in Cancer Cells Suggesting an Improved Therapeutic Strategy. Abecassis I, Sedgewick AJ, Romkes M, Buch S, Nukui T, Kapetanaki MG, Vogt A, Kirkwood JM, Benos PV and Tawbi H (2019) Scientific reports;9(1):3309. Epub 2019/03/03. doi: 10.1038/s41598-019-39542-2. PubMed PMID: 30824778.

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A Quantitative Systems Pharmacology Approach to Infer Pathways Involved in Complex Disease Phenotypes. Schurdak ME, Pei F, Lezon TR, Carlisle D, Friedlander R, Taylor DL and Stern AM (2018) Methods Mol Biol;1787:207-22. Epub 2018/05/08. doi: 10.1007/978-1-4939-7847-2_16. PubMed PMID: 29736721.

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A High-Content Screen Reveals New Small-Molecule Enhancers of Ras/Mapk Signaling as Probes for Zebrafish Heart Development. Saydmohammed M, Vollmer LL, Onuoha EO, Maskrey TS, Gibson G, Watkins SC, Wipf P, Vogt A and Tsang M (2018) Molecules;23(7). Epub 2018/07/13. doi: 10.3390/molecules23071691. PubMed PMID: 29997348.

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A glass-based, continuously zonated and vascularized human liver acinus microphysiological system (vLAMPS) designed for experimental modeling of diseases and ADME/TOX. Li X, George SM, Vernetti L, Gough AH and Taylor DL (2018) Lab Chip;18:2614-31. doi: 10.1039/C8LC00418H. PubMed PMID: 30063238.

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Opportunities and Challenges in Implementation of Multiparameter Single Cell Analysis Platforms for Clinical Translation. Keating SM, Taylor DL, Plant AL, Litwack ED, Kuhn P, Greenspan EJ, Hartshorn CM, Sigman CC, Kelloff GJ, Chang DD, Friberg G, Lee JSH and Kuida K (2018) Clin Transl Sci;11(3):267-76. Epub 2018/03/03. doi: 10.1111/cts.12536. PubMed PMID: 29498218.

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Clinically Observed Estrogen Receptor Alpha Mutations within the Ligand-Binding Domain Confer Distinguishable Phenotypes. Jia S, Miedel MT, Ngo M, Hessenius R, Chen N, Wang P, Bahreini A, Li Z, Ding Z, Shun TY, Zuckerman DM, Taylor DL, Puhalla SL, Lee AV, Oesterreich S and Stern AM (2018) Oncology;94(3):176-89. Epub 2018/01/08. doi: 10.1159/000485510. PubMed PMID: 29306943.

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Integrating Analysis of Cellular Heterogeneity in High-Content Dose-Response Studies. Gough A, Shun TY, Taylor DL and Schurdak M (2018) Methods Mol Biol;1745:25-46. Epub 2018/02/25. doi: 10.1007/978-1-4939-7680-5_2. PubMed PMID: 29476461.

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Profilin-1 deficiency leads to SMAD3 upregulation and impaired 3D outgrowth of breast cancer cells. Chakraborty S, Jiang C, Gau D, Oddo M, Ding Z, Vollmer L, Joy M, Schiemann W, Stolz DB, Vogt A, Ghosh S and Roy P (2018) Br J Cancer;119(9):1106-17. Epub 2018/10/16. doi: 10.1038/s41416-018-0284-6. PubMed PMID: 30318519.

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Liver ‘organ on a chip’. Beckwitt CH, Clark AM, Wheeler S, Taylor DL, Stolz DB, Griffith L and Wells A (2018) Exp Cell Res;363(1):15-25. Epub 2018/01/02. doi: 10.1016/j.yexcr.2017.12.023. PubMed PMID: 29291400.

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New insights into shear stress-induced endothelial signalling and barrier function: cell-free fluid versus blood flow. Xu S, Li X, LaPenna KB, Yokota SD, Huke S and He P (2017) Cardiovascular research;113(5):508-18. Epub 2017/02/06. doi: 10.1093/cvr/cvx021. PubMed PMID: 28158679.

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Functional Coupling of Human Microphysiology Systems: Intestine, Liver, Kidney Proximal Tubule, Blood-Brain Barrier and Skeletal Muscle. Vernetti L, Gough A, Baetz N, Blutt S, Broughman JR, Brown JA, Foulke-Abel J, Hasan N, In J, Kelly E, Kovbasnjuk O, Repper J, Senutovitch N, Stabb J, Yeung C, Zachos NC, Donowitz M, Estes M, Himmelfarb J, Truskey G, Wikswo JP and Taylor DL (2017) Scientific reports;7:42296. doi: 10.1038/srep42296. PubMed PMID: 28176881.

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Dual role of mitochondria in producing melatonin and driving GPCR signaling to block cytochrome c release. Suofu Y, Li W, Jean-Alphonse FG, Jia J, Khattar NK, Li J, Baranov SV, Leronni D, Mihalik AC, He Y, Cecon E, Wehbi VL, Kim J, Heath BE, Baranova OV, Wang X, Gable MJ, Kretz ES, Di Benedetto G, Lezon TR, Ferrando LM, Larkin TM, Sullivan M, Yablonska S, Wang J, Minnigh MB, Guillaumet G, Suzenet F, Richardson RM, Poloyac SM, Stolz DB, Jockers R, Witt-Enderby PA, Carlisle DL, Vilardaga JP and Friedlander RM (2017) Proceedings of the National Academy of Sciences of the United States of America;114(38):E7997-e8006. Epub 2017/09/07. doi: 10.1073/pnas.1705768114. PubMed PMID: 28874589.

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Platform for Quantitative Evaluation of Spatial Intratumoral Heterogeneity in Multiplexed Fluorescence Images. Spagnolo DM, Al-Kofahi Y, Zhu P, Lezon TR, Gough A, Stern AM, Lee AV, Ginty F, Sarachan B, Taylor DL and Chennubhotla SC (2017) Cancer Res;77(21):e71-e4. Epub 2017/11/03. doi: 10.1158/0008-5472.can-17-0676. PubMed PMID: 29092944.

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Evolution of Experimental Models of the Liver to Predict Human Drug Hepatotoxicity and Efficacy. Vernetti LA, Vogt A, Gough A and Taylor DL (2017) Clin Liver Dis;21(1):197-214. Epub 2016/11/16. doi: 10.1016/j.cld.2016.08.013. PubMed PMID: 27842772.

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Pre-clinical and clinical investigations of metabolic zonation in liver diseases: The potential of microphysiology systems. Soto-Gutierrez A, Gough A, Vernetti LA, Taylor DL and Monga SP (2017) Exp Biol Med (Maywood):1535370217707731. Epub 2017/05/04. doi: 10.1177/1535370217707731. PubMed PMID: 28467181.

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Exploiting Analysis of Heterogeneity to Increase the Information Content Extracted from Fluorescence Micrographs of Transgenic Zebrafish Embryos. Shun T, Gough AH, Sanker S, Hukriede NA and Vogt A (2017) Assay Drug Dev Technol;15(6):257-66. Epub 2017/08/12. doi: 10.1089/adt.2017.793. PubMed PMID: 28800244.

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Connecting Neuronal Cell Protective Pathways and Drug Combinations in a Huntington’s Disease Model through the Application of Quantitative Systems Pharmacology. Pei F, Li H, Henderson MJ, Titus SA, Jadhav A, Simeonov A, Cobanoglu MC, Mousavi SH, Shun T, McDermott L, Iyer P, Fioravanti M, Carlisle D, Friedlander RM, Bahar I, Taylor DL, Lezon TR, Stern AM and Schurdak ME (2017) Scientific reports;7(1):17803. Epub 2017/12/21. doi: 10.1038/s41598-017-17378-y. PubMed PMID: 29259176.

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ARCHITECTURAL PATTERNS FOR DIFFERENTIAL DIAGNOSIS OF PROLIFERATIVE BREAST LESIONS FROM HISTOPATHOLOGICAL IMAGES. Nguyen L, Tosun AB, Fine JL, Taylor DL and Chennubhotla SC (2017) Proc IEEE Int Symp Biomed Imaging;2017:152-5. Epub 2017/09/12. doi: 10.1109/isbi.2017.7950490. PubMed PMID: 28890755.

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Spatial Statistics for Segmenting Histological Structures in H&E Stained Tissue Images. Nguyen L, Tosun AB, Fine JL, Lee AV, Taylor DL and Chennubhotla SC (2017) IEEE Trans Med Imaging;36(7):1522-32. Epub 2017/03/23. doi: 10.1109/tmi.2017.2681519. PubMed PMID: 28328502.

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Control of oxygen tension recapitulates zone-specific functions in human liver microphysiology systems. Lee-Montiel FT, George SM, Gough AH, Sharma AD, Wu J, DeBiasio R, Vernetti LA and Taylor DL (2017) Exp Biol Med (Maywood);242(16):1617-32. Epub 2017/04/15. doi: 10.1177/1535370217703978. PubMed PMID: 28409533.

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A Tumor Cell-Selective Inhibitor of Mitogen-Activated Protein Kinase Phosphatases Sensitizes Breast Cancer Cells to Lymphokine-Activated Killer Cell Activity. Kaltenmeier CT, Vollmer LL, Vernetti LA, Caprio L, Davis K, Korotchenko VN, Day BW, Tsang M, Hulkower KI, Lotze MT and Vogt A (2017) J Pharmacol Exp Ther;361(1):39-50. Epub 2017/02/06. doi: 10.1124/jpet.116.239756. PubMed PMID: 28154014.

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Drug Discovery to Halt the Progression of Acute Kidney Injury to Chronic Kidney Disease: A Case for Phenotypic Drug Discovery in Acute Kidney Injury. Hukriede N, Vogt A and de Caestecker M (2017) Nephron;137(4):268-72. Epub 2017/06/15. doi: 10.1159/000476079. PubMed PMID: 28614822.

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Biologically Relevant Heterogeneity: Metrics and Practical Insights. Gough A, Stern AM, Maier J, Lezon T, Shun TY, Chennubhotla C, Schurdak ME, Haney SA and Taylor DL (2017) SLAS Discov;22(3):213-37. doi: 10.1177/2472555216682725. PubMed PMID: 28231035.

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Comparison of three cell-based drug screening platforms for HSV-1 infection. D’Aiuto L, Williamson K, Dimitrion P, McNulty J, Brown CE, Dokuburra CB, Nielsen AJ, Lin WJ, Piazza P, Schurdak ME, Wood J, Yolken RH, Kinchington PR, Bloom DC and Nimgaonkar VL (2017) Antiviral Res;142:136-40. Epub 2017/03/28. doi: 10.1016/j.antiviral.2017.03.016. PubMed PMID: 28342892.

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Modeling global changes induced by local perturbations to the HIV-1 capsid. Bergman S and Lezon TR (2017) Journal of molecular graphics & modelling;71:218-26. Epub 2016/12/13. doi: 10.1016/j.jmgm.2016.12.003. PubMed PMID: 27951510.

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Mutation site and context dependent effects of ESR1 mutation in genome-edited breast cancer cell models. Bahreini A, Li Z, Wang P, Levine KM, Tasdemir N, Cao L, Weir HM, Puhalla SL, Davidson NE, Stern AM, Chu D, Park BH, Lee AV and Oesterreich S (2017) Breast Cancer Res;19(1):60. Epub 2017/05/26. doi: 10.1186/s13058-017-0851-4. PubMed PMID: 28535794.

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Proteomic Screening and Lasso Regression Reveal Differential Signaling in Insulin and Insulin-like Growth Factor I (IGF1) Pathways. Erdem C, Nagle AM, Casa AJ, Litzenburger BC, Wang YF, Taylor DL, Lee AV and Lezon TR (2016) Mol Cell Proteomics;15(9):3045-57. doi: 10.1074/mcp.M115.057729. PubMed PMID: 27364358.

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High expression of orphan nuclear receptor NR4A1 in a subset of ovarian tumors with worse outcome. Delgado E, Boisen MM, Laskey R, Chen R, Song C, Sallit J, Yochum ZA, Andersen CL, Sikora MJ, Wagner J, Safe S, Elishaev E, Lee A, Edwards RP, Haluska P, Tseng G, Schurdak M and Oesterreich S (2016) Gynecologic oncology;141(2):348-56. doi: 10.1016/j.ygyno.2016.02.030. PubMed PMID: 26946093.

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A human liver microphysiology platform for investigating physiology, drug safety, and disease models. Vernetti LA, Senutovitch N, Boltz R, DeBiasio R, Shun TY, Gough A and Taylor DL (2016) Exp Biol Med (Maywood);241(1):101-14. Epub 2015/07/24. doi: 10.1177/1535370215592121. PubMed PMID: 26202373.

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A Perspective on Implementing a Quantitative Systems Pharmacology Platform for Drug Discovery and the Advancement of Personalized Medicine. Stern AM, Schurdak ME, Bahar I, Berg JM and Taylor DL (2016) J Biomol Screen;21(6):521-34. doi: 10.1177/1087057116635818.

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Pointwise mutual information quantifies intratumor heterogeneity in tissue sections labeled with multiple fluorescent biomarkers. Spagnolo D, Gyanchandani R, Al-Kofahi Y, Stern A, Lezon T, Gough A, Meyer D, Ginty F, Sarachan B, Fine J, Lee A, Taylor D and Chennubhotla S (2016) Journal of pathology informatics;7(1):47-. doi: 10.4103/2153-3539.194839.

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The Microphysiology Systems Database for Analyzing and Modeling Compound Interactions with Human and Animal Organ Models. Gough A, Vernetti L, Bergenthal L, Shun TY and Taylor DL (2016) Appl In Vitro Toxicol;2(2):103-17. Epub 2016/06/01. doi: 10.1089/aivt.2016.0011. PubMed PMID: 28781990.

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A metric and workflow for quality control in the analysis of heterogeneity in phenotypic profiles and screens. Gough A, Shun TY, Lansing Taylor D and Schurdak M (2016) Methods;96:12-26. doi: http://dx.doi.org/10.1016/j.ymeth.2015.10.007.

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Selection of a potential diagnostic biomarker for HIV infection from a random library of non-biological synthetic peptoid oligomers. Gearhart TL, Montelaro RC, Schurdak ME, Pilcher CD, Rinaldo CR, Kodadek T, Park Y, Islam K, Yurko R, Marques ET, Jr. and Burke DS (2016) J Immunol Methods;435:85-9. doi: 10.1016/j.jim.2016.05.001. PubMed PMID: 27182050.

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Fluorescent protein biosensors applied to microphysiological systems. Senutovitch N, Vernetti L, Boltz R, DeBiasio R, Gough A and Taylor DL (2015) Exp Biol Med (Maywood);240:795–808. doi: 10.1177/1535370215584934. PubMed PMID: 25990438.

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High-Content Analysis with Cellular and Tissue Systems Biology: a Bridge between Cancer Cell Biology and Tissue-Based Diagnostics. Gough A, Lezon T, Faeder JR, Chennubhotla C, Murphy RF, Critchley-Thorne R and Taylor DL. In: Mendelsohn J, Howley PM, Israel MA, Gray JW, Thompson C, editors. The molecular basis of cancer. 4th ed. Philadelphia, PA: Saunders/Elsevier; 2015. p. 369-92.

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A high-content, multiplexed screen in human breast cancer cells identifies profilin-1 inducers with anti-migratory activities. Joy ME, Vollmer LL, Hulkower K, Stern AM, Peterson CK, Boltz RC, Roy P and Vogt A (2014) PloS one;9(2):e88350. doi: 10.1371/journal.pone.0088350. PubMed PMID: 24520372.

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Identifying and Quantifying Heterogeneity in High Content Analysis: Application of Heterogeneity Indices to Drug Discovery. Gough AH, Chen N, Shun TY, Lezon TR, Boltz RC, Reese CE, Wagner J, Vernetti LA, Grandis JR, Lee AV, Stern AM, Schurdak ME and Taylor DL (2014) PloS one;9(7):e102678. doi: 10.1371/journal.pone.0102678. PubMed PMID: 25036749.

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Large-scale generation of human iPSC-derived neural stem cells/early neural progenitor cells and their neuronal differentiation. D’Aiuto L, Zhi Y, Kumar Das D, Wilcox MR, Johnson JW, McClain L, MacDonald ML, Di Maio R, Schurdak ME, Piazza P, Viggiano L, Sweet R, Kinchington PR, Bhattacharjee AG, Yolken R and Nimgaonkar VL (2014) Organogenesis;10(4):365-77. doi: 10.1080/15476278.2015.1011921. PubMed PMID: 25629202.

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