Antibody-Based Proteomics Publications

Zhongcheng Shi, Michael Hoang Nguyen, Yuan Yao, Shixia Huang. High-Throughput Post-Translational Modification Analyses by Reverse Phase Protein Array. Protein Arrays: methods and applications. 2024 (In press)

Murthy D, Dutta D, Attri KS, Samanta T, Yang S, Jung KH, Latario SG, Putluri V, Huang S, Putluri N, Park JH, Kaipparettu BA. CD24 negativity reprograms mitochondrial metabolism to PPARα and NF-κB-driven fatty acid β-oxidation in triple-negative breast cancer. Cancer Lett. 2024 Apr 10;587:216724. doi: 10.1016/j.canlet.2024.216724. Epub 2024 Feb 17. PMID: 38373689; PMCID: PMC11068061.

Amara CS, Kami Reddy KR, Yuntao Y, Chan YS, Piyarathna DWB, Dobrolecki LE, Shih DJH, Shi Z, Xu J, Huang S, Ellis MJ, Apolo AB, Ballester LY, Gao J, Hansel DE, Lotan Y, Hodges HC, Lerner SP, Creighton CJ, Sreekumar A, Zheng WJ, Msaouel P, Kavuri SM, Putluri N. The IL6/JAK/STAT3 signaling axis is a therapeutic vulnerability in SMARCB1-deficient bladder cancer. Nat Commun. 2024 Feb 14;15(1):1373. doi: 10.1038/s41467-024-45132-2. PMID: 38355560; PMCID: PMC10867091

Oturkar CC, Rosario SR, Hutson AD, Groman A, Edge SB, Morrison CD, Swetzig WM, Wang J, Park JH, Kaipparettu BA, Singh PK, Kumar S, Cappuccino HH, Ranjan M, Adjei A, Ghasemi M, Goey AKL, Kulkarni S, Das GM. ESR1 and p53 interactome alteration defines mechanisms of tamoxifen response in luminal breast cancer. iScience. 2024 May 15;27(6):109995. doi: 10.1016/j.isci.2024.109995. PMID: 38868185; PMCID: PMC11166704.

Xia F, Shi S, Palacios E, Liu W, Buscho SE, Li J, Huang S, Vizzeri G, Dong XC, Motamedi M, Zhang W, Liu H. Sirt6 protects retinal ganglion cells and optic nerve from degeneration during aging and glaucoma. Mol Ther. 2024 Jun 5;32(6):1760-1778. doi: 10.1016/j.ymthe.2024.04.030. Epub 2024 Apr 24. PMID: 38659223; PMCID: PMC11184404.

Xuan Wang, Zhongcheng Shi, Nicolas L. Young, Dean P. Edwards, Shixia Huang. Profiling histone post-translational modifications and chromatin modifying proteins by high-throughput reverse phase protein array. In: Trygve O. Tollefsbol, Editor. Epigenetics in Human Disease Epigenetics in Human Disease Third Edition, In Press (2024). Elsevier Academic Press, Cambridge, MA, USA & Oxford, United Kingdom. Book chapter

Zhang L, Hsu JI, Braekeleer ED, Chen CW, Patel TD, Urya H, Guzman AG, Martell AG, Waldvogel SM, Tovy A, Callen E, Murdaugh R, Richard R, Jansen S, Vissers L, de Vries BBA, Nussenzweig A, Huang S, Coarfa C, Anastas JN, Takahashi K, Vassiliou G, Goodell MA. SOD1 is a synthetic lethal target in PPM1D-mutant leukemia cells. bioRxiv [Preprint]. 2023 Sep 1:2023.08.31.555634. doi: 10.1101/2023.08.31.555634. PMID: 37693622; PMCID: PMC10491179.

Yu X, He T, Tong Z, Liao L, Huang S, Fakhouri WD, Edwards DP, Xu J. Molecular mechanisms of TWIST1-regulated transcription in EMT and cancer metastasis. EMBO Rep. 2023 Nov 6;24(11):e56902. doi: 10.15252/embr.202356902. Epub 2023 Sep 8. PMID: 37680145; PMCID: PMC10626429.

Bu W, Creighton CJ, Heavener KS, Gutierrez C, Dou Y, Ku AT, Zhang Y, Jiang W, Urrutia J, Jiang W, Yue F, Jia L, Ibrahim AA, Zhang B, Huang S, Li Y. Efficient cancer modeling through CRISPR-Cas9/HDR-based somatic precision gene editing in mice. Sci Adv. 2023 May 12;9(19):eade0059. doi: 10.1126/sciadv.ade0059. Epub 2023 May 12. PMID: 37172086; PMCID: PMC10181191.

Chen X, Li H, Liu Y, Qi J, Dong B, Huang S, Zhao S, Zhu Y. Dimethyl Sulfoxide Inhibits Bile Acid Synthesis in Healthy Mice but Does Not Protect Mice from Bile-Acid-Induced Liver Damage. Biology (Basel). 2023 Aug 9;12(8):1105. doi: 10.3390/biology12081105. PMID: 37626991; PMCID: PMC10452260.

Yu X, He T, Tong Z, Liao L, Huang S, Fakhouri WD, Edwards DP, Xu J. Molecular mechanisms of TWIST1-regulated transcription in EMT and cancer metastasis. EMBO Rep. 2023 Nov 6;24(11):e56902. doi: 10.15252/embr.202356902. Epub 2023 Sep 8. PMID: 37680145.

Cook AA, Jayabal S, Sheng J, Fields E, Leung TCS, Quilez S, McNicholas E, Lau L, Huang S, Watt AJ. Activation of TrkB-Akt signaling rescues deficits in a mouse model of SCA6. Sci Adv. 2022 Sep 16;8(37):eabh3260. doi: 10.1126/sciadv.abh3260. Epub 2022 Sep 16. PMID: 36112675; PMCID: PMC9481119.

Lin M, Ku AT, Dong J, Yue F, Jiang W, Ibrahim AA, Peng F, Creighton CJ, Nagi C, Gutierrez C, Rosen JM, Zhang XH, Hilsenbeck SG, Chen X, Du YN, Huang S, Shi A, Fan Z, Li Y. STAT5 confers lactogenic properties in breast tumorigenesis and restricts metastatic potential. Oncogene. 2022 Nov;41(48):5214-5222. doi: 10.1038/s41388-022-02500-w. Epub 2022 Oct 19. PMID: 36261627; PMCID: PMC9701164.

Song IW, Nagamani SC, Nguyen D, Grafe I, Sutton VR, Gannon FH, Munivez E, Jiang MM, Tran A, Wallace M, Esposito P, Musaad S, Strudthoff E, McGuire S, Thornton M, Shenava V, Rosenfeld S, Huang S, Shypailo R, Orwoll E, Lee B. Targeting TGF-β for treatment of osteogenesis imperfecta. J Clin Invest. 2022 Apr 1;132(7):e152571. doi: 10.1172/JCI152571. PMID: 35113812; PMCID: PMC8970679.

Tsang SV, Rainusso N, Liu M, Nomura M, Patel TD, Nakahata K, Kim HR, Huang S, Rajapakshe K, Coarfa C, Man TK, Rao PH, Yustein JT. LncRNA PVT-1 promotes osteosarcoma cancer stem-like properties through direct interaction with TRIM28 and TSC2 ubiquitination. Oncogene. 2022 Dec;41(50):5373-5384. doi: 10.1038/s41388-022-02538-w. Epub 2022 Nov 8. PMID: 36348010.

Wang X, Shi Z, Lu HY, Kim JJ, Bu W, Villalobos JA, Perera DN, Jung SY, Wang T, Grimm SL, Taylor BC, Rajapakshe K, Park H, Wulfkuhle J, Young NL, Li Y, Coarfa C, Edwards DP, Huang S. High-throughput profiling of histone post-translational modifications and chromatin modifying proteins by reverse phase protein array. J Proteomics. 2022 Jun 30;262:104596. doi: 10.1016/j.jprot.2022.104596. Epub 2022 Apr 27. PMID: 35489683; PMCID: PMC10165948.

Bado IL, Zhang W, Hu J, Xu Z, Wang H, Sarkar P, Li L, Wan YW, Liu J, Wu W, Lo HC, Kim IS, Singh S, Janghorban M, Muscarella AM, Goldstein A, Singh P, Jeong HH, Liu C, Schiff R, Huang S, Ellis MJ, Gaber MW, Gugala Z, Liu Z, Zhang XH. The bone microenvironment increases phenotypic plasticity of ER+ breast cancer cells. Dev Cell. 2021 Apr 19;56(8):1100-1117.e9. doi: 10.1016/j.devcel.2021.03.008. PMID: 33878299; PMCID: PMC8062036.

Coarfa C, Grimm SL, Rajapakshe K, Perera D, Lu HY, Wang X, Christensen KR, Mo Q, Edwards DP, Huang S. Reverse-Phase Protein Array: Technology, Application, Data Processing, and Integration. J Biomol Tech. 2021 Apr;32(1):15-29. doi: 10.7171/jbt.21-3202-001. PMID: 34025221; PMCID: PMC7861052.

Hebert KA, Jaramillo S, Yu W, Wang M, Veeramachaneni R, Sandulache VC, Sikora AG, Bonnen MD, Annapragada AV, Corry D, Kheradmand F, Pandita RK, Ludwig MS, Pandita TK, Huang S, Coarfa C, Grimm SL, Perera D, Miles G, Ghebre YT. Esomeprazole enhances the effect of ionizing radiation to improve tumor control. Oncotarget. 2021 Jul 6;12(14):1339-1353. doi: 10.18632/oncotarget.28008. PMID: 34262645; PMCID: PMC8274720.

Kaochar S, Rusin A, Foley C, Rajapakshe K, Robertson M, Skapura D, Mason C, Berman De Ruiz K, Tyryshkin AM, Deng J, Shin JN, Fiskus W, Dong J, Huang S, Navone NM, Davis CM, Ehli EA, Coarfa C, Mitsiades N. Inhibition of GATA2 in prostate cancer by a clinically available small molecule. Endocr Relat Cancer. 2021 Nov 24;29(1):15-31. doi: 10.1530/ERC-21-0085. PMID: 34636746

Hsin-Yi Lu, Jian Xiong, Dimuthu Nuwan Perera, Kimal Rajapakshe, Xuan Wang, Fuli Jia, Myra Costello, Kimberly Holloway, Danli Wu, Carlos Ramos, Cristian Coarfa, Dean P. Edwards, Michael X. Zhu, Shixia Huang. High Throughput Evaluation of Metabolic Activities Using Reverse Phase Protein Array (RPPA). In: Tong, Q., ed. Neuronal Signaling in Neuron Signaling in Metabolic Regulation, 1st Ed. 2021, p. 293, CRC Press, Boca Raton and London.

Napierala JS, Rajapakshe K, Clark A, Chen YY, Huang S, Mesaros C, Xu P, Blair IA, Hauser LA, Farmer J, Lynch DR, Edwards DP, Coarfa C, Napierala M. Reverse Phase Protein Array Reveals Correlation of Retinoic Acid Metabolism With Cardiomyopathy in Friedreich's Ataxia. Mol Cell Proteomics. 2021;20:100094. doi: 10.1016/j.mcpro.2021.100094. Epub 2021 May 13. PMID: 33991687; PMCID: PMC8214145.

Yue F, Jiang W, Ku AT, Young AIJ, Zhang W, Souto EP, Gao Y, Yu Z, Wang Y, Creighton CJ, Nagi C, Wang T, Hilsenbeck SG, Feng XH, Huang S, Coarfa C, Zhang XH, Liu Q, Lin X, Li Y. A Wnt-Independent LGR4-EGFR Signaling Axis in Cancer Metastasis. Cancer Res. 2021 Sep 1;81(17):4441-4454. doi: 10.1158/0008-5472.CAN-21-1112. Epub 2021 Jun 7. PMID: 34099494; PMCID: PMC8416783.

Corn PG, Zhang M, Nogueras-Gonzalez GM, Xiao L, Zurita AJ, Subudhi SK, Tu SM, Aparicio AM, Coarfa C, Rajapakshe K, Huang S, Navone NM, Lin SH, Wang G,Ramachandran S, Titus MA, Panaretakis T, Gallick GE, Efstathiou E, Troncoso P,Logothetis C. A Phase II Study of Cabozantinib and Androgen Ablation in Patients with Hormone-Naïve Metastatic Prostate Cancer. Clin Cancer Res. 2020 Mar 1;26(5):990-999. doi: 10.1158/1078-0432.CCR-19-2389. Epub 2020 Jan 15. PubMed PMID: 31941830.

Elsarraj HS, Hong Y, Limback D, Zhao R, Berger J, Bishop SC, Sabbagh A, Oppenheimer L, Harper HE, Tsimelzon A, Huang S, Hilsenbeck SG, Edwards DP, Fontes J, Fan F, Madan R, Fangman B, Ellis A, Tawfik O, Persons DL, Fields T, Godwin AK, Hagan CR, Swenson-Fields K, Coarfa C, Thompson J, Behbod F. BCL9/STAT3 regulation of transcriptional enhancer networks promote DCIS progression. NPJ Breast Cancer. 2020 Apr 24;6:12. doi: 10.1038/s41523-020-0157-z. PMID: 32352029; PMCID: PMC7181646.

Guo, Z.; Primeau, T.; Luo, J.; Zhang, C.; Sun, H.; Hoog, J.; Gao, F.; Huang, S.; Edwards, D.P.; Davies, S.R.; Aft, R.; Ding, L.; Ellis, M.J.; Li, S.; Ma, C.X. Proteomic Resistance Biomarkers for PI3K Inhibitor in Triple Negative Breast Cancer Patient-Derived Xenograft Models. Cancers 2020, 12, 3857. Guo, Z.; Primeau, T.; Luo, J.; Zhang, C.; Sun, H.; Hoog, J.; Gao, F.; Huang, S.; Edwards, D.P.; Davies, S.R.; Aft, R.; Ding, L.; Ellis, M.J.; Li, S.; Ma, C.X. Proteomic Resistance Biomarkers for PI3K Inhibitor in Triple Negative Breast Cancer Patient-Derived Xenograft Models. Cancers 2020, 12, 3857.

Sharma M, Khong H, Fa'ak F, Bentebibel SE, Janssen LME, Chesson BC, Creasy CA, Forget MA, Kahn LMS, Pazdrak B, Karki B, Hailemichael Y, Singh M, Vianden C, Vennam S, Bharadwaj U, Tweardy DJ, Haymaker C, Bernatchez C, Huang S, Rajapakshe K, Coarfa C, Hurwitz ME, Sznol M, Hwu P, Hoch U, Addepalli M, Charych DH, Zalevsky J, Diab A, Overwijk WW. Bempegaldesleukin selectively depletes intratumoral Tregs and potentiates T cell-mediated cancer therapy. Nat Commun. 2020 Jan 31;11(1):661. doi: 10.1038/s41467-020-14471-1. PMID: 32005826; PMCID: PMC6994577.

Shneider BL, Cortes-Santiago N, Schady DA, Krishnamoorthy S, Thevananther S, Rajapakshe K, Perera D, Huang S, Coarfa C. Constitutive activation of mitogen-activated protein kinase kinase (MEK1) in ileal enterocytes leads to dysplasia and a predisposition to cancer. Am J Physiol Gastrointest Liver Physiol. 2021 Mar 1;320(3):G366-G379. doi: 10.1152/ajpgi.00065.2020. Epub 2021 Jan 20. PMID: 33470189.

Subramonian D, Phanhthilath N, Rinehardt H, Flynn S, Huo Y, Zhang J, Messer K, Mo Q, Huang S, Lesperance J, Zage PE. Regorafenib is effective against neuroblastoma in vitro and in vivo and inhibits the RAS/MAPK, PI3K/Akt/mTOR and Fos/Jun pathways. Br J Cancer. 2020 Aug;123(4):568-579. doi: 10.1038/s41416-020-0905-8. Epub 2020 May 27. PMID: 32457362; PMCID: PMC7434894.

Xue L, Chen F, Yue F, Camacho L, Kothapalli S, Wei G, Huang S, Mo Q, Ma F, Li Y, Jiralerspong S. Metformin and an insulin/IGF-1 receptor inhibitor are synergistic in blocking growth of triple-negative breast cancer. Breast Cancer Res Treat. 2021 Jan;185(1):73-84. doi: 10.1007/s10549-020-05927-5. Epub 2020 Sep 17. PMID: 32940848; PMCID: PMC7855212.

Zhang T, Choi S, Zhang T, Chen Z, Chi Y, Huang S, Xiang JZ, Du YN. miR-431 Promotes Metastasis of Pancreatic Neuroendocrine Tumors by Targeting DAB2 Interacting Protein, a Ras GTPase Activating Protein Tumor Suppressor. Am J Pathol. 2020 Mar;190(3):689-701. doi: 10.1016/j.ajpath.2019.11.007. Epub 2020 Jan 14. PubMed PMID: 31953039; PubMed Central PMCID: PMC7074368. 

Bu W, Liu Z, Jiang W, Nagi C, Huang S, Edwards DP, Jo E, Mo Q, Creighton CJ, Hilsenbeck SG, Leavitt AD, Lewis MT, Wong STC, Li Y. Mammary Precancerous Stem and Non-Stem Cells Evolve into Cancers of Distinct Subtypes. Cancer Res. 2019 Jan 1;79(1):61-71. doi: 10.1158/0008-5472.CAN-18-1087. Epub 2018 Nov 6. PMID: 30401712; PMCID: PMC6318055.

Finnerty BM, Moore MD, Verma A, Aronova A, Huang S, Edwards DP, Chen Z, Seandel M, Scognamiglio T, Du YN, Elemento O, Zarnegar R, Min IM, Fahey TJ. UCHL1 loss alters the cell-cycle in metastatic pancreatic neuroendocrine tumors. Endocr Relat Cancer. 2019 Apr 1;26(4):411-423. doi: 10.1530/ERC-18-0507. Epub 2019 Jan 1. PMID: 30689542.

Fu X, Pereira R, De Angelis C, Veeraraghavan J, Nanda S, Qin L, Cataldo ML, Sethunath V, Mehravaran S, Gutierrez C, Chamness GC, Feng Q, O'Malley BW, Selenica P, Weigelt B, Reis-Filho JS, Cohen O, Wagle N, Nardone A, Jeselsohn R, Brown M, Rimawi MF, Osborne CK, Schiff R. FOXA1 upregulation promotes enhancer and transcriptional reprogramming in endocrine-resistant breast cancer. Proc Natl Acad Sci U S A. 2019 Dec 26;116(52):26823-26834. doi: 10.1073/pnas.1911584116. Epub 2019 Dec 11. PMID: 31826955; PMCID: PMC6936436.

Lee YJ, Ho SR, Graves JD, Xiao Y, Huang S, Lin WC. CGRRF1, a growth suppressor, regulates EGFR ubiquitination in breast cancer. Breast Cancer Res. 2019 Dec 4;21(1):134. PubMed PMID: 31801577.

Sethunath V, Hu H, De Angelis C, Veeraraghavan J, Qin L, Wang N, Simon LM,Wang T, Fu X, Nardone A, Pereira R, Nanda S, Griffith OL, Tsimelzon A, Shaw C, Chamness GC, Reis-Filho JS, Weigelt B, Heiser LM, Hilsenbeck SG, Huang S, Rimawi MF, Gray JW, Osborne CK, Schiff R. Targeting the Mevalonate Pathway to Overcome Acquired Anti-HER2 Treatment Resistance in Breast Cancer. Mol Cancer Res. 2019 Nov;17(11):2318-2330. doi: 10.1158/1541-7786.MCR-19-0756. Epub 2019 Aug 16. PubMed PMID: 31420371; PubMed Central PMCID: PMC6825570.

Yao M, Fang W, Smart C, Hu Q, Huang S, Alvarez N, Fields P, Cheng N. CCR2 Chemokine Receptors Enhance Growth and Cell-Cycle Progression of Breast Cancer Cells Through SRC and PKC Activation. Mol Cancer Res. 2019 Feb;17(2):604-617. PMID: 30446625; PubMed Central PMCID: PMC6359961.