DATASET BRIEF A large set of estrogen receptor b-interacting proteins identified by tandem affinity purification in hormone- responsive human breast cancer cell nuclei Giovanni Nassa 1 , Roberta Tarallo 1 , Concetta Ambrosino 2 , Angela Bamundo 1 , Lorenzo Ferraro 1 , Ornella Paris 1 , Maria Ravo 1 , Pietro H. Guzzi 3 , Mario Cannataro 3 , Marc Baumann 4,5 , Tuula A. Nyman 6 , Ernesto Nola 1 and Alessandro Weisz 1,7 1 Department of General Pathology, Second University of Naples, Napoli, Italy 2 Department of Biological and Environmental Sciences, University of Sannio, Benevento, Italy 3 Department of Experimental and Clinical Medicine, University ‘Magna Graecia’, Catanzaro, Italy 4 Institute of Biomedicine (Physiology), Biomedicum Helsinki, University of Helsinki, Helsinki, Finland 5 Protein Chemistry Unit, Biomedicum Helsinki, University of Helsinki, Helsinki, Finland 6 Protein Chemistry Research Group, Institute of Biotechnology, University of Helsinki, Helsinki, Finland 7 Molecular Medicine Laboratory, Faculty of Medicine and Surgery, University of Salerno, Baronissi, Italy Received: June 1, 2010 Revised: August 4, 2010 Accepted: September 27, 2010 Estrogen receptors a (ER-a) and b (ER-b) play distinct biological roles in onset and progression of hormone-responsive breast cancer, with ER-b exerting a modulatory activity on ER-a-mediated estrogen signaling and stimulation of cell proliferation by mechanisms still not fully understood. We stably expressed human ER-b fused to a tandem affinity purification-tag in estrogen-responsive MCF-7 cells and applied tandem affinity purification and nanoLC-MS/MS to identify the ER-b interactome of this cell type. Functional annotation by bioinformatics analyses of the 303 proteins that co-purify with ER-b from nuclear extracts identify several new molecular partners of this receptor subtype that repre- sents nodal points of a large protein network controlling multiple processes and functions in breast cancer cells. Keywords: Breast cancer / Cell biology / Estrogen receptor / Nuclear signaling / Tandem affinity purification Estrogens exert their biological actions in the mammary gland by promoting cell growth and differentiation. Estro- gen-responsive cells are endowed with estrogen receptors (ER-a and ER-b) of the steroid/nuclear receptors super- family of trans-acting factors [1]. According to the genomic model of action, ER ligands induce a change in the receptor conformation resulting in nuclear translocation, protein dimerization and binding to chromatin at regulatory sites. This leads to enhancement or repression of target gene transcription [2–4] that represents, in breast cancer (BC) cells, the causal relationships between estrogen actions and the hormone-responsive tumor phenotype. On the other hand, estrogens are able to trigger also rapid and transient cellular responses through mechanism(s) independent from this genomic pathway, via ER crosstalk with different signal transduction pathways [5]. The genomic and extra- genomic pathways do integrate with each other to mediate the mitogenic actions of estrogens, and both molecular cascades involve multiprotein complexes that physically and functionally interact with ERs [6]. ER-a and ER-b are often co-expressed in the same cell, where they exert their Abbreviations: BC, breast cancer; CBP, Calmodulin-binding peptide; E2, 17-b-estradiol; ER, estrogen receptor; MW, mole- cular weight; TAP, tandem affinity purification Correspondence: Dr. Alessandro Weisz, Dipartimento di Patolo- gia generale, Seconda Universita ` degli Studi di Napoli, vico L. De Crecchio 7, 80138 Napoli, Italy E-mail: alessandro.weisz@unina2.it Fax: 139-081-441655 & 2010 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim www.proteomics-journal.com Proteomics 2011, 11, 159–165 159 DOI 10.1002/pmic.201000344