molecules Communication Proteomic Analysis of Zeb1 Interactome in Breast Carcinoma Cells Sergey E. Parfenyev 1 , Sergey V. Shabelnikov 1 , Danila Y. Pozdnyakov 1 , Olga O. Gnedina 1 , Leonid S. Adonin 2 , Nickolai A. Barlev 1,2 and Alexey G. Mittenberg 1, *   Citation: Parfenyev, S.E.; Shabelnikov, S.V.; Pozdnyakov, D.Y.; Gnedina, O.O.; Adonin, L.S.; Barlev, N.A.; Mittenberg, A.G. Proteomic Analysis of Zeb1 Interactome in Breast Carcinoma Cells. Molecules 2021, 26, 3143. https://doi.org/ 10.3390/molecules26113143 Academic Editors: Kamelija Zarkovic and Neven Zarkovic Received: 8 December 2020 Accepted: 21 May 2021 Published: 24 May 2021 Publisher’s Note: MDPI stays neutral with regard to jurisdictional claims in published maps and institutional affil- iations. Copyright: © 2021 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https:// creativecommons.org/licenses/by/ 4.0/). 1 Institute of Cytology of the Russian Academy of Sciences, 194064 St. Petersburg, Russia; gen21eration@gmail.com(S.E.P.); buddasvami@gmail.com(S.V.S.); 9apdu179@gmail.com (D.Y.P.); olga.o.gnedina@gmail.com (O.O.G.); nick.a.barlev@gmail.com (N.A.B.) 2 Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia; leo.adonin@gmail.com * Correspondence: mittenberg@incras.ru or a.mittenberg@gmail.com Abstract: Breast cancer is the most frequently diagnosed malignant neoplasm and the second leading cause of cancer death among women. Epithelial-to-mesenchymal Transition (EMT) plays a critical role in the organism development, providing cell migration and tissue formation. However, its erroneous activation in malignancies can serve as the basis for the dissemination of cancer cells and metastasis. The Zeb1 transcription factor, which regulates the EMT activation, has been shown to play an essential role in malignant transformation. This factor is involved in many signaling pathways that influence a wide range of cellular functions via interacting with many proteins that affect its transcriptional functions. Importantly, the interactome of Zeb1 depends on the cellular context. Here, using the inducible expression of Zeb1 in epithelial breast cancer cells, we identified a substantial list of novel potential Zeb1 interaction partners, including proteins involved in the formation of malignant neoplasms, such as ATP-dependent RNA helicase DDX17and a component of the NURD repressor complex, CTBP2. We confirmed the presence of the selected interactors by immunoblotting with specific antibodies. Further, we demonstrated that co-expression of Zeb1 and CTBP2 in breast cancer patients correlated with the poor survival prognosis, thus signifying the functionality of the Zeb1–CTBP2 interaction. Keywords: breast cancer; Zeb1; metastasis; epithelial to mesenchymal transition (EMT) 1. Introduction Breast cancer (BC) is the most commonly diagnosed malignant tumor in humans. More than 50,000 new cases of breast cancer are recorded annually in Russia, and in the whole world, the number exceeds 1 million [1–3]. Breast carcinomas are also considered the second leading cause of cancer death in women [4]. Among patients, more than 90% of deaths associated with breast cancer are caused not by the primary tumor, but by metastases. In 6–10% of breast cancer diagnoses, the tumor has already metastasized to other sites, and in 30% of patients with early stages of breast cancer, metastatic or recurrent disease is observed. Understanding the mechanisms of metastasis of this tumor is important for the early diagnosis and treatment of breast cancer. The exact mechanisms involved in the transition of non-invasive tumor cells to those with metastatic potential are still not fully understood. However, recent literature data indicate that one of the main mechanisms of breast cancer metastasis is the epithelial–mesenchymal transition [5]. The epithelial–mesenchymal transition (EMT) is a reversible genetic program im- plemented during embryonic development and pathologically activated in cancer [6,7]. This process is accompanied by a loss of intercellular contacts and polarity of epithelial cells, a global reorganization of the cytoskeleton, leading to a loss of epithelial properties and an increase in mesenchymal morphology, as well as increased cell motility and resis- tance to therapy [8,9]. The EMT phenomenon has been examined in the context of distant metastases in different types of carcinomas, including breast tumors. The EMT program is Molecules 2021, 26, 3143. https://doi.org/10.3390/molecules26113143 https://www.mdpi.com/journal/molecules