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Mares-Quiñones MD, Galán-Vásquez E, Pérez-Rueda E, Pérez-Ishiwara DG, Medel-Flores MO, Gómez-García MDC. Identification of modules and key genes associated with breast cancer subtypes through network analysis. Sci Rep 2024; 14:12350. [PMID: 38811600 PMCID: PMC11137066 DOI: 10.1038/s41598-024-61908-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 05/10/2024] [Indexed: 05/31/2024] Open
Abstract
Breast cancer is the most common malignancy in women around the world. Intratumor and intertumoral heterogeneity persist in mammary tumors. Therefore, the identification of biomarkers is essential for the treatment of this malignancy. This study analyzed 28,143 genes expressed in 49 breast cancer cell lines using a Weighted Gene Co-expression Network Analysis to determine specific target proteins for Basal A, Basal B, Luminal A, Luminal B, and HER2 ampl breast cancer subtypes. Sixty-five modules were identified, of which five were characterized as having a high correlation with breast cancer subtypes. Genes overexpressed in the tumor were found to participate in the following mechanisms: regulation of the apoptotic process, transcriptional regulation, angiogenesis, signaling, and cellular survival. In particular, we identified the following genes, considered as hubs: IFIT3, an inhibitor of viral and cellular processes; ETS1, a transcription factor involved in cell death and tumorigenesis; ENSG00000259723 lncRNA, expressed in cancers; AL033519.3, a hypothetical gene; and TMEM86A, important for regulating keratinocyte membrane properties, considered as a key in Basal A, Basal B, Luminal A, Luminal B, and HER2 ampl breast cancer subtypes, respectively. The modules and genes identified in this work can be used to identify possible biomarkers or therapeutic targets in different breast cancer subtypes.
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Affiliation(s)
- María Daniela Mares-Quiñones
- Laboratorio de Biomedicina Molecular, Programa de Doctorado en Biotecnología, Escuela Nacional de Medicina y Homeopatía, Instituto Politécnico Nacional, Ciudad de México, Mexico
| | - Edgardo Galán-Vásquez
- Departamento de Ingeniería de Sistemas Computacionales y Automatización, Instituto de Investigaciones en Matemáticas Aplicadas y en Sistemas, Universidad Nacional Autónoma de México, Ciudad Universitaria, Ciudad de México, Mexico
| | - Ernesto Pérez-Rueda
- Instituto de Investigaciones en Matemáticas Aplicadas y en Sistemas, Universidad Nacional Autónoma de México, Unidad Académica del Estado de Yucatán, Mérida, Mexico
| | - D Guillermo Pérez-Ishiwara
- Laboratorio de Biomedicina Molecular, Programa de Doctorado en Biotecnología, Escuela Nacional de Medicina y Homeopatía, Instituto Politécnico Nacional, Ciudad de México, Mexico
| | - María Olivia Medel-Flores
- Laboratorio de Biomedicina Molecular, Programa de Doctorado en Biotecnología, Escuela Nacional de Medicina y Homeopatía, Instituto Politécnico Nacional, Ciudad de México, Mexico
| | - María Del Consuelo Gómez-García
- Laboratorio de Biomedicina Molecular, Programa de Doctorado en Biotecnología, Escuela Nacional de Medicina y Homeopatía, Instituto Politécnico Nacional, Ciudad de México, Mexico.
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2
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Dagostino R, Gottlieb A. Tissue-specific atlas of trans-models for gene regulation elucidates complex regulation patterns. BMC Genomics 2024; 25:377. [PMID: 38632500 PMCID: PMC11022497 DOI: 10.1186/s12864-024-10317-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 04/16/2024] [Indexed: 04/19/2024] Open
Abstract
BACKGROUND Deciphering gene regulation is essential for understanding the underlying mechanisms of healthy and disease states. While the regulatory networks formed by transcription factors (TFs) and their target genes has been mostly studied with relation to cis effects such as in TF binding sites, we focused on trans effects of TFs on the expression of their transcribed genes and their potential mechanisms. RESULTS We provide a comprehensive tissue-specific atlas, spanning 49 tissues of TF variations affecting gene expression through computational models considering two potential mechanisms, including combinatorial regulation by the expression of the TFs, and by genetic variants within the TF. We demonstrate that similarity between tissues based on our discovered genes corresponds to other types of tissue similarity. The genes affected by complex TF regulation, and their modelled TFs, were highly enriched for pharmacogenomic functions, while the TFs themselves were also enriched in several cancer and metabolic pathways. Additionally, genes that appear in multiple clusters are enriched for regulation of immune system while tissue clusters include cluster-specific genes that are enriched for biological functions and diseases previously associated with the tissues forming the cluster. Finally, our atlas exposes multilevel regulation across multiple tissues, where TFs regulate other TFs through the two tested mechanisms. CONCLUSIONS Our tissue-specific atlas provides hierarchical tissue-specific trans genetic regulations that can be further studied for association with human phenotypes.
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Affiliation(s)
- Robert Dagostino
- McWilliams School of Biomedical Informatics, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Assaf Gottlieb
- McWilliams School of Biomedical Informatics, University of Texas Health Science Center at Houston, Houston, TX, USA.
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3
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Chen J, Li J, Sun X, Lu H, Liu K, Li Z, Guan J, Song H, Wei W, Ge Y, Fan Q, Bao W, Ma B, Du Z. Precision Therapy of Recurrent Breast Cancer through Targeting Different Malignant Tumor Cells with a HER2/CD44-Targeted Hydrogel Nanobot. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2301043. [PMID: 37154208 DOI: 10.1002/smll.202301043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 04/20/2023] [Indexed: 05/10/2023]
Abstract
Heterogeneity and drug resistance of tumor cells are the leading causes of incurability and poor survival for patients with recurrent breast cancer. In order to accurately deliver the biological anticancer drugs to different subtypes of malignant tumor cells for omnidirectional targeted treatment of recurrent breast cancer, a distinct design is demonstrated by embedding liposome-based nanocomplexes containing pro-apoptotic peptide and survivin siRNA drugs (LPR) into Herceptin/hyaluronic acid cross-linked nanohydrogels (Herceptin-HA) to fabricate a HER2/CD44-targeted hydrogel nanobot (named as ALPR). ALPR delivered cargoes to the cells overexpressing CD44 and HER2, followed by Herceptin-HA biodegradation, subsequently, the exposed lipid component containing DOPE fused with the endosomal membrane and released peptide and siRNA into the cytoplasm. These experiments indicated that ALPR can specifically deliver Herceptin, peptide, and siRNA drugs to HER2-positive SKBR-3, triple-negative MDA-MB-231, and HER2-negative drug-resistant MCF-7 human breast cancer cells. ALPR completely inhibited the growth of heterogeneous breast tumors via multichannel synergistic effects: disrupting mitochondria, downregulating the survivin gene, and blocking HER2 receptors on the surface of HER2-positive cells. The present design overcomes the chemical drug resistance and opens a feasible route for the combinative treatment of recurrent breast cancer, even other solid tumors, utilizing different kinds of biological drugs.
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Affiliation(s)
- Juan Chen
- Engineering Research Center of Cell & Therapeutic Antibody, Ministry of Education, and School of Pharmacy, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
- Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, 600 Yi-Shan Road, Shanghai, 200233, China
| | - Jinjin Li
- Engineering Research Center of Cell & Therapeutic Antibody, Ministry of Education, and School of Pharmacy, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Xiaolu Sun
- Engineering Research Center of Cell & Therapeutic Antibody, Ministry of Education, and School of Pharmacy, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Huixia Lu
- Engineering Research Center of Cell & Therapeutic Antibody, Ministry of Education, and School of Pharmacy, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Kuai Liu
- Engineering Research Center of Cell & Therapeutic Antibody, Ministry of Education, and School of Pharmacy, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Zhenbo Li
- Engineering Research Center of Cell & Therapeutic Antibody, Ministry of Education, and School of Pharmacy, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Jianyue Guan
- Engineering Research Center of Cell & Therapeutic Antibody, Ministry of Education, and School of Pharmacy, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Huiling Song
- Engineering Research Center of Cell & Therapeutic Antibody, Ministry of Education, and School of Pharmacy, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Wei Wei
- Engineering Research Center of Cell & Therapeutic Antibody, Ministry of Education, and School of Pharmacy, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Yanhong Ge
- Engineering Research Center of Cell & Therapeutic Antibody, Ministry of Education, and School of Pharmacy, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Qiong Fan
- The International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, 910 Hengshan Road, Shanghai, 200030, China
| | - Wei Bao
- Department of Obstetrics and Gynecology, Shanghai General Hospital affiliated with Shanghai Jiao Tong University, 100 Haining Road, Shanghai, 200080, China
| | - Buyong Ma
- Engineering Research Center of Cell & Therapeutic Antibody, Ministry of Education, and School of Pharmacy, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Zixiu Du
- Engineering Research Center of Cell & Therapeutic Antibody, Ministry of Education, and School of Pharmacy, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
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4
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Zhang W, Li Y, Xin S, Yang L, Jiang M, Xin Y, Wang Y, Cao P, Zhang S, Yang Y, Lu J. The emerging roles of IFIT3 in antiviral innate immunity and cellular biology. J Med Virol 2023; 95:e28259. [PMID: 36305096 DOI: 10.1002/jmv.28259] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 08/23/2022] [Accepted: 10/25/2022] [Indexed: 01/11/2023]
Abstract
The interferon-inducible protein with tetrapeptide repeats 3 (IFIT3) is one of the most important members in both the IFIT family and interferon-stimulated genes family. IFIT3 has typical features of the IFIT family in terms of gene and protein structures, and is able to be activated through the classical PRRs-IFN-JAK/STAT pathway. A variety of viruses can induce the expression of IFIT3, which in turn inhibits the replication of viruses, with the underlying mechanism showing its crucial role in antiviral innate immunity. Emerging studies have also identified that IFIT3 is involved in cellular biology changes, including cell proliferation, apoptosis, differentiation, and cancer development. In this review, we summarize the characteristics of IFIT3 with respect to molecular structure and regulatory pathways, highlighting the role of IFIT3 in antiviral innate immunity, as well as its diverse biological roles. We also discuss the potential of IFIT3 as a biomarker in disease diagnosis and therapy.
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Affiliation(s)
- Wentao Zhang
- Hunan Cancer Hospital/the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Hunan, Changsha, China.,Department of Microbiology, School of Basic Medical Science, Central South University, Hunan, Changsha, China.,NHC Key Laboratory of Carcinogenesis, The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Hunan, Changsha, China.,Department of Hematology, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Hunan, Changsha, China.,China-Africa Research Center of Infectious Diseases, Central South University, Hunan, Changsha, China
| | - Yanling Li
- Hunan Cancer Hospital/the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Hunan, Changsha, China.,Department of Microbiology, School of Basic Medical Science, Central South University, Hunan, Changsha, China.,NHC Key Laboratory of Carcinogenesis, The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Hunan, Changsha, China.,Department of Hematology, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Hunan, Changsha, China.,China-Africa Research Center of Infectious Diseases, Central South University, Hunan, Changsha, China
| | - Shuyu Xin
- Hunan Cancer Hospital/the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Hunan, Changsha, China.,Department of Microbiology, School of Basic Medical Science, Central South University, Hunan, Changsha, China.,NHC Key Laboratory of Carcinogenesis, The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Hunan, Changsha, China.,Department of Hematology, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Hunan, Changsha, China.,China-Africa Research Center of Infectious Diseases, Central South University, Hunan, Changsha, China
| | - Li Yang
- Hunan Cancer Hospital/the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Hunan, Changsha, China.,Department of Microbiology, School of Basic Medical Science, Central South University, Hunan, Changsha, China.,NHC Key Laboratory of Carcinogenesis, The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Hunan, Changsha, China.,Department of Hematology, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Hunan, Changsha, China.,China-Africa Research Center of Infectious Diseases, Central South University, Hunan, Changsha, China
| | - Mingjuan Jiang
- Hunan Cancer Hospital/the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Hunan, Changsha, China.,Department of Microbiology, School of Basic Medical Science, Central South University, Hunan, Changsha, China.,NHC Key Laboratory of Carcinogenesis, The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Hunan, Changsha, China.,Department of Hematology, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Hunan, Changsha, China.,China-Africa Research Center of Infectious Diseases, Central South University, Hunan, Changsha, China
| | - Yujie Xin
- Hunan Cancer Hospital/the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Hunan, Changsha, China.,Department of Microbiology, School of Basic Medical Science, Central South University, Hunan, Changsha, China.,NHC Key Laboratory of Carcinogenesis, The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Hunan, Changsha, China.,Department of Hematology, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Hunan, Changsha, China.,China-Africa Research Center of Infectious Diseases, Central South University, Hunan, Changsha, China
| | - Yiwei Wang
- Hunan Cancer Hospital/the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Hunan, Changsha, China.,Department of Microbiology, School of Basic Medical Science, Central South University, Hunan, Changsha, China.,NHC Key Laboratory of Carcinogenesis, The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Hunan, Changsha, China.,Department of Hematology, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Hunan, Changsha, China.,China-Africa Research Center of Infectious Diseases, Central South University, Hunan, Changsha, China
| | - Pengfei Cao
- NHC Key Laboratory of Carcinogenesis, The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Hunan, Changsha, China.,Department of Hematology, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Hunan, Changsha, China
| | - Senmiao Zhang
- Hunan Cancer Hospital/the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Hunan, Changsha, China.,Department of Microbiology, School of Basic Medical Science, Central South University, Hunan, Changsha, China.,NHC Key Laboratory of Carcinogenesis, The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Hunan, Changsha, China.,Department of Hematology, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Hunan, Changsha, China.,China-Africa Research Center of Infectious Diseases, Central South University, Hunan, Changsha, China
| | - Yang Yang
- Hunan Cancer Hospital/the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Hunan, Changsha, China.,Department of Microbiology, School of Basic Medical Science, Central South University, Hunan, Changsha, China.,NHC Key Laboratory of Carcinogenesis, The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Hunan, Changsha, China.,Department of Hematology, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Hunan, Changsha, China.,China-Africa Research Center of Infectious Diseases, Central South University, Hunan, Changsha, China
| | - Jianhong Lu
- Hunan Cancer Hospital/the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Hunan, Changsha, China.,Department of Microbiology, School of Basic Medical Science, Central South University, Hunan, Changsha, China.,NHC Key Laboratory of Carcinogenesis, The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Hunan, Changsha, China.,Department of Hematology, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Hunan, Changsha, China.,China-Africa Research Center of Infectious Diseases, Central South University, Hunan, Changsha, China
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5
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Prokhorova DV, Vokhtantsev IP, Tolstova PO, Zhuravlev ES, Kulishova LM, Zharkov DO, Stepanov GA. Natural Nucleoside Modifications in Guide RNAs Can Modulate the Activity of the CRISPR-Cas9 System In Vitro. CRISPR J 2022; 5:799-812. [PMID: 36350691 DOI: 10.1089/crispr.2022.0069] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
At the present time, the clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated protein 9 (Cas9) system has been widely adopted as an efficient genomic editing tool. However, there are some actual problems such as the off-target effects, cytotoxicity, and immunogenicity. The incorporation of modifications into guide RNAs permits enhancing both the efficiency and the specificity of the CRISPR-Cas9 system. In this study, we demonstrate that the inclusion of N6-methyladenosine, 5-methylcytidine, and pseudouridine in trans-activating RNA (tracrRNA) or in single guide RNA (sgRNA) enables efficient gene editing in vitro. We found that the complexes of modified guide RNAs with Cas9 protein promoted cleavage of the target short/long duplexes and plasmid substrates. In addition, the modified monomers in guide RNAs allow increasing the specificity of CRISPR-Cas9 system in vitro and promote diminishing both the immunostimulating and the cytotoxic effects of sgRNAs.
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Affiliation(s)
- Daria V Prokhorova
- Institute of Chemical Biology and Fundamental Medicine of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.,Department of Natural Sciences, Novosibirsk State University, Novosibirsk, Russia
| | - Ivan P Vokhtantsev
- Institute of Chemical Biology and Fundamental Medicine of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.,Department of Natural Sciences, Novosibirsk State University, Novosibirsk, Russia
| | - Polina O Tolstova
- Institute of Chemical Biology and Fundamental Medicine of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.,Department of Natural Sciences, Novosibirsk State University, Novosibirsk, Russia
| | - Evgenii S Zhuravlev
- Institute of Chemical Biology and Fundamental Medicine of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Lilia M Kulishova
- Institute of Chemical Biology and Fundamental Medicine of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Dmitry O Zharkov
- Institute of Chemical Biology and Fundamental Medicine of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.,Department of Natural Sciences, Novosibirsk State University, Novosibirsk, Russia
| | - Grigory A Stepanov
- Institute of Chemical Biology and Fundamental Medicine of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
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6
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Ermakov MS, Nushtaeva AA, Richter VA, Koval OA. Cancer-associated fibroblasts and their role in tumor progression. Vavilovskii Zhurnal Genet Selektsii 2022; 26:14-21. [PMID: 35342854 PMCID: PMC8894099 DOI: 10.18699/vjgb-22-03] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 11/10/2021] [Accepted: 11/12/2021] [Indexed: 12/12/2022] Open
Abstract
The stromal elements of a malignant tumor can promote cancer progression and metastasis. The structure of the tumor stroma includes connective tissue elements, blood vessels, nerves, and extracellular matrix (ECM). Some of the cellular elements of the tumor stroma are cancer-associated fibroblasts (CAFs). The origin and function of CAFs have been actively studied over the past thirty years. CAFs produce collagen, the main scaffold protein of the extracellular matrix. Collagen in the tumor stroma stimulates fibrosis, enhances the rigidity of tumor tissue, and disrupts the transmission of proliferation and differentiation signaling pathways. CAFs control tumor angiogenesis, cell motility, tumor immunogenic properties, and the development of resistance to chemo- and immunotherapy. As a result of metabolic adaptation of rapidly growing tumor tissue to the nutrients and oxygen deprivation, the main type of energy production in cells changes from oxidative phosphorylation to anaerobic glycolysis. These changes lead to sequential molecular alterations, including the induction of specified transcriptional factors that result in the CAFs activation. The molecular phenotype of activated CAFs is similar to fibroblasts activated during inflammation. In activated CAFs, alpha-smooth muscle actin (α-SMA) is synthetized de novo and various proteases and fibronectin are produced. Since CAFs are found in all types of carcinomas, these cells are potential targets for the development of new approaches for anticancer therapy. Some CAFs originate from resident fibroblasts of the organs invaded by the tumor, while others originate from epithelial tumor cells, which are undergoing an epithelial-mesenchymal transition (EMT). To date, many molecular and metabolic inducers of the EMT have been discovered including the transforming growth factor-beta (TGF-β), hypoxia, and inflammation. This review classifies modern concepts of molecular markers of CAFs, their functional features, and discusses the stages of epithelial-mesenchymal transition, and the potential of CAFs as a target for antitumor therapy.
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Affiliation(s)
- M. S. Ermakov
- Institute of Chemical Biology and Fundamental Medicine of the Siberian Branch of the Russian Academy of Sciences
| | - A. A. Nushtaeva
- Institute of Chemical Biology and Fundamental Medicine of the Siberian Branch of the Russian Academy of Sciences
| | - V. A. Richter
- Institute of Chemical Biology and Fundamental Medicine of the Siberian Branch of the Russian Academy of Sciences
| | - O. A. Koval
- Institute of Chemical Biology and Fundamental Medicine of the Siberian Branch of the Russian Academy of Sciences; Novosibirsk State University
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7
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Troitskaya O, Novak D, Nushtaeva A, Savinkova M, Varlamov M, Ermakov M, Richter V, Koval O. EGFR Transgene Stimulates Spontaneous Formation of MCF7 Breast Cancer Cells Spheroids with Partly Loss of HER3 Receptor. Int J Mol Sci 2021; 22:12937. [PMID: 34884742 PMCID: PMC8657849 DOI: 10.3390/ijms222312937] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 11/26/2021] [Accepted: 11/27/2021] [Indexed: 12/12/2022] Open
Abstract
Multicellular spheroids with 3D cell-cell interactions are a useful model to simulate the growth conditions of cancer. There is evidence that in tumor spheroids, the expression of various essential molecules is changed compared to the adherent form of cell cultures. These changes include growth factor receptors and ABC transporters and result in the enhanced invasiveness of the cells and drug resistance. It is known that breast adenocarcinoma MCF7 cells can spontaneously form 3D spheroids and such spheroids are characterized by high expression of EGFR/HER2, while the natural phenotype of MCF7 cells is EGFRlow/HER2low. Therefore, it was interesting to reveal if high epidermal growth factor receptor (EGFR) expression is sufficient for the conversion of adherent MCF7 to spheroids. In this study, an MCF7 cell line with high expression of EGFR was engineered using the retroviral transduction method. These MCF7-EGFR cells assembled in spheroids very quickly and grew predominantly as a 3D suspension culture with no special plates, scaffolds, growth supplements, or exogenous matrixes. These spheroids were characterized by a rounded shape with a well-defined external border and 100 µM median diameter. The sphere-forming ability of MCF7-EGFR cells was up to 5 times stronger than in MCF7wt cells. Thus, high EGFR expression was the initiation factor of conversion of adherent MCF7wt cells to spheroids. MCF7-EGFR spheroids were enriched by the cells with a cancer stem cell (CSC) phenotype CD24-/low/CD44- in comparison with parental MCF7wt cells and MCF7-EGFR adhesive cells. We suppose that these properties of MCF7-EGFR spheroids originate from the typical features of parental MCF7 cells. We showed the decreasing of HER3 receptors in MCF7-EGFR spheroids compared to that in MCFwt and in adherent MCF7-EGFR cells, and the same decrease was observed in the MCF7wt spheroids growing under the growth factors stimulation. To summarize, the expression of EGFR transgene in MCF7 cells stimulates rapid spheroids formation; these spheroids are enriched by CSC-like CD24-/CD44- cells, they partly lose HER3 receptors, and are characterized by a lower potency in drug resistance pomp activation compared to MCF7wt. These MCF7-EGFR spheroids are a useful cancer model for the development of anticancer drugs, including EGFR-targeted therapeutics.
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Affiliation(s)
- Olga Troitskaya
- Institute of Chemical Biology and Fundamental Medicine SB RAS, 630090 Novosibirsk, Russia; (A.N.); (M.S.); (M.V.); (M.E.); (V.R.); (O.K.)
| | - Diana Novak
- Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia;
| | - Anna Nushtaeva
- Institute of Chemical Biology and Fundamental Medicine SB RAS, 630090 Novosibirsk, Russia; (A.N.); (M.S.); (M.V.); (M.E.); (V.R.); (O.K.)
| | - Maria Savinkova
- Institute of Chemical Biology and Fundamental Medicine SB RAS, 630090 Novosibirsk, Russia; (A.N.); (M.S.); (M.V.); (M.E.); (V.R.); (O.K.)
- Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia;
| | - Mikhail Varlamov
- Institute of Chemical Biology and Fundamental Medicine SB RAS, 630090 Novosibirsk, Russia; (A.N.); (M.S.); (M.V.); (M.E.); (V.R.); (O.K.)
- Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia;
| | - Mikhail Ermakov
- Institute of Chemical Biology and Fundamental Medicine SB RAS, 630090 Novosibirsk, Russia; (A.N.); (M.S.); (M.V.); (M.E.); (V.R.); (O.K.)
| | - Vladimir Richter
- Institute of Chemical Biology and Fundamental Medicine SB RAS, 630090 Novosibirsk, Russia; (A.N.); (M.S.); (M.V.); (M.E.); (V.R.); (O.K.)
| | - Olga Koval
- Institute of Chemical Biology and Fundamental Medicine SB RAS, 630090 Novosibirsk, Russia; (A.N.); (M.S.); (M.V.); (M.E.); (V.R.); (O.K.)
- Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia;
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8
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Wessels DJ, Pujol C, Pradhan N, Lusche DF, Gonzalez L, Kelly SE, Martin EM, Voss ER, Park YN, Dailey M, Sugg SL, Phadke S, Bashir A, Soll DR. Directed movement toward, translocation along, penetration into and exit from vascular networks by breast cancer cells in 3D. Cell Adh Migr 2021; 15:224-248. [PMID: 34338608 PMCID: PMC8331046 DOI: 10.1080/19336918.2021.1957527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
We developed a computer-assisted platform using laser scanning confocal microscopy to 3D reconstruct in real-time interactions between metastatic breast cancer cells and human umbilical vein endothelial cells (HUVECs). We demonstrate that MB-231 cancer cells migrate toward HUVEC networks, facilitated by filopodia, migrate along the network surfaces, penetrate into and migrate within the HUVEC networks, exit and continue migrating along network surfaces. The system is highly amenable to 3D reconstruction and computational analyses, and assessments of the effects of potential anti-metastasis monoclonal antibodies and other drugs. We demonstrate that an anti-RHAMM antibody blocks filopodium formation and all of the behaviors that we found take place between MB-231 cells and HUVEC networks.
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Affiliation(s)
- Deborah J Wessels
- Developmental Studies Hybridoma Bank and W.M. Keck Dynamic Image Analysis Facility, Department of Biology, The University of Iowa, Iowa City, IA, USA
| | - Claude Pujol
- Developmental Studies Hybridoma Bank and W.M. Keck Dynamic Image Analysis Facility, Department of Biology, The University of Iowa, Iowa City, IA, USA
| | - Nikash Pradhan
- Developmental Studies Hybridoma Bank and W.M. Keck Dynamic Image Analysis Facility, Department of Biology, The University of Iowa, Iowa City, IA, USA
| | - Daniel F Lusche
- Developmental Studies Hybridoma Bank and W.M. Keck Dynamic Image Analysis Facility, Department of Biology, The University of Iowa, Iowa City, IA, USA
| | - Luis Gonzalez
- Developmental Studies Hybridoma Bank and W.M. Keck Dynamic Image Analysis Facility, Department of Biology, The University of Iowa, Iowa City, IA, USA
| | - Sydney E Kelly
- Developmental Studies Hybridoma Bank and W.M. Keck Dynamic Image Analysis Facility, Department of Biology, The University of Iowa, Iowa City, IA, USA
| | - Elizabeth M Martin
- Developmental Studies Hybridoma Bank and W.M. Keck Dynamic Image Analysis Facility, Department of Biology, The University of Iowa, Iowa City, IA, USA
| | - Edward R Voss
- Developmental Studies Hybridoma Bank and W.M. Keck Dynamic Image Analysis Facility, Department of Biology, The University of Iowa, Iowa City, IA, USA
| | - Yang-Nim Park
- Developmental Studies Hybridoma Bank and W.M. Keck Dynamic Image Analysis Facility, Department of Biology, The University of Iowa, Iowa City, IA, USA
| | - Michael Dailey
- Developmental Studies Hybridoma Bank and W.M. Keck Dynamic Image Analysis Facility, Department of Biology, The University of Iowa, Iowa City, IA, USA
| | - Sonia L Sugg
- Department of Surgery, The University of Iowa Hospitals and Clinics, Iowa City, IA, USA
| | - Sneha Phadke
- Department of Internal Medicine, The University of Iowa Hospitals and Clinics, Iowa City, IA, USA
| | - Amani Bashir
- Department of Pathology, The University of Iowa Hospitals and Clinics, Iowa City, IA, USA
| | - David R Soll
- Developmental Studies Hybridoma Bank and W.M. Keck Dynamic Image Analysis Facility, Department of Biology, The University of Iowa, Iowa City, IA, USA
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Pidugu VK, Pidugu HB, Wu MM, Liu CJ, Lee TC. Emerging Functions of Human IFIT Proteins in Cancer. Front Mol Biosci 2019; 6:148. [PMID: 31921891 PMCID: PMC6930875 DOI: 10.3389/fmolb.2019.00148] [Citation(s) in RCA: 85] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 12/04/2019] [Indexed: 12/14/2022] Open
Abstract
Interferon-induced protein with tetratricopeptide repeats (IFIT) genes are prominent interferon-stimulated genes (ISGs). The human IFIT gene family consists of four genes named IFIT1, IFIT2, IFIT3, and IFIT5. The expression of IFIT genes is very low in most cell types, whereas their expression is greatly enhanced by interferon treatment, viral infection, and pathogen-associated molecular patterns (PAMPs). The proteins encoded by IFIT genes have multiple tetratricopeptide repeat (TPR) motifs. IFIT proteins do not have any known enzymatic roles. However, they execute a variety of cellular functions by mediating protein-protein interactions and forming multiprotein complexes with cellular and viral proteins through their multiple TPR motifs. The versatile tertiary structure of TPR motifs in IFIT proteins enables them to be involved in distinct biological functions, including host innate immunity, antiviral immune response, virus-induced translation initiation, replication, double-stranded RNA signaling, and PAMP recognition. The current understanding of the IFIT proteins and their role in cellular signaling mechanisms is limited to the antiviral immune response and innate immunity. However, recent studies on IFIT protein functions and their involvement in various molecular signaling mechanisms have implicated them in cancer progression and metastasis. In this article, we focused on critical molecular, biological and oncogenic functions of human IFIT proteins by reviewing their prognostic significance in health and cancer. Research suggests that IFIT proteins could be novel therapeutic targets for cancer therapy.
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Affiliation(s)
| | | | - Meei-Maan Wu
- Department of Public Health, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Chung-Ji Liu
- Department of Oral and Maxillofacial Surgery, Mackay Memorial Hospital, Taipei, Taiwan
| | - Te-Chang Lee
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan.,Institute of Pharmacology, National Yang-Ming University, Taipei, Taiwan
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10
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Chinak O, Golubitskaya E, Pyshnaya I, Stepanov G, Zhuravlev E, Richter V, Koval O. Nucleic Acids Delivery Into the Cells Using Pro-Apoptotic Protein Lactaptin. Front Pharmacol 2019; 10:1043. [PMID: 31619993 PMCID: PMC6759801 DOI: 10.3389/fphar.2019.01043] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 08/16/2019] [Indexed: 11/30/2022] Open
Abstract
Cell penetrating peptides (CPP) are promising agents for transporting diverse cargo into the cells. The amino acid sequence and the mechanism of lactaptin entry into the cells allow it to be included into CPP group. Lactaptin, the fragment of human milk kappa-casein, and recombinant lactaptin (RL2) were initially discovered as molecules that induced apoptosis of cultured cancer cells and did not affect non-malignant cells. Here, we analyzed the recombinant lactaptin potency to form complexes with nucleic acids and to act as a gene delivery system. To study RL2-dependent delivery, three type of nucleic acid were used as a models: plasmid DNA (pDNA), siRNA, and non-coding RNA which allow to detect intracellular localization through their functional activity. We have demonstrated that RL2 formed positively charged noncovalent 110-nm-sized complexes with enhanced green fluorescent protein (EGFP)-expressing plasmid DNA. Ca2+ ions stabilized these complexes, whereas polyanion heparin displaced DNA from the complexes. The functional activity of delivered nucleic acids were assessed by fluorescent microscopy using A549 lung adenocarcinoma cells and A431 epidermoid carcinoma cells. We observed that RL2:pDNA complexes provided EGFP expression in the treated cells and that strongly confirmed the entering pDNA into the cells. The efficiency of cell transformation by these complexes increased when RL2:pDNA ratio increased. Pre-treatment of the cells with anti-RL2 antibodies partly inhibited the entry of pDNA into the cells. RL2-mediated delivery of siRNA against EGFP was analyzed when A549 cells were co-transfected with EGFP-pDNA and RL2:siRNA complexes. siRNA against EGFP efficiently inhibited the expression of EGFP being delivered as RL2:siRNA complexes. We have previously demonstrated that non-coding U25 small nucleolar RNA (snoRNA) can decrease cell viability. Cancer cell transfection with RL2-snoRNA U25 complexes lead to a substantial decrease of cell viability, confirming the efficiency of snoRNA U25 delivery. Collectively, these findings indicate that recombinant lactaptin is able to deliver noncovalently associated nucleic acids into cancer cells in vitro.
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Affiliation(s)
- Olga Chinak
- Laboratory of Biotechnology, Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Ekaterina Golubitskaya
- Laboratory of Genome Editing, Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.,Department of Natural Sciences, Novosibirsk State University, Novosibirsk, Russia
| | - Inna Pyshnaya
- Laboratory of Biomedical Chemistry, Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Grigory Stepanov
- Laboratory of Genome Editing, Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Evgenii Zhuravlev
- Laboratory of Genome Editing, Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Vladimir Richter
- Laboratory of Biotechnology, Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Olga Koval
- Laboratory of Biotechnology, Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.,Department of Natural Sciences, Novosibirsk State University, Novosibirsk, Russia
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11
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Nushtaeva AA, Karpushina AA, Ermakov MS, Gulyaeva LF, Gerasimov AV, Sidorov SV, Gayner TA, Yunusova AY, Tkachenko AV, Richter VA, Koval OA. Establishment of primary human breast cancer cell lines using "pulsed hypoxia" method and development of metastatic tumor model in immunodeficient mice. Cancer Cell Int 2019; 19:46. [PMID: 30858763 PMCID: PMC6394017 DOI: 10.1186/s12935-019-0766-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 02/21/2019] [Indexed: 12/14/2022] Open
Abstract
Background Among breast cancer (BC) patients the outcomes of anticancer therapy vary dramatically due to the highly heterogeneous molecular characteristics of BC. Therefore, an extended panel of BC cell lines are required for in vitro and in vivo studies to find out new characteristic of carcinogenesis and metastasis. The purpose of this study was to develop patient-derived BC cell cultures and metastatic tumor models representing a tool for personal therapy and translational research. Methods Breast cancer cells were prepared by optimizing technique from tumor samples. We used real-time RT-PCR, flow cytometry, western blotting, cytotoxicity assay, karyotyping and fluorescent and electron microscopy analyses to characterize the established cell lines. BC xenografts in scid mice were used for in vivo tumorigenicity studies. Results The technique of preparing primary cells was optimized and this resulted in a high output of viable and active proliferated cells of nine patient-derived breast cancer cell lines and one breast non-malignant cell line. High E-cadherine and EpCAM expression correlated positively with epithelial phenotype while high expression of N-cadherine and Vimentin were shown in cells with mesenchymal phenotype. All mesenchymal-like cell lines were high HER3-positive—up to 90%. More interesting than that, is that two cell lines under specific culturing conditions (pulsed hypoxia and conditioned media) progressively transformed from mesenchymal to epithelial phenotypes displaying the expression of respective molecular markers proving that the mesenchymal-to-epithelial transition occurred. Becoming epithelial, these cells have lost HER3 and decreased HER2 membrane receptors. Three of the established epithelial cancer cell lines were tumorigenic in SCID mice and the generated tumors exhibited lobules-like structures. Ultrastructure analysis revealed low-differentiate phenotype of tumorigenic cell lines. These cells were in near-triploid range with multiple chromosome rearrangements. Tumorigenic BrCCh4e cells, originated from the patient of four-course chemotherapy, initiated metastasis when they were grafted subcutaneous with colonization of mediastinum lymph nodes. Conclusions The developed BC cells metastasizing to mediastinum lymph nodes are a relevant model for downstream applications. Moreover, our findings demonstrate that pulsed hypoxia induces transformation of primary fibroblastoid breast cancer cells to epithelial-like cells and both of these cultures—induced and original—don’t show tumor initiating capacity. Electronic supplementary material The online version of this article (10.1186/s12935-019-0766-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Anna A Nushtaeva
- 1Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, Lavrentiev Avenue, 8, Novosibirsk, 630090 Russia
| | - Anastasia A Karpushina
- 1Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, Lavrentiev Avenue, 8, Novosibirsk, 630090 Russia
| | - Mikhail S Ermakov
- 2Novosibirsk State University, Pirogova Str. 1, Novosibirsk, 630090 Russia
| | - Ludmila F Gulyaeva
- 2Novosibirsk State University, Pirogova Str. 1, Novosibirsk, 630090 Russia.,3Institute of Molecular Biology and Biophysics, Siberian Branch, Russian Academy of Medical Sciences, Ac. Timakov Str. 2, Novosibirsk, 630117 Russia
| | - Alexey V Gerasimov
- National Novosibirsk Regional Oncology Dispensary, Plakhotnogo Str. 2, Novosibirsk, 630000 Russia
| | - Sergey V Sidorov
- Novosibirsk Municipal Budgetary Healthcare Institution "Municipal Clinical Hospital #1", Zalessky Str. 6, Novosibirsk, 630047 Russia
| | - Tatyana A Gayner
- 1Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, Lavrentiev Avenue, 8, Novosibirsk, 630090 Russia
| | - Anastasia Y Yunusova
- 1Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, Lavrentiev Avenue, 8, Novosibirsk, 630090 Russia
| | - Anastasia V Tkachenko
- 1Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, Lavrentiev Avenue, 8, Novosibirsk, 630090 Russia
| | - Vladimir A Richter
- 1Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, Lavrentiev Avenue, 8, Novosibirsk, 630090 Russia
| | - Olga A Koval
- 1Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, Lavrentiev Avenue, 8, Novosibirsk, 630090 Russia.,2Novosibirsk State University, Pirogova Str. 1, Novosibirsk, 630090 Russia
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12
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Nucleotide Modifications Decrease Innate Immune Response Induced by Synthetic Analogs of snRNAs and snoRNAs. Genes (Basel) 2018; 9:genes9110531. [PMID: 30400232 PMCID: PMC6266926 DOI: 10.3390/genes9110531] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 10/26/2018] [Indexed: 12/25/2022] Open
Abstract
Short nuclear regulatory RNAs play a key role in the main stages of maturation of the precursors of the major RNA species. Small nuclear RNAs (snRNAs) form the core of the spliceosome and are responsible for the splicing of pre-mRNA molecules. Small nucleolar RNAs (snoRNAs) direct post-transcriptional modification of pre-rRNAs. A promising strategy for the development of non-coding RNA (ncRNAs) mimicking molecules is the introduction of modified nucleotides, which are normally present in natural ncRNAs, into the structure of synthetic RNAs. We have created a set of snoRNAs and snRNA analogs and studied the effect of base modifications, specifically, pseudouridine (Ψ) and 5-methylcytidine (m⁵C), on the immune-stimulating and cytotoxic properties of these RNAs. Here, we performed a whole-transcriptome study of the influence of synthetic snoRNA analogs with various modifications on gene expression in human cells. Moreover, we confirmed the role of PKR in the recognition of snoRNA and snRNA analogs using the short hairpin RNA (shRNA) technique. We believe that the data obtained will contribute to the understanding of the role of nucleotide modification in ncRNA functions, and can be useful for creating the agents for gene regulation based on the structure of natural snoRNAs and snRNAs.
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