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Mussa A, Ismail NH, Hamid M, Al-Hatamleh MAI, Bragoli A, Hajissa K, Mokhtar NF, Mohamud R, Uskoković V, Hassan R. Understanding the role of TNFR2 signaling in the tumor microenvironment of breast cancer. J Exp Clin Cancer Res 2024; 43:312. [PMID: 39609700 PMCID: PMC11603874 DOI: 10.1186/s13046-024-03218-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2024] [Accepted: 10/29/2024] [Indexed: 11/30/2024] Open
Abstract
Breast cancer (BC) is the most frequently diagnosed malignancy among women. It is characterized by a high level of heterogeneity that emerges from the interaction of several cellular and soluble components in the tumor microenvironment (TME), such as cytokines, tumor cells and tumor-associated immune cells. Tumor necrosis factor (TNF) receptor 2 (TNFR2) appears to play a significant role in microenvironmental regulation, tumor progression, immune evasion, drug resistance, and metastasis of many types of cancer, including BC. However, the significance of TNFR2 in BC biology is not fully understood. This review provides an overview of TNFR2 biology, detailing its activation and its interactions with important signaling pathways in the TME (e.g., NF-κB, MAPK, and PI3K/Akt pathways). We discuss potential therapeutic strategies targeting TNFR2, with the aim of enhancing the antitumor immune response to BC. This review provides insights into role of TNFR2 as a major immune checkpoint for the future treatment of patients with BC.
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Affiliation(s)
- Ali Mussa
- Department of Haematology, School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian, Kota Bharu , Kelantan, 16150, Malaysia
- Department of Biology, Faculty of Education, Omdurman Islamic University, P.O. Box 382, Omdurman, Sudan
| | - Nor Hayati Ismail
- Department of Haematology, School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian, Kota Bharu , Kelantan, 16150, Malaysia
| | - Mahasin Hamid
- Department of Pharmaceutics, Xiangya School of Pharmaceutical Sciences, Central South University, Hunan Province, Changsha, 410013, China
- Department of Zoology, Faculty of Sciences and Information Technology, University of Nyala, Nyala, 63311, Sudan
| | - Mohammad A I Al-Hatamleh
- Division of Hematology and Oncology, Department of Medicine, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, 15213, USA
| | - Anthony Bragoli
- Department of Immunology, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Khalid Hajissa
- Department of Zoology, Faculty of Science and Technology, Omdurman Islamic University, P.O. Box 382, Omdurman, Sudan
| | - Noor Fatmawati Mokhtar
- Institute for Research in Molecular Medicine (iNFORMM), Universiti Sains Malaysia, Kubang Kerian, Kota Bharu , Kelantan, 16150, Malaysia
| | - Rohimah Mohamud
- Department of Immunology, School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian, Kota Bharu , Kelantan, 16150, Malaysia.
| | - Vuk Uskoković
- TardigradeNano LLC, Irvine, CA, 92604, USA
- Division of Natural Sciences, Fullerton College, Fullerton, CA, 92832, USA
| | - Rosline Hassan
- Department of Haematology, School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian, Kota Bharu , Kelantan, 16150, Malaysia.
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Al-Lamki RS, Tolkovsky AM, Alawwami M, Lu W, Field SF, Wang J, Pober JS, Bradley JR. Tumor Necrosis Factor Receptor-2 Signals Clear-Cell Renal Carcinoma Proliferation via Phosphorylated 4E Binding Protein-1 and Mitochondrial Gene Translation. THE AMERICAN JOURNAL OF PATHOLOGY 2024; 194:1374-1387. [PMID: 38537932 DOI: 10.1016/j.ajpath.2024.02.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 02/08/2024] [Accepted: 02/21/2024] [Indexed: 04/09/2024]
Abstract
Clear-cell renal cell carcinoma (ccRCC), a tubular epithelial malignancy, secretes tumor necrosis factor (TNF), which signals ccRCC cells in an autocrine manner via two cell surface receptors, TNFR1 and TNFR2, to activate shared and distinct signaling pathways. Selective ligation of TNFR2 drives cell cycle entry of malignant cells via a signaling pathway involving epithelial tyrosine kinase, vascular endothelial cell growth factor receptor type 2, phosphatidylinositol-3-kinase, Akt, pSer727-Stat3, and mammalian target of rapamycin. In this study, phosphorylated 4E binding protein-1 (4EBP1) serine 65 (pSer65-4EBP1) was identified as a downstream target of this TNFR2 signaling pathway. pSer65-4EBP1 expression was significantly elevated relative to total 4EBP1 in ccRCC tissue compared with that in normal kidneys, with signal intensity increasing with malignant grade. Selective ligation of TNFR2 with the TNFR2-specific mutein increased pSer65-4EBP1 expression in organ cultures that co-localized with internalized TNFR2 in mitochondria and increased expression of mitochondrially encoded COX (cytochrome c oxidase subunit) Cox1, as well as nuclear-encoded Cox4/5b subunits. Pharmacologic inhibition of mammalian target of rapamycin reduced both TNFR2-specific mutein-mediated phosphorylation of 4EBP1 and cell cycle activation in tumor cells while increasing cell death. These results signify the importance of pSer65-4EBP1 in mediating TNFR2-driven cell-cycle entry in tumor cells in ccRCC and implicate a novel relationship between the TNFR2/pSer65-4EBP1/COX axis and mitochondrial function.
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MESH Headings
- Humans
- Adaptor Proteins, Signal Transducing/metabolism
- Adaptor Proteins, Signal Transducing/genetics
- Carcinoma, Renal Cell/metabolism
- Carcinoma, Renal Cell/pathology
- Carcinoma, Renal Cell/genetics
- Cell Cycle Proteins/metabolism
- Cell Cycle Proteins/genetics
- Cell Line, Tumor
- Cell Proliferation
- Kidney Neoplasms/metabolism
- Kidney Neoplasms/pathology
- Kidney Neoplasms/genetics
- Mitochondria/metabolism
- Phosphoproteins/metabolism
- Phosphorylation
- Protein Biosynthesis
- Receptors, Tumor Necrosis Factor, Type II/metabolism
- Receptors, Tumor Necrosis Factor, Type II/genetics
- Signal Transduction
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Affiliation(s)
- Rafia S Al-Lamki
- Department of Medicine, National Institute of Health Research Cambridge Biomedical Research Centre, University of Cambridge, Cambridge, United Kingdom.
| | - Aviva M Tolkovsky
- Department of Clinical Neurosciences, The Clifford Allbutt Building, University of Cambridge, Cambridge, United Kingdom
| | - Mohammad Alawwami
- Department of Medicine, National Institute of Health Research Cambridge Biomedical Research Centre, University of Cambridge, Cambridge, United Kingdom
| | - WanHua Lu
- Department of Medicine, National Institute of Health Research Cambridge Biomedical Research Centre, University of Cambridge, Cambridge, United Kingdom
| | - Sarah F Field
- Dementia Research Institute, Island Research Building, University of Cambridge, Cambridge, United Kingdom
| | - Jun Wang
- Department of Medicine, National Institute of Health Research Cambridge Biomedical Research Centre, University of Cambridge, Cambridge, United Kingdom
| | - Jordan S Pober
- Department of Immunobiology, Yale University, New Haven, Connecticut
| | - John R Bradley
- Department of Medicine, National Institute of Health Research Cambridge Biomedical Research Centre, University of Cambridge, Cambridge, United Kingdom
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Li S, Liu W, Liu J, Yang Z, Zhang L, Nie F, Yang P, Guo H, Yang C. Low-dose TNF-α promotes angiogenesis of oral squamous cell carcinoma cells via TNFR2/Akt/mTOR axis. Oral Dis 2024; 30:3004-3017. [PMID: 37964399 DOI: 10.1111/odi.14802] [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: 10/12/2022] [Revised: 10/08/2023] [Accepted: 10/23/2023] [Indexed: 11/16/2023]
Abstract
OBJECTIVES To assess the role of TNF-α/TNFR2 axis on promoting angiogenesis in oral squamous cell carcinoma (OSCC) cells and uncover the underlying mechanisms. MATERIALS AND METHODS The expression of TNFR2 and CD31 in OSCC tissues was examined; gene expression relationship between TNF-α/TNFR2 and angiogenic markers or signaling molecules was analyzed; the expression of angiogenic markers, signaling molecules, TNFR1, and TNFR2 in TNF-α-stimulated OSCC cells treated with or without TNFR2 neutralizing antibody (TNFR2 Nab) were assessed; the concentration of angiogenic markers in the supernatant of OSCC cells was detected; conditioned mediums of OSCC cells treated with TNF-α or TNF-α + TNFR2 Nab were applied to human umbilical vein endothelial cells (HUVECs), followed by tube formation and cell migration assays. RESULTS Significantly elevated expression of TNFR2 and CD31 in OSCC tissues was observed. A positive gene expression correlation was identified between TNF-α/TNFR2 and angiogenic markers or signaling molecules. TNFR2 Nab inhibited the effects of TNF-α on enhancing the expression of angiogenic factors and TNFR2, the phosphorylation of the Akt/mTOR signaling pathway, HUVECs migration, and tube formation. CONCLUSIONS TNFR2 Nab counteracts the effect of TNF-α on OSCC cells through the TNFR2/Akt/mTOR axis, indicating that blocking TNFR2 might be a promising strategy against cancer.
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Affiliation(s)
- Shutong Li
- Department of Periodontology, School and Hospital of Stomatology, Cheeloo College of Medicine, Shandong University and Shandong Key Laboratory of Oral Tissue Regeneration and Shandong Engineering Laboratory for Dental Materials and Oral Tissue Regeneration and Shandong Provincial Clinical Research Center for Oral Diseases, Jinan, Shandong, China
| | - Wenchuan Liu
- Department of Periodontology, School and Hospital of Stomatology, Cheeloo College of Medicine, Shandong University and Shandong Key Laboratory of Oral Tissue Regeneration and Shandong Engineering Laboratory for Dental Materials and Oral Tissue Regeneration and Shandong Provincial Clinical Research Center for Oral Diseases, Jinan, Shandong, China
| | - Junze Liu
- School of Information and Computer Sciences, Institute for Genomics and Bioinformatics, University of California Irvine, Irvine, California, USA
| | - Zongcheng Yang
- Division of Life Sciences and Medicine, Department of Stomatology, The First Affiliated Hospital of USTC, University of Science and Technology of China, Hefei, Anhui, China
| | - Liguo Zhang
- Department of Periodontology, School and Hospital of Stomatology, Cheeloo College of Medicine, Shandong University and Shandong Key Laboratory of Oral Tissue Regeneration and Shandong Engineering Laboratory for Dental Materials and Oral Tissue Regeneration and Shandong Provincial Clinical Research Center for Oral Diseases, Jinan, Shandong, China
| | - Fujiao Nie
- Department of Periodontology, School and Hospital of Stomatology, Cheeloo College of Medicine, Shandong University and Shandong Key Laboratory of Oral Tissue Regeneration and Shandong Engineering Laboratory for Dental Materials and Oral Tissue Regeneration and Shandong Provincial Clinical Research Center for Oral Diseases, Jinan, Shandong, China
| | - Pishan Yang
- Department of Periodontology, School and Hospital of Stomatology, Cheeloo College of Medicine, Shandong University and Shandong Key Laboratory of Oral Tissue Regeneration and Shandong Engineering Laboratory for Dental Materials and Oral Tissue Regeneration and Shandong Provincial Clinical Research Center for Oral Diseases, Jinan, Shandong, China
| | - Hongmei Guo
- Department of Periodontology, School and Hospital of Stomatology, Cheeloo College of Medicine, Shandong University and Shandong Key Laboratory of Oral Tissue Regeneration and Shandong Engineering Laboratory for Dental Materials and Oral Tissue Regeneration and Shandong Provincial Clinical Research Center for Oral Diseases, Jinan, Shandong, China
| | - Chengzhe Yang
- Department of Oral and Maxillofacial Surgery, Qilu Hospital of Shandong University, Jinan, Shandong, China
- Institute of Stomatology, Shandong University, Jinan, Shandong, China
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Takahashi H, Yoshimatsu G, Faustman DL. The Roles of TNFR2 Signaling in Cancer Cells and the Tumor Microenvironment and the Potency of TNFR2 Targeted Therapy. Cells 2022; 11:1952. [PMID: 35741080 DOI: 10.3390/cells11121952pubmedhttps:/www.ncbi.nlm.nih.gov/pubmed/35741080pubmed] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Revised: 06/08/2022] [Accepted: 06/14/2022] [Indexed: 08/02/2024] Open
Abstract
The appreciation that cancer growth is promoted by a dynamic tumor microenvironment (TME) has spawned novel approaches to cancer treatment. New therapies include agents that activate quiescent T effector cells and agents that interfere with abnormal neovascularity. Although promising, many experimental therapies targeted at the TME have systemic toxicity. Another approach is to target the TME with greater specificity by taking aim at the tumor necrosis factor receptor 2 (TNFR2) signaling pathway. TNFR2 is an attractive molecular target because it is rarely expressed in normal tissues (thus, has low potential for systemic toxicity) and because it is overexpressed on many types of cancer cells as well as on associated TME components, such as T regulatory cells (Tregs), tumor-associated macrophages, and other cells that facilitate tumor progression and spread. Novel therapies that block TNFR2 signaling show promise in cell culture studies, animal models, and human studies. Novel antibodies have been developed that expressly kill only rapidly proliferating cells expressing newly synthesized TNFR2 protein. This review traces the origins of our understanding of TNFR2's multifaceted roles in the TME and discusses the therapeutic potential of agents designed to block TNFR2 as the cornerstone of a TME-specific strategy.
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Affiliation(s)
- Hiroyuki Takahashi
- Department of Gastroenterological Surgery, Fukuoka University Hospital, Fukuoka 814-0180, Japan
- Immunobiology Department, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA 02129, USA
| | - Gumpei Yoshimatsu
- Department of Gastroenterological Surgery, Fukuoka University Hospital, Fukuoka 814-0180, Japan
| | - Denise Louise Faustman
- Immunobiology Department, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA 02129, USA
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Takahashi H, Yoshimatsu G, Faustman DL. The Roles of TNFR2 Signaling in Cancer Cells and the Tumor Microenvironment and the Potency of TNFR2 Targeted Therapy. Cells 2022; 11:cells11121952. [PMID: 35741080 PMCID: PMC9222015 DOI: 10.3390/cells11121952] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Revised: 06/08/2022] [Accepted: 06/14/2022] [Indexed: 11/16/2022] Open
Abstract
The appreciation that cancer growth is promoted by a dynamic tumor microenvironment (TME) has spawned novel approaches to cancer treatment. New therapies include agents that activate quiescent T effector cells and agents that interfere with abnormal neovascularity. Although promising, many experimental therapies targeted at the TME have systemic toxicity. Another approach is to target the TME with greater specificity by taking aim at the tumor necrosis factor receptor 2 (TNFR2) signaling pathway. TNFR2 is an attractive molecular target because it is rarely expressed in normal tissues (thus, has low potential for systemic toxicity) and because it is overexpressed on many types of cancer cells as well as on associated TME components, such as T regulatory cells (Tregs), tumor-associated macrophages, and other cells that facilitate tumor progression and spread. Novel therapies that block TNFR2 signaling show promise in cell culture studies, animal models, and human studies. Novel antibodies have been developed that expressly kill only rapidly proliferating cells expressing newly synthesized TNFR2 protein. This review traces the origins of our understanding of TNFR2’s multifaceted roles in the TME and discusses the therapeutic potential of agents designed to block TNFR2 as the cornerstone of a TME-specific strategy.
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Affiliation(s)
- Hiroyuki Takahashi
- Department of Gastroenterological Surgery, Fukuoka University Hospital, Fukuoka 814-0180, Japan; (H.T.); (G.Y.)
- Immunobiology Department, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA 02129, USA
| | - Gumpei Yoshimatsu
- Department of Gastroenterological Surgery, Fukuoka University Hospital, Fukuoka 814-0180, Japan; (H.T.); (G.Y.)
| | - Denise Louise Faustman
- Immunobiology Department, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA 02129, USA
- Correspondence: ; Tel.: +1-617-726-4084; Fax: +1-617-726-4095
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6
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Ben-Baruch A. Tumor Necrosis Factor α: Taking a Personalized Road in Cancer Therapy. Front Immunol 2022; 13:903679. [PMID: 35663982 PMCID: PMC9157545 DOI: 10.3389/fimmu.2022.903679] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 04/25/2022] [Indexed: 11/29/2022] Open
Affiliation(s)
- Adit Ben-Baruch
- The Shmunis School of Biomedicine and Cancer Research, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
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7
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Filipiak-Duliban A, Brodaczewska K, Majewska A, Kieda C. Spheroid culture models adequately imitate distinctive features of the renal cancer or melanoma microenvironment. In Vitro Cell Dev Biol Anim 2022; 58:349-364. [PMID: 35536385 DOI: 10.1007/s11626-022-00685-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 04/24/2022] [Indexed: 11/05/2022]
Abstract
Tumor development studies should adapt to cancer cells' specific mechanisms in connection with their microenvironment. Standard two-dimensional cultures and gas composition are not relevant to the real cancer environment. Existing three-dimensional models are often requiring sophisticated conditions. Here, we propose and characterize, in two cancer models, melanoma (B16F10) and kidney cancer (RenCa), a three-dimensional culture method, reporting the presence of hypoxia-related genes/proteins and aggressiveness mechanisms (epithelial mesenchymal transition and cancer stem cells). We validate the designed three-dimensional method by comparing it with in vivo growing tumors. The developed method brings simplicity and data reproducibility. Melanoma spheroid-growing cells reached a cell cycle arrest at the G0/G1 phase and showed induction of hypoxia. Spheroid-recovered RenCa cells were enriched in proliferating cells and displayed delayed hypoxia. Moreover, the responses to hypoxia observed in spheroids were validated by in vivo tumor studies for both lines. Three-dimensional shapes induced cancer stem cells in renal cancer, whereas epithelial to mesenchymal transition occurred in the melanoma model. Such distinction in the use of different aggressiveness-leading pathways was observed in in vivo melanoma vs kidney tumors. Thus, this 3D culture model approach is adequate to uncover crucial molecular pathways using distinct mechanisms to reach aggressiveness; i.e., B16F10 cells perform epithelial to mesenchymal transition while RenCa cells dedifferentiate into cancer stem cells. Such three-dimensional models help mimic the in vivo tumor features, i.e., hypoxia and aggressiveness mechanisms as validated here by next-generation sequencing analysis, and are proposed for further alternative methods to in vivo studies.
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Affiliation(s)
- Aleksandra Filipiak-Duliban
- Laboratory of Molecular Oncology and Innovative Therapies, Military Institute of Medicine, Warsaw, Poland. .,Postgraduate School of Molecular Medicine, Medical University of Warsaw, Warsaw, Poland.
| | - Klaudia Brodaczewska
- Laboratory of Molecular Oncology and Innovative Therapies, Military Institute of Medicine, Warsaw, Poland
| | - Aleksandra Majewska
- Laboratory of Molecular Oncology and Innovative Therapies, Military Institute of Medicine, Warsaw, Poland.,Postgraduate School of Molecular Medicine, Medical University of Warsaw, Warsaw, Poland
| | - Claudine Kieda
- Laboratory of Molecular Oncology and Innovative Therapies, Military Institute of Medicine, Warsaw, Poland.,Center for Molecular Biophysics UPR 4301 CNRS, 45071, Orleans, France
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Trisolini L, Laera L, Favia M, Muscella A, Castegna A, Pesce V, Guerra L, De Grassi A, Volpicella M, Pierri CL. Differential Expression of ADP/ATP Carriers as a Biomarker of Metabolic Remodeling and Survival in Kidney Cancers. Biomolecules 2020; 11:38. [PMID: 33396658 PMCID: PMC7824283 DOI: 10.3390/biom11010038] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 12/19/2020] [Accepted: 12/24/2020] [Indexed: 02/07/2023] Open
Abstract
ADP/ATP carriers (AACs) are mitochondrial transport proteins playing a strategic role in maintaining the respiratory chain activity, fueling the cell with ATP, and also regulating mitochondrial apoptosis. To understand if AACs might represent a new molecular target for cancer treatment, we evaluated AAC expression levels in cancer/normal tissue pairs available on the Tissue Cancer Genome Atlas database (TCGA), observing that AACs are dysregulated in most of the available samples. It was observed that at least two AACs showed a significant differential expression in all the available kidney cancer/normal tissue pairs. Thus, we investigated AAC expression in the corresponding kidney non-cancer (HK2)/cancer (RCC-Shaw and CaKi-1) cell lines, grown in complete medium or serum starvation, for investigating how metabolic alteration induced by different growth conditions might influence AAC expression and resistance to mitochondrial apoptosis initiators, such as "staurosporine" or the AAC highly selective inhibitor "carboxyatractyloside". Our analyses showed that AAC2 and AAC3 transcripts are more expressed than AAC1 in all the investigated kidney cell lines grown in complete medium, whereas serum starvation causes an increase of at least two AAC transcripts in kidney cancer cell lines compared to non-cancer cells. However, the total AAC protein content is decreased in the investigated cancer cell lines, above all in the serum-free medium. The observed decrease in AAC protein content might be responsible for the decrease of OXPHOS activity and for the observed lowered sensitivity to mitochondrial apoptosis induced by staurosporine or carboxyatractyloside. Notably, the cumulative probability of the survival of kidney cancer patients seriously decreases with the decrease of AAC1 expression in KIRC and KIRP tissues making AAC1 a possible new biomarker of metabolic remodeling and survival in kidney cancers.
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Affiliation(s)
- Lucia Trisolini
- Department of Biosciences, Biotechnologies, Biopharmaceutics, University “Aldo Moro” of Bari, Via E. Orabona, 4, 70125 Bari, Italy; (L.T.); (L.L.); (M.F.); (A.C.); (V.P.); (L.G.)
| | - Luna Laera
- Department of Biosciences, Biotechnologies, Biopharmaceutics, University “Aldo Moro” of Bari, Via E. Orabona, 4, 70125 Bari, Italy; (L.T.); (L.L.); (M.F.); (A.C.); (V.P.); (L.G.)
| | - Maria Favia
- Department of Biosciences, Biotechnologies, Biopharmaceutics, University “Aldo Moro” of Bari, Via E. Orabona, 4, 70125 Bari, Italy; (L.T.); (L.L.); (M.F.); (A.C.); (V.P.); (L.G.)
| | - Antonella Muscella
- Dipartimento di Scienze e Tecnologie Biologiche e Ambientali (Di.S.Te.B.A.), Università del Salento, 73100 Lecce, Italy;
| | - Alessandra Castegna
- Department of Biosciences, Biotechnologies, Biopharmaceutics, University “Aldo Moro” of Bari, Via E. Orabona, 4, 70125 Bari, Italy; (L.T.); (L.L.); (M.F.); (A.C.); (V.P.); (L.G.)
| | - Vito Pesce
- Department of Biosciences, Biotechnologies, Biopharmaceutics, University “Aldo Moro” of Bari, Via E. Orabona, 4, 70125 Bari, Italy; (L.T.); (L.L.); (M.F.); (A.C.); (V.P.); (L.G.)
| | - Lorenzo Guerra
- Department of Biosciences, Biotechnologies, Biopharmaceutics, University “Aldo Moro” of Bari, Via E. Orabona, 4, 70125 Bari, Italy; (L.T.); (L.L.); (M.F.); (A.C.); (V.P.); (L.G.)
| | - Anna De Grassi
- Department of Biosciences, Biotechnologies, Biopharmaceutics, University “Aldo Moro” of Bari, Via E. Orabona, 4, 70125 Bari, Italy; (L.T.); (L.L.); (M.F.); (A.C.); (V.P.); (L.G.)
- BROWSer S.r.l. c/o, Department of Biosciences, Biotechnologies, Biopharmaceutics, University “Aldo Moro” of Bari, Via E. Orabona, 4, 70126 Bari, Italy
| | - Mariateresa Volpicella
- Department of Biosciences, Biotechnologies, Biopharmaceutics, University “Aldo Moro” of Bari, Via E. Orabona, 4, 70125 Bari, Italy; (L.T.); (L.L.); (M.F.); (A.C.); (V.P.); (L.G.)
| | - Ciro Leonardo Pierri
- Department of Biosciences, Biotechnologies, Biopharmaceutics, University “Aldo Moro” of Bari, Via E. Orabona, 4, 70125 Bari, Italy; (L.T.); (L.L.); (M.F.); (A.C.); (V.P.); (L.G.)
- BROWSer S.r.l. c/o, Department of Biosciences, Biotechnologies, Biopharmaceutics, University “Aldo Moro” of Bari, Via E. Orabona, 4, 70126 Bari, Italy
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Panov J, Simchi L, Feuermann Y, Kaphzan H. Bioinformatics Analyses of the Transcriptome Reveal Ube3a-Dependent Effects on Mitochondrial-Related Pathways. Int J Mol Sci 2020; 21:ijms21114156. [PMID: 32532103 PMCID: PMC7312912 DOI: 10.3390/ijms21114156] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 06/07/2020] [Accepted: 06/08/2020] [Indexed: 12/14/2022] Open
Abstract
The UBE3A gene encodes the ubiquitin E3-ligase protein, UBE3A, which is implicated in severe neurodevelopmental disorders. Lack of UBE3A expression results in Angelman syndrome, while UBE3A overexpression, due to genomic 15q duplication, results in autism. The cellular roles of UBE3A are not fully understood, yet a growing body of evidence indicates that these disorders involve mitochondrial dysfunction and increased oxidative stress. We utilized bioinformatics approaches to delineate the effects of murine Ube3a deletion on the expression of mitochondrial-related genes and pathways. For this, we generated an mRNA sequencing dataset from mouse embryonic fibroblasts (MEFs) in which both alleles of Ube3a gene were deleted and their wild-type controls. Since oxidative stress and mitochondrial dysregulation might not be exhibited in the resting baseline state, we also activated mitochondrial functioning in the cells of these two genotypes using TNFα application. Transcriptomes of the four groups of MEFs, Ube3a+/+ and Ube3a-/-, with or without the application of TNFα, were analyzed using various bioinformatics tools and machine learning approaches. Our results indicate that Ube3a deletion affects the gene expression profiles of mitochondrial-associated pathways. We further confirmed these results by analyzing other publicly available human transcriptome datasets of Angelman syndrome and 15q duplication syndrome.
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