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Lin L, Zou X, Nong W, Ge Y, Li F, Luo B, Zhang Q, Xie X. The potential value of cancer-testis antigens in ovarian cancer: Prognostic markers and targets for immunotherapy. Immun Inflamm Dis 2024; 12:e1284. [PMID: 38896069 PMCID: PMC11186301 DOI: 10.1002/iid3.1284] [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: 01/23/2024] [Revised: 05/11/2024] [Accepted: 05/15/2024] [Indexed: 06/21/2024] Open
Abstract
BACKGROUND Tumor immunotherapy has become an important adjuvant therapy after surgery, radiotherapy, and chemotherapy. In recent years, the role of tumor-associated antigen (TAA) in tumor immunotherapy has become increasingly prominent. Cancer-testis antigen (CTA) is a kind of TAA that is highly restricted in a variety of tumors and can induce an immune response. AIMS This review article aimed to evaluate the role of CTA on the progression of ovarian cancer, its diagnostic efficacy, and the potential for immunotherapy. METHODS We analyzed publications and outlined a comprehensive of overview the regulatory mechanism, immunogenicity, clinical expression significance, tumorigenesis, and application prospects of CTA in ovarian cancer, with a particular focus on recent progress in CTA-based immunotherapy. RESULTS The expression of CTA affects the occurrence, development, and prognosis of ovarian cancer and is closely related to tumor immunity. CONCLUSION CTA can be used as a biomarker for the diagnosis and prognosis evaluation of ovarian cancer and is an ideal target for antitumor immunotherapy. These findings provide novel insights on CTA in the improvement of diagnosis and treatment for ovarian cancer. The successes, current challenges and future prospects were also discussed to portray its significant potential.
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Affiliation(s)
- Lina Lin
- Department of Histology and Embryology, School of Basic Medicine ScienceGuangxi Medical UniversityNanningGuangxiPeople's Republic of China
- Department of Obstetrics and GynecologyThe First Affiliated Hospital of Guangxi Medical UniversityNanningGuangxiPeople's Republic of China
| | - Xiaoqiong Zou
- Department of Histology and Embryology, School of Basic Medicine ScienceGuangxi Medical UniversityNanningGuangxiPeople's Republic of China
| | - Weixia Nong
- Department of Histology and Embryology, School of Basic Medicine ScienceGuangxi Medical UniversityNanningGuangxiPeople's Republic of China
| | - Yingying Ge
- Department of Histology and Embryology, School of Basic Medicine ScienceGuangxi Medical UniversityNanningGuangxiPeople's Republic of China
| | - Feng Li
- Department of Histology and Embryology, School of Basic Medicine ScienceGuangxi Medical UniversityNanningGuangxiPeople's Republic of China
| | - Bin Luo
- Department of Histology and Embryology, School of Basic Medicine ScienceGuangxi Medical UniversityNanningGuangxiPeople's Republic of China
- Education Department of Guangxi Zhuang Autonomous RegionKey Laboratory of Basic Research on Regional Diseases (Guangxi Medical University)NanningGuangxiPeople's Republic of China
| | - Qingmei Zhang
- Department of Histology and Embryology, School of Basic Medicine ScienceGuangxi Medical UniversityNanningGuangxiPeople's Republic of China
- Education Department of Guangxi Zhuang Autonomous RegionKey Laboratory of Basic Research on Regional Diseases (Guangxi Medical University)NanningGuangxiPeople's Republic of China
| | - Xiaoxun Xie
- Department of Histology and Embryology, School of Basic Medicine ScienceGuangxi Medical UniversityNanningGuangxiPeople's Republic of China
- Education Department of Guangxi Zhuang Autonomous RegionKey Laboratory of Basic Research on Regional Diseases (Guangxi Medical University)NanningGuangxiPeople's Republic of China
- Ministry of Education, Key Laboratory of Early Prevention and Treatment of Regional High Frequency Tumor (Guangxi Medical University)NanningGuangxiPeople's Republic of China
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Liu C, Vorderbruggen M, Muñoz-Trujillo C, Kim SH, Katzenellenbogen JA, Katzenellenbogen BS, Karpf AR. NB compounds are potent and efficacious FOXM1 inhibitors in high-grade serous ovarian cancer cells. J Ovarian Res 2024; 17:94. [PMID: 38704607 PMCID: PMC11069232 DOI: 10.1186/s13048-024-01421-4] [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: 01/30/2024] [Accepted: 04/20/2024] [Indexed: 05/06/2024] Open
Abstract
BACKGROUND Genetic studies implicate the oncogenic transcription factor Forkhead Box M1 (FOXM1) as a potential therapeutic target in high-grade serous ovarian cancer (HGSOC). We evaluated the activity of different FOXM1 inhibitors in HGSOC cell models. RESULTS We treated HGSOC and fallopian tube epithelial (FTE) cells with a panel of previously reported FOXM1 inhibitors. Based on drug potency, efficacy, and selectivity, determined through cell viability assays, we focused on two compounds, NB-73 and NB-115 (NB compounds), for further investigation. NB compounds potently and selectively inhibited FOXM1 with lesser effects on other FOX family members. NB compounds decreased FOXM1 expression via targeting the FOXM1 protein by promoting its proteasome-mediated degradation, and effectively suppressed FOXM1 gene targets at both the protein and mRNA level. At the cellular level, NB compounds promoted apoptotic cell death. Importantly, while inhibition of apoptosis using a pan-caspase inhibitor rescued HGSOC cells from NB compound-induced cell death, it did not rescue FOXM1 protein degradation, supporting that FOXM1 protein loss from NB compound treatment is specific and not a general consequence of cytotoxicity. Drug washout studies indicated that FOXM1 reduction was retained for at least 72 h post-treatment, suggesting that NB compounds exhibit long-lasting effects in HGSOC cells. NB compounds effectively suppressed both two-dimensional and three-dimensional HGSOC cell colony formation at sub-micromolar concentrations. Finally, NB compounds exhibited synergistic activity with carboplatin in HGSOC cells. CONCLUSIONS NB compounds are potent, selective, and efficacious inhibitors of FOXM1 in HGSOC cells and are worthy of further investigation as HGSOC therapeutics.
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Affiliation(s)
- Cassie Liu
- Eppley Institute, University of Nebraska Medical Center, Omaha, NE, 68918-6805, USA
- Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, 68918-6805, USA
| | - Makenzie Vorderbruggen
- Eppley Institute, University of Nebraska Medical Center, Omaha, NE, 68918-6805, USA
- Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, 68918-6805, USA
| | - Catalina Muñoz-Trujillo
- Eppley Institute, University of Nebraska Medical Center, Omaha, NE, 68918-6805, USA
- Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, 68918-6805, USA
| | - Sung Hoon Kim
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - John A Katzenellenbogen
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Cancer Center, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Benita S Katzenellenbogen
- Department of Molecular and Integrative Physiology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Cancer Center, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Adam R Karpf
- Eppley Institute, University of Nebraska Medical Center, Omaha, NE, 68918-6805, USA.
- Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, 68918-6805, USA.
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Martínez‐López A, García‐Casas A, Infante G, González‐Fernández M, Salvador N, Lorente M, Mendiburu‐Eliçabe M, Gonzalez‐Moreno S, Villarejo‐Campos P, Velasco G, Malliri A, Castillo‐Lluva S. POTEE promotes breast cancer cell malignancy by inducing invadopodia formation through the activation of SUMOylated Rac1. Mol Oncol 2024; 18:620-640. [PMID: 38098337 PMCID: PMC10920093 DOI: 10.1002/1878-0261.13568] [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: 08/03/2023] [Revised: 11/23/2023] [Accepted: 12/13/2023] [Indexed: 12/29/2023] Open
Abstract
The small GTPase Rac1 (Ras-related C3 botulinum toxin substrate 1) has been implicated in cancer progression and in the poor prognosis of various types of tumors. Rac1 SUMOylation occurs during epithelial-mesenchymal transition (EMT), and it is required for tumor cell migration and invasion. Here we identify POTEE (POTE Ankyrin domain family member E) as a novel Rac1-SUMO1 effector involved in breast cancer malignancy that controls invadopodium formation through the activation of Rac1-SUMO1. POTEE activates Rac1 in the invadopodium by recruiting TRIO-GEF (triple functional domain protein), and it induces tumor cell proliferation and metastasis in vitro and in vivo. We found that the co-localization of POTEE with Rac1 is correlated with more aggressive breast cancer subtypes. Given its role in tumor dissemination, the leading cause of cancer-related deaths, POTEE could represent a potential therapeutic target for these types of cancer.
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Affiliation(s)
- Angélica Martínez‐López
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias QuímicasUniversidad Complutense de MadridSpain
- Instituto de Investigaciones Sanitarias San Carlos (IdISSC)MadridSpain
| | - Ana García‐Casas
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias QuímicasUniversidad Complutense de MadridSpain
- Instituto de Investigaciones Sanitarias San Carlos (IdISSC)MadridSpain
| | - Guiomar Infante
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias QuímicasUniversidad Complutense de MadridSpain
- Instituto de Investigaciones Sanitarias San Carlos (IdISSC)MadridSpain
| | - Mónica González‐Fernández
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias QuímicasUniversidad Complutense de MadridSpain
- Instituto de Investigaciones Sanitarias San Carlos (IdISSC)MadridSpain
| | - Nélida Salvador
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias QuímicasUniversidad Complutense de MadridSpain
- Instituto de Investigaciones Sanitarias San Carlos (IdISSC)MadridSpain
| | - Mar Lorente
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias QuímicasUniversidad Complutense de MadridSpain
- Instituto de Investigaciones Sanitarias San Carlos (IdISSC)MadridSpain
| | - Marina Mendiburu‐Eliçabe
- Departamento de Estadística e Investigación Operativa, Facultad de Ciencias MatemáticasUniversidad Complutense de MadridSpain
| | | | | | - Guillermo Velasco
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias QuímicasUniversidad Complutense de MadridSpain
- Instituto de Investigaciones Sanitarias San Carlos (IdISSC)MadridSpain
| | - Angeliki Malliri
- Cancer Research UK Manchester InstituteThe University of ManchesterUK
| | - Sonia Castillo‐Lluva
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias QuímicasUniversidad Complutense de MadridSpain
- Instituto de Investigaciones Sanitarias San Carlos (IdISSC)MadridSpain
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Edris A, Voorhies K, Lutz SM, Iribarren C, Hall I, Wu AC, Tobin M, Fawcett K, Lahousse L. Asthma exacerbations and eosinophilia in the UK Biobank: a genome-wide association study. ERJ Open Res 2024; 10:00566-2023. [PMID: 38196893 PMCID: PMC10772900 DOI: 10.1183/23120541.00566-2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 10/31/2023] [Indexed: 01/11/2024] Open
Abstract
Background Asthma exacerbations reflect disease severity, affect morbidity and mortality, and may lead to declining lung function. Inflammatory endotypes (e.g. T2-high (eosinophilic)) may play a key role in asthma exacerbations. We aimed to assess whether genetic susceptibility underlies asthma exacerbation risk and additionally tested for an interaction between genetic variants and eosinophilia on exacerbation risk. Methods UK Biobank data were used to perform a genome-wide association study of individuals with asthma and at least one exacerbation compared to individuals with asthma and no history of exacerbations. Individuals with asthma were identified using self-reported data, hospitalisation data and general practitioner records. Exacerbations were identified as either asthma-related hospitalisation, general practitioner record of asthma exacerbation or an oral corticosteroid burst prescription. A logistic regression model adjusted for age, sex, smoking status and genetic ancestry via principal components was used to assess the association between genetic variants and asthma exacerbations. We sought replication for suggestive associations (p<5×10-6) in the GERA cohort. Results In the UK Biobank, we identified 11 604 cases and 37 890 controls. While no variants reached genome-wide significance (p<5×10-8) in the primary analysis, 116 signals were suggestively significant (p<5×10-6). In GERA, two single nucleotide polymorphisms (rs34643691 and rs149721630) replicated (p<0.05), representing signals near the NTRK3 and ABCA13 genes. Conclusions Our study has identified reproducible associations with asthma exacerbations in the UK Biobank and GERA cohorts. Confirmation of these findings in different asthma subphenotypes in diverse ancestries and functional investigation will be required to understand their mechanisms of action and potentially inform therapeutic development.
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Affiliation(s)
- Ahmed Edris
- Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium
- Genetic Epidemiology Group, Department of Health Sciences, University of Leicester, Leicester, UK
| | - Kirsten Voorhies
- Precision Medicine Translational Research Center, Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, MA, USA
| | - Sharon M. Lutz
- Precision Medicine Translational Research Center, Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, MA, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Carlos Iribarren
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
| | - Ian Hall
- Faculty of Medicine and Health Sciences, University of Nottingham, Nottingham, UK
| | - Ann Chen Wu
- Precision Medicine Translational Research Center, Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, MA, USA
| | - Martin Tobin
- Genetic Epidemiology Group, Department of Health Sciences, University of Leicester, Leicester, UK
| | - Katherine Fawcett
- Genetic Epidemiology Group, Department of Health Sciences, University of Leicester, Leicester, UK
- These authors contributed equally
| | - Lies Lahousse
- Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium
- These authors contributed equally
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Gozzellino L, Nannini M, Urbini M, Pizzi C, Leone O, Corti B, Baldovini C, Angeli F, Foà A, Pacini D, Folesani G, Costa A, Palumbo T, Nigro MC, Pasquinelli G, Astolfi A, Pantaleo MA. Genomic Landscape Comparison of Cardiac versus Extra-Cardiac Angiosarcomas. Biomedicines 2023; 11:3290. [PMID: 38137511 PMCID: PMC10741871 DOI: 10.3390/biomedicines11123290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 11/29/2023] [Accepted: 12/07/2023] [Indexed: 12/24/2023] Open
Abstract
Angiosarcomas (ASs) are rare malignant vascular entities that can affect several regions in our body, including the heart. Cardiac ASs comprise 25-40% of cardiac sarcomas and can cause death within months of diagnosis. Thus, our aim was to identify potential differences and/or similarities between cardiac and extra-cardiac ASs to enhance targeted therapies and, consequently, patients' prognosis. Whole-transcriptome analysis of three cardiac and eleven extra-cardiac non-cutaneous samples was performed to investigate differential gene expression and mutational events between the two groups. The gene signature of cardiac and extra-cardiac non-cutaneous ASs was also compared to that of cutaneous angiosarcomas (n = 9). H/N/K-RAS and TP53 alterations were more recurrent in extra-cardiac ASs, while POTE-gene family overexpression was peculiar to cardiac ASs. Additionally, in vitro functional analyses showed that POTEH upregulation conferred a growth advantage to recipient cells, partly supporting the cardiac AS aggressive phenotype and patients' scarce survival rate. These features should be considered when investigating alternative treatments.
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Affiliation(s)
- Livia Gozzellino
- Department of Medical and Surgical Sciences (DIMEC), Alma Mater Studiorum—University of Bologna, 40138 Bologna, Italy; (L.G.); (M.N.); (F.A.); (M.C.N.); (M.A.P.)
| | - Margherita Nannini
- Department of Medical and Surgical Sciences (DIMEC), Alma Mater Studiorum—University of Bologna, 40138 Bologna, Italy; (L.G.); (M.N.); (F.A.); (M.C.N.); (M.A.P.)
- Division of Oncology, IRCCS Azienda Ospedaliero-Universitaria di Bologna, 40138 Bologna, Italy
| | - Milena Urbini
- Biosciences Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, 47014 Meldola, Italy;
| | - Carmine Pizzi
- Unit of Cardiology, Department of Medical and Surgical Sciences, University of Bologna, 40138 Bologna, Italy; (C.P.); (A.F.)
| | - Ornella Leone
- Division of Pathology, Cardiovascular and Cardiac Transplant Pathology Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, 40138 Bologna, Italy; (O.L.); (B.C.); (C.B.)
| | - Barbara Corti
- Division of Pathology, Cardiovascular and Cardiac Transplant Pathology Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, 40138 Bologna, Italy; (O.L.); (B.C.); (C.B.)
| | - Chiara Baldovini
- Division of Pathology, Cardiovascular and Cardiac Transplant Pathology Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, 40138 Bologna, Italy; (O.L.); (B.C.); (C.B.)
| | - Francesco Angeli
- Department of Medical and Surgical Sciences (DIMEC), Alma Mater Studiorum—University of Bologna, 40138 Bologna, Italy; (L.G.); (M.N.); (F.A.); (M.C.N.); (M.A.P.)
| | - Alberto Foà
- Unit of Cardiology, Department of Medical and Surgical Sciences, University of Bologna, 40138 Bologna, Italy; (C.P.); (A.F.)
| | - Davide Pacini
- Cardiac Surgery Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, 40138 Bologna, Italy; (D.P.); (G.F.)
| | - Gianluca Folesani
- Cardiac Surgery Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, 40138 Bologna, Italy; (D.P.); (G.F.)
| | - Alice Costa
- IRCCS Azienda Ospedaliero-Universitaria di Bologna, 40138 Bologna, Italy;
| | - Teresa Palumbo
- Interdepartmental Center Alma Mater Institute on Healthy Planet, Alma Mater Studiorum—University of Bologna, 40138 Bologna, Italy;
| | - Maria Concetta Nigro
- Department of Medical and Surgical Sciences (DIMEC), Alma Mater Studiorum—University of Bologna, 40138 Bologna, Italy; (L.G.); (M.N.); (F.A.); (M.C.N.); (M.A.P.)
| | - Gianandrea Pasquinelli
- Division of Pathology, IRCCS Azienda Ospedaliero-Universitaria di Bologna, 40138 Bologna, Italy;
| | - Annalisa Astolfi
- Department of Medical and Surgical Sciences (DIMEC), Alma Mater Studiorum—University of Bologna, 40138 Bologna, Italy; (L.G.); (M.N.); (F.A.); (M.C.N.); (M.A.P.)
- IRCCS Azienda Ospedaliero-Universitaria di Bologna, 40138 Bologna, Italy;
| | - Maria Abbondanza Pantaleo
- Department of Medical and Surgical Sciences (DIMEC), Alma Mater Studiorum—University of Bologna, 40138 Bologna, Italy; (L.G.); (M.N.); (F.A.); (M.C.N.); (M.A.P.)
- Division of Oncology, IRCCS Azienda Ospedaliero-Universitaria di Bologna, 40138 Bologna, Italy
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Kast DJ, Jansen S. Purification of modified mammalian actin isoforms for in vitro reconstitution assays. Eur J Cell Biol 2023; 102:151363. [PMID: 37778219 PMCID: PMC10872616 DOI: 10.1016/j.ejcb.2023.151363] [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: 06/19/2023] [Revised: 08/19/2023] [Accepted: 09/26/2023] [Indexed: 10/03/2023] Open
Abstract
In vitro reconstitution assays using purified actin have greatly improved our understanding of cytoskeletal dynamics and their regulation by actin-binding proteins. However, early purification methods consisted of harsh conditions to obtain pure actin and often did not include correct maturation and obligate modification of the isolated actin monomers. Novel insights into the folding requirements and N-terminal processing of actin as well as a better understanding of the interaction of actin with monomer sequestering proteins such as DNaseI, profilin and gelsolin, led to the development of more gentle approaches to obtain pure recombinant actin isoforms with known obligate modifications. This review summarizes the approaches that can be employed to isolate natively folded endogenous and recombinant actin from tissues and cells. We further emphasize the use and limitations of each method and describe how these methods can be implemented to study actin PTMs, disease-related actin mutations and novel actin-like proteins.
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Affiliation(s)
- David J Kast
- Department of Cell Biology and Physiology, Washington University in St. Louis, Saint Louis, MO, 63110, United States.
| | - Silvia Jansen
- Department of Cell Biology and Physiology, Washington University in St. Louis, Saint Louis, MO, 63110, United States.
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Investigating the Function of Human Jumping Translocation Breakpoint Protein (hJTB) and Its Interacting Partners through In-Solution Proteomics of MCF7 Cells. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27238301. [PMID: 36500393 PMCID: PMC9740069 DOI: 10.3390/molecules27238301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 11/16/2022] [Accepted: 11/16/2022] [Indexed: 11/30/2022]
Abstract
Human jumping translocation breakpoint (hJTB) gene is located on chromosome 1q21 and is involved in unbalanced translocation in many types of cancer. JTB protein is ubiquitously present in normal cells but it is found to be overexpressed or downregulated in various types of cancer cells, where this protein and its isoforms promote mitochondrial dysfunction, resistance to apoptosis, genomic instability, proliferation, invasion and metastasis. Hence, JTB could be a tumor biomarker for different types of cancer, such as breast cancer (BC), and could be used as a drug target for therapy. However, the functions of the protein or the pathways through which it increases cell proliferation and invasiveness of cancer cells are not well-known. Therefore, we aim to investigate the functions of JTB by using in-solution digestion-based cellular proteomics of control and upregulated and downregulated JTB protein in MCF7 breast cancer cell line, taking account that in-solution digestion-based proteomics experiments are complementary to the initial in-gel based ones. Proteomics analysis allows investigation of protein dysregulation patterns that indicate the function of the protein and its interacting partners, as well as the pathways and biological processes through which it functions. We concluded that JTB dysregulation increases the epithelial-mesenchymal transition (EMT) potential and cell proliferation, harnessing cytoskeleton organization, apical junctional complex, metabolic reprogramming, and cellular proteostasis. Deregulated JTB expression was found to be associated with several proteins involved in mitochondrial organization and function, oxidative stress (OS), apoptosis, and interferon alpha and gamma signaling. Consistent and complementary to our previous results emerged by using in-gel based proteomics of transfected MCF7 cells, JTB-related proteins that are overexpressed in this experiment suggest the development of a more aggressive phenotype and behavior for this luminal type A non-invasive/poor-invasive human BC cell line that does not usually migrate or invade compared with the highly metastatic MDA-MB-231 cells. This more aggressive phenotype of MCF7 cells related to JTB dysregulation and detected by both in-gel and in-solution proteomics could be promoted by synergistic upregulation of EMT, Mitotic spindle and Fatty acid metabolism pathways. However, in both JTB dysregulated conditions, several downregulated JTB-interacting proteins predominantly sustain antitumor activities, attenuating some of the aggressive phenotypical and behavioral traits promoted by the overexpressed JTB-related partners.
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Saha C, Bojdo J, Dunne NJ, Duary RK, Buckley N, McCarthy HO. Nucleic acid vaccination strategies for ovarian cancer. Front Bioeng Biotechnol 2022; 10:953887. [PMID: 36420446 PMCID: PMC9677957 DOI: 10.3389/fbioe.2022.953887] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 10/26/2022] [Indexed: 09/19/2023] Open
Abstract
High grade serous carcinoma (HGSC) is one of the most lethal ovarian cancers that is characterised by asymptomatic tumour growth, insufficient knowledge of malignant cell origin and sub-optimal detection. HGSC has been recently shown to originate in the fallopian tube and not in the ovaries. Conventional treatments such as chemotherapy and surgery depend upon the stage of the disease and have resulted in higher rates of relapse. Hence, there is a need for alternative treatments. Differential antigen expression levels have been utilised for early detection of the cancer and could be employed in vaccination strategies using nucleic acids. In this review the different vaccination strategies in Ovarian cancer are discussed and reviewed. Nucleic acid vaccination strategies have been proven to produce a higher CD8+ CTL response alongside CD4+ T-cell response when compared to other vaccination strategies and thus provide a good arena for antitumour immune therapy. DNA and mRNA need to be delivered into the intracellular matrix. To overcome ineffective naked delivery of the nucleic acid cargo, a suitable delivery system is required. This review also considers the suitability of cell penetrating peptides as a tool for nucleic acid vaccine delivery in ovarian cancer.
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Affiliation(s)
- Chayanika Saha
- School of Pharmacy, Queen’s University of Belfast, Belfast, United Kingdom
| | - James Bojdo
- School of Pharmacy, Queen’s University of Belfast, Belfast, United Kingdom
| | - Nicholas J. Dunne
- School of Mechanical and Manufacturing Engineering, Dublin City University, Dublin, Ireland
- Centre for Medical Engineering Research, School of Mechanical and Manufacturing Engineering, Dublin City University, Dublin, Ireland
- Department of Mechanical and Manufacturing Engineering, School of Engineering, Trinity College Dublin, Dublin, Ireland
- Advanced Manufacturing Research Centre (I-Form), School of Mechanical and Manufacturing Engineering, Dublin City University, Dublin, Ireland
- Advanced Materials and Bioengineering Research Centre (AMBER), Royal College of Surgeons in Ireland and Trinity College Dublin, Dublin, Ireland
- Advanced Processing Technology Research Centre, Dublin City University, Dublin, Ireland
- Trinity Centre for Biomedical Engineering, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin, Ireland
| | - Raj Kumar Duary
- Department of Food Engineering and Technology, Tezpur University, Tezpur, India
| | - Niamh Buckley
- School of Pharmacy, Queen’s University of Belfast, Belfast, United Kingdom
| | - Helen O. McCarthy
- School of Pharmacy, Queen’s University of Belfast, Belfast, United Kingdom
- School of Chemical Sciences, Dublin City University, Dublin, Ireland
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Spirocyclic dimer SpiD7 activates the unfolded protein response to selectively inhibit growth and induce apoptosis of cancer cells. J Biol Chem 2022; 298:101890. [PMID: 35378132 PMCID: PMC9062249 DOI: 10.1016/j.jbc.2022.101890] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 03/22/2022] [Accepted: 03/24/2022] [Indexed: 11/25/2022] Open
Abstract
The unfolded protein response (UPR) is an adaptation mechanism activated to resolve transient accumulation of unfolded/misfolded proteins in the endoplasmic reticulum. Failure to resolve the transient accumulation of such proteins results in UPR-mediated programmed cell death. Loss of tumor suppressor gene or oncogene addiction in cancer cells can result in sustained higher basal UPR levels; however, it is not clear if these higher basal UPR levels in cancer cells can be exploited as a therapeutic strategy. We hypothesized that covalent modification of surface-exposed cysteine (SEC) residues could simulate unfolded/misfolded proteins to activate the UPR, and that higher basal UPR levels in cancer cells would provide the necessary therapeutic window. To test this hypothesis, here we synthesized analogs that can covalently modify multiple SEC residues and evaluated them as UPR activators. We identified a spirocyclic dimer, SpiD7, and evaluated its effects on UPR activation signals, that is, XBP1 splicing, phosphorylation of eIF2α, and a decrease in ATF 6 levels, in normal and cancer cells, which were further confirmed by RNA-Seq analyses. We found that SpiD7 selectively induced caspase-mediated apoptosis in cancer cells, whereas normal cells exhibited robust XBP1 splicing, indicating adaptation to stress. Furthermore, SpiD7 inhibited the growth of high-grade serous carcinoma cell lines ~3-15-fold more potently than immortalized fallopian tube epithelial (paired normal control) cells and reduced clonogenic growth of high-grade serous carcinoma cell lines. Our results suggest that induction of the UPR by covalent modification of SEC residues represents a cancer cell vulnerability and can be exploited to discover novel therapeutics.
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10
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Zhao J, Xu Z, Liu Y, Wang X, Liu X, Gao Y, Jin Y. The expression of cancer-testis antigen in ovarian cancer and the development of immunotherapy. Am J Cancer Res 2022; 12:681-694. [PMID: 35261795 PMCID: PMC8899981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 01/26/2022] [Indexed: 06/14/2023] Open
Abstract
Ovarian cancer is a relatively common tumor in women with the highest mortality among female reproductive system tumors. The lack of apparent early symptoms and effective screening strategies often leads to ovarian cancer being diagnosed at an advanced stage. Immunotherapy relying on tumor-associated antigens might improve the treatment of ovarian cancer. Cancer-testis antigens (CTAs) are ideal tumor-associated antigens, and MAGE-A, NY-ESO-1, CT45, and Sp17 are classic CTAs highly expressed in ovarian cancer. Here, we review the research on CTAs in ovarian cancer, including prognostic value and advances in immunotherapy, all of which are essential for developing a theoretical basis for targeted therapy strategies.
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Affiliation(s)
- Jianhang Zhao
- Department of Pharmacology, School of Pharmacy, China Medical UniversityShenyang, Liaoning, China
| | - Zhaoxu Xu
- Department of Pharmacology, School of Pharmacy, China Medical UniversityShenyang, Liaoning, China
| | - Yan Liu
- Liaoning Research Institute of Family Planning (Reproductive Hospital Affiliated to China Medical University), Key Laboratory of Reproductive Health and Genetic Medicine, National Health Commission of ChinaShenyang, Liaoning, China
| | - Xiaobin Wang
- Center of Reproductive Medicine, Shengjing Hospital of China Medical UniversityShenyang, Liaoning, China
| | - Xinli Liu
- Medical Oncology Department of Gastrointestinal Cancer, Liaoning Cancer Hospital & Institute, Cancer Hospital of China Medical UniversityShenyang, Liaoning, China
| | - Yanan Gao
- Department of Pharmacology, School of Pharmacy, China Medical UniversityShenyang, Liaoning, China
| | - Ying Jin
- Liaoning Research Institute of Family Planning (Reproductive Hospital Affiliated to China Medical University), Key Laboratory of Reproductive Health and Genetic Medicine, National Health Commission of ChinaShenyang, Liaoning, China
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11
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Tarabichi M, Demeulemeester J, Verfaillie A, Flanagan AM, Van Loo P, Konopka T. A pan-cancer landscape of somatic mutations in non-unique regions of the human genome. Nat Biotechnol 2021; 39:1589-1596. [PMID: 34282324 PMCID: PMC7612106 DOI: 10.1038/s41587-021-00971-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 06/02/2021] [Indexed: 12/27/2022]
Abstract
A substantial fraction of the human genome displays high sequence similarity with at least one other genomic sequence, posing a challenge for the identification of somatic mutations from short-read sequencing data. Here we annotate genomic variants in 2,658 cancers from the Pan-Cancer Analysis of Whole Genomes (PCAWG) cohort with links to similar sites across the human genome. We train a machine learning model to use signals distributed over multiple genomic sites to call somatic events in non-unique regions and validate the data against linked-read sequencing in an independent dataset. Using this approach, we uncover previously hidden mutations in ~1,700 coding sequences and in thousands of regulatory elements, including in known cancer genes, immunoglobulins and highly mutated gene families. Mutations in non-unique regions are consistent with mutations in unique regions in terms of mutation burden and substitution profiles. The analysis provides a systematic summary of the mutation events in non-unique regions at a genome-wide scale across multiple human cancers.
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Affiliation(s)
- Maxime Tarabichi
- The Francis Crick Institute, London, UK.
- Institute for Interdisciplinary Research, Université Libre de Bruxelles, Brussels, Belgium.
| | - Jonas Demeulemeester
- The Francis Crick Institute, London, UK
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | | | - Adrienne M Flanagan
- Research Department of Pathology, Cancer Institute, University College London, London, UK
- Department of Cellular and Molecular Pathology, Royal National Orthopaedic Hospital NHS Trust, Stanmore, UK
| | | | - Tomasz Konopka
- The Francis Crick Institute, London, UK.
- William Harvey Research Institute, Queen Mary University of London, London, UK.
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12
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Qazi S, Raza K. In silico approach to understand epigenetics of POTEE in ovarian cancer. J Integr Bioinform 2021; 18:jib-2021-0028. [PMID: 34788504 PMCID: PMC8709732 DOI: 10.1515/jib-2021-0028] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 11/04/2021] [Indexed: 12/20/2022] Open
Abstract
Ovarian cancer is the third leading cause of cancer-related deaths in India. Epigenetics mechanisms seemingly plays an important role in ovarian cancer. This paper highlights the crucial epigenetic changes that occur in POTEE that get hypomethylated in ovarian cancer. We utilized the POTEE paralog mRNA sequence to identify major motifs and also performed its enrichment analysis. We identified 6 motifs of varying lengths, out of which only three motifs, including CTTCCAGCAGATGTGGATCA, GGAACTGCC, and CGCCACATGCAGGC were most likely to be present in the nucleotide sequence of POTEE. By enrichment and occurrences identification analyses, we rectified the best match motif as CTTCCAGCAGATGT. Since there is no experimentally verified structure of POTEE paralog, thus, we predicted the POTEE structure using an automated workflow for template-based modeling using the power of a deep neural network. Additionally, to validate our predicted model we used AlphaFold predicted POTEE structure and observed that the residual stretch starting from 237-958 had a very high confidence per residue. Furthermore, POTEE predicted model stability was evaluated using replica exchange molecular dynamic simulation for 50 ns. Our network-based epigenetic analysis discerns only 10 highly significant, direct, and physical associators of POTEE. Our finding aims to provide new insights about the POTEE paralog.
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Affiliation(s)
- Sahar Qazi
- Department of Computer Science, Jamia Millia Islamia, New Delhi 110025, India
| | - Khalid Raza
- Department of Computer Science, Jamia Millia Islamia, New Delhi 110025, India
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13
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Zhang Y, Qazi S, Raza K. Differential expression analysis in ovarian cancer: A functional genomics and systems biology approach. Saudi J Biol Sci 2021; 28:4069-4081. [PMID: 34220265 PMCID: PMC8241591 DOI: 10.1016/j.sjbs.2021.04.022] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 04/01/2021] [Accepted: 04/07/2021] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Ovarian cancer is one of the rarest lethal oncologic diseases that have hardly any specific biomarkers. The availability of high-throughput genomic data and advancement in bioinformatics tools allow us to predict gene biomarkers and apply systems biology approaches to get better diagnosis, and prognosis of the disease with a tentative drug that may be repurposed. OBJECTIVE To perform genome-wide association studies using microarray gene expression of ovarian cancer and identify gene biomarkers, construction and analyze networks, perform survival analysis, and drug interaction studies for better diagnosis, prognosis, and treatment of ovarian cancer. METHOD The gene expression profiles of both healthy and serous ovarian cancer epithelial samples were considered. We applied a series of bioinformatics methods and tools, including fold-change statistics for differential expression analysis, DisGeNET and NCBI-Gene databases for gene-disease association mapping, DAVID 6.8 for GO enrichment analysis, GeneMANIA for network construction, Cytoscape 3.8 with its plugins for network visualization, analysis, and module detection, the UALCAN for patient survival analysis, and PubChem, DrugBank and DGIdb for gene-drug interaction. RESULTS We identified 8 seed genes that were subjected for drug-gene interaction studies. Because of over-expression in all the four stages of ovarian cancer, we discern that genes HMGA1 and PSAT1 are potential therapeutic biomarkers for its diagnosis at an early stage (stage I). Our analysis suggests that there are 11 drugs common in the seed genes. However, hypermethylated seed genes HMGA1 and PSAT1 showcased a good interaction affinity with drugs cisplatin, cyclosporin, bisphenol A, progesterone, and sunitinib, and are crucial in the proliferation of ovarian cancer. CONCLUSION Our study reveals that HMGA1 and PSAT1 can be deployed for initial screening of ovarian cancer and drugs cisplatin, bisphenol A, cyclosporin, progesterone, and sunitinib are effective in curbing the epigenetic alteration.
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Affiliation(s)
- Yinbing Zhang
- College of Chemistry & Chemical Engineering, Hubei University, Wuhan 430062, China
| | - Sahar Qazi
- Department of Computer Science, Jamia Millia Islamia, New Delhi 110025, India
| | - Khalid Raza
- Department of Computer Science, Jamia Millia Islamia, New Delhi 110025, India
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14
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Fan C, Qu H, Wang X, Sobhani N, Wang L, Liu S, Xiong W, Zeng Z, Li Y. Cancer/testis antigens: from serology to mRNA cancer vaccine. Semin Cancer Biol 2021; 76:218-231. [PMID: 33910064 DOI: 10.1016/j.semcancer.2021.04.016] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 04/19/2021] [Accepted: 04/20/2021] [Indexed: 02/01/2023]
Abstract
Cancer/testis antigens (CTAs) are a group of tumor antigens expressed in numerous cancer tissues, as well as in the testis and placental tissues. There are over 200 CTAs supported by serology and expression data. The expression patterns of CTAs reflect the similarities between the processes of gametogenesis and tumorigenesis. It is notable that CTAs are highly expressed in three types of cancers (lung cancer, bladder cancer, and skin cancer), all of which have a metal etiology. Here, we review the expression, regulation, and function of CTAs and their translational prospects as cancer biomarkers and treatment targets. Many CTAs are highly immunogenic, tissue-specific, and frequently expressed in cancer tissues but not under physiological conditions, rendering them promising candidates for cancer detection. Some CTAs are associated with clinical outcomes, so they may serve as prognostic biomarkers. A small number of CTAs are membrane-bound, making them ideal targets for chimeric antigen receptor (CAR) T cells. Mounting evidence suggests that CTAs induce humoral or cellular immune responses, providing cancer immunotherapeutic opportunities for T-cell receptors (TCRs), CAR T cell, antibody-based therapy and peptide- or mRNA-based vaccines. Indeed, CTAs are the dominating non-mutated targets in mRNA cancer vaccine development. Clinical trials on CTA TCR and vaccines have shown effectiveness, safety, and tolerance, but these successes are limited to a small number of patients. In-depth studies on CTA expression and function are needed to improve CTA-based immunotherapy.
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Affiliation(s)
- Chunmei Fan
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and School of Basic Medicine, Central South University, Changsha, Hunan, China; Section of Epidemiology and Population Science, Department of Medicine, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, United States
| | - Hongke Qu
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and School of Basic Medicine, Central South University, Changsha, Hunan, China
| | - Xu Wang
- Section of Epidemiology and Population Science, Department of Medicine, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, United States
| | - Navid Sobhani
- Section of Epidemiology and Population Science, Department of Medicine, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, United States
| | - Leiming Wang
- Section of Epidemiology and Population Science, Department of Medicine, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, United States
| | - Shuanglin Liu
- Section of Epidemiology and Population Science, Department of Medicine, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, United States
| | - Wei Xiong
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and School of Basic Medicine, Central South University, Changsha, Hunan, China
| | - Zhaoyang Zeng
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and School of Basic Medicine, Central South University, Changsha, Hunan, China.
| | - Yong Li
- Section of Epidemiology and Population Science, Department of Medicine, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, United States.
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15
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Barger CJ, Chee L, Albahrani M, Munoz-Trujillo C, Boghean L, Branick C, Odunsi K, Drapkin R, Zou L, Karpf AR. Co-regulation and function of FOXM1/ RHNO1 bidirectional genes in cancer. eLife 2021; 10:e55070. [PMID: 33890574 PMCID: PMC8104967 DOI: 10.7554/elife.55070] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2020] [Accepted: 04/22/2021] [Indexed: 12/14/2022] Open
Abstract
The FOXM1 transcription factor is an oncoprotein and a top biomarker of poor prognosis in human cancer. Overexpression and activation of FOXM1 is frequent in high-grade serous carcinoma (HGSC), the most common and lethal form of human ovarian cancer, and is linked to copy number gains at chromosome 12p13.33. We show that FOXM1 is co-amplified and co-expressed with RHNO1, a gene involved in the ATR-Chk1 signaling pathway that functions in the DNA replication stress response. We demonstrate that FOXM1 and RHNO1 are head-to-head (i.e., bidirectional) genes (BDG) regulated by a bidirectional promoter (BDP) (named F/R-BDP). FOXM1 and RHNO1 each promote oncogenic phenotypes in HGSC cells, including clonogenic growth, DNA homologous recombination repair, and poly-ADP ribosylase inhibitor resistance. FOXM1 and RHNO1 are one of the first examples of oncogenic BDG, and therapeutic targeting of FOXM1/RHNO1 BDG is a potential therapeutic approach for ovarian and other cancers.
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MESH Headings
- Ataxia Telangiectasia Mutated Proteins/genetics
- Ataxia Telangiectasia Mutated Proteins/metabolism
- Carboplatin/pharmacology
- Carrier Proteins/genetics
- Carrier Proteins/metabolism
- Cell Line, Tumor
- Cell Proliferation
- Checkpoint Kinase 1/genetics
- Checkpoint Kinase 1/metabolism
- Databases, Genetic
- Drug Resistance, Neoplasm
- Female
- Forkhead Box Protein M1/genetics
- Forkhead Box Protein M1/metabolism
- Gene Expression Regulation, Neoplastic
- Humans
- Neoplasms, Cystic, Mucinous, and Serous/drug therapy
- Neoplasms, Cystic, Mucinous, and Serous/genetics
- Neoplasms, Cystic, Mucinous, and Serous/metabolism
- Neoplasms, Cystic, Mucinous, and Serous/pathology
- Ovarian Neoplasms/drug therapy
- Ovarian Neoplasms/genetics
- Ovarian Neoplasms/metabolism
- Ovarian Neoplasms/pathology
- Poly(ADP-ribose) Polymerase Inhibitors/pharmacology
- Promoter Regions, Genetic
- Recombinational DNA Repair
- Signal Transduction
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Affiliation(s)
- Carter J Barger
- Eppley Institute for Cancer Research and Fred & Pamela Buffett Cancer Center, University of Nebraska Medical CenterOmahaUnited States
| | - Linda Chee
- Eppley Institute for Cancer Research and Fred & Pamela Buffett Cancer Center, University of Nebraska Medical CenterOmahaUnited States
| | - Mustafa Albahrani
- Eppley Institute for Cancer Research and Fred & Pamela Buffett Cancer Center, University of Nebraska Medical CenterOmahaUnited States
| | - Catalina Munoz-Trujillo
- Eppley Institute for Cancer Research and Fred & Pamela Buffett Cancer Center, University of Nebraska Medical CenterOmahaUnited States
| | - Lidia Boghean
- Eppley Institute for Cancer Research and Fred & Pamela Buffett Cancer Center, University of Nebraska Medical CenterOmahaUnited States
| | - Connor Branick
- Eppley Institute for Cancer Research and Fred & Pamela Buffett Cancer Center, University of Nebraska Medical CenterOmahaUnited States
| | - Kunle Odunsi
- Departments of Gynecologic Oncology, Immunology, and Center for Immunotherapy, Roswell Park Comprehensive Cancer CenterBuffaloUnited States
| | - Ronny Drapkin
- Penn Ovarian Cancer Research Center, University of Pennsylvania Perelman School of MedicinePhiladelphiaUnited States
| | - Lee Zou
- Massachusetts General Hospital Cancer Center, Harvard Medical SchoolCharlestownUnited States
| | - Adam R Karpf
- Eppley Institute for Cancer Research and Fred & Pamela Buffett Cancer Center, University of Nebraska Medical CenterOmahaUnited States
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16
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Kundu S, Ray MD, Sharma A. Interplay between genome organization and epigenomic alterations of pericentromeric DNA in cancer. J Genet Genomics 2021; 48:184-197. [PMID: 33840602 DOI: 10.1016/j.jgg.2021.02.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2020] [Revised: 02/07/2021] [Accepted: 02/20/2021] [Indexed: 12/16/2022]
Abstract
In eukaryotic genome biology, the genomic organization inside the three-dimensional (3D) nucleus is highly complex, and whether this organization governs gene expression is poorly understood. Nuclear lamina (NL) is a filamentous meshwork of proteins present at the lining of inner nuclear membrane that serves as an anchoring platform for genome organization. Large chromatin domains termed as lamina-associated domains (LADs), play a major role in silencing genes at the nuclear periphery. The interaction of the NL and genome is dynamic and stochastic. Furthermore, many genes change their positions during developmental processes or under disease conditions such as cancer, to activate certain sorts of genes and/or silence others. Pericentromeric heterochromatin (PCH) is mostly in the silenced region within the genome, which localizes at the nuclear periphery. Studies show that several genes located at the PCH are aberrantly expressed in cancer. The interesting question is that despite being localized in the pericentromeric region, how these genes still manage to overcome pericentromeric repression. Although epigenetic mechanisms control the expression of the pericentromeric region, recent studies about genome organization and genome-nuclear lamina interaction have shed light on a new aspect of pericentromeric gene regulation through a complex and coordinated interplay between epigenomic remodeling and genomic organization in cancer.
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Affiliation(s)
- Subhadip Kundu
- Laboratory of Chromatin and Cancer Epigenetics, Department of Biochemistry, All India Institute of Medical Sciences, Ansari Nagar, New Delhi 110029, India
| | - M D Ray
- Department of Surgical Oncology, IRCH, All India Institute of Medical Sciences, Ansari Nagar, New Delhi 110029, India
| | - Ashok Sharma
- Laboratory of Chromatin and Cancer Epigenetics, Department of Biochemistry, All India Institute of Medical Sciences, Ansari Nagar, New Delhi 110029, India.
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17
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18
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Evolutionary Dynamics of the POTE Gene Family in Human and Nonhuman Primates. Genes (Basel) 2020; 11:genes11020213. [PMID: 32085667 PMCID: PMC7073761 DOI: 10.3390/genes11020213] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 02/06/2020] [Accepted: 02/13/2020] [Indexed: 12/20/2022] Open
Abstract
POTE (prostate, ovary, testis, and placenta expressed) genes belong to a primate-specific gene family expressed in prostate, ovary, and testis as well as in several cancers including breast, prostate, and lung cancers. Due to their tumor-specific expression, POTEs are potential oncogenes, therapeutic targets, and biomarkers for these malignancies. This gene family maps within human and primate segmental duplications with a copy number ranging from two to 14 in different species. Due to the high sequence identity among the gene copies, specific efforts are needed to assemble these loci in order to correctly define the organization and evolution of the gene family. Using single-molecule, real-time (SMRT) sequencing, in silico analyses, and molecular cytogenetics, we characterized the structure, copy number, and chromosomal distribution of the POTE genes, as well as their expression in normal and disease tissues, and provided a comparative analysis of the POTE organization and gene structure in primate genomes. We were able, for the first time, to de novo sequence and assemble a POTE tandem duplication in marmoset that is misassembled and collapsed in the reference genome, thus revealing the presence of a second POTE copy. Taken together, our findings provide comprehensive insights into the evolutionary dynamics of the primate-specific POTE gene family, involving gene duplications, deletions, and long interspersed nuclear element (LINE) transpositions to explain the actual repertoire of these genes in human and primate genomes.
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19
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Shen Z, Feng X, Fang Y, Li Y, Li Z, Zhan Y, Lin M, Li G, Ding Y, Deng H. POTEE drives colorectal cancer development via regulating SPHK1/p65 signaling. Cell Death Dis 2019; 10:863. [PMID: 31723122 PMCID: PMC6853991 DOI: 10.1038/s41419-019-2046-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Revised: 09/08/2019] [Accepted: 10/03/2019] [Indexed: 12/24/2022]
Abstract
Aberrant gene expression plays critical roles in the development of colorectal cancer (CRC). Here we show that POTEE, which was identified as a member E of POTE ankyrin domain family, was significantly upregulated in colorectal tumors and predicted poor overall survival of CRC patients. In CRC cells, POTEE could act as an oncogene and could promote cell growth, cell-cycle progression, inhibit apoptosis, and elevates xenograft tumor growth. Mechanically, we used microarray analysis and identified a POTEE/SPHK1/p65 signaling axis, which affected the biological functions of CRC cells. Further evaluation showed that overexpression of POTEE could increase the protein expression of SPHK1, followed by promoting the phosphorylation and activation of p65 protein. Altogether, our findings suggested a POTEE/SPHK1/p65 signaling axis could promote colorectal tumorigenesis and POTEE might potentially serve as a novel biomarker for the diagnosis and an intervention of colorectal cancer.
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Affiliation(s)
- Zhiyong Shen
- Department of General Surgery, Nanfang Hospital, Southern Medical University, 1838 North Guangzhou Ave., 510515, Guangzhou, Guangdong Province, China
| | - Xiaochuang Feng
- Department of General Surgery, Nanfang Hospital, Southern Medical University, 1838 North Guangzhou Ave., 510515, Guangzhou, Guangdong Province, China
| | - Yuan Fang
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, 1838 North Guangzhou Ave., 510515, Guangzhou, Guangdong Province, China
| | - Yongsheng Li
- Department of General Surgery, Nanfang Hospital, Southern Medical University, 1838 North Guangzhou Ave., 510515, Guangzhou, Guangdong Province, China
| | - Zhenkang Li
- Department of General Surgery, Nanfang Hospital, Southern Medical University, 1838 North Guangzhou Ave., 510515, Guangzhou, Guangdong Province, China
| | - Yizhi Zhan
- Department of Pathology, Nanfang Hospital, Southern Medical University, 1838 North Guangzhou Ave., 510515, Guangzhou, Guangdong Province, China
| | - Mingdao Lin
- Department of General Surgery, Nanfang Hospital, Southern Medical University, 1838 North Guangzhou Ave., 510515, Guangzhou, Guangdong Province, China
| | - Guoxin Li
- Department of General Surgery, Nanfang Hospital, Southern Medical University, 1838 North Guangzhou Ave., 510515, Guangzhou, Guangdong Province, China
| | - Yi Ding
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, 1838 North Guangzhou Ave., 510515, Guangzhou, Guangdong Province, China.
| | - Haijun Deng
- Department of General Surgery, Nanfang Hospital, Southern Medical University, 1838 North Guangzhou Ave., 510515, Guangzhou, Guangdong Province, China.
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20
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Hillman JC, Pugacheva EM, Barger CJ, Sribenja S, Rosario S, Albahrani M, Truskinovsky AM, Stablewski A, Liu S, Loukinov DI, Zentner GE, Lobanenkov VV, Karpf AR, Higgins MJ. BORIS Expression in Ovarian Cancer Precursor Cells Alters the CTCF Cistrome and Enhances Invasiveness through GALNT14. Mol Cancer Res 2019; 17:2051-2062. [PMID: 31292201 DOI: 10.1158/1541-7786.mcr-19-0310] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Revised: 06/07/2019] [Accepted: 07/03/2019] [Indexed: 11/16/2022]
Abstract
High-grade serous carcinoma (HGSC) is the most aggressive and predominant form of epithelial ovarian cancer and the leading cause of gynecologic cancer-related death. We have previously shown that CTCFL (also known as BORIS, Brother of the Regulator of Imprinted Sites) is expressed in most ovarian cancers, and is associated with global and promoter-specific DNA hypomethylation, advanced tumor stage, and poor prognosis. To explore its role in HGSC, we expressed BORIS in human fallopian tube secretory epithelial cells (FTSEC), the presumptive cells of origin for HGSC. BORIS-expressing cells exhibited increased motility and invasion, and BORIS expression was associated with alterations in several cancer-associated gene expression networks, including fatty acid metabolism, TNF signaling, cell migration, and ECM-receptor interactions. Importantly, GALNT14, a glycosyltransferase gene implicated in cancer cell migration and invasion, was highly induced by BORIS, and GALNT14 knockdown significantly abrogated BORIS-induced cell motility and invasion. In addition, in silico analyses provided evidence for BORIS and GALNT14 coexpression in several cancers. Finally, ChIP-seq demonstrated that expression of BORIS was associated with de novo and enhanced binding of CTCF at hundreds of loci, many of which correlated with activation of transcription at target genes, including GALNT14. Taken together, our data indicate that BORIS may promote cell motility and invasion in HGSC via upregulation of GALNT14, and suggests BORIS as a potential therapeutic target in this malignancy. IMPLICATIONS: These studies provide evidence that aberrant expression of BORIS may play a role in the progression to HGSC by enhancing the migratory and invasive properties of FTSEC.
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Affiliation(s)
- Joanna C Hillman
- Department of Molecular and Cellular Biology, Roswell Park Comprehensive Cancer Center, Buffalo, New York
| | - Elena M Pugacheva
- Molecular Pathology Section, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, NIH, Rockville, Maryland
| | - Carter J Barger
- Eppley Institute and Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska
| | - Sirinapa Sribenja
- Department of Molecular and Cellular Biology, Roswell Park Comprehensive Cancer Center, Buffalo, New York
| | - Spencer Rosario
- Department of Cancer Genetics, Roswell Park Comprehensive Cancer Center, Buffalo, New York
| | - Mustafa Albahrani
- Eppley Institute and Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska
| | | | - Aimee Stablewski
- Department of Molecular and Cellular Biology, Roswell Park Comprehensive Cancer Center, Buffalo, New York
| | - Song Liu
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, New York
| | - Dmitri I Loukinov
- Molecular Pathology Section, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, NIH, Rockville, Maryland
| | - Gabriel E Zentner
- Department of Biology, Indiana University, Bloomington, Indiana.,Indiana University Melvin and Bren Simon Cancer Center, Indianapolis, Indiana
| | - Victor V Lobanenkov
- Molecular Pathology Section, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, NIH, Rockville, Maryland
| | - Adam R Karpf
- Eppley Institute and Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska.
| | - Michael J Higgins
- Department of Molecular and Cellular Biology, Roswell Park Comprehensive Cancer Center, Buffalo, New York.
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Sharma A, Albahrani M, Zhang W, Kufel CN, James SR, Odunsi K, Klinkebiel D, Karpf AR. Epigenetic activation of POTE genes in ovarian cancer. Epigenetics 2019; 14:185-197. [PMID: 30764732 DOI: 10.1080/15592294.2019.1581590] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Abstract
The POTE gene family consists of 14 homologous genes localized to autosomal pericentromeres, and a sub-set of POTEs are cancer-testis antigen (CTA) genes. POTEs are over-expressed in epithelial ovarian cancer (EOC), including the high-grade serous subtype (HGSC), and expression of individual POTEs correlates with chemoresistance and reduced survival in HGSC. The mechanisms driving POTE overexpression in EOC and other cancers is unknown. Here, we investigated the role of epigenetics in regulating POTE expression, with a focus on DNA hypomethylation. Consistent with their pericentromeric localization, Pan-POTE expression in EOC correlated with expression of the pericentromeric repeat NBL2, which was not the case for non-pericentromeric CTAs. POTE genomic regions contain LINE-1 (L1) sequences, and Pan-POTE expression correlated with both global and POTE-specific L1 hypomethylation in EOC. Analysis of individual POTEs using RNA-seq and DNA methylome data from fallopian tube epithelia (FTE) and HGSC revealed that POTEs C, E, and F have increased expression in HGSC in conjunction with DNA hypomethylation at 5' promoter or enhancer regions. Moreover, POTEs C/E/F showed additional increased expression in recurrent HGSC in conjunction with 5' hypomethylation, using patient-matched samples. Experiments using decitabine treatment and DNMT knockout cell lines verified a functional contribution of DNA methylation to POTE repression, and epigenetic drug combinations targeting histone deacetylases (HDACs) and histone methyltransferases (HMTs) in combination with decitabine further increased POTE expression. In summary, several alterations of the cancer epigenome, including pericentromeric activation, global and locus-specific L1 hypomethylation, and locus-specific 5' CpG hypomethylation, converge to promote POTE expression in ovarian cancer.
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Affiliation(s)
- Ashok Sharma
- a Eppley Institute , University of Nebraska Medical Center , Omaha , NE , USA.,b Fred & Pamela Buffett Cancer Center , University of Nebraska Medical Center , Omaha , NE , USA
| | - Mustafa Albahrani
- a Eppley Institute , University of Nebraska Medical Center , Omaha , NE , USA.,b Fred & Pamela Buffett Cancer Center , University of Nebraska Medical Center , Omaha , NE , USA
| | - Wa Zhang
- a Eppley Institute , University of Nebraska Medical Center , Omaha , NE , USA.,b Fred & Pamela Buffett Cancer Center , University of Nebraska Medical Center , Omaha , NE , USA
| | - Christina N Kufel
- c Department of Pharmacology and Therapeutics , Roswell Park Comprehensive Cancer Center , Buffalo , NY , USA
| | - Smitha R James
- c Department of Pharmacology and Therapeutics , Roswell Park Comprehensive Cancer Center , Buffalo , NY , USA
| | - Kunle Odunsi
- d Department of Immunology , Roswell Park Comprehensive Cancer Center , Buffalo , NY , USA.,e Department of Gynecologic Oncology , Roswell Park Comprehensive Cancer Center , Buffalo , NY , USA.,f Center for Immunotherapy , Roswell Park Comprehensive Cancer Center , Buffalo , NY , USA
| | - David Klinkebiel
- b Fred & Pamela Buffett Cancer Center , University of Nebraska Medical Center , Omaha , NE , USA.,g Department of Biochemistry and Molecular Biology , University of Nebraska Medical Center , Omaha , NE , USA
| | - Adam R Karpf
- a Eppley Institute , University of Nebraska Medical Center , Omaha , NE , USA.,b Fred & Pamela Buffett Cancer Center , University of Nebraska Medical Center , Omaha , NE , USA.,c Department of Pharmacology and Therapeutics , Roswell Park Comprehensive Cancer Center , Buffalo , NY , USA
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