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Murtadha M, Park M, Zhu Y, Caserta E, Napolitano O, Tandoh T, Moloudizargari M, Pozhitkov A, Singer M, Dona AA, Vahed H, Gonzalez A, Ly K, Ouyang C, Sanchez JF, Nigam L, Duplan A, Chowdhury A, Ghoda L, Li L, Zhang B, Krishnan A, Marcucci G, Williams JC, Pichiorri F. A CD38-directed, single-chain T-cell engager targets leukemia stem cells through IFN-γ-induced CD38 expression. Blood 2024; 143:1599-1615. [PMID: 38394668 PMCID: PMC11103097 DOI: 10.1182/blood.2023021570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 12/22/2023] [Accepted: 12/25/2023] [Indexed: 02/25/2024] Open
Abstract
ABSTRACT Treatment resistance of leukemia stem cells (LSCs) and suppression of the autologous immune system represent major challenges to achieve a cure in acute myeloid leukemia (AML). Although AML blasts generally retain high levels of surface CD38 (CD38pos), LSCs are frequently enriched in the CD34posCD38neg blast fraction. Here, we report that interferon gamma (IFN-γ) reduces LSCs clonogenic activity and induces CD38 upregulation in both CD38pos and CD38neg LSC-enriched blasts. IFN-γ-induced CD38 upregulation depends on interferon regulatory factor 1 transcriptional activation of the CD38 promoter. To leverage this observation, we created a novel compact, single-chain CD38-CD3 T-cell engager (BN-CD38) designed to promote an effective immunological synapse between CD38pos AML cells and both CD8pos and CD4pos T cells. We demonstrate that BN-CD38 engages autologous CD4pos and CD8pos T cells and CD38pos AML blasts, leading to T-cell activation and expansion and to the elimination of leukemia cells in an autologous setting. Importantly, BN-CD38 engagement induces the release of high levels of IFN-γ, driving the expression of CD38 on CD34posCD38neg LSC-enriched blasts and their subsequent elimination. Critically, although BN-CD38 showed significant in vivo efficacy across multiple disseminated AML cell lines and patient-derived xenograft models, it did not affect normal hematopoietic stem cell clonogenicity and the development of multilineage human immune cells in CD34pos humanized mice. Taken together, this study provides important insights to target and eliminate AML LSCs.
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Affiliation(s)
- Mariam Murtadha
- Department of Hematology and Hematopoietic Cell Transplantation, Judy and Bernard Briskin Center for Multiple Myeloma Research, City of Hope, Duarte, CA
- Department of Hematologic Malignancies Translational Science, Beckman Research Institute, City of Hope, Duarte, CA
| | - Miso Park
- Department of Cancer Biology and Molecular Medicine, Beckman Research Institute, City of Hope, Duarte, CA
| | - Yinghui Zhu
- Department of Hematology and Hematopoietic Cell Transplantation, Judy and Bernard Briskin Center for Multiple Myeloma Research, City of Hope, Duarte, CA
- Department of Hematologic Malignancies Translational Science, Beckman Research Institute, City of Hope, Duarte, CA
- Research Center for Translational Medicine, Shanghai East Hospital, Frontier Science Center for Stem Cell Research, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Enrico Caserta
- Department of Hematology and Hematopoietic Cell Transplantation, Judy and Bernard Briskin Center for Multiple Myeloma Research, City of Hope, Duarte, CA
- Department of Hematologic Malignancies Translational Science, Beckman Research Institute, City of Hope, Duarte, CA
| | - Ottavio Napolitano
- Department of Hematology and Hematopoietic Cell Transplantation, Judy and Bernard Briskin Center for Multiple Myeloma Research, City of Hope, Duarte, CA
- Department of Hematologic Malignancies Translational Science, Beckman Research Institute, City of Hope, Duarte, CA
| | - Theophilus Tandoh
- Department of Hematology and Hematopoietic Cell Transplantation, Judy and Bernard Briskin Center for Multiple Myeloma Research, City of Hope, Duarte, CA
- Department of Hematologic Malignancies Translational Science, Beckman Research Institute, City of Hope, Duarte, CA
| | - Milad Moloudizargari
- Department of Hematology and Hematopoietic Cell Transplantation, Judy and Bernard Briskin Center for Multiple Myeloma Research, City of Hope, Duarte, CA
- Department of Hematologic Malignancies Translational Science, Beckman Research Institute, City of Hope, Duarte, CA
| | - Alex Pozhitkov
- Department of Hematology and Hematopoietic Cell Transplantation, Judy and Bernard Briskin Center for Multiple Myeloma Research, City of Hope, Duarte, CA
- Department of Hematologic Malignancies Translational Science, Beckman Research Institute, City of Hope, Duarte, CA
| | - Mahmoud Singer
- Department of Hematology and Hematopoietic Cell Transplantation, Judy and Bernard Briskin Center for Multiple Myeloma Research, City of Hope, Duarte, CA
- Department of Hematologic Malignancies Translational Science, Beckman Research Institute, City of Hope, Duarte, CA
| | - Ada Alice Dona
- Department of Hematology and Hematopoietic Cell Transplantation, Judy and Bernard Briskin Center for Multiple Myeloma Research, City of Hope, Duarte, CA
- Department of Hematologic Malignancies Translational Science, Beckman Research Institute, City of Hope, Duarte, CA
| | - Hawa Vahed
- Department of Hematology and Hematopoietic Cell Transplantation, Judy and Bernard Briskin Center for Multiple Myeloma Research, City of Hope, Duarte, CA
- Department of Hematologic Malignancies Translational Science, Beckman Research Institute, City of Hope, Duarte, CA
| | - Asaul Gonzalez
- Department of Cancer Biology and Molecular Medicine, Beckman Research Institute, City of Hope, Duarte, CA
| | - Kevin Ly
- Department of Cancer Biology and Molecular Medicine, Beckman Research Institute, City of Hope, Duarte, CA
| | - Ching Ouyang
- Integrative Genomics Core, City of Hope Comprehensive Cancer Center, City of Hope, Duarte, CA
| | - James F. Sanchez
- Department of Hematology and Hematopoietic Cell Transplantation, Judy and Bernard Briskin Center for Multiple Myeloma Research, City of Hope, Duarte, CA
| | - Lokesh Nigam
- Department of Hematology and Hematopoietic Cell Transplantation, Judy and Bernard Briskin Center for Multiple Myeloma Research, City of Hope, Duarte, CA
- Department of Hematologic Malignancies Translational Science, Beckman Research Institute, City of Hope, Duarte, CA
| | - Amanda Duplan
- Department of Hematologic Malignancies Translational Science, Beckman Research Institute, City of Hope, Duarte, CA
| | - Arnab Chowdhury
- Department of Hematology and Hematopoietic Cell Transplantation, Judy and Bernard Briskin Center for Multiple Myeloma Research, City of Hope, Duarte, CA
- Department of Computational and Quantitative Medicine, Beckman Research Institute, City of Hope, Duarte, CA
| | - Lucy Ghoda
- Department of Hematologic Malignancies Translational Science, Beckman Research Institute, City of Hope, Duarte, CA
| | - Ling Li
- Department of Hematologic Malignancies Translational Science, Beckman Research Institute, City of Hope, Duarte, CA
| | - Bin Zhang
- Department of Hematologic Malignancies Translational Science, Beckman Research Institute, City of Hope, Duarte, CA
| | - Amrita Krishnan
- Department of Hematology and Hematopoietic Cell Transplantation, Judy and Bernard Briskin Center for Multiple Myeloma Research, City of Hope, Duarte, CA
| | - Guido Marcucci
- Department of Hematologic Malignancies Translational Science, Beckman Research Institute, City of Hope, Duarte, CA
| | - John C. Williams
- Department of Cancer Biology and Molecular Medicine, Beckman Research Institute, City of Hope, Duarte, CA
| | - Flavia Pichiorri
- Department of Hematology and Hematopoietic Cell Transplantation, Judy and Bernard Briskin Center for Multiple Myeloma Research, City of Hope, Duarte, CA
- Department of Hematologic Malignancies Translational Science, Beckman Research Institute, City of Hope, Duarte, CA
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2
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Hasan A, Khan NA, Uddin S, Khan AQ, Steinhoff M. Deregulated transcription factors in the emerging cancer hallmarks. Semin Cancer Biol 2024; 98:31-50. [PMID: 38123029 DOI: 10.1016/j.semcancer.2023.12.001] [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: 09/28/2023] [Revised: 11/25/2023] [Accepted: 12/14/2023] [Indexed: 12/23/2023]
Abstract
Cancer progression is a multifaceted process that entails several stages and demands the persistent expression or activation of transcription factors (TFs) to facilitate growth and survival. TFs are a cluster of proteins with DNA-binding domains that attach to promoter or enhancer DNA strands to start the transcription of genes by collaborating with RNA polymerase and other supporting proteins. They are generally acknowledged as the major regulatory molecules that coordinate biological homeostasis and the appropriate functioning of cellular components, subsequently contributing to human physiology. TFs proteins are crucial for controlling transcription during the embryonic stage and development, and the stability of different cell types depends on how they function in different cell types. The development and progression of cancer cells and tumors might be triggered by any anomaly in transcription factor function. It has long been acknowledged that cancer development is accompanied by the dysregulated activity of TF alterations which might result in faulty gene expression. Recent studies have suggested that dysregulated transcription factors play a major role in developing various human malignancies by altering and rewiring metabolic processes, modifying the immune response, and triggering oncogenic signaling cascades. This review emphasizes the interplay between TFs involved in metabolic and epigenetic reprogramming, evading immune attacks, cellular senescence, and the maintenance of cancer stemness in cancerous cells. The insights presented herein will facilitate the development of innovative therapeutic modalities to tackle the dysregulated transcription factors underlying cancer.
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Affiliation(s)
- Adria Hasan
- Molecular Cell Biology Laboratory, Integral Information and Research Centre-4 (IIRC-4), Integral University, Lucknow 226026, India; Department of Bioengineering, Faculty of Engineering, Integral University, Lucknow 226026, India
| | - Naushad Ahmad Khan
- Department of Surgery, Trauma and Vascular Surgery Clinical Research, Hamad General Hospital, Doha 3050, Qatar
| | - Shahab Uddin
- Translational Research Institute, Academic Health System, Hamad Medical Corporation, Doha 3050, Qatar; Department of Biosciences, Integral University, Lucknow 226026, India; Animal Research Center, Qatar University, Doha, Qatar; Dermatology Institute, Academic Health System, Hamad Medical Corporation, Doha 3050, Qatar
| | - Abdul Q Khan
- Translational Research Institute, Academic Health System, Hamad Medical Corporation, Doha 3050, Qatar.
| | - Martin Steinhoff
- Translational Research Institute, Academic Health System, Hamad Medical Corporation, Doha 3050, Qatar; Animal Research Center, Qatar University, Doha, Qatar; Department of Dermatology and Venereology, Rumailah Hospital, Hamad Medical Corporation, Doha 3050, Qatar; Department of Medicine, Weill Cornell Medicine Qatar, Qatar Foundation-Education City, Doha 24144, Qatar; Department of Medicine, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA; College of Medicine, Qatar University, Doha 2713, Qatar
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Sun X, Yang Y, Meng X, Li J, Liu X, Liu H. PANoptosis: Mechanisms, biology, and role in disease. Immunol Rev 2024; 321:246-262. [PMID: 37823450 DOI: 10.1111/imr.13279] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 09/16/2023] [Accepted: 09/19/2023] [Indexed: 10/13/2023]
Abstract
Cell death can be executed through distinct subroutines. PANoptosis is a unique inflammatory cell death modality involving the interactions between pyroptosis, apoptosis, and necroptosis, which can be mediated by multifaceted PANoptosome complexes assembled via integrating components from other cell death modalities. There is growing interest in the process and function of PANoptosis. Accumulating evidence suggests that PANoptosis occurs under diverse stimuli, for example, viral or bacterial infection, cytokine storm, and cancer. Given the impact of PANoptosis across the disease spectrum, this review briefly describes the relationships between pyroptosis, apoptosis, and necroptosis, highlights the key molecules in PANoptosome formation and PANoptosis activation, and outlines the multifaceted roles of PANoptosis in diseases together with a potential for therapeutic targeting. We also discuss important concepts and pressing issues for future PANoptosis research. Improved understanding of PANoptosis and its mechanisms is crucial for identifying novel therapeutic targets and strategies.
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Affiliation(s)
- Xu Sun
- Department of Integrated Chinese and Western Medicine, Affiliated Cancer Hospital of Zhengzhou University and Henan Cancer Hospital, Zhengzhou, China
| | - Yanpeng Yang
- Cardiac Care Unit, Zhengzhou Central Hospital Affiliated to Zhengzhou University, Zhengzhou, China
| | - Xiaona Meng
- Department of Integrated Chinese and Western Medicine, Affiliated Cancer Hospital of Zhengzhou University and Henan Cancer Hospital, Zhengzhou, China
| | - Jia Li
- Department of Integrated Chinese and Western Medicine, Affiliated Cancer Hospital of Zhengzhou University and Henan Cancer Hospital, Zhengzhou, China
| | - Xiaoli Liu
- Department of Integrated Chinese and Western Medicine, Affiliated Cancer Hospital of Zhengzhou University and Henan Cancer Hospital, Zhengzhou, China
| | - Huaimin Liu
- Department of Integrated Chinese and Western Medicine, Affiliated Cancer Hospital of Zhengzhou University and Henan Cancer Hospital, Zhengzhou, China
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4
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Yang X, Wang H, Zhang L, Yao S, Dai J, Wen G, An J, Jin H, Du Q, Hu Y, Zheng L, Chen X, Yi Z, Tuo B. Novel roles of karyopherin subunit alpha 2 in hepatocellular carcinoma. Biomed Pharmacother 2023; 163:114792. [PMID: 37121148 DOI: 10.1016/j.biopha.2023.114792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 04/05/2023] [Accepted: 04/24/2023] [Indexed: 05/02/2023] Open
Abstract
Hepatocellular carcinoma is the most common type of liver cancer and associated with a high fatality rate. This disease poses a major threat to human health worldwide. A considerable number of genetic and epigenetic factors are involved in the development of hepatocellular carcinoma. However, the molecular mechanism underlying the progression of hepatocellular carcinoma remains unclear. Karyopherin subunit alpha 2 (KPNA2), also termed importin α1, is a member of the nuclear transporter family. In recent years, KPNA2 has been gradually linked to the nuclear transport pathway for a variety of tumor-associated proteins. Furthermore, it promotes tumor development by participating in various pathophysiological processes such as cell proliferation, apoptosis, immune response, and viral infection. In hepatocellular carcinoma, it has been found that KPNA2 expression is significantly higher in liver cancer tissues versus paracancerous tissues. Moreover, it has been identified as a marker of poor prognosis and early recurrence in patients with hepatocellular carcinoma. Nevertheless, the role of KPNA2 in the development of hepatocellular carcinoma remains to be determined. This review summarizes the current knowledge on the pathogenesis and role of KPNA2 in hepatocellular carcinoma, and provides new directions and strategies for the diagnosis, treatment, and prediction of prognosis of this disease.
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Affiliation(s)
- Xingyue Yang
- Department of Gastroenterology, Digestive Disease Hospital, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Hu Wang
- Department of General Surgery, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Li Zhang
- Department of Gastroenterology, Digestive Disease Hospital, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Shun Yao
- Department of Gastroenterology, Digestive Disease Hospital, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Jing Dai
- Department of Gastroenterology, Digestive Disease Hospital, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Guorong Wen
- Department of Gastroenterology, Digestive Disease Hospital, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Jiaxing An
- Department of Gastroenterology, Digestive Disease Hospital, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Hai Jin
- Department of Gastroenterology, Digestive Disease Hospital, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Qian Du
- Department of Gastroenterology, Digestive Disease Hospital, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Yanxia Hu
- Department of Gastroenterology, Digestive Disease Hospital, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Liming Zheng
- Department of Gastroenterology, Digestive Disease Hospital, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Xingyue Chen
- Department of Gastroenterology, Digestive Disease Hospital, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Zhiqiang Yi
- Department of Gastroenterology, Digestive Disease Hospital, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Biguang Tuo
- Department of Gastroenterology, Digestive Disease Hospital, Affiliated Hospital of Zunyi Medical University, Zunyi, China; The Collaborative Innovation Center of Tissue Damage Repair and Regenerative Medicine of Zunyi Medical University, Zunyi, China.
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5
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Numpadit S, Ito C, Nakaya T, Hagiwara K. Investigation of oncolytic effect of recombinant Newcastle disease virus in primary and metastatic oral melanoma. Med Oncol 2023; 40:138. [PMID: 37022566 PMCID: PMC10079733 DOI: 10.1007/s12032-023-02002-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 03/20/2023] [Indexed: 04/07/2023]
Abstract
Malignant melanoma is aggressive cancer with a high rate of local invasiveness and metastasis. Currently, the treatment options for patients with advanced-stage and metastatic oral melanoma are limited. A promising treatment option is oncolytic viral therapy. This study aimed to evaluate novel therapies for malignant melanoma using a canine model. Oral melanoma, which frequently occurs in dogs is used as a model for human melanoma, was isolated and cultured and used for the evaluation of the tumor lytic effect induced by viral infection. We constructed a recombinant Newcastle disease virus (rNDV) that promotes the extracellular release of IFNγ from the virus-infected melanoma. The expression of oncolytic and apoptosis-related genes, the immune response by lymphocytes, and IFNγ expression were evaluated in virus-infected melanoma cells. The results showed that the rate of rNDV infection varied according to the isolated melanoma cells and the oncolytic effect differed between melanoma cells owing to the infectivity of the virus. The oncolytic effect tended to be greater for the IFNγ-expressing virus than for the GFP-expressing prototype virus. Additionally, lymphocytes co-cultured with the virus showed induced expression of Th1 cytokines. Therefore, recombinant NDV expressing IFNγ is expected to induce cellular immunity and oncolytic activity. This oncolytic treatment shows promise as a therapeutic approach for melanoma treatment once evaluated using clinical samples from humans.
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Affiliation(s)
- Supaporn Numpadit
- School of Veterinary Medicine, Rakuno Gakuen University, Ebetsu, Hokkaido, 069-8501, Japan
| | - Chiaki Ito
- School of Veterinary Medicine, Rakuno Gakuen University, Ebetsu, Hokkaido, 069-8501, Japan
| | - Takaaki Nakaya
- Department of Infectious Disease, Kyoto Prefectural University of Medicine, Kamigyo-ku Kajii-cho, Kawaramachi-Hirokoji, Kyoto-shi, 602-8566, Japan
| | - Katsuro Hagiwara
- School of Veterinary Medicine, Rakuno Gakuen University, Ebetsu, Hokkaido, 069-8501, Japan.
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Merhi M, Ahmad F, Taib N, Inchakalody V, Uddin S, Shablak A, Dermime S. The complex network of transcription factors, immune checkpoint inhibitors and stemness features in colorectal cancer: A recent update. Semin Cancer Biol 2023; 89:1-17. [PMID: 36621515 DOI: 10.1016/j.semcancer.2023.01.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 12/19/2022] [Accepted: 01/04/2023] [Indexed: 01/07/2023]
Abstract
Cancer immunity is regulated by several mechanisms that include co-stimulatory and/or co-inhibitory molecules known as immune checkpoints expressed by the immune cells. In colorectal cancer (CRC), CTLA-4, LAG3, TIM-3 and PD-1 are the major co-inhibitory checkpoints involved in tumor development and progression. On the other hand, the deregulation of transcription factors and cancer stem cells activity plays a major role in the development of drug resistance and in the spread of metastatic disease in CRC. In this review, we describe how the modulation of such transcription factors affects the response of CRC to therapies. We also focus on the role of cancer stem cells in tumor metastasis and chemoresistance and discuss both preclinical and clinical approaches for targeting stem cells to prevent their tumorigenic effect. Finally, we provide an update on the clinical applications of immune checkpoint inhibitors in CRC and discuss the regulatory effects of transcription factors on the expression of the immune inhibitory checkpoints with specific focus on the PD-1 and PD-L1 molecules.
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Affiliation(s)
- Maysaloun Merhi
- Translational Cancer Research Facility, Translational Research Institute, Hamad Medical Corporation, Doha, Qatar; National Center for Cancer Care and Research, Hamad Medical Corporation, Doha, Qatar
| | - Fareed Ahmad
- Translational Research Institute and Dermatology Institute, Academic Health System, Hamad Medical Corporation, Doha, Qatar
| | - Nassiba Taib
- Translational Cancer Research Facility, Translational Research Institute, Hamad Medical Corporation, Doha, Qatar
| | - Varghese Inchakalody
- Translational Cancer Research Facility, Translational Research Institute, Hamad Medical Corporation, Doha, Qatar; National Center for Cancer Care and Research, Hamad Medical Corporation, Doha, Qatar
| | - Shahab Uddin
- Translational Research Institute and Dermatology Institute, Academic Health System, Hamad Medical Corporation, Doha, Qatar; Laboratory Animal Research Center, Qatar University, Doha, Qatar
| | - Alaaeldin Shablak
- National Center for Cancer Care and Research, Hamad Medical Corporation, Doha, Qatar
| | - Said Dermime
- Translational Cancer Research Facility, Translational Research Institute, Hamad Medical Corporation, Doha, Qatar; National Center for Cancer Care and Research, Hamad Medical Corporation, Doha, Qatar; College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar.
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7
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Orbach SM, Brooks MD, Zhang Y, Campit SE, Bushnell GG, Decker JT, Rebernick RJ, Chandrasekaran S, Wicha MS, Jeruss JS, Shea LD. Single-cell RNA-sequencing identifies anti-cancer immune phenotypes in the early lung metastatic niche during breast cancer. Clin Exp Metastasis 2022; 39:865-881. [PMID: 36002598 DOI: 10.1007/s10585-022-10185-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 07/28/2022] [Indexed: 11/29/2022]
Abstract
Microenvironmental changes in the early metastatic niche may be exploited to identify therapeutic targets to inhibit secondary tumor formation and improve disease outcomes. We dissected the developing lung metastatic niche in a model of metastatic, triple-negative breast cancer using single-cell RNA-sequencing. Lungs were extracted from mice at 7-, 14-, or 21 days after tumor inoculation corresponding to the pre-metastatic, micro-metastatic, and metastatic niche, respectively. The progression of the metastatic niche was marked by an increase in neutrophil infiltration (5% of cells at day 0 to 81% of cells at day 21) and signaling pathways corresponding to the hallmarks of cancer. Importantly, the pre-metastatic and early metastatic niche were composed of immune cells with an anti-cancer phenotype not traditionally associated with metastatic disease. As expected, the metastatic niche exhibited pro-cancer phenotypes. The transition from anti-cancer to pro-cancer phenotypes was directly associated with neutrophil and monocyte behaviors at these time points. Predicted metabolic, transcription factor, and receptor-ligand signaling suggested that changes in the neutrophils likely induced the transitions in the other immune cells. Conditioned medium generated by cells extracted from the pre-metastatic niche successfully inhibited tumor cell proliferation and migration in vitro and the in vivo depletion of pre-metastatic neutrophils and monocytes worsened survival outcomes, thus validating the anti-cancer phenotype of the developing niche. Genes associated with the early anti-cancer response could act as biomarkers that could serve as targets for the treatment of early metastatic disease. Such therapies have the potential to revolutionize clinical outcomes in metastatic breast cancer.
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Affiliation(s)
- Sophia M Orbach
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, USA
| | - Michael D Brooks
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Yining Zhang
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI, USA
| | - Scott E Campit
- Program in Chemical Biology, University of Michigan, Ann Arbor, MI, USA
| | - Grace G Bushnell
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, USA
| | - Joseph T Decker
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, USA
| | - Ryan J Rebernick
- Medical Science Training Program, University of Michigan, Ann Arbor, MI, USA
| | - Sriram Chandrasekaran
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, USA.,Program in Chemical Biology, University of Michigan, Ann Arbor, MI, USA.,Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA.,Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA
| | - Max S Wicha
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA.,Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA
| | - Jacqueline S Jeruss
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, USA.,Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA.,Department of Surgery, University of Michigan, Ann Arbor, MI, USA.,Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Lonnie D Shea
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, USA. .,Department of Chemical Engineering, University of Michigan, Ann Arbor, MI, USA. .,Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA.
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8
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Tsai KK, Huang SS, Northey JJ, Liao WY, Hsu CC, Cheng LH, Werner ME, Chuu CP, Chatterjee C, Lakins JN, Weaver VM. Screening of organoids derived from patients with breast cancer implicates the repressor NCOR2 in cytotoxic stress response and antitumor immunity. NATURE CANCER 2022; 3:734-752. [PMID: 35618935 PMCID: PMC9246917 DOI: 10.1038/s43018-022-00375-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 04/08/2022] [Indexed: 12/31/2022]
Abstract
Resistance to antitumor treatment contributes to patient mortality. Functional proteomic screening of organoids derived from chemotherapy-treated patients with breast cancer identified nuclear receptor corepressor 2 (NCOR2) histone deacetylase as an inhibitor of cytotoxic stress response and antitumor immunity. High NCOR2 in the tumors of patients with breast cancer predicted chemotherapy refractoriness, tumor recurrence and poor prognosis. Molecular studies revealed that NCOR2 inhibits antitumor treatment by regulating histone deacetylase 3 (HDAC3) to repress interferon regulatory factor 1 (IRF-1)-dependent gene expression and interferon (IFN) signaling. Reducing NCOR2 or impeding its epigenetic activity by modifying its interaction with HDAC3 enhanced chemotherapy responsiveness and restored antitumor immunity. An adeno-associated viral NCOR2-HDAC3 competitor potentiated chemotherapy and immune checkpoint therapy in culture and in vivo by permitting transcription of IRF-1-regulated proapoptosis and inflammatory genes to increase IFN-γ signaling. The findings illustrate the utility of patient-derived organoids for drug discovery and suggest that targeting stress and inflammatory-repressor complexes such as NCOR2-HDAC3 could overcome treatment resistance and improve the outcome of patients with cancer.
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Affiliation(s)
- Kelvin K Tsai
- Department of Surgery and Center for Bioengineering and Tissue Regeneration, University of California, San Francisco, CA, USA.
- Department of Radiation Oncology, Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.
- Department of Bioengineering and Therapeutic Sciences, Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.
- Laboratory of Advanced Molecular Therapeutics, Graduate Institute of Clinical Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan.
- Department of Medicine, Wan Fang Hospital, Taipei Medical University, Taipei, Taiwan.
| | - Shenq-Shyang Huang
- Laboratory of Advanced Molecular Therapeutics, Graduate Institute of Clinical Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Jason J Northey
- Department of Surgery and Center for Bioengineering and Tissue Regeneration, University of California, San Francisco, CA, USA
| | - Wen-Ying Liao
- Laboratory of Advanced Molecular Therapeutics, Graduate Institute of Clinical Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Chung-Chi Hsu
- Laboratory of Advanced Molecular Therapeutics, Graduate Institute of Clinical Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Li-Hsin Cheng
- Laboratory of Advanced Molecular Therapeutics, Graduate Institute of Clinical Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Michael E Werner
- Department of Surgery and Center for Bioengineering and Tissue Regeneration, University of California, San Francisco, CA, USA
| | - Chih-Pin Chuu
- Institute of Cellular and System Medicine, National Health Research Institutes, Miaoli, Taiwan
| | - Chandrima Chatterjee
- Department of Pathology and Institute for Medicine and Engineering, University of Pennsylvania, Philadelphia, PA, USA
| | - Jonathon N Lakins
- Department of Surgery and Center for Bioengineering and Tissue Regeneration, University of California, San Francisco, CA, USA
- Department of Pathology and Institute for Medicine and Engineering, University of Pennsylvania, Philadelphia, PA, USA
| | - Valerie M Weaver
- Department of Surgery and Center for Bioengineering and Tissue Regeneration, University of California, San Francisco, CA, USA.
- Department of Radiation Oncology, Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.
- Department of Bioengineering and Therapeutic Sciences, Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.
- Department of Pathology and Institute for Medicine and Engineering, University of Pennsylvania, Philadelphia, PA, USA.
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9
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Cooperative effects of RIG-I-like receptor signaling and IRF1 on DNA damage-induced cell death. Cell Death Dis 2022; 13:364. [PMID: 35436994 PMCID: PMC9016077 DOI: 10.1038/s41419-022-04797-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 03/17/2022] [Accepted: 03/30/2022] [Indexed: 12/19/2022]
Abstract
Properly responding to DNA damage is vital for eukaryotic cells, including the induction of DNA repair, growth arrest and, as a last resort to prevent neoplastic transformation, cell death. Besides being crucial for ensuring homeostasis, the same pathways and mechanisms are at the basis of chemoradiotherapy in cancer treatment, which involves therapeutic induction of DNA damage by chemical or physical (radiological) measures. Apart from typical DNA damage response mediators, the relevance of cell-intrinsic antiviral signaling pathways in response to DNA breaks has recently emerged. Originally known for combatting viruses via expression of antiviral factors including interferons (IFNs) and establishing of an antiviral state, RIG-I-like receptors (RLRs) were found to be critical for adequate induction of cell death upon the introduction of DNA double-strand breaks. We here show that presence of IRF3 is crucial in this process, most likely through direct activation of pro-apoptotic factors rather than transcriptional induction of canonical downstream components, such as IFNs. Investigating genes reported to be involved in both DNA damage response and antiviral signaling, we demonstrate that IRF1 is an obligatory factor for DNA damage-induced cell death. Interestingly, its regulation does not require activation of RLR signaling, but rather sensing of DNA double-strand breaks by ATM and ATR. Hence, even though independently regulated, both RLR signaling and IRF1 are essential for full-fledged induction/execution of DNA damage-mediated cell death programs. Our results not only support more broadly developing IRF1 as a biomarker predictive for the effectiveness of chemoradiotherapy, but also suggest investigating a combined pharmacological stimulation of RLR and IRF1 signaling as a potential adjuvant regimen in tumor therapy.
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10
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Ji X, Meng W, Liu Z, Mu X. Emerging Roles of lncRNAs Regulating RNA-Mediated Type-I Interferon Signaling Pathway. Front Immunol 2022; 13:811122. [PMID: 35280983 PMCID: PMC8914027 DOI: 10.3389/fimmu.2022.811122] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 02/01/2022] [Indexed: 12/14/2022] Open
Abstract
The type-I interferon (IFN-I) signaling pathway plays pivot roles in defending against pathogen invasion. Exogenous ssRNA and dsRNA could be immunogenic. RNA-mediated IFN signaling is extensively studied in the field. The incorrect functioning of this pathway leads to either autoimmune diseases or suffering from microorganism invasion. From the discrimination of “self” and “non-self” molecules by receptors to the fine-tune modulations in downstream cascades, all steps are under the surveillance featured by complex feedbacks and regulators. Studies in recent years highlighted the emerging roles of long noncoding RNAs (lncRNAs) as a reservoir for signaling regulation. LncRNAs bind to targets through the structure and sequence, and thus the mechanisms of action can be complex and specific. Here, we summarized lncRNAs modulating the RNA-activated IFN-I signaling pathway according to the event order during the signaling. We hope this review help understand how lncRNAs are participating in the regulation of IFN-I signaling.
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Affiliation(s)
- Xiaoxin Ji
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
- Tianjin University and Health-Biotech United Group Joint Laboratory of Innovative Drug Development and Translational Medicine, Tianjin University, Tianjin, China
| | - Wei Meng
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
- Tianjin University and Health-Biotech United Group Joint Laboratory of Innovative Drug Development and Translational Medicine, Tianjin University, Tianjin, China
| | - Zichuan Liu
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
- Tianjin University and Health-Biotech United Group Joint Laboratory of Innovative Drug Development and Translational Medicine, Tianjin University, Tianjin, China
- *Correspondence: Zichuan Liu, ; Xin Mu,
| | - Xin Mu
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
- Tianjin University and Health-Biotech United Group Joint Laboratory of Innovative Drug Development and Translational Medicine, Tianjin University, Tianjin, China
- *Correspondence: Zichuan Liu, ; Xin Mu,
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11
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Sauerer T, Lischer C, Weich A, Berking C, Vera J, Dörrie J. Single-Molecule RNA Sequencing Reveals IFNγ-Induced Differential Expression of Immune Escape Genes in Merkel Cell Polyomavirus-Positive MCC Cell Lines. Front Microbiol 2021; 12:785662. [PMID: 35003017 PMCID: PMC8727593 DOI: 10.3389/fmicb.2021.785662] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 11/18/2021] [Indexed: 12/15/2022] Open
Abstract
Merkel cell carcinoma (MCC) is a rare and highly aggressive cancer, which is mainly caused by genomic integration of the Merkel cell polyomavirus and subsequent expression of a truncated form of its large T antigen. The resulting primary tumor is known to be immunogenic and under constant pressure to escape immune surveillance. Because interferon gamma (IFNγ), a key player of immune response, is secreted by many immune effector cells and has been shown to exert both anti-tumoral and pro-tumoral effects, we studied the transcriptomic response of MCC cells to IFNγ. In particular, immune modulatory effects that may help the tumor evade immune surveillance were of high interest to our investigation. The effect of IFNγ treatment on the transcriptomic program of three MCC cell lines (WaGa, MKL-1, and MKL-2) was analyzed using single-molecule sequencing via the Oxford Nanopore platform. A significant differential expression of several genes was detected across all three cell lines. Subsequent pathway analysis and manual annotation showed a clear upregulation of genes involved in the immune escape of tumor due to IFNγ treatment. The analysis of selected genes on protein level underlined our sequencing results. These findings contribute to a better understanding of immune escape of MCC and may help in clinical treatment of MCC patients. Furthermore, we demonstrate that single-molecule sequencing can be used to assess characteristics of large eukaryotic transcriptomes and thus contribute to a broader access to sequencing data in the community due to its low cost of entry.
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Affiliation(s)
- Tatjana Sauerer
- RNA-based Immunotherapy, Hautklinik, Comprehensive Cancer Center Erlangen European Metropolitan Area of Nuremberg, Deutsches Zentrum Immuntherapie, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Christopher Lischer
- Systems Tumor Immunology, Hautklinik, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Comprehensive Cancer Center Erlangen European Metropolitan Area of Nuremberg, Deutsches Zentrum Immuntherapie, Erlangen, Germany
| | - Adrian Weich
- Systems Tumor Immunology, Hautklinik, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Comprehensive Cancer Center Erlangen European Metropolitan Area of Nuremberg, Deutsches Zentrum Immuntherapie, Erlangen, Germany
| | - Carola Berking
- Hautklinik, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Comprehensive Cancer Center Erlangen European Metropolitan Area of Nuremberg, Deutsches Zentrum Immuntherapie, Erlangen, Germany
| | - Julio Vera
- Systems Tumor Immunology, Hautklinik, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Comprehensive Cancer Center Erlangen European Metropolitan Area of Nuremberg, Deutsches Zentrum Immuntherapie, Erlangen, Germany
| | - Jan Dörrie
- RNA-based Immunotherapy, Hautklinik, Comprehensive Cancer Center Erlangen European Metropolitan Area of Nuremberg, Deutsches Zentrum Immuntherapie, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
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12
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Shi Y, Castro-Gonzalez S, Chen Y, Serra-Moreno R. Effects of the SUMO Ligase BCA2 on Metabolic Activity, Cell Proliferation, Cell Migration, Cell Cycle, and the Regulation of NF-κB and IRF1 in Different Breast Epithelial Cellular Contexts. Front Cell Dev Biol 2021; 9:711481. [PMID: 34589482 PMCID: PMC8473798 DOI: 10.3389/fcell.2021.711481] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 08/25/2021] [Indexed: 12/28/2022] Open
Abstract
Breast cancer-associated gene 2 (BCA2) is an E3 ubiquitin and SUMO ligase with antiviral properties against HIV. Specifically, BCA2 (i) enhances the restriction imposed by BST2/Tetherin, impeding viral release; (ii) promotes the ubiquitination and degradation of the HIV protein Gag, limiting virion production; (iii) down-regulates NF-κB, which is necessary for HIV RNA synthesis; and (iv) activates the innate transcription factor IRF1. Due to its antiviral properties, ectopic expression of BCA2 in infected cells represents a promising therapeutic approach against HIV infection. However, BCA2 up-regulation is often observed in breast tumors. To date, the studies about BCA2 and cancer development are controversial, stating both pro- and anti-oncogenic roles. Here, we investigated the impact of BCA2 on cellular metabolic activity, cell proliferation, cell migration, and cell cycle progression. In addition, we also examined the ability of BCA2 to regulate NF-κB and IRF1 in transformed and non-tumor breast epithelial environments. Despite the fact that BCA2 promotes the transition from G1 to S phase of the cell cycle, it did not increase cell proliferation, migration nor metabolic activity. As expected, BCA2 maintains its enzymatic function at inhibiting NF-κB in different breast cancer cell lines. However, the effect of BCA2 on IRF1 differs depending on the cellular context. Specifically, BCA2 activates IRF1 in ER+ breast cell lines while it inhibits this transcription factor in ER– breast cancer cells. We hypothesize that the distinct actions of BCA2 over IRF1 may explain, at least in part, the different proposed roles for BCA2 in these cancers.
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Affiliation(s)
- Yuhang Shi
- Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY, United States
| | | | - Yuexuan Chen
- Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY, United States
| | - Ruth Serra-Moreno
- Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY, United States
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13
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Samadi M, Majidzadeh-A K, Salehi M, Jalili N, Noorinejad Z, Mosayebzadeh M, Muhammadnejad A, Sharif Khatibi A, Moradi-Kalbolandi S, Farahmand L. Engineered hypoxia-responding Escherichia coli carrying cardiac peptide genes, suppresses tumor growth, angiogenesis and metastasis in vivo. J Biol Eng 2021; 15:20. [PMID: 34344421 PMCID: PMC8330025 DOI: 10.1186/s13036-021-00269-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 06/07/2021] [Indexed: 12/11/2022] Open
Abstract
Development of engineered non-pathogenic bacteria, capable of expressing anti-cancer proteins under tumor-specific conditions, is an ideal approach for selectively eradicating proliferating cancer cells. Herein, using an engineered hypoxia responding nirB promoter, we developed an engineered Escherichia coli BW25133 strain capable of expressing cardiac peptides and GFP signaling protein under hypoxic condition for spatiotemporal targeting of mice mammary tumors. Following determination of the in vitro cytotoxicity profile of the engineered bacteria, selective accumulation of bacteria in tumor microenvironment was studied 48 h after tail vein injection of 108 cfu bacteria in animals. For in vivo evaluation of antitumoral activities, mice with establishment mammary tumors received 3 consecutive intravenous injections of transformed bacteria with 4-day intervals and alterations in expression of tumor growth, invasion and angiogenesis specific biomarkers (Ki-67, VEGFR, CD31and MMP9 respectively), as well as fold changes in concentration of proinflammatory cytokines were examined at the end of the 24-day study period. Intravenously injected bacteria could selectively accumulate in tumor site and temporally express GFP and cardiac peptides in response to hypoxia, enhancing survival rate of tumor bearing mice, suppressing tumor growth rate and expression of MMP-9, VEGFR2, CD31 and Ki67 biomarkers. Applied engineered bacteria could also significantly reduce concentrations of IL-1β, IL-6, GC-SF, IL-12 and TNF-α proinflammatory cytokines while increasing those of IL-10, IL-17A and INF-γ. Overall, administration of hypoxia-responding E. coli bacteria, carrying cardiac peptide expression construct could effectively suppress tumor growth, angiogenesis, invasion and metastasis and enhance overall survival of mice bearing mammary tumors.
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Affiliation(s)
- Mitra Samadi
- Recombinant Proteins Department, Breast Cancer Research Center, Motamed Cancer Institute, ACECR, Tehran, Iran
| | - Keivan Majidzadeh-A
- Recombinant Proteins Department, Breast Cancer Research Center, Motamed Cancer Institute, ACECR, Tehran, Iran
| | - Malihe Salehi
- Recombinant Proteins Department, Breast Cancer Research Center, Motamed Cancer Institute, ACECR, Tehran, Iran
| | - Neda Jalili
- Recombinant Proteins Department, Breast Cancer Research Center, Motamed Cancer Institute, ACECR, Tehran, Iran
| | - Zeinab Noorinejad
- Recombinant Proteins Department, Breast Cancer Research Center, Motamed Cancer Institute, ACECR, Tehran, Iran
| | - Marjan Mosayebzadeh
- Recombinant Proteins Department, Breast Cancer Research Center, Motamed Cancer Institute, ACECR, Tehran, Iran
| | - Ahad Muhammadnejad
- Cancer Biology Research Center, Cancer Institute of Iran, Tehran University of Medical Sciences, Tehran, Iran
| | - Azadeh Sharif Khatibi
- Recombinant Proteins Department, Breast Cancer Research Center, Motamed Cancer Institute, ACECR, Tehran, Iran
| | - Shima Moradi-Kalbolandi
- Recombinant Proteins Department, Breast Cancer Research Center, Motamed Cancer Institute, ACECR, Tehran, Iran
| | - Leila Farahmand
- Recombinant Proteins Department, Breast Cancer Research Center, Motamed Cancer Institute, ACECR, Tehran, Iran.
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14
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Adedokun B, Du Z, Gao G, Ahearn TU, Lunetta KL, Zirpoli G, Figueroa J, John EM, Bernstein L, Zheng W, Hu JJ, Ziegler RG, Nyante S, Bandera EV, Ingles SA, Press MF, Deming-Halverson SL, Rodriguez-Gil JL, Yao S, Ogundiran TO, Ojengbede O, Blot W, Troester MA, Nathanson KL, Hennis A, Nemesure B, Ambs S, Fiorica PN, Sucheston-Campbell LE, Bensen JT, Kushi LH, Torres-Mejia G, Hu D, Fejerman L, Bolla MK, Dennis J, Dunning AM, Easton DF, Michailidou K, Pharoah PDP, Wang Q, Sandler DP, Taylor JA, O'Brien KM, Kitahara CM, Falusi AG, Babalola C, Yarney J, Awuah B, Addai-Wiafe B, Chanock SJ, Olshan AF, Ambrosone CB, Conti DV, Ziv E, Olopade OI, Garcia-Closas M, Palmer JR, Haiman CA, Huo D. Cross-ancestry GWAS meta-analysis identifies six breast cancer loci in African and European ancestry women. Nat Commun 2021; 12:4198. [PMID: 34234117 PMCID: PMC8263739 DOI: 10.1038/s41467-021-24327-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 06/02/2021] [Indexed: 02/06/2023] Open
Abstract
Our study describes breast cancer risk loci using a cross-ancestry GWAS approach. We first identify variants that are associated with breast cancer at P < 0.05 from African ancestry GWAS meta-analysis (9241 cases and 10193 controls), then meta-analyze with European ancestry GWAS data (122977 cases and 105974 controls) from the Breast Cancer Association Consortium. The approach identifies four loci for overall breast cancer risk [1p13.3, 5q31.1, 15q24 (two independent signals), and 15q26.3] and two loci for estrogen receptor-negative disease (1q41 and 7q11.23) at genome-wide significance. Four of the index single nucleotide polymorphisms (SNPs) lie within introns of genes (KCNK2, C5orf56, SCAMP2, and SIN3A) and the other index SNPs are located close to GSTM4, AMPD2, CASTOR2, and RP11-168G16.2. Here we present risk loci with consistent direction of associations in African and European descendants. The study suggests that replication across multiple ancestry populations can help improve the understanding of breast cancer genetics and identify causal variants.
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Affiliation(s)
- Babatunde Adedokun
- Center for Clinical Cancer Genetics and Global Health, Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Zhaohui Du
- Department of Preventative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Guimin Gao
- Department of Public Health Sciences, University of Chicago, Chicago, IL, USA
| | - Thomas U Ahearn
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Kathryn L Lunetta
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Gary Zirpoli
- Slone Epidemiology Center, Boston University, Boston, MA, USA
| | - Jonine Figueroa
- Usher Institute and CRUK Edinburgh Centre, University of Edinburgh, Edinburgh, UK
| | - Esther M John
- Departments of Epidemiology & Population Health and of Medicine (Oncology) and Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Leslie Bernstein
- Biomarkers of Early Detection and Prevention, Department of Population Sciences, Beckman Research Institute, City of Hope Comprehensive Cancer Center, Duarte, CA, USA
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, TN, USA
| | - Jennifer J Hu
- Department of Public Health Sciences, University of Miami, Miami, FL, USA
| | - Regina G Ziegler
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Sarah Nyante
- Department of Radiology, University of North Carolina, Chapel Hill, NC, USA
| | - Elisa V Bandera
- Cancer Prevention and Control Program, Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA
| | - Sue A Ingles
- Department of Preventative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Michael F Press
- Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Sandra L Deming-Halverson
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, TN, USA
| | - Jorge L Rodriguez-Gil
- Genomics, Development and Disease Section, Genetic Disease Research Branch, National Human Genome Research Institute, NIH, Bethesda, MD, USA
| | - Song Yao
- Department of Cancer Prevention and Control, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Temidayo O Ogundiran
- Department of Surgery, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Oladosu Ojengbede
- Center for Population and Reproductive Health, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - William Blot
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, TN, USA
| | - Melissa A Troester
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, USA
| | - Katherine L Nathanson
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Anselm Hennis
- University of the West Indies, Bridgetown, Barbados
- Department of Family, Population and Preventive Medicine, Stony Brook University, Stony Brook, NY, USA
| | - Barbara Nemesure
- Department of Family, Population and Preventive Medicine, Stony Brook University, Stony Brook, NY, USA
| | - Stefan Ambs
- Laboratory of Human Carcinogenesis, National Cancer Institute, Bethesda, MD, USA
| | - Peter N Fiorica
- Department of Public Health Sciences, University of Chicago, Chicago, IL, USA
| | - Lara E Sucheston-Campbell
- Department of Veterinary Biosciences, College of Veterinary Medicine, The Ohio State University, Columbus, OH, USA
| | - Jeannette T Bensen
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, USA
| | - Lawrence H Kushi
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
| | - Gabriela Torres-Mejia
- Center for Population Health Research, Instituto Nacional de Salud Publica, Cuernavaca, Mexico
| | - Donglei Hu
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Laura Fejerman
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Manjeet K Bolla
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Joe Dennis
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Alison M Dunning
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Douglas F Easton
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Kyriaki Michailidou
- Biostatistics Unit, The Cyprus Institute of Neurology & Genetics, Nicosia, Cyprus
| | - Paul D P Pharoah
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Qin Wang
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Dale P Sandler
- Epidemiology Branch, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC, USA
| | - Jack A Taylor
- Epidemiology Branch, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC, USA
| | - Katie M O'Brien
- Epidemiology Branch, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC, USA
| | - Cari M Kitahara
- Radiation Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Adeyinka G Falusi
- Institute for Advanced Medical Research and Training, College of Medicine, University of Ibadan, Ibadan, Oyo, Nigeria
| | - Chinedum Babalola
- Department of Pharmaceutical Chemistry, University of Ibadan, Ibadan, Oyo, Nigeria
| | | | | | | | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Andrew F Olshan
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, USA
| | - Christine B Ambrosone
- Department of Cancer Prevention and Control, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - David V Conti
- Department of Preventative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Elad Ziv
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Olufunmilayo I Olopade
- Center for Clinical Cancer Genetics and Global Health, Department of Medicine, University of Chicago, Chicago, IL, USA
| | | | - Julie R Palmer
- Slone Epidemiology Center, Boston University, Boston, MA, USA
| | - Christopher A Haiman
- Department of Preventative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.
| | - Dezheng Huo
- Center for Clinical Cancer Genetics and Global Health, Department of Medicine, University of Chicago, Chicago, IL, USA.
- Department of Public Health Sciences, University of Chicago, Chicago, IL, USA.
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15
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Li W, Ling L, Wang Z, Liang Y, Huang W, Nie P, Huang B. Functional domains and amino acid residues of Japanese eel IRF1, AjIRF1, regulate its nuclear import and IFN/Mx promoter activation. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2021; 116:103923. [PMID: 33186561 DOI: 10.1016/j.dci.2020.103923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 11/05/2020] [Accepted: 11/05/2020] [Indexed: 06/11/2023]
Abstract
Interferon regulatory factors (IRFs) are a family of transcriptional factors capable of regulating the expression of distinct subsets of interferon (IFN)-stimulated genes by binding to their promoters. IRF1 was the first member identified for its ability to regulate the IFNβ gene and has now been revealed to exhibit remarkable functional diversity in the regulation of different cellular responses. In the present study, the IRF1 gene was identified and characterized in Japanese eel, Anguilla japonica (AjIRF1). The open reading frame of AjIRF1 was 804 bp in length, encoding a protein of 267 amino acids (aa) that encompasses a conserved N-terminal DNA binding domain (DBD). Sequence alignment shows the presence of six highly conserved tryptophan (W) residues in the DBD of IRF1, IRF2 and IRF11, while other IRF members have only five tryptophans. Expression analysis showed that AjIRF1 was significantly upregulated in all tested organs/tissues in response to Poly I:C stimulation or Edwardsiella tarda infection. Furthermore, the functional activity of AjIRF1 was confirmed in driving the transcription of AjIFN promoters, which depends on the highly conserved residues within DBD. Subcellular distribution analysis revealed that AjIRF1 was localized exclusively in the nucleus, which is cooperatively regulated by a bipartite NLS embedded within the DBD and a monopartite NLS located immediately downstream of the DBD. Taken together, this study presents the expression profile of AjIRF1 and defines the functional motifs required for its nuclear import and its role in activating IFN promoters, thus providing helpful information for further research on the regulatory mechanisms of teleost IRF1.
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Affiliation(s)
- Wenxing Li
- Fisheries College, Jimei University, Xiamen, 361021, China
| | - Lulu Ling
- Fisheries College, Jimei University, Xiamen, 361021, China
| | - Zhixuan Wang
- Fisheries College, Jimei University, Xiamen, 361021, China
| | - Ying Liang
- Fisheries College, Jimei University, Xiamen, 361021, China; Engineering Research Center of the Modern Technology for Eel Industry, Ministry of Education, PR China, Xiamen, 361021, China
| | - Wenshu Huang
- Fisheries College, Jimei University, Xiamen, 361021, China; Engineering Research Center of the Modern Technology for Eel Industry, Ministry of Education, PR China, Xiamen, 361021, China
| | - Pin Nie
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, Shandong Province, 266237, China; School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, Shandong Province, 266109, China.
| | - Bei Huang
- Fisheries College, Jimei University, Xiamen, 361021, China; Engineering Research Center of the Modern Technology for Eel Industry, Ministry of Education, PR China, Xiamen, 361021, China.
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16
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Rueschenbaum S, Cai C, Schmidt M, Schwarzkopf K, Dittmer U, Zeuzem S, Welsch C, Lange CM. Translation of IRF-1 Restricts Hepatic Interleukin-7 Production to Types I and II Interferons: Implications for Hepatic Immunity. Front Immunol 2021; 11:581352. [PMID: 33584648 PMCID: PMC7874116 DOI: 10.3389/fimmu.2020.581352] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 11/30/2020] [Indexed: 12/18/2022] Open
Abstract
Interleukin-7 (IL-7) is an important cytokine with pivotal pro-survival functions in the adaptive immune system. However, the role of IL-7 in innate immunity is not fully understood. In the present study, the impact of hepatic IL-7 on innate immune cells was assessed by functional experiments as well as in patients with different stages of liver cirrhosis or acute-on-chronic liver failure (ACLF). Human hepatocytes and liver sinusoidal endothelial cells secreted IL-7 in response to stimulation with interferons (IFNs) of type I and II, yet not type III. De novo translation of interferon-response factor-1 (IRF-1) restricted IL-7 production to stimulation with type I and II IFNs. LPS-primed human macrophages were identified as innate immune target cells responding to IL-7 signaling by inactivation of Glycogen synthase kinase-3 (GSK3). IL-7-mediated GSK3 inactivation augmented LPS-induced secretion of pro-inflammatory cytokines and blunted LPS tolerance of macrophages. The IFN-IRF-1-IL-7 axis was present in liver cirrhosis patients. However, liver cirrhosis patients with or without ACLF had significantly lower concentrations of IL-7 in serum compared to healthy controls, which might contribute to LPS-tolerance in these patients. In conclusion, we propose the presence of an inflammatory cascade where IFNs of type I/II induce hepatocellular IL-7 in an IRF-1-restriced way. Beyond its role in adaptive immune responses, IL-7 appears to augment the response of macrophages to LPS and to ameliorate LPS tolerance, which may improve innate immune responses against invading pathogens.
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Affiliation(s)
- Sabrina Rueschenbaum
- Department of Gastroenterology and Hepatology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany.,Department of Medicine 1, J.W. Goethe University Hospital, Frankfurt, Germany
| | - Chengcong Cai
- Department of Medicine 1, J.W. Goethe University Hospital, Frankfurt, Germany
| | - Matthias Schmidt
- Department of Medicine 1, J.W. Goethe University Hospital, Frankfurt, Germany
| | | | - Ulf Dittmer
- Institute for Virology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Stefan Zeuzem
- Department of Medicine 1, J.W. Goethe University Hospital, Frankfurt, Germany
| | - Christoph Welsch
- Department of Medicine 1, J.W. Goethe University Hospital, Frankfurt, Germany
| | - Christian M Lange
- Department of Gastroenterology and Hepatology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany.,Department of Medicine 1, J.W. Goethe University Hospital, Frankfurt, Germany
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17
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Chen W, Zhang W, Zhou T, Cai J, Yu Z, Wu Z. A Newly Defined Pyroptosis-Related Gene Signature for the Prognosis of Bladder Cancer. Int J Gen Med 2021; 14:8109-8120. [PMID: 34803395 PMCID: PMC8594790 DOI: 10.2147/ijgm.s337735] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 10/19/2021] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Bladder cancer (BC), as the most common urinary system tumor type and the main cause of tumor-related death, has an unsatisfactory prognosis. In recent years, related literature has proposed that cell pyroptosis is an inflammatory form of programmed cell death. However, in BC, the relationship between the expression of pyroptosis-related genes and the prognosis has not been elucidated. METHODS We got the RNA sequencing data from TCGA and GEO datasets. Fifty-two pyroptosis-related genes were extracted for further explore. Then, we compared the gene expression levels between the normal bladder and BC tissues. After that, we develop and validate a pyroptosis-related gene prognostic model and made following functional enrichment analysis and single-sample gene set enrichment analysis of the differentially expressed genes between the high- and low-risk groups. RESULTS Twenty-nine differentially expressed genes (DEGs) were found between normal and tumor tissues. Based on the median score calculated by the risk score formula from 8 pyroptosis-related genes, 414 patients were equally divided into low- and high-risk subgroups. The survival probability of BC patients in the high-risk group was significantly lower than that in the low-risk group (P < 0.001). Through multivariate analysis, our risk score is an independent factor predicting OS in BC patients. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis show that high-risk populations are rich in immune-related genes and have a decreased immune status. All the above results have been externally verified from GEO cohort. CONCLUSION Pyroptosis-related genes are closely related to tumor immunity and are a potential prognostic tool for predicting BCs.
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Affiliation(s)
- Weikang Chen
- Department of Urology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, 325000, People’s Republic of China
| | - Wenhao Zhang
- The Fourth School of Clinical Medicine, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, 325000, People’s Republic of China
- Department of Urology, Affiliated Hangzhou First People’s Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 325000, People’s Republic of China
| | - Tao Zhou
- Department of Urology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, 325000, People’s Republic of China
| | - Jian Cai
- Department of Urology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, 325000, People’s Republic of China
| | - Zhixian Yu
- Department of Urology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, 325000, People’s Republic of China
- Correspondence: Zhixian Yu; Zhigang Wu Department of Urology, The First Affiliated Hospital of Wenzhou Medical University, No. 2, Fuxue Road Lucheng District, Wenzhou, Zhejiang, 325000, People’s Republic of China Email ;
| | - Zhigang Wu
- Department of Urology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, 325000, People’s Republic of China
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18
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Venkatraman S, Meller J, Hongeng S, Tohtong R, Chutipongtanate S. Transcriptional Regulation of Cancer Immune Checkpoints: Emerging Strategies for Immunotherapy. Vaccines (Basel) 2020; 8:E735. [PMID: 33291616 PMCID: PMC7761936 DOI: 10.3390/vaccines8040735] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 12/01/2020] [Accepted: 12/02/2020] [Indexed: 12/19/2022] Open
Abstract
The study of immune evasion has gained a well-deserved eminence in cancer research by successfully developing a new class of therapeutics, immune checkpoint inhibitors, such as pembrolizumab and nivolumab, anti-PD-1 antibodies. By aiming at the immune checkpoint blockade (ICB), these new therapeutics have advanced cancer treatment with notable increases in overall survival and tumor remission. However, recent reports reveal that 40-60% of patients fail to benefit from ICB therapy due to acquired resistance or tumor relapse. This resistance may stem from increased expression of co-inhibitory immune checkpoints or alterations in the tumor microenvironment that promotes immune suppression. Because these mechanisms are poorly elucidated, the transcription factors that regulate immune checkpoints, known as "master regulators", have garnered interest. These include AP-1, IRF-1, MYC, and STAT3, which are known to regulate PD/PD-L1 and CTLA-4. Identifying these and other potential master regulators as putative therapeutic targets or biomarkers can be facilitated by mining cancer literature, public datasets, and cancer genomics resources. In this review, we describe recent advances in master regulator identification and characterization of the mechanisms underlying immune checkpoints regulation, and discuss how these master regulators of immune checkpoint molecular expression can be targeted as a form of auxiliary therapeutic strategy to complement traditional immunotherapy.
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Affiliation(s)
- Simran Venkatraman
- Graduate Program in Molecular Medicine, Faculty of Science Joint Program Faculty of Medicine Ramathibodi Hospital, Faculty of Medicine Siriraj Hospital, Faculty of Dentistry, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand;
| | - Jarek Meller
- Departments of Environmental and Public Health Sciences, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA;
- Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45267, USA
| | - Suradej Hongeng
- Division of Hematology and Oncology, Department of Pediatrics, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand;
| | - Rutaiwan Tohtong
- Graduate Program in Molecular Medicine, Faculty of Science Joint Program Faculty of Medicine Ramathibodi Hospital, Faculty of Medicine Siriraj Hospital, Faculty of Dentistry, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand;
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
| | - Somchai Chutipongtanate
- Pediatric Translational Research Unit, Department of Pediatrics, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand
- Department of Clinical Epidemiology and Biostatistics, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand
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19
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Safdar M, Zaheer S, Khailany RA, Parvez S, Naveed M, Bhuiyan P, Ozaslan M, Moatasam R, Al-Attar MS, Khan MA, Junejo Y. The Relevance of SNPs at 3'UTR Region of CASP7 and miR-371b-5p Associated Diseases: A Computational Analysis. Cell Biochem Biophys 2020; 78:541-557. [PMID: 32951155 DOI: 10.1007/s12013-020-00941-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The process of genetically programmed cell death, or apoptosis, plays a crucialrolein cellular homeostasis and gene expression. Disruption of apoptosis may lead to aberrant immune responses, cancer, and neurodegenerative diseases. Single nucleotide polymorphisms (SNPs) present in various microRNA (miRNA) genes and targets being an alteration of miRNA activity resulting in human diseases. Evidence reported that SNPs increase/decrease the effectiveness of the interaction between miRNAs and their target genes associated with diseases. The primary purpose of this study is not only to identify miRSNPs on the CASP7 gene (caspase-7) and SNPs in miRNA genes targeting 3'UTR but also to evaluate the effect of thesegene variations in apoptosis and their associated diseases. We detected 120 miRNAs binding sites and 27 different SNPs in binding sites of miRNA in 3'UTR of the CASP7 gene by ten different online softwares. Interestingly, miR-371b-5p's binding site on CASP7 has an SNP (rs576198588, G/T) on CASP7 3'UTR, and its genomic sequence has an SNP (rs751339395, G/T) at the same nucleotide with rs576198588. Similarly, two other SNPs (rs774879764, C/G rs750389063, C/T) were identified at the first position binding site of miR-371b-5p. Here, miRSNP (rs576198588) at CASP7 3'UTR and SNP (rs751339395) at miR-371b-5p genomic sequence cross-matches at the same site of binding region. Besides, miR-371b-5p targets many apoptosis-related genes (HIP1, TRIAP1, GSKIP, NIN, DAP, CAAP1, XIAP, TMBIM1, TMBIM4, TNFRSF10A, RAD21, AKT1, BAG1, BAG4) even though it had no apoptosis correlated interaction demonstrated formerly. It assures that CASP7 could have a significant consequence on apoptosis through different pathways. Henceforth, this study was representing and signifying an influential connotation among miR-371b-5p and apoptosis via computational exploration and recommended to have better insight.
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Affiliation(s)
- Muhammad Safdar
- Department of Breeding and Genetics, Cholistan University of Veterinary and Animal Sciences, Bahawalpur, 63100, Pakistan.
- Department of Biology, Division of Molecular Biology and Genetics, Gaziantep University, 27310, Gaziantep, Turkey.
| | - Sana Zaheer
- Department of Biotechnology, Virtual University of Pakistan, Lahore, 60000, Pakistan
| | - Rozhgar A Khailany
- Department of Biology, College of Science, Salahaddin University-Erbil, 44001, Erbil, Iraq
- Department of Biology, Faculty of Education, Tishk International University, 44001, Erbil, Iraq
| | - Sadaf Parvez
- Department of Biology, Virtual University of Pakistan, Lahore, 54000, Pakistan
| | - Muhammad Naveed
- School of Pharmacy, Nanjing Medical University, Nanjing, 211166, PR China
| | - Piplu Bhuiyan
- School of Basic Life Sciences, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 20029, PR China
| | - Mehmet Ozaslan
- Department of Biology, Division of Molecular Biology and Genetics, Gaziantep University, 27310, Gaziantep, Turkey
| | - Rebaz Moatasam
- Department of Medical Microbiology, Koya University, Koya-Erbil, Iraq
| | - Mustafa S Al-Attar
- Department of Environmental Science, College of Science, Salahaddin University-Erbil, Erbil, Iraq
| | - Musarrat Abbas Khan
- Department of Animal Breeding and Genetics, University College of Veterinary and Animal Sciences, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
| | - Yasmeen Junejo
- Department of Physiology and Biochemistry, Cholistan University of Veterinary and Animal Sciences, Bahawalpur, 63100, Pakistan
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20
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Rho SB, Lee SH, Byun HJ, Kim BR, Lee CH. IRF-1 Inhibits Angiogenic Activity of HPV16 E6 Oncoprotein in Cervical Cancer. Int J Mol Sci 2020; 21:ijms21207622. [PMID: 33076322 PMCID: PMC7589982 DOI: 10.3390/ijms21207622] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 10/13/2020] [Indexed: 12/15/2022] Open
Abstract
HPV16 E6 oncoprotein is a member of the human papillomavirus (HPV) family that contributes to enhanced cellular proliferation and risk of cervical cancer progression via viral infection. In this study, interferon regulatory factor-1 (IRF-1) regulates cell growth inhibition and transcription factors in immune response, and acts as an HPV16 E6-binding cellular molecule. Over-expression of HPV16 E6 elevated cell growth by attenuating IRF-1-induced apoptosis and repressing p21 and p53 expression, but activating cyclin D1 and nuclear factor kappa B (NF-κB) expression. The promoter activities of p21 and p53 were suppressed, whereas NF-κB activities were increased by HPV16 E6. Additionally, the cell viability of HPV16 E6 was diminished by IRF-1 in a dose-dependent manner. We found that HPV16 E6 activated vascular endothelial growth factor (VEGF)-induced endothelial cell migration and proliferation as well as phosphorylation of VEGFR-2 via direct interaction in vitro. HPV16 E6 exhibited potent pro-angiogenic activity and clearly enhanced the levels of hypoxia-inducible factor-1α (HIF-1α). By contrast, the loss of function of HPV16 E6 by siRNA-mediated knockdown inhibited the cellular events. These data provide direct evidence that HPV16 E6 facilitates tumour growth and angiogenesis. HPV16 E6 also activates the PI3K/mTOR signalling cascades, and IRF-1 suppresses HPV16 E6-induced tumourigenesis and angiogenesis. Collectively, these findings suggest a biological mechanism underlying the HPV16 E6-related activity in cervical tumourigenesis.
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Affiliation(s)
- Seung Bae Rho
- Division of Translational Science, Research Institute, National Cancer Center, Goyang, Gyeonggido 411-769, Korea;
| | - Seung-Hoon Lee
- Department of Life Science, Yong In University, Yongin, Gyeonggido 449-714, Korea;
| | - Hyun-Jung Byun
- Phamaceutical Biochemistry, College of Pharmacy and Integrated Research Institute for Drug, Dongguk University, Goyang 100-715, Korea;
| | - Boh-Ram Kim
- Phamaceutical Biochemistry, College of Pharmacy and Integrated Research Institute for Drug, Dongguk University, Goyang 100-715, Korea;
- Correspondence: (B.-R.K.); (C.H.L.); Tel.: +82-31-961-5213 (B.-R.K. & C.H.L.)
| | - Chang Hoon Lee
- Phamaceutical Biochemistry, College of Pharmacy and Integrated Research Institute for Drug, Dongguk University, Goyang 100-715, Korea;
- Correspondence: (B.-R.K.); (C.H.L.); Tel.: +82-31-961-5213 (B.-R.K. & C.H.L.)
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21
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Remoli AL, Sgarbanti M, Perrotti E, Acchioni M, Orsatti R, Acchioni C, Battistini A, Clarke R, Marsili G. IκB kinase-ε-mediated phosphorylation triggers IRF-1 degradation in breast cancer cells. Neoplasia 2020; 22:459-469. [PMID: 32784074 PMCID: PMC7419274 DOI: 10.1016/j.neo.2020.07.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Accepted: 07/06/2020] [Indexed: 11/24/2022]
Abstract
Interferon Regulatory Factors (IRFs) are key regulators of immunity, cell survival and apoptosis. IRF transcriptional activity and subcellular localization are tightly regulated by posttranscriptional modifications including phosphorylation. The IκB kinase family member IKK-ε is essential in regulating antiviral innate immunity mediated by IRFs but is now also recognized as an oncoprotein amplified and overexpressed in breast cancer cell lines and patient-derived tumors. In the present study, we report that the tumor suppressor IRF-1 is a specific target of IKK-ε in breast cancer cells. IKK-ε-mediated phosphorylation of IRF-1 dramatically decreases IRF-1 protein stability, accelerating IRF-1 degradation and quenching IRF-1 transcriptional activity. Chemical inhibition of IKK-ε activity, fully restores IRF-1 levels and function and positively correlates with inhibition of cell growth and proliferation of breast cancer cells. By using a breast cancer cell line stably expressing a dominant negative version of IRF-1 we were able to demonstrate that IKK-ε preferentially exerts its oncogenic potential in breast cancer through the regulation of IRF-1 and point to the IKK-ε-mediated phosphorylation of IRF-1 as a therapeutic target to overcome IKK-ε-mediated tumorigenesis.
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Affiliation(s)
- Anna Lisa Remoli
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Marco Sgarbanti
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Edvige Perrotti
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Marta Acchioni
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Roberto Orsatti
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Chiara Acchioni
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Angela Battistini
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Robert Clarke
- Department of Oncology, Georgetown University, Washington, District of Columbia, United States; Hormel Institute, University of Minnesota, Austin, Minnesota, United States
| | - Giulia Marsili
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy.
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22
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Karki R, Sharma BR, Lee E, Banoth B, Malireddi RKS, Samir P, Tuladhar S, Mummareddy H, Burton AR, Vogel P, Kanneganti TD. Interferon regulatory factor 1 regulates PANoptosis to prevent colorectal cancer. JCI Insight 2020; 5:136720. [PMID: 32554929 DOI: 10.1172/jci.insight.136720] [Citation(s) in RCA: 120] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Accepted: 05/20/2020] [Indexed: 12/11/2022] Open
Abstract
Interferon regulatory factor 1 (IRF1) regulates diverse biological functions, including modulation of cellular responses involved in tumorigenesis. Genetic mutations and altered IRF1 function are associated with several cancers. Although the function of IRF1 in the immunobiology of cancer is emerging, IRF1-specific mechanisms regulating tumorigenesis and tissue homeostasis in vivo are not clear. Here, we found that mice lacking IRF1 were hypersusceptible to colorectal tumorigenesis. IRF1 functions in both the myeloid and epithelial compartments to confer protection against AOM/DSS-induced colorectal tumorigenesis. We further found that IRF1 also prevents tumorigenesis in a spontaneous mouse model of colorectal cancer. The attenuated cell death in the colons of Irf1-/- mice was due to defective pyroptosis, apoptosis, and necroptosis (PANoptosis). IRF1 does not regulate inflammation and the inflammasome in the colon. Overall, our study identified IRF1 as an upstream regulator of PANoptosis to induce cell death during colitis-associated tumorigenesis.
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Affiliation(s)
- Rajendra Karki
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Bhesh Raj Sharma
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Ein Lee
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA.,Integrated Biomedical Sciences Program, University of Tennessee Health Science Center, Memphis, Tennessee, USA
| | - Balaji Banoth
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - R K Subbarao Malireddi
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Parimal Samir
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Shraddha Tuladhar
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Harisankeerth Mummareddy
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA.,Emory College of Arts and Sciences, Emory University, Atlanta, Georgia, USA
| | - Amanda R Burton
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Peter Vogel
- Animal Resources Center and Veterinary Pathology Core, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
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23
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A dual role of Irf1 in maintaining epithelial identity but also enabling EMT and metastasis formation of breast cancer cells. Oncogene 2020; 39:4728-4740. [PMID: 32404986 DOI: 10.1038/s41388-020-1326-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 05/02/2020] [Accepted: 05/05/2020] [Indexed: 01/06/2023]
Abstract
An epithelial to mesenchymal transition (EMT) is an embryonic dedifferentiation program which is aberrantly activated in cancer cells to acquire cellular plasticity. This plasticity increases the ability of breast cancer cells to invade into surrounding tissue, to seed metastasis at distant sites and to resist to chemotherapy. In this study, we have observed a higher expression of interferon-related factors in basal-like and claudin-low subtypes of breast cancer in patients, known to be associated with EMT. Notably, Irf1 exerts essential functions during the EMT process, yet it is also required for the maintenance of an epithelial differentiation status of mammary gland epithelial cells: RNAi-mediated ablation of Irf1 in mammary epithelial cells results in the expression of mesenchymal factors and Smad transcriptional activity. Conversely, ablation of Irf1 during TGFβ-induced EMT prevents a mesenchymal transition and stabilizes the expression of E-cadherin. In the basal-like murine breast cancer cell line 4T1, RNAi-mediated ablation of Irf1 reduces colony formation and cell migration in vitro and shedding of circulating tumor cells and metastasis formation in vivo. This context-dependent dual role of Irf1 in the regulation of epithelial-mesenchymal plasticity provides important new insights into the functional contribution and therapeutic potential of interferon-regulated factors in breast cancer.
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24
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Cheng Y, Wang D, Jiang J, Huang W, Li D, Luo J, Gu W, Mo W, Wang C, Li Y, Gu S, Xu Y. Integrative analysis of AR-mediated transcriptional regulatory network reveals IRF1 as an inhibitor of prostate cancer progression. Prostate 2020; 80:640-652. [PMID: 32282098 DOI: 10.1002/pros.23976] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/23/2019] [Accepted: 03/16/2020] [Indexed: 12/19/2022]
Abstract
BACKGROUND Androgen receptor (AR) is crucial for prostate cancer (PCa) initiation and malignant progression. Only half of androgen-responsive genes have been identified as having androgen-responsive elements, suggesting that AR regulates downstream genes through other transcriptional factors. However, whether and how AR regulates the progression via regulating these androgen-responsive genes remains unclear. METHODS Androgen-responsive and activity-changed (AC) transcriptional factors (TFs) were identified based on the time-course gene-expression array and gene promoter regions analysis. The intersection of androgen-responsive and AC TFs was selected the core TFs, which were used to construct the core transcriptional regulatory network. GO enrichment analysis, cell proliferation assays, glycolysis experiments, and reverse transcription polymerase chain reaction analysis were used to analyze and validate the functions of the network. As one of the core TFs, the function and mechanism of IRF1 have been further explored. RESULTS We devised a new integrated approach to select core TFs and construct core transcriptional regulatory network in PCa. The 24 core TFs and core transcriptional regulatory network participate in regulating PCa cell proliferation, RNA splicing, and cancer metabolism. Further validations showed that AR signaling could promote glycolysis via inducing glycolytic enzymes in PCa cells. IRF1, a novel target of AR, served as a tumor suppressor by inhibiting PCa proliferation, cell cycle, and glycolysis. CONCLUSIONS It is the first time to demonstrate the regulating role of the AR-mediated transcriptional regulatory network in a series of important biological processes in PCa cells. IRF1, an AR-regulated TF, acts as tumor suppressor in this core transcriptional regulatory network, which highlights the therapeutic potential of targeting this regulatory network for PCa.
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Affiliation(s)
- Yihang Cheng
- State Key Laboratory of Genetic Engineering, Shanghai Engineering Research Center of Industrial Microorganisms, School of Life Science, Shanghai, China
| | - Dan Wang
- State Key Laboratory of Genetic Engineering, Shanghai Engineering Research Center of Industrial Microorganisms, School of Life Science, Shanghai, China
| | - Jun Jiang
- State Key Laboratory of Genetic Engineering, Shanghai Engineering Research Center of Industrial Microorganisms, School of Life Science, Shanghai, China
| | - Wenhua Huang
- State Key Laboratory of Genetic Engineering, Shanghai Engineering Research Center of Industrial Microorganisms, School of Life Science, Shanghai, China
| | - Dujian Li
- Department of Urology, Shanghai Fourth People's Hospital Affiliated to Tongji University School of Medicine, Shanghai, China
| | - Jun Luo
- Department of Urology, Shanghai Fourth People's Hospital Affiliated to Tongji University School of Medicine, Shanghai, China
| | - Wei Gu
- Department of Urology, Shanghai Fourth People's Hospital Affiliated to Tongji University School of Medicine, Shanghai, China
| | - Wenjuan Mo
- State Key Laboratory of Genetic Engineering, Shanghai Engineering Research Center of Industrial Microorganisms, School of Life Science, Shanghai, China
| | - Chenji Wang
- State Key Laboratory of Genetic Engineering, Shanghai Engineering Research Center of Industrial Microorganisms, School of Life Science, Shanghai, China
| | - Yao Li
- State Key Laboratory of Genetic Engineering, Shanghai Engineering Research Center of Industrial Microorganisms, School of Life Science, Shanghai, China
| | - Shaohua Gu
- State Key Laboratory of Genetic Engineering, Shanghai Engineering Research Center of Industrial Microorganisms, School of Life Science, Shanghai, China
| | - Yaoting Xu
- Department of Urology, Shanghai Fourth People's Hospital Affiliated to Tongji University School of Medicine, Shanghai, China
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25
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Vidal P. Interferon α in cancer immunoediting: From elimination to escape. Scand J Immunol 2020; 91:e12863. [PMID: 31909839 DOI: 10.1111/sji.12863] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 11/11/2019] [Accepted: 01/03/2020] [Indexed: 12/25/2022]
Abstract
Interferon α (IFNα) is a cytokine that mediates diverse immune responses to tumours. It is the oldest immune-based oncologic drug and has been widely used to treat various malignancies in humans. Yet, the use of IFNα in cancer therapy has only resulted in limited success and even led to worse clinical outcomes under certain instances. The emergence of the cancer immunoediting concept-which implicates the host immune system in promoting tumour growth-recapitulates the need to evaluate the immune functions of IFNα. This review proposes that IFNα has dual opposing roles in cancer development based on the mutational status of its signalling components, which determines the expression of anti- or pro-tumorigenic IFN-stimulated genes (ISGs). This duality may translate into new applications of IFNα in cancer immunotherapy.
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Affiliation(s)
- Paolo Vidal
- Department of Medical Microbiology, College of Public Health, University of the Philippines Manila, Philippines
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26
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Overexpression of PSAT1 promotes metastasis of lung adenocarcinoma by suppressing the IRF1-IFNγ axis. Oncogene 2020; 39:2509-2522. [PMID: 31988456 DOI: 10.1038/s41388-020-1160-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Revised: 12/26/2019] [Accepted: 01/15/2020] [Indexed: 12/16/2022]
Abstract
An increasing number of enzymes involved in serine biosynthesis have been identified and correlated with malignant evolution in various types of cancer. Here we showed that the overexpression of phosphoserine aminotransferase 1 (PSAT1) is widely found in lung cancer tissues compared with nontumor tissues and predicts a poorer prognosis in patients with lung adenocarcinoma. PSAT1 expression was examined in a tissue microarray by immunohistochemistry. The data show that the knockdown of PSAT1 dramatically inhibits the in vitro and in vivo metastatic potential of highly metastatic lung cancer cells; conversely, the enforced expression of exogenous PSAT1 predominantly enhances the metastatic potential of lung cancer cells. Importantly, manipulating PSAT1 expression regulates the in vivo tumor metastatic abilities in lung cancer cells. Adjusting the glucose and glutamine concentrations did not alter the PSAT1-driven cell invasion properties, indicating that this process might not rely on the activation of its enzymatic function. RNA microarray analysis of transcriptional profiling from PSAT1 alternation in CL1-5 and CL1-0 cells demonstrated that interferon regulatory factor 1 (IRF1) acts as a crucial regulator of PSAT1-induced gene expression upon metastatic progression. Decreasing the IRF1-IFIH1 axis compromised the PSAT1-prompted transcriptional reprogramming in cancer cells. Our results identify PSAT1 as a key regulator by a novel PSAT1/IRF1 axis in lung cancer progression, which may serve as a potential biomarker and therapeutic target for the treatment of lung cancer patients.
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Otálora-Otálora BA, Florez M, López-Kleine L, Canas Arboleda A, Grajales Urrego DM, Rojas A. Joint Transcriptomic Analysis of Lung Cancer and Other Lung Diseases. Front Genet 2019; 10:1260. [PMID: 31867044 PMCID: PMC6908522 DOI: 10.3389/fgene.2019.01260] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 11/14/2019] [Indexed: 12/09/2022] Open
Abstract
Background: Epidemiological and clinical evidence points cancer comorbidity with pulmonary chronic disease. The acquisition of some hallmarks of cancer by cells affected with lung pathologies as a cell adaptive mechanism to a shear stress, suggests that could be associated with the establishment of tumoral processes. Objective: To propose a bioinformatic pipeline for the identification of all deregulated genes and the transcriptional regulators (TFs) that are coexpressed during lung cancer establishment, and therefore could be important for the acquisition of the hallmarks of cancer. Methods: Ten microarray datasets (six of lung cancer, four of lung diseases) comparing normal and diseases-related lung tissue were selected to identify hub differentiated expressed genes (DEGs) in common between lung pathologies and lung cancer, along with transcriptional regulators through the utilization of specialized libraries from R language. DAVID bioinformatics tool for gene enrichment analyses was used to identify genes with experimental evidence associated to tumoral processes and signaling pathways. Coexpression networks of DEGs and TFs in lung cancer establishment were created with Coexnet library, and a survival analysis of the main hub genes was made. Results: Two hundred ten DEGs were identified in common between lung cancer and other lung diseases related to the acquisition of tumoral characteristics, which are coexpressed in a lung cancer network with TFs, suggesting that could be related to the establishment of the tumoral pathology in lung. The comparison of the coexpression networks of lung cancer and other lung diseases allowed the identification of common connectivity patterns (CCPs) with DEGs and TFs correlated to important tumoral processes and signaling pathways, that haven´t been studied to experimentally validate their role in the early stages of lung cancer. Some of the TFs identified showed a correlation between its expression levels and the survival of lung cancer patients. Conclusion: Our findings indicate that lung diseases share genes with lung cancer which are coexpressed in lung cancer, and might be able to explain the epidemiological observations that point to direct and inverse comorbid associations between some chronic lung diseases and lung cancer and represent a complex transcriptomic scenario.
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Affiliation(s)
| | - Mauro Florez
- Departamento de Estadística, Grupo de Investigación en Bioinformática y Biología de sistemas – GiBBS, Facultad de Ciencias, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Liliana López-Kleine
- Departamento de Estadística, Grupo de Investigación en Bioinformática y Biología de sistemas – GiBBS, Facultad de Ciencias, Universidad Nacional de Colombia, Bogotá, Colombia
| | | | | | - Adriana Rojas
- Instituto de Genética Humana, Facultad de Medicina, Pontificia Universidad Javeriana, Bogotá, Colombia
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Alshabi AM, Shaikh IA, Vastrad C. Exploring the Molecular Mechanism of the Drug-Treated Breast Cancer Based on Gene Expression Microarray. Biomolecules 2019; 9:biom9070282. [PMID: 31311202 PMCID: PMC6681318 DOI: 10.3390/biom9070282] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Revised: 06/24/2019] [Accepted: 07/09/2019] [Indexed: 02/07/2023] Open
Abstract
: Breast cancer (BRCA) remains the leading cause of cancer morbidity and mortality worldwide. In the present study, we identified novel biomarkers expressed during estradiol and tamoxifen treatment of BRCA. The microarray dataset of E-MTAB-4975 from Array Express database was downloaded, and the differential expressed genes (DEGs) between estradiol-treated BRCA sample and tamoxifen-treated BRCA sample were identified by limma package. The pathway and gene ontology (GO) enrichment analysis, construction of protein-protein interaction (PPI) network, module analysis, construction of target genes-miRNA interaction network and target genes-transcription factor (TF) interaction network were performed using bioinformatics tools. The expression, prognostic values, and mutation of hub genes were validated by SurvExpress database, cBioPortal, and human protein atlas (HPA) database. A total of 856 genes (421 up-regulated genes and 435 down-regulated genes) were identified in T47D (overexpressing Split Ends (SPEN) + estradiol) samples compared to T47D (overexpressing Split Ends (SPEN) + tamoxifen) samples. Pathway and GO enrichment analysis revealed that the DEGs were mainly enriched in response to lysine degradation II (pipecolate pathway), cholesterol biosynthesis pathway, cell cycle pathway, and response to cytokine pathway. DEGs (MCM2, TCF4, OLR1, HSPA5, MAP1LC3B, SQSTM1, NEU1, HIST1H1B, RAD51, RFC3, MCM10, ISG15, TNFRSF10B, GBP2, IGFBP5, SOD2, DHF and MT1H) , which were significantly up- and down-regulated in estradiol and tamoxifen-treated BRCA samples, were selected as hub genes according to the results of protein-protein interaction (PPI) network, module analysis, target genes-miRNA interaction network and target genes-TF interaction network analysis. The SurvExpress database, cBioPortal, and Human Protein Atlas (HPA) database further confirmed that patients with higher expression levels of these hub genes experienced a shorter overall survival. A comprehensive bioinformatics analysis was performed, and potential therapeutic applications of estradiol and tamoxifen were predicted in BRCA samples. The data may unravel the future molecular mechanisms of BRCA.
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Affiliation(s)
- Ali Mohamed Alshabi
- Department of Clinical Pharmacy, College of Pharmacy, Najran University, Najran, 66237, Saudi Arabia
| | - Ibrahim Ahmed Shaikh
- Department of Pharmacology, College of Pharmacy, Najran University, Najran, 66237, Saudi Arabia
| | - Chanabasayya Vastrad
- Biostatistics and Bioinformatics, ChanabasavaNilaya, Bharthinagar, Dharwad 580001, Karnataka, India.
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Moon SK, Woo JI, Lim DJ. Involvement of TNF-α and IFN-γ in Inflammation-Mediated Cochlear Injury. Ann Otol Rhinol Laryngol 2019; 128:8S-15S. [DOI: 10.1177/0003489419837689] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Objectives: Inflammation is crucial for the pathogenesis of acquired sensorineural hearing loss, but the precise mechanism involved remains elusive. Among a number of inflammatory mediators, tumor necrosis factor-alpha (TNF-α) plays a pivotal role in cisplatin ototoxicity. However, TNF-α alone is cytotoxic to cochlear sensory cells only at the extremely high concentrations, suggesting the involvement of other factors that may sensitize cells to TNF-α cytotoxicity. Since interferon gamma (IFN-γ) importantly contributes to the cochlear inflammatory processes, we aim to determine whether and how IFN-γ affects TNF-α cytotoxicity to cochlear sensory cells. Methods: TNF-α expression was determined with western blotting in RSL cells and immunolabeling of mouse temporal bone sections. HEI-OC1 cell viability was determined with MTT assays, cytotoxicity assays, and cytometric analysis with methylene blue staining. Cochlear sensory cell injury was determined in the organotypic culture of the mouse organ of Corti. Results: Spiral ligament fibrocytes were shown to upregulate TNF-α in response to pro-inflammatory stimulants. We demonstrated IFN-γ increases the susceptibility of HEI-OC1 cells to TNF-α cytotoxicity via JAK1/2-STAT1 signaling. TNFR1-mediated Caspase-1 activation was found to mediate the sensitization effect of IFN-γ on TNF-α cytotoxicity. The combination of IFN-γ and TNF-α appeared to augment cisplatin cytotoxicity to cochlear sensory cells ex vivo. Conclusions: Taken together, these findings suggest the involvement of IFN-γ in the sensitization of cochlear cells to TNF-α cytotoxicity, which would enable us to better understand the complex mechanisms underlying inflammation-mediated cochlear injury.
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Affiliation(s)
- Sung K. Moon
- Department of Head and Neck Surgery, David Geffen School of Medicine, UCLA, Los Angeles, California, USA
| | - Jeong-Im Woo
- Department of Head and Neck Surgery, David Geffen School of Medicine, UCLA, Los Angeles, California, USA
| | - David J. Lim
- Department of Head and Neck Surgery, David Geffen School of Medicine, UCLA, Los Angeles, California, USA
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Stoltz KP, Jondle CN, Pulakanti K, Sylvester PA, Urrutia R, Rao S, Tarakanova VL. Tumor suppressor Interferon Regulatory Factor 1 selectively blocks expression of endogenous retrovirus. Virology 2019; 526:52-60. [PMID: 30342302 PMCID: PMC6875439 DOI: 10.1016/j.virol.2018.10.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 10/01/2018] [Accepted: 10/01/2018] [Indexed: 01/23/2023]
Abstract
Endogenous retroviruses (ERVs) comprise 10% of the genome, with many of these transcriptionally silenced post early embryogenesis. Several stimuli, including exogenous virus infection and cellular transformation can reactivate ERV expression via a poorly understood mechanism. We identified Interferon Regulatory Factor 1 (IRF-1), a tumor suppressor and an antiviral host factor, as a suppressor of ERV expression. IRF-1 decreased expression of a specific mouse ERV in vitro and in vivo. IRF-3, but not IRF-7, also decreased expression of distinct ERV families, suggesting that suppression of ERVs is a relevant biological function of the IRF family. Given the emerging appreciation of the physiological relevance of ERV expression in cancer, IRF-1-mediated suppression of specific ERVs may contribute to the overall tumor suppressor activity of this host factor.
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Affiliation(s)
- K P Stoltz
- Microbiology and Immunology Department, Medical College of Wisconsin, Milwaukee, Wisconsin, United States
| | - C N Jondle
- Microbiology and Immunology Department, Medical College of Wisconsin, Milwaukee, Wisconsin, United States
| | - K Pulakanti
- Blood Research Institute, BloodCenter of Wisconsin, a Part of Versiti, 8727 West Watertown Plank Road, Milwaukee, WI 53226, United States
| | - P A Sylvester
- Microbiology and Immunology Department, Medical College of Wisconsin, Milwaukee, Wisconsin, United States
| | - R Urrutia
- Cancer Center, Medical College of Wisconsin, Milwaukee, Wisconsin, United States; Department of Surgery, Medical College of Wisconsin, Milwaukee, Wisconsin, United States
| | - S Rao
- Blood Research Institute, BloodCenter of Wisconsin, a Part of Versiti, 8727 West Watertown Plank Road, Milwaukee, WI 53226, United States.
| | - V L Tarakanova
- Microbiology and Immunology Department, Medical College of Wisconsin, Milwaukee, Wisconsin, United States; Cancer Center, Medical College of Wisconsin, Milwaukee, Wisconsin, United States.
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Olney KC, Nyer DB, Vargas DA, Wilson Sayres MA, Haynes KA. The synthetic histone-binding regulator protein PcTF activates interferon genes in breast cancer cells. BMC SYSTEMS BIOLOGY 2018; 12:83. [PMID: 30253781 PMCID: PMC6156859 DOI: 10.1186/s12918-018-0608-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Accepted: 09/12/2018] [Indexed: 02/06/2023]
Abstract
Background Mounting evidence from genome-wide studies of cancer shows that chromatin-mediated epigenetic silencing at large cohorts of genes is strongly linked to a poor prognosis. This mechanism is thought to prevent cell differentiation and enable evasion of the immune system. Drugging the cancer epigenome with small molecule inhibitors to release silenced genes from the repressed state has emerged as a powerful approach for cancer research and drug development. Targets of these inhibitors include chromatin-modifying enzymes that can acquire drug-resistant mutations. In order to directly target a generally conserved feature, elevated trimethyl-lysine 27 on histone H3 (H3K27me3), we developed the Polycomb-based Transcription Factor (PcTF), a fusion activator that targets methyl-histone marks via its N-terminal H3K27me3-binding motif, and co-regulates sets of silenced genes. Results Here, we report transcriptome profiling analyses of PcTF-treated breast cancer model cell lines. We identified a set of 19 PcTF-upregulated genes, or PUGs, that were consistent across three distinct breast cancer cell lines. These genes are associated with the interferon response pathway. Conclusions Our results demonstrate for the first time a chromatin-mediated interferon-related transcriptional response driven by an engineered fusion protein that physically links repressive histone marks with active transcription. Electronic supplementary material The online version of this article (10.1186/s12918-018-0608-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Kimberly C Olney
- School of Life Sciences, Arizona State University, 427 E Tyler Mall, Tempe, 85287-4501, AZ, USA
| | - David B Nyer
- School of Biological and Health Systems Engineering, Arizona State University, 501 E Tyler Mall, Tempe, AZ, 85287-9709, USA
| | - Daniel A Vargas
- School of Biological and Health Systems Engineering, Arizona State University, 501 E Tyler Mall, Tempe, AZ, 85287-9709, USA
| | - Melissa A Wilson Sayres
- School of Life Sciences, Arizona State University, 427 E Tyler Mall, Tempe, 85287-4501, AZ, USA.,Center for Evolution and Medicine, Arizona State University, 427 E Tyler Mall, Tempe, 85287-1701, AZ, USA
| | - Karmella A Haynes
- School of Biological and Health Systems Engineering, Arizona State University, 501 E Tyler Mall, Tempe, AZ, 85287-9709, USA.
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Xie Y, He S, Wang J. MicroRNA-373 facilitates HSV-1 replication through suppression of type I IFN response by targeting IRF1. Biomed Pharmacother 2018; 97:1409-1416. [DOI: 10.1016/j.biopha.2017.11.071] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2017] [Revised: 10/23/2017] [Accepted: 11/10/2017] [Indexed: 01/31/2023] Open
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Chen P, Song W, Liu L. Genome-Wide Transcriptome Analysis of Estrogen Receptor-Positive and Human Epithelial Growth Factor Receptor 2-Positive Breast Cancers by Ribonucleic Acid Sequencing. Gynecol Obstet Invest 2017; 83:338-348. [PMID: 29241203 DOI: 10.1159/000484244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Accepted: 10/13/2017] [Indexed: 11/19/2022]
Abstract
AIM The aim is to identify complex pathogenesis of breast cancer subtypes and disclose the whole landscape of altered transcriptional activities in these cancers. METHODS We downloaded raw expression data from public database, and performed transcriptome analysis of 8 estrogen receptor-positive (ER+) breast cancer tissue samples, 8 human epithelial growth factor receptor 2-positive (HER2+) breast cancer tissue samples, and 3 normal breast tissues by identification, functional annotation, and prediction of upstream regulators and cell-surface biomarkers of differentially expressed genes (DEGs). RESULTS We identified over 5,000 DEGs in each of ER+ and HER2+ breast cancers compared to normal tissues. Functional enrichment analysis of shared DEGs indicated significant changes in the regulation of immune -systems in the 2 subtypes. We further identified 1,871 DEGs between the 2 subtypes and disclosed great tumor heterogeneity. We identified 533 shared upregulated genes and predicted 17 upstream transcription factors, as well as identified differentially expressed cell-surface biomarkers for distinguishing our ER+ and HER2+ breast cancers. Further analysis also highlighted the limitation of the usage of HER2 alone in breast cancer classification. CONCLUSION Our findings in ER+ and HER2+ breast cancers provided novel insights into heterogeneous transcriptional activities underlying complex mechanisms of oncogenesis in breast cancers.
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Affiliation(s)
- Pengtao Chen
- Thyroid and Breast Surgery, Zhoukou Central Hospital of Henan Province, Zhoukou, China
| | - Wei Song
- School of Life Science, Shanghai University, Shanghai, China
| | - Liangli Liu
- Intensive Care Unit, Zhoukou Hospital of Traditional Chinese Medicine of Henan Province, Zhoukou, China
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Wan P, Zhang J, Du Q, Geller DA. The clinical significance and biological function of interferon regulatory factor 1 in cholangiocarcinoma. Biomed Pharmacother 2017; 97:771-777. [PMID: 29107934 DOI: 10.1016/j.biopha.2017.10.096] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2017] [Revised: 10/18/2017] [Accepted: 10/21/2017] [Indexed: 12/19/2022] Open
Abstract
Interferon regulatory factor 1 (IRF1) has been suggested to act as a tumor suppressor in human cancers. However, the clinical significance and biological function of IRF1 in cholangiocarcinoma is poorly understood. In our results, IRF1 mRNA and protein expressions were decreased in cholangiocarcinoma tissues and cell lines compared with paired normal hepatic tissues and intrahepatic bile duct epithelial cell line. IRF1 protein low-expression was associated with tumor stage, tumor size, vascular invasion and metastasis and served as a poor independent prognostic parameter in cholangiocarcinoma patients. Up-regulation of IRF1 expression suppressed cholangiocarcinoma cells proliferation, migration and invasion, and blocked cell cycle progression, but has no effect on apoptosis. In conclusion, IRF1 is low-expressed in cholangiocarcinoma tissues and cell lines, and correlated with malignant status and prognosis in cholangiocarcinoma patients. IRF1 served as tumor suppressor in the regulation of cholangiocarcinoma cells proliferation, cell cycle, migration and invasion.
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Affiliation(s)
- Peiqi Wan
- Department of Surgery, University of Pittsburgh, Pittsburgh, PA 15213, USA; Department of infectious diseases, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530021, PR China.
| | - Junhong Zhang
- Department of Surgery, University of Pittsburgh, Pittsburgh, PA 15213, USA; Department of Gastroenterology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530021, PR China
| | - Qiang Du
- Department of Surgery, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - David A Geller
- Department of Surgery, University of Pittsburgh, Pittsburgh, PA 15213, USA.
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BRCA1-mimetic compound NSC35446.HCl inhibits IKKB expression by reducing estrogen receptor-α occupancy in the IKKB promoter and inhibits NF-κB activity in antiestrogen-resistant human breast cancer cells. Breast Cancer Res Treat 2017; 166:681-693. [PMID: 28808806 DOI: 10.1007/s10549-017-4442-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Accepted: 08/04/2017] [Indexed: 10/19/2022]
Abstract
PURPOSE We previously identified small molecules that fit into a BRCA1-binding pocket within estrogen receptor-alpha (ERα), mimic the ability of BRCA1 to inhibit ERα activity ("BRCA1-mimetics"), and overcome antiestrogen resistance. One such compound, the hydrochloride salt of NSC35446 ("NSC35446.HCl"), also inhibited the growth of antiestrogen-resistant LCC9 tumor xenografts. The purpose of this study was to investigate the down-stream effects of NSC35446.HCl and its mechanism of action. METHODS Here, we studied antiestrogen-resistant (LCC9, T47DCO, MCF-7/RR, LY2), ERα-negative (MDA-MB-231, HCC1806, MDA-MB-468), and antiestrogen-sensitive (MCF-7) cell lines. Techniques utilized include RNA-seq, qRT-PCR, cell growth analysis, cell-cycle analysis, Western blotting, luciferase reporter assays, TUNEL assays, in silico analysis of the IKKB gene, and ChIP assays. RESULTS SC35446.HCl inhibited proliferation and induced apoptosis in antiestrogen-resistant LCC9, T47DCO, MCF-7/RR, and LY2 cells but not in ERα-negative breast cancer cell lines. IKKB (IKKβ, IKBKB), an upstream activator of NF-κB, was identified as a BRCA1-mimetic-regulated gene based on an RNA-seq analysis. NSC35446.HCl inhibited IKKB, IKKA, and IKKG/NEMO mRNA and protein expression in LCC9 cells. NSC35446.HCl also inhibited NF-κB activity and expression of NF-κB target genes. In silico analysis of the IKKB promoter identified nine estrogen response element (ERE) half-sites and one ERE-like full-site. ChIP assays revealed that ERα was recruited to the ERE-like full-site and five of the nine half-sites and that ERα recruitment was inhibited by NSC35446.HCl in LCC9 and T47DCO cells. CONCLUSIONS These studies identify functional EREs in the IKKB promoter and identify IKKB as an ERα and NSC35446.HCl-regulated gene, and they suggest that NF-κB and IKKB, which were previously linked to antiestrogen resistance, are targets for NSC35446.HCl in reversing antiestrogen resistance.
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Wang X, Wang SS, Zhou L, Yu L, Zhang LM. A network-pathway based module identification for predicting the prognosis of ovarian cancer patients. J Ovarian Res 2016; 9:73. [PMID: 27806724 PMCID: PMC5093979 DOI: 10.1186/s13048-016-0285-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2016] [Accepted: 10/25/2016] [Indexed: 12/19/2022] Open
Abstract
Background This study aimed to screen multiple genes biomarkers based on gene expression data for predicting the survival of ovarian cancer patients. Methods Two microarray data of ovarian cancer samples were collected from The Cancer Genome Atlas (TCGA) database. The data in the training set were used to construct Reactome functional interactions network, which then underwent Markov clustering, supervised principal components, Cox proportional hazard model to screen significantly prognosis related modules. The distinguishing ability of each module for survival was further evaluated by the testing set. Gene Ontology (GO) functional and pathway annotations were performed to identify the roles of genes in each module for ovarian cancer. Results The network based approach identified two 7-gene functional interaction modules (31: DCLRE1A, EXO1, KIAA0101, KIN, PCNA, POLD3, POLD2; 35: DKK3, FABP3, IRF1, AIM2, GBP1, GBP2, IRF2) that are associated with prognosis of ovarian cancer patients. These network modules are related to DNA repair, replication, immune and cytokine mediated signaling pathways. Conclusions The two 7-gene expression signatures may be accurate predictors of clinical outcome in patients with ovarian cancer and has the potential to develop new therapeutic strategies for ovarian cancer patients.
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Affiliation(s)
- Xin Wang
- Department of Gynaecology and Obstetrics, The 306 Hospital of PLA, Beijing, 100037, China
| | - Shan-Shan Wang
- Outpatient Pharmacy, Outpatient Department, NO.16 Chengzhuang Fengtai Distinct, Beijing, 100071, China
| | - Lin Zhou
- Department of Gynaecology and Obstetrics, The 306 Hospital of PLA, Beijing, 100037, China
| | - Li Yu
- Department of Gynaecology and Obstetrics, The 306 Hospital of PLA, Beijing, 100037, China
| | - Lan-Mei Zhang
- Department of Gynaecology and Obstetrics, The 306 Hospital of PLA, Beijing, 100037, China.
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Beheshti A, Wage J, McDonald JT, Lamont C, Peluso M, Hahnfeldt P, Hlatky L. Tumor-host signaling interaction reveals a systemic, age-dependent splenic immune influence on tumor development. Oncotarget 2016; 6:35419-32. [PMID: 26497558 PMCID: PMC4742115 DOI: 10.18632/oncotarget.6214] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Accepted: 09/29/2015] [Indexed: 01/23/2023] Open
Abstract
The concept of age-dependent host control of cancer development raises the natural question of how these effects manifest across the host tissue/organ types with which a tumor interacts, one important component of which is the aging immune system. To investigate this, changes in the spleen, an immune nexus in the mouse, was examined for its age-dependent interactive influence on the carcinogenesis process. The model is the C57BL/6 male mice (adolescent, young adult, middle-aged, and old or 68, 143, 551 and 736 days old respectively) with and without a syngeneic murine tumor implant. Through global transcriptome analysis, immune-related functions were found to be key regulators in the spleen associated with tumor progression as a function of age with CD2, CD3ε, CCL19, and CCL5 being the key molecules involved. Surprisingly, other than CCL5, all key factors and immune-related functions were not active in spleens from non-tumor bearing old mice. Our findings of age-dependent tumor-spleen signaling interaction suggest the existence of a global role of the aging host in carcinogenesis. Suggested is a new avenue for therapeutic improvement that capitalizes on the pervasive role of host aging in dictating the course of this disease.
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Affiliation(s)
- Afshin Beheshti
- Division of Hematology/Oncology, Molecular Oncology Research Institute, Tufts Medical Center, Boston, MA, USA.,Center of Cancer Systems Biology, Tufts University School of Medicine, Boston, MA, USA
| | - Justin Wage
- Center of Cancer Systems Biology, Tufts University School of Medicine, Boston, MA, USA
| | | | - Clare Lamont
- Center of Cancer Systems Biology, Tufts University School of Medicine, Boston, MA, USA
| | - Michael Peluso
- Center of Cancer Systems Biology, Tufts University School of Medicine, Boston, MA, USA
| | - Philip Hahnfeldt
- Center of Cancer Systems Biology, Tufts University School of Medicine, Boston, MA, USA
| | - Lynn Hlatky
- Center of Cancer Systems Biology, Tufts University School of Medicine, Boston, MA, USA
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Ahmed F, Mahmood N, Shahid S, Hussain Z, Ahmed I, Jalal A, Ijaz B, Shahid A, Mujtaba G, Mustafa T. Mutations in Human Interferon α2b Gene and Potential as Risk Factor Associated with Female Breast Cancer. Cancer Biother Radiopharm 2016; 31:199-208. [PMID: 27403569 DOI: 10.1089/cbr.2016.2046] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The current study explored the potential links between breast cancer and human interferon α-2b (hIFNα-2b) gene mutations. The hIFNα-2b gene was amplified from breast cancer tumor tissue samples (N = 60) by polymerase chain reaction (PCR) and the products were subjected to gene sequencing. A total of 38 (63.3%) samples showed positive PCR amplification results. Several of these also exhibited frequent alterations (mutations) after 400 bp and, in particular, adenine was replaced by other bases. A total of 19 selected mutated amino acids were analyzed for local/general fold pattern changes. Human IFNα-2b receptor (IFNAR): ligand (hIFNα-2b protein) interactions through a Z-DOCK (3.0.2) server were also evaluated to assess the binding patterns of each ligand to receptor to induce Janus-Kinase-signal transducer and activator of transcription antiproliferative signal transduction pathway inside the cancer cells. Certain local structural and conformational changes were predicted to be induced by mutations in the ligand. The variant models of the hIFNα-2b displayed structural and conformational changes that signified that changes to hIFNα-2b may be a risk factor in addition to other known factors associated with onset/progression of female breast carcinoma. It was hoped that others might build upon the research in this study evaluating protein structural models with mutations and their consequent interactions with receptors in the development of potent immune therapeutic drugs for breast cancer that are based on recombinant hIFNα-2b.
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Affiliation(s)
- Fayyaz Ahmed
- 1 Institute of Industrial Biotechnology, GC University, Lahore , Pakistan
| | - Nasir Mahmood
- 2 Department of Allied Health Sciences and Chemical Pathology, Department of Human Genetics and Molecular Biology, University of Health Sciences , Lahore, Pakistan
| | - Saman Shahid
- 3 National University of Computer and Emerging Sciences (NUCES) , Foundation of Advancement of Science and Technology (FAST), Lahore, Pakistan
| | - Zahid Hussain
- 1 Institute of Industrial Biotechnology, GC University, Lahore , Pakistan
| | - Ishtiaq Ahmed
- 1 Institute of Industrial Biotechnology, GC University, Lahore , Pakistan
| | - Amir Jalal
- 4 Departement of Biochemistry, Sahara Medical College , Narowal, Pakistan
| | - Bushra Ijaz
- 5 National Center of Excellence in Molecular Biology, University of the Punjab , Lahore, Pakistan
| | - Abubaker Shahid
- 6 Institute of Nuclear Medicine and Oncology (INMOL) , Hospital, Lahore, Pakistan
| | - Ghulam Mujtaba
- 6 Institute of Nuclear Medicine and Oncology (INMOL) , Hospital, Lahore, Pakistan
| | - Tanveer Mustafa
- 7 Fatima Jinnah Medical College and University , Lahore, Pakistan
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Armstrong MJ, Stang MT, Liu Y, Yan J, Pizzoferrato E, Yim JH. IRF-1 inhibits NF-κB activity, suppresses TRAF2 and cIAP1 and induces breast cancer cell specific growth inhibition. Cancer Biol Ther 2016; 16:1029-41. [PMID: 26011589 DOI: 10.1080/15384047.2015.1046646] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Abstract
Interferon Regulatory Factor (IRF)-1, originally identified as a transcription factor of the human interferon (IFN)-β gene, mediates tumor suppression and may inhibit oncogenesis. We have shown that IRF-1 in human breast cancer cells results in the down-regulation of survivin, tumor cell death, and the inhibition of tumor growth in vivo in xenogeneic mouse models. In this current report, we initiate studies comparing the effect of IRF-1 in human nonmalignant breast cell and breast cancer cell lines. While IRF-1 in breast cancer cells results in growth inhibition and cell death, profound growth inhibition and cell death are not observed in nonmalignant human breast cells. We show that TNF-α or IFN-γ induces IRF-1 in breast cancer cells and results in enhanced cell death. Abrogation of IRF-1 diminishes TNF-α and IFN-γ-induced apoptosis. We test the hypothesis that IRF-1 augments TNF-α-induced apoptosis in breast cancer cells. Potential signaling networks elicited by IRF-1 are investigated by evaluating the NF-κB pathway. TNF-α and/or IFN-γ results in decreased presence of NF-κB p65 in the nucleus of breast cancer cells. While TNF-α and/or IFN-γ can induce IRF-1 in nonmalignant breast cells, a marked change in NF-κB p65 is not observed. Moreover, the ectopic expression of IRF-1 in breast cancer cells results in caspase-3, -7, -8 cleavage, inhibits NF-κB activity, and suppresses the expression of molecules involved in the NF-κB pathway. These data show that IRF-1 in human breast cancer cells elicits multiple signaling networks including intrinsic and extrinsic cell death and down-regulates molecules involved in the NF-κB pathway.
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Key Words
- Ad, adenovirus
- Cdk, cyclin-dependent kinase
- DISC, death-inducing signaling complex
- DMEM, Dulbecco's Modified Eagle's Medium
- DR, death receptor
- EGFP, enhanced green fluorescent protein
- ER, estrogen receptor
- FADD, fas-associated death domain
- FBS, Fetal Bovine Serum
- FITC, fluorescein isothiocyanate
- FLICE, fas-associated death domain protein interleukin-1 β-converting enzyme
- IAP
- IFN-β, interferon-β
- IFN-γ, interferon-gamma
- IKK, IκB, kinase complex
- IRF-1
- IRF-1, interferon regulatory factor-1
- IκB, Inhibitory kappaB
- MOI, multiplicity of infection
- MTT, methylthiazoltetrazolium
- NEMO, NF-κB essential modulator
- NF-κB
- NF-κB, nuclear factor of kappa Beta
- RIP1, receptor interacting protein 1
- SCID, severe combined immunodeficiency
- STAT, signal transducer and activator of transcription
- Smac/DIABLO, Second mitochondria-derived activator of caspase/Direct IAP-binding protein with low pI
- TNF-α, tumor necrosis factor-α
- TNFR, tumor necrosis factor receptor
- TRADD, TNF receptor associated protein with a death domain
- TRAF2, tumor necrosis factor receptor-associated factor 2
- TRAIL, tumor necrosis factor-related apoptosis-inducing ligand
- XIAP, X-linked inhibitor of apoptosis protein
- apoptosis
- breast cancer
- cFLIP, cellular FLICE inhibitory protein
- cIAP1, c-inhibitor of apoptosis
- p53
- siRNA, small interfering RNA
- tumor suppressor
- β-gal, β-galactosidase
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Affiliation(s)
- Michaele J Armstrong
- a Department of Surgery; University of Pittsburgh School of Medicine ; Pittsburgh , PA , USA
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Walch-Rückheim B, Pahne-Zeppenfeld J, Fischbach J, Wickenhauser C, Horn LC, Tharun L, Büttner R, Mallmann P, Stern P, Kim YJ, Bohle RM, Rübe C, Ströder R, Juhasz-Böss I, Solomayer EF, Smola S. STAT3/IRF1 Pathway Activation Sensitizes Cervical Cancer Cells to Chemotherapeutic Drugs. Cancer Res 2016; 76:3872-83. [DOI: 10.1158/0008-5472.can-14-1306] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Accepted: 03/21/2016] [Indexed: 11/16/2022]
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Wlochowitz D, Haubrock M, Arackal J, Bleckmann A, Wolff A, Beißbarth T, Wingender E, Gültas M. Computational Identification of Key Regulators in Two Different Colorectal Cancer Cell Lines. Front Genet 2016; 7:42. [PMID: 27092172 PMCID: PMC4820448 DOI: 10.3389/fgene.2016.00042] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2015] [Accepted: 03/14/2016] [Indexed: 12/12/2022] Open
Abstract
Transcription factors (TFs) are gene regulatory proteins that are essential for an effective regulation of the transcriptional machinery. Today, it is known that their expression plays an important role in several types of cancer. Computational identification of key players in specific cancer cell lines is still an open challenge in cancer research. In this study, we present a systematic approach which combines colorectal cancer (CRC) cell lines, namely 1638N-T1 and CMT-93, and well-established computational methods in order to compare these cell lines on the level of transcriptional regulation as well as on a pathway level, i.e., the cancer cell-intrinsic pathway repertoire. For this purpose, we firstly applied the Trinity platform to detect signature genes, and then applied analyses of the geneXplain platform to these for detection of upstream transcriptional regulators and their regulatory networks. We created a CRC-specific position weight matrix (PWM) library based on the TRANSFAC database (release 2014.1) to minimize the rate of false predictions in the promoter analyses. Using our proposed workflow, we specifically focused on revealing the similarities and differences in transcriptional regulation between the two CRC cell lines, and report a number of well-known, cancer-associated TFs with significantly enriched binding sites in the promoter regions of the signature genes. We show that, although the signature genes of both cell lines show no overlap, they may still be regulated by common TFs in CRC. Based on our findings, we suggest that canonical Wnt signaling is activated in 1638N-T1, but inhibited in CMT-93 through cross-talks of Wnt signaling with the VDR signaling pathway and/or LXR-related pathways. Furthermore, our findings provide indication of several master regulators being present such as MLK3 and Mapk1 (ERK2) which might be important in cell proliferation, migration, and invasion of 1638N-T1 and CMT-93, respectively. Taken together, we provide new insights into the invasive potential of these cell lines, which can be used for development of effective cancer therapy.
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Affiliation(s)
- Darius Wlochowitz
- Institute of Bioinformatics, University Medical Center Göttingen Göttingen, Germany
| | - Martin Haubrock
- Institute of Bioinformatics, University Medical Center Göttingen Göttingen, Germany
| | - Jetcy Arackal
- Department of Hematology/Medical Oncology, University Medical Center Göttingen Göttingen, Germany
| | - Annalen Bleckmann
- Department of Hematology/Medical Oncology, University Medical Center Göttingen Göttingen, Germany
| | - Alexander Wolff
- Department of Medical Statistics, University Medical Center Göttingen Göttingen, Germany
| | - Tim Beißbarth
- Department of Medical Statistics, University Medical Center Göttingen Göttingen, Germany
| | - Edgar Wingender
- Institute of Bioinformatics, University Medical Center Göttingen Göttingen, Germany
| | - Mehmet Gültas
- Institute of Bioinformatics, University Medical Center Göttingen Göttingen, Germany
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Kochupurakkal BS, Wang ZC, Hua T, Culhane AC, Rodig SJ, Rajkovic-Molek K, Lazaro JB, Richardson AL, Biswas DK, Iglehart JD. RelA-Induced Interferon Response Negatively Regulates Proliferation. PLoS One 2015; 10:e0140243. [PMID: 26460486 PMCID: PMC4604146 DOI: 10.1371/journal.pone.0140243] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Accepted: 09/23/2015] [Indexed: 12/21/2022] Open
Abstract
Both oncogenic and tumor-suppressor activities are attributed to the Nuclear Factor kappa B (NF-kB) pathway. Moreover, NF-kB may positively or negatively regulate proliferation. The molecular determinants of these opposing roles of NF-kB are unclear. Using primary human mammary epithelial cells (HMEC) as a model, we show that increased RelA levels and consequent increase in basal transcriptional activity of RelA induces IRF1, a target gene. Induced IRF1 upregulates STAT1 and IRF7, and in consort, these factors induce the expression of interferon response genes. Activation of the interferon pathway down-regulates CDK4 and up-regulates p27 resulting in Rb hypo-phosphorylation and cell cycle arrest. Stimulation of HMEC with IFN-γ elicits similar phenotypic and molecular changes suggesting that basal activity of RelA and IFN-γ converge on IRF1 to regulate proliferation. The anti-proliferative RelA-IRF1-CDK4 signaling axis is retained in ER+/HER2- breast tumors analyzed by The Cancer Genome Atlas (TCGA). Using immuno-histochemical analysis of breast tumors, we confirm the negative correlation between RelA levels and proliferation rate in ER+/HER2- breast tumors. These findings attribute an anti-proliferative tumor-suppressor role to basal RelA activity. Inactivation of Rb, down-regulation of RelA or IRF1, or upregulation of CDK4 or IRF2 rescues the RelA-IRF1-CDK4 induced proliferation arrest in HMEC and are points of disruption in aggressive tumors. Activity of the RelA-IRF1-CDK4 axis may explain favorable response to CDK4/6 inhibition observed in patients with ER+ Rb competent tumors.
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Affiliation(s)
- Bose S. Kochupurakkal
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
- * E-mail: (JDI); (BSK)
| | - Zhigang C. Wang
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
| | - Tony Hua
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
| | - Aedin C. Culhane
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
| | - Scott J. Rodig
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts, United States of America
| | | | - Jean-Bernard Lazaro
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
| | - Andrea L. Richardson
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts, United States of America
| | - Debajit K. Biswas
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
| | - J. Dirk Iglehart
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
- Department of Surgery, Brigham and Women's Hospital, Boston, Massachusetts, United States of America
- * E-mail: (JDI); (BSK)
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Exploring the Potential of Venom from Nasonia vitripennis as Therapeutic Agent with High-Throughput Screening Tools. Toxins (Basel) 2015; 7:2051-70. [PMID: 26046700 PMCID: PMC4488689 DOI: 10.3390/toxins7062051] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Accepted: 05/29/2015] [Indexed: 11/16/2022] Open
Abstract
The venom from the ectoparasitoid wasp Nasonia vitripennis (Hymenoptera: Pteromalidae) contains at least 80 different proteins and possibly even more peptides or other small chemical compounds, demonstrating its appealing therapeutic application. To better understand the dynamics of the venom in mammalian cells, two high-throughput screening tools were performed. The venom induced pathways related to an early stress response and activated reporters that suggest the involvement of steroids. Whether these steroids reside from the venom itself or show an induced release/production caused by the venom, still remains unsolved. The proinflammatory cytokine IL-1β was found to be down-regulated after venom and LPS co-treatment, confirming the anti-inflammatory action of N. vitripennis venom. When analyzing the expression levels of the NF-κB target genes, potentially not only the canonical but also the alternative NF-κB pathway can be affected, possibly explaining some counterintuitive results. It is proposed that next to an NF-κB binding site, the promoter of the genes tested by the PCR array may also contain binding sites for other transcription factors, resulting in a complex puzzle to connect the induced target gene with its respective transcription factor. Interestingly, Nasonia venom altered the expression of some drug targets, presenting the venom with an exciting therapeutical potential.
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Li Z, Chen B, Feng M, Ouyang H, Zheng M, Ye Q, Nie Q, Zhang X. MicroRNA-23b Promotes Avian Leukosis Virus Subgroup J (ALV-J) Replication by Targeting IRF1. Sci Rep 2015; 5:10294. [PMID: 25980475 PMCID: PMC4434839 DOI: 10.1038/srep10294] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2014] [Accepted: 04/08/2015] [Indexed: 12/31/2022] Open
Abstract
Avian leukosis virus subgroup J (ALV-J) can cause several different leukemia-like proliferative diseases in the hemopoietic system of chickens. Here, we investigated the transcriptome profiles and miRNA expression profiles of ALV-J-infected and uninfected chicken spleens to identify the genes and miRNAs related to ALV-J invasion. In total, 252 genes and 167 miRNAs were differentially expressed in ALV-J-infected spleens compared to control uninfected spleens. miR-23b expression was up-regulated in ALV-J-infected spleens compared with the control spleens, and transcriptome analysis revealed that the expression of interferon regulatory factor 1 (IRF1) was down-regulated in ALV-J-infected spleens compared to uninfected spleens. A dual-luciferase reporter assay showed that IRF1 was a direct target of miR-23b. miR-23b overexpression significantly (P = 0.0022) decreased IRF1 mRNA levels and repressed IRF1-3′-UTR reporter activity. In vitro experiments revealed that miR-23b overexpression strengthened ALV-J replication, whereas miR-23b loss of function inhibited ALV-J replication. IRF1 overexpression inhibited ALV-J replication, and IRF1 knockdown enhanced ALV-J replication. Moreover, IRF1 overexpression significantly (P = 0.0014) increased IFN-β expression. In conclusion, these results suggested that miR-23b may play an important role in ALV-J replication by targeting IRF1.
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Affiliation(s)
- Zhenhui Li
- 1] Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, Guangdong, China [2] Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, Guangdong, China
| | - Biao Chen
- 1] Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, Guangdong, China [2] Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, Guangdong, China
| | - Min Feng
- 1] Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, Guangdong, China [2] Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, Guangdong, China
| | - Hongjia Ouyang
- 1] Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, Guangdong, China [2] Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, Guangdong, China
| | - Ming Zheng
- 1] Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, Guangdong, China [2] Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, Guangdong, China
| | - Qiao Ye
- 1] Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, Guangdong, China [2] Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, Guangdong, China
| | - Qinghua Nie
- 1] Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, Guangdong, China [2] Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, Guangdong, China
| | - Xiquan Zhang
- 1] Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, Guangdong, China [2] Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, Guangdong, China
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Wang L, Wang Y, Song Z, Chu J, Qu X. Deficiency of interferon-gamma or its receptor promotes colorectal cancer development. J Interferon Cytokine Res 2015; 35:273-80. [PMID: 25383957 DOI: 10.1089/jir.2014.0132] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Genetic variations in interferon-gamma (IFN-γ) and its receptor (IFNγR) subunits are closely associated with the risk of colorectal cancer (CRC) and survival after diagnosis. However, the role of loss of IFN-γ or IFNγR function in the pathogenesis of CRC remains unclear. Here, we investigated the role of endogenous IFN-γ deficiency in adenomatous polyposis coli (Apc)-mediated intestinal tumor by developing a variant of Apc(Min/+) mice. The Apc(Min/+)IFN-γ(+/-) mice presented with increased number and size of adenomas, and 41.7% of these mice developed adenocarcinoma. Molecular analyses of the adenomas suggested that heterozygous deletion of IFN-γ promoted EGFR/Erk1/2 and Wnt/β-catenin signaling. In vitro, IFN-γ administration inhibited Apc-mutated HT-29 colon cancer cell proliferation and had no effect on the proliferation of HCT-116 colon cancer cells that express wild-type Apc. Besides, we challenged HT-29 cells with small interfering RNA targeting one of its receptor subunits IFNγR1. We found that knockdown of IFNγR1 in HT-29 cells stimulated cell proliferation and colony formation, which was also related to the regulation of EGFR/Erk1/2 and Wnt/β-catenin signaling. Thus, our results strongly support the notion that IFN-γ and IFNγR1 act as a rate-limiting factor in the development of CRC, uncovering a novel role for them in cancer biology.
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Affiliation(s)
- Lu Wang
- 1 Department of Pharmacology, School of Pharmaceutical Sciences, Shandong University , Jinan, China
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Schwartz-Roberts JL, Cook KL, Chen C, Shajahan-Haq AN, Axelrod M, Wärri A, Riggins RB, Jin L, Haddad BR, Kallakury BV, Baumann WT, Clarke R. Interferon regulatory factor-1 signaling regulates the switch between autophagy and apoptosis to determine breast cancer cell fate. Cancer Res 2015; 75:1046-55. [PMID: 25576084 PMCID: PMC4359953 DOI: 10.1158/0008-5472.can-14-1851] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Interferon regulatory factor-1 (IRF1) is a tumor suppressor that regulates cell fate in several cell types. Here, we report an inverse correlation in expression of nuclear IRF1 and the autophagy regulator ATG7 in human breast cancer cells that directly affects their cell fate. In mice harboring mutant Atg7, nuclear IRF1 was increased in mammary tumors, spleen, and kidney. Mechanistic investigations identified ATG7 and the cell death modulator beclin-1 (BECN1) as negative regulators of IRF1. Silencing ATG7 or BECN1 caused estrogen receptor-α to exit the nucleus at the time when IRF1 nuclear localization occurred. Conversely, silencing IRF1 promoted autophagy by increasing BECN1 and blunting IGF1 receptor and mTOR survival signaling. Loss of IRF1 promoted resistance to antiestrogens, whereas combined silencing of ATG7 and IRF1 restored sensitivity to these agents. Using a mathematical model to prompt signaling hypotheses, we developed evidence that ATG7 silencing could resensitize IRF1-attenuated cells to apoptosis through mechanisms that involve other estrogen-regulated genes. Overall, our work shows how inhibiting the autophagy proteins ATG7 and BECN1 can regulate IRF1-dependent and -independent signaling pathways in ways that engender a new therapeutic strategy to attack breast cancer.
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Affiliation(s)
- Jessica L Schwartz-Roberts
- Department of Physiology and Biophysics, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC. Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC
| | - Katherine L Cook
- Department of Physiology and Biophysics, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC. Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC
| | - Chun Chen
- Department of Biological Sciences, Virginia Polytechnic Institute and State University, Blacksburg, Virginia. Department of Electrical and Computer Engineering, Virginia Polytechnic Institute and State University, Blacksburg, Virginia
| | - Ayesha N Shajahan-Haq
- Department of Physiology and Biophysics, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC. Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC
| | - Margaret Axelrod
- Department of Physiology and Biophysics, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC. Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC
| | - Anni Wärri
- Department of Physiology and Biophysics, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC. Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC
| | - Rebecca B Riggins
- Department of Physiology and Biophysics, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC. Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC
| | - Lu Jin
- Department of Physiology and Biophysics, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC. Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC
| | - Bassem R Haddad
- Department of Physiology and Biophysics, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC. Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC
| | - Bhaskar V Kallakury
- Department of Pathology, Georgetown University Medical Center, Washington, DC
| | - William T Baumann
- Department of Biological Sciences, Virginia Polytechnic Institute and State University, Blacksburg, Virginia. Department of Electrical and Computer Engineering, Virginia Polytechnic Institute and State University, Blacksburg, Virginia
| | - Robert Clarke
- Department of Physiology and Biophysics, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC. Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC.
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Identification of IRF1 as critical dual regulator of Smac mimetic-induced apoptosis and inflammatory cytokine response. Cell Death Dis 2014; 5:e1562. [PMID: 25501823 PMCID: PMC4454156 DOI: 10.1038/cddis.2014.498] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2014] [Revised: 10/13/2014] [Accepted: 10/20/2014] [Indexed: 12/02/2022]
Abstract
Smac (second mitochondria-derived activator of caspase) mimetics are considered as promising anticancer therapeutics and used to induce apoptosis by antagonizing inhibitor of apoptosis proteins, which are often abundantly expressed in cancer cells. Here, we identify interferon regulatory factor 1 (IRF1) as a novel critical regulator of Smac mimetic BV6-induced apoptosis and proinflammatory cytokine secretion with impact on the immune response. IRF1 knockdown rescues cells from BV6-induced apoptosis and attenuates BV6-stimulated upregulation of tumor necrosis factor-α (TNFα), indicating that IRF1 mediates BV6-triggered cell death, at least in part, by inducing TNFα. This notion is supported by data showing that exogenous supply of TNFα restores BV6-induced cell death in IRF-knockdown cells. Interestingly, IRF1 selectively controls the induction of nuclear factor-κB (NF-κB) target genes, as IRF1 depletion attenuates BV6-stimulated upregulation of TNFα and interleukin-8 (IL-8) but not p100 and RelB. Concomitant knockdown of IRF1 and p65 cooperate to inhibit BV6-induced cell death, implying a cooperative interaction of IRF1 and NF-κB. In addition, IRF1 silencing hampers TNFα induction by TNFα itself as an another prototypical NF-κB stimulus. Importantly, IRF1 depletion impedes BV6-stimulated secretion of additional proinflammatory cytokines such as granulocyte–macrophage colony-stimulating factor (GM-CSF), IL-8, IL-6 and monocyte chemoattractant protein-1, and migration of primary monocytes to BV6-treated tumor cells. In conclusion, this identification of IRF1 as a dual regulator of BV6-induced apoptosis and inflammatory cytokine secretion provides novel insights into determinants of sensitivity towards Smac mimetic and possible implications of Smac mimetic treatment on tumor microenvironment and immune response.
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Xu H, Xian J, Vire E, McKinney S, Wong J, Wei V, Tong R, Kouzarides T, Caldas C, Aparicio S. Up-regulation of the interferon-related genes in BRCA2 knockout epithelial cells. J Pathol 2014; 234:386-97. [PMID: 25043256 PMCID: PMC4882165 DOI: 10.1002/path.4404] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2014] [Revised: 07/03/2014] [Accepted: 07/06/2014] [Indexed: 12/30/2022]
Abstract
BRCA2 mutations are significantly associated with early-onset breast cancer, and the tumour-suppressing function of BRCA2 has been attributed to its involvement in homologous recombination (HR)-mediated DNA repair. In order to identify additional functions of BRCA2, we generated BRCA2-knockout HCT116 human colorectal carcinoma cells. Using genome-wide microarray analyses, we have discovered a link between the loss of BRCA2 and the up-regulation of a subset of interferon (IFN)-related genes, including APOBEC3F and APOBEC3G. The over-expression of IFN-related genes was confirmed in different human BRCA2(-/-) and mouse Brca2(-/-) tumour cell lines, and was independent of senescence and apoptosis. In isogenic wild-type BRCA2 cells, we observed over-expression of IFN-related genes after treatment with DNA-damaging agents, and following ionizing radiation. Cells with endogenous DNA damage because of defective BRCA1 or RAD51 also exhibited over-expression of IFN-related genes. Transcriptional activity of the IFN-stimulated response element (ISRE) was increased in BRCA2 knockout cells, and the expression of BRCA2 greatly decreased IFNα-stimulated ISRE reporter activity, suggesting that BRCA2 directly represses the expression of IFN-related genes through the ISRE. Finally, the colony-forming capacity of BRCA2 knockout cells was significantly reduced in the presence of either IFNβ or IFNγ, suggesting that IFNs may have potential as therapeutic agents in cancer cells with BRCA2 mutations. The GEO Accession No. for microarray analysis is GSE54830.
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Affiliation(s)
- Hong Xu
- Department of Molecular Oncology, British Columbia Cancer Agency, 675 West 10th Avenue, Vancouver, BC, V5Z 1L3, Canada
| | - Jian Xian
- Department of Oncology, University of Cambridge and Cancer Research UK Cambridge Research Institute, Li Ka Shing Centre, Cambridge, CB2 0RE, UK
| | - Emmanuelle Vire
- Wellcome Trust/Cancer Research UK Gurdon Institute, The Henry Wellcome Building of Cancer and Developmental Biology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK
| | - Steven McKinney
- Department of Molecular Oncology, British Columbia Cancer Agency, 675 West 10th Avenue, Vancouver, BC, V5Z 1L3, Canada
| | - Jason Wong
- Department of Molecular Oncology, British Columbia Cancer Agency, 675 West 10th Avenue, Vancouver, BC, V5Z 1L3, Canada
| | - Vivien Wei
- Department of Microbiology and Immunology, University of British Columbia, 1365 - 2350 Health Sciences Mall, Vancouver, British Columbia, Canada, V6T 1Z3
| | - Rebecca Tong
- Department of Microbiology and Immunology, University of British Columbia, 1365 - 2350 Health Sciences Mall, Vancouver, British Columbia, Canada, V6T 1Z3
| | - Tony Kouzarides
- Wellcome Trust/Cancer Research UK Gurdon Institute, The Henry Wellcome Building of Cancer and Developmental Biology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK
| | - Carlos Caldas
- Department of Oncology, University of Cambridge and Cancer Research UK Cambridge Research Institute, Li Ka Shing Centre, Cambridge, CB2 0RE, UK
| | - Samuel Aparicio
- Department of Molecular Oncology, British Columbia Cancer Agency, 675 West 10th Avenue, Vancouver, BC, V5Z 1L3, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Wesbrook Mall, Vancouver, BC, V6T 2B5 Vancouver, BC
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Arockiaraj J, Sathyamoorthi A, Kumaresan V, Palanisamy R, Chaurasia MK, Bhatt P, Gnanam AJ, Pasupuleti M, Arasu A. A murrel interferon regulatory factor-1: molecular characterization, gene expression and cell protection activity. Mol Biol Rep 2014; 41:5299-309. [PMID: 24859976 DOI: 10.1007/s11033-014-3401-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Accepted: 05/06/2014] [Indexed: 01/27/2023]
Abstract
In this study, we have reported a first murrel interferon regulatory factor-1 (designated as Murrel IRF-1) which is identified from a constructed cDNA library of striped murrel Channa striatus. The identified sequence was obtained by internal sequencing method from the library. The Murrel IRF-1 varies in size of the polypeptide from the earlier reported fish IRF-1. It contains a DNA binding domain along with a tryptophan pentad repeats, a nuclear localization signal and a transactivation domain. The homologous analysis showed that the Murrel IRF-1 had a significant sequence similarity with other known fish IRF-1 groups. The phylogenetic analysis exhibited that the Murrel IRF-1 clustered together with IRF-1 members, but the other members including IRF-2, 3, 4, 5, 6, 7, 8, 9 and 10 were clustered individually. The secondary structure of Murrel IRF-1 contains 27% α-helices (85 aa residues), 5.7% β-sheets (19 aa residues) and 67.19% random coils (210 aa residues). Furthermore, we predicted a tertiary structure of Murrel IRF-1 using I-Tasser program and analyzed the structure on PyMol surface view. The RNA structure of the Murrel IRF-1 along with its minimum free energy (-284.43 kcal/mol) was also predicted. The highest gene expression was observed in spleen and its expression was inducted with pathogenic microbes which cause epizootic ulcerative syndrome in murrels such as fungus, Aphanomyces invadans and bacteria, Aeromonas hydrophila, and poly I:C, a viral RNA analog. The results of cell protection assay suggested that the Murrel IRF-1 regulates the early defense response in C. striatus. Moreover, it showed Murrel IRF-1 as a potential candidate which can be developed as a therapeutic agent to control microbial infections in striped murrel. Overall, these results indicate the immune importance of IRF-1, however, the interferon signaling mechanism in murrels upon infection is yet to be studied at proteomic level.
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Affiliation(s)
- Jesu Arockiaraj
- Division of Fisheries Biotechnology & Molecular Biology, Department of Biotechnology, Faculty of Science and Humanities, SRM University, Kattankulathur, Chennai, 603 203, Tamil Nadu, India,
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Construction of pancreatic cancer double-factor regulatory network based on chip data on the transcriptional level. Mol Biol Rep 2014; 41:2875-83. [PMID: 24469724 DOI: 10.1007/s11033-014-3143-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2013] [Accepted: 01/11/2014] [Indexed: 12/24/2022]
Abstract
Transcription factor (TF) and microRNA (miRNA) have been discovered playing crucial roles in cancer development. However, the effect of TFs and miRNAs in pancreatic cancer pathogenesis remains vague. We attempted to reveal the possible mechanism of pancreatic cancer based on transcription level. Using GSE16515 datasets downloaded from gene expression omnibus database, we first identified the differentially expressed genes (DEGs) in pancreatic cancer by the limma package in R. Then the DEGs were mapped into DAVID to conduct the kyoto encyclopedia of genes and genomes (KEGG) pathway enrichment analysis. TFs and miRNAs that DEGs significantly enriched were identified by Fisher's test, and then the pancreatic cancer double-factor regulatory network was constructed. In our study, total 1117 DEGs were identified and they significantly enriched in 4 KEGG pathways. A double-factor regulatory network was established, including 29 DEGs, 24 TFs, 25 miRNAs. In the network, LAMC2, BRIP1 and miR155 were identified which may be involved in pancreatic cancer development. In conclusion, the double-factor regulatory network was found to play an important role in pancreatic cancer progression and our results shed new light on the molecular mechanism of pancreatic cancer.
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