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Murillo Carrasco AG, Giovanini G, Ramos AF, Chammas R, Bustos SO. Insights from a Computational-Based Approach for Analyzing Autophagy Genes across Human Cancers. Genes (Basel) 2023; 14:1550. [PMID: 37628602 PMCID: PMC10454514 DOI: 10.3390/genes14081550] [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: 06/30/2023] [Revised: 07/25/2023] [Accepted: 07/26/2023] [Indexed: 08/27/2023] Open
Abstract
In the last decade, there has been a boost in autophagy reports due to its role in cancer progression and its association with tumor resistance to treatment. Despite this, many questions remain to be elucidated and explored among the different tumors. Here, we used omics-based cancer datasets to identify autophagy genes as prognostic markers in cancer. We then combined these findings with independent studies to further characterize the clinical significance of these genes in cancer. Our observations highlight the importance of innovative approaches to analyze tumor heterogeneity, potentially affecting the expression of autophagy-related genes with either pro-tumoral or anti-tumoral functions. In silico analysis allowed for identifying three genes (TBC1D12, KERA, and TUBA3D) not previously described as associated with autophagy pathways in cancer. While autophagy-related genes were rarely mutated across human cancers, the expression profiles of these genes allowed the clustering of different cancers into three independent groups. We have also analyzed datasets highlighting the effects of drugs or regulatory RNAs on autophagy. Altogether, these data provide a comprehensive list of targets to further the understanding of autophagy mechanisms in cancer and investigate possible therapeutic targets.
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Affiliation(s)
- Alexis Germán Murillo Carrasco
- Center for Translational Research in Oncology (LIM24), Instituto do Cancer do Estado de Sao Paulo (ICESP), Hospital das Clinicas da Faculdade de Medicina da Universidade de Sao Paulo (HCFMUSP), São Paulo 01246-000, Brazil; (A.G.M.C.); (S.O.B.)
- Comprehensive Center for Precision Oncology, Universidade de São Paulo, São Paulo 01246-000, Brazil
| | - Guilherme Giovanini
- Escola de Artes, Ciências e Humanidades, Universidade de São Paulo, Av. Arlindo Béttio, 1000, São Paulo 03828-000, Brazil; (G.G.); (A.F.R.)
| | - Alexandre Ferreira Ramos
- Escola de Artes, Ciências e Humanidades, Universidade de São Paulo, Av. Arlindo Béttio, 1000, São Paulo 03828-000, Brazil; (G.G.); (A.F.R.)
| | - Roger Chammas
- Center for Translational Research in Oncology (LIM24), Instituto do Cancer do Estado de Sao Paulo (ICESP), Hospital das Clinicas da Faculdade de Medicina da Universidade de Sao Paulo (HCFMUSP), São Paulo 01246-000, Brazil; (A.G.M.C.); (S.O.B.)
- Comprehensive Center for Precision Oncology, Universidade de São Paulo, São Paulo 01246-000, Brazil
| | - Silvina Odete Bustos
- Center for Translational Research in Oncology (LIM24), Instituto do Cancer do Estado de Sao Paulo (ICESP), Hospital das Clinicas da Faculdade de Medicina da Universidade de Sao Paulo (HCFMUSP), São Paulo 01246-000, Brazil; (A.G.M.C.); (S.O.B.)
- Comprehensive Center for Precision Oncology, Universidade de São Paulo, São Paulo 01246-000, Brazil
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Műzes G, Sipos F. Autoimmunity and Carcinogenesis: Their Relationship under the Umbrella of Autophagy. Biomedicines 2023; 11:biomedicines11041130. [PMID: 37189748 DOI: 10.3390/biomedicines11041130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Revised: 04/04/2023] [Accepted: 04/06/2023] [Indexed: 04/11/2023] Open
Abstract
The immune system and autophagy share a functional relationship. Both innate and adaptive immune responses involve autophagy and, depending on the disease’s origin and pathophysiology, it may have a detrimental or positive role on autoimmune disorders. As a “double-edged sword” in tumors, autophagy can either facilitate or impede tumor growth. The autophagy regulatory network that influences tumor progression and treatment resistance is dependent on cell and tissue types and tumor stages. The connection between autoimmunity and carcinogenesis has not been sufficiently explored in past studies. As a crucial mechanism between the two phenomena, autophagy may play a substantial role, though the specifics remain unclear. Several autophagy modifiers have demonstrated beneficial effects in models of autoimmune disease, emphasizing their therapeutic potential as treatments for autoimmune disorders. The function of autophagy in the tumor microenvironment and immune cells is the subject of intensive study. The objective of this review is to investigate the role of autophagy in the simultaneous genesis of autoimmunity and malignancy, shedding light on both sides of the issue. We believe our work will assist in the organization of current understanding in the field and promote additional research on this urgent and crucial topic.
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Affiliation(s)
- Györgyi Műzes
- Immunology Division, Department of Internal Medicine and Hematology, Semmelweis University, 1088 Budapest, Hungary
| | - Ferenc Sipos
- Immunology Division, Department of Internal Medicine and Hematology, Semmelweis University, 1088 Budapest, Hungary
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Rubio-Tomás T, Sotiriou A, Tavernarakis N. The interplay between selective types of (macro)autophagy: Mitophagy and xenophagy. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2023; 374:129-157. [PMID: 36858654 DOI: 10.1016/bs.ircmb.2022.10.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Autophagy is a physiological response, activated by a myriad of endogenous and exogenous cues, including DNA damage, perturbation of proteostasis, depletion of nutrients or oxygen and pathogen infection. Upon sensing those stimuli, cells employ multiple non-selective and selective autophagy pathways to promote fitness and survival. Importantly, there are a variety of selective types of autophagy. In this review we will focus on autophagy of bacteria (xenophagy) and autophagy of mitochondria (mitophagy). We provide a brief introduction to bulk autophagy, as well as xenophagy and mitophagy, highlighting their common molecular factors. We also describe the role of xenophagy and mitophagy in the detection and elimination of pathogens by the immune system and the adaptive mechanisms that some pathogens have developed through evolution to escape the host autophagic response. Finally, we summarize the recent articles (from the last five years) linking bulk autophagy with xenophagy and/or mitophagy in the context on developmental biology, cancer and metabolism.
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Affiliation(s)
- Teresa Rubio-Tomás
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Crete, Greece
| | - Aggeliki Sotiriou
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Crete, Greece; Division of Basic Sciences, School of Medicine, University of Crete, Heraklion, Crete, Greece
| | - Nektarios Tavernarakis
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Crete, Greece; Division of Basic Sciences, School of Medicine, University of Crete, Heraklion, Crete, Greece.
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Cancer Stem Cell Relationship with Pro-Tumoral Inflammatory Microenvironment. Biomedicines 2023; 11:biomedicines11010189. [PMID: 36672697 PMCID: PMC9855358 DOI: 10.3390/biomedicines11010189] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 01/05/2023] [Accepted: 01/10/2023] [Indexed: 01/15/2023] Open
Abstract
Inflammatory processes and cancer stem cells (CSCs) are increasingly recognized as factors in the development of tumors. Emerging evidence indicates that CSCs are associated with cancer properties such as metastasis, treatment resistance, and disease recurrence. However, the precise interaction between CSCs and the immune microenvironment remains unexplored. Although evasion of the immune system by CSCs has been extensively studied, new research demonstrates that CSCs can also control and even profit from the immune response. This review provides an overview of the reciprocal interplay between CSCs and tumor-infiltrating immune cells, collecting pertinent data about how CSCs stimulate leukocyte reprogramming, resulting in pro-tumor immune cells that promote metastasis, chemoresistance, tumorigenicity, and even a rise in the number of CSCs. Tumor-associated macrophages, neutrophils, Th17 and regulatory T cells, mesenchymal stem cells, and cancer-associated fibroblasts, as well as the signaling pathways involved in these pro-tumor activities, are among the immune cells studied. Although cytotoxic leukocytes have the potential to eliminate CSCs, immune evasion mechanisms in CSCs and their clinical implications are also known. We intended to compile experimental findings that provide direct evidence of interactions between CSCs and the immune system and CSCs and the inflammatory milieu. In addition, we aimed to summarize key concepts in order to comprehend the cross-talk between CSCs and the tumor microenvironment as a crucial process for the effective design of anti-CSC therapies.
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Fehri E, Ennaifer E, Bel Haj Rhouma R, Ardhaoui M, Boubaker S. TLR9 and Glioma: Friends or Foes? Cells 2022; 12:cells12010152. [PMID: 36611945 PMCID: PMC9818384 DOI: 10.3390/cells12010152] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 12/18/2022] [Accepted: 12/26/2022] [Indexed: 12/31/2022] Open
Abstract
Toll-like receptor 9 (TLR9) is an intracellular innate immunity receptor that plays a vital role in chronic inflammation and in recognizing pathogenic and self-DNA in immune complexes. This activation of intracellular signaling leads to the transcription of either immune-related or malignancy genes through specific transcription factors. Thus, it has been hypothesized that TLR9 may cause glioma. This article reviews the roles of TLR9 in the pathogenesis of glioma and its related signaling molecules in either defending or promoting glioma. TLR9 mediates the invasion-induced hypoxia of brain cancer cells by the activation of matrix metalloproteinases (2, 9, and 13) in brain tissues. In contrast, the combination of the TLR9 agonist CpG ODN to radiotherapy boosts the role of T cells in antitumor effects. The TLR9 agonist CpG ODN 107 also enhances the radiosensitivity of human glioma U87 cells by blocking tumor angiogenesis. CpG enhances apoptosis in vitro and in vivo. Furthermore, it can enhance the antigen-presenting capacity of microglia, switch immune response toward CD8 T cells, and reduce the number of CD4CD25 Treg cells. CpG ODN shows promise as a potent immunotherapeutic drug against cancer, but specific cautions should be taken when activating TLR9, especially in the case of glioblastoma.
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Affiliation(s)
- Emna Fehri
- HPV Unit Research, Laboratory of Molecular Epidemiology and Experimental Pathology Applied to Infectious Diseases, Pasteur Institute of Tunis, Tunis 1002, Tunisia
- Department of Human and Experimental Pathology, Pasteur Institute of Tunis, Tunis 1002, Tunisia
- Correspondence:
| | - Emna Ennaifer
- HPV Unit Research, Laboratory of Molecular Epidemiology and Experimental Pathology Applied to Infectious Diseases, Pasteur Institute of Tunis, Tunis 1002, Tunisia
- Department of Human and Experimental Pathology, Pasteur Institute of Tunis, Tunis 1002, Tunisia
| | - Rahima Bel Haj Rhouma
- HPV Unit Research, Laboratory of Molecular Epidemiology and Experimental Pathology Applied to Infectious Diseases, Pasteur Institute of Tunis, Tunis 1002, Tunisia
| | - Monia Ardhaoui
- HPV Unit Research, Laboratory of Molecular Epidemiology and Experimental Pathology Applied to Infectious Diseases, Pasteur Institute of Tunis, Tunis 1002, Tunisia
- Department of Human and Experimental Pathology, Pasteur Institute of Tunis, Tunis 1002, Tunisia
| | - Samir Boubaker
- Department of Human and Experimental Pathology, Pasteur Institute of Tunis, Tunis 1002, Tunisia
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Műzes G, Bohusné Barta B, Szabó O, Horgas V, Sipos F. Cell-Free DNA in the Pathogenesis and Therapy of Non-Infectious Inflammations and Tumors. Biomedicines 2022; 10:biomedicines10112853. [PMID: 36359370 PMCID: PMC9687442 DOI: 10.3390/biomedicines10112853] [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: 10/15/2022] [Revised: 10/31/2022] [Accepted: 11/07/2022] [Indexed: 11/09/2022] Open
Abstract
The basic function of the immune system is the protection of the host against infections, along with the preservation of the individual antigenic identity. The process of self-tolerance covers the discrimination between self and foreign antigens, including proteins, nucleic acids, and larger molecules. Consequently, a broken immunological self-tolerance results in the development of autoimmune or autoinflammatory disorders. Immunocompetent cells express pattern-recognition receptors on their cell membrane and cytoplasm. The majority of endogenous DNA is located intracellularly within nuclei and mitochondria. However, extracellular, cell-free DNA (cfDNA) can also be detected in a variety of diseases, such as autoimmune disorders and malignancies, which has sparked interest in using cfDNA as a possible biomarker. In recent years, the widespread use of liquid biopsies and the increasing demand for screening, as well as monitoring disease activity and therapy response, have enabled the revival of cfDNA research. The majority of studies have mainly focused on the function of cfDNA as a biomarker. However, research regarding the immunological consequences of cfDNA, such as its potential immunomodulatory or therapeutic benefits, is still in its infancy. This article discusses the involvement of various DNA-sensing receptors (e.g., absent in melanoma-2; Toll-like receptor 9; cyclic GMP-AMP synthase/activator of interferon genes) in identifying host cfDNA as a potent danger-associated molecular pattern. Furthermore, we aim to summarize the results of the experimental studies that we recently performed and highlight the immunomodulatory capacity of cfDNA, and thus, the potential for possible therapeutic consideration.
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Affiliation(s)
| | | | | | | | - Ferenc Sipos
- Correspondence: ; Tel.: +36-20-478-0752; Fax: +36-1-266-0816
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Sipos F, Bohusné Barta B, Simon Á, Nagy L, Dankó T, Raffay RE, Petővári G, Zsiros V, Wichmann B, Sebestyén A, Műzes G. Survival of HT29 Cancer Cells Is Affected by IGF1R Inhibition via Modulation of Self-DNA-Triggered TLR9 Signaling and the Autophagy Response. Pathol Oncol Res 2022; 28:1610322. [PMID: 35651701 PMCID: PMC9148969 DOI: 10.3389/pore.2022.1610322] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 04/27/2022] [Indexed: 02/05/2023]
Abstract
Purpose: In HT29 colon cancer cells, a close interplay between self-DNA-induced TLR9 signaling and autophagy response was found, with remarkable effects on cell survival and differentiation. IGF1R activation drives the development and malignant progression of colorectal cancer. IGF1R inhibition displays a controversial effect on autophagy. The interrelated roles of IGF1R inhibition and TLR9/autophagy signaling in HT29 cancer cells have not yet been clarified. In our study, we aimed to investigate the complex interplay of IGF1R inhibition and TLR9/autophagy signaling in HT29 cells. Methods: HT29 cells were incubated with tumor-originated self-DNA with or without inhibitors of IGF1R (picropodophyllin), autophagy (chloroquine), and TLR9 (ODN2088), respectively. Cell proliferation and metabolic activity measurements, direct cell counting, NanoString and Taqman gene expression analyses, immunocytochemistry, WES Simple Western blot, and transmission electron microscopy investigations were performed. Results: The concomitant use of tumor-derived self-DNA and IGF1R inhibitors displays anti-proliferative potential, which can be reversed by parallel TLR9 signaling inhibition. The distinct effects of picropodophyllin, ODN2088, and chloroquine per se or in combination on HT29 cell proliferation and autophagy suggest that either the IGF1R-associated or non-associated autophagy machinery is "Janus-faced" regarding its actions on cell proliferation. Autophagy, induced by different combinations of self-DNA and inhibitors is not sufficient to rescue HT29 cells from death but results in the survival of some CD133-positive stem-like HT29 cells. Conclusion: The creation of new types of combined IGF1R, autophagy, and/or TLR9 signaling inhibitors would play a significant role in the development of more personalized anti-tumor therapies for colorectal cancer.
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Affiliation(s)
- Ferenc Sipos
- Department of Internal Medicine and Hematology, Semmelweis University, Budapest, Hungary
- *Correspondence: Ferenc Sipos,
| | - Bettina Bohusné Barta
- Department of Internal Medicine and Hematology, Semmelweis University, Budapest, Hungary
| | - Ágnes Simon
- Department of Internal Medicine and Hematology, Semmelweis University, Budapest, Hungary
| | - Lőrinc Nagy
- Department of Internal Medicine and Hematology, Semmelweis University, Budapest, Hungary
| | - Titanilla Dankó
- Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - Regina Eszter Raffay
- Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - Gábor Petővári
- Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - Viktória Zsiros
- Department of Anatomy, Histology and Embryology, Semmelweis University, Budapest, Hungary
| | | | - Anna Sebestyén
- Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - Györgyi Műzes
- Department of Internal Medicine and Hematology, Semmelweis University, Budapest, Hungary
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Bohusné Barta B, Simon Á, Nagy L, Dankó T, Raffay RE, Petővári G, Zsiros V, Sebestyén A, Sipos F, Műzes G. Survival of HT29 cancer cells is influenced by hepatocyte growth factor receptor inhibition through modulation of self-DNA-triggered TLR9-dependent autophagy response. PLoS One 2022; 17:e0268217. [PMID: 35551547 PMCID: PMC9098092 DOI: 10.1371/journal.pone.0268217] [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: 09/07/2021] [Accepted: 04/25/2022] [Indexed: 02/05/2023] Open
Abstract
HGFR activation drives the malignant progression of colorectal cancer, and its inhibition displays anti-autophagic activity. The interrelated role of HGFR inhibition and TLR9/autophagy signaling in HT29 cancer cells subjected to modified self-DNA treatments has not been clarified. We analyzed this complex interplay with cell metabolism and proliferation measurements, TLR9, HGFR and autophagy inhibitory assays and WES Simple Western blot-based autophagy flux measurements, gene expression analyses, immunocytochemistry, and transmission electron microscopy. The overexpression of MyD88 and caspase-3 was associated with enhanced HT29 cell proliferation, suggesting that incubation with self-DNAs could suppress the apoptosis-induced compensatory cell proliferation. HGFR inhibition blocked the proliferation-reducing effect of genomic and hypermethylated, but not that of fragmented DNA. Lowest cell proliferation was achieved with the concomitant use of genomic DNA, HGFR inhibitor, and chloroquine, when the proliferation stimulating effect of STAT3 overexpression could be outweighed by the inhibitory effect of LC3B, indicating the putative involvement of HGFR-mTOR-ULK1 molecular cascade in HGFR inhibitor-mediated autophagy. The most intense cell proliferation was caused by the co-administration of hypermethylated DNA, TLR9 and HGFR inhibitors, when decreased expression of both canonical and non-canonical HGFR signaling pathways and autophagy-related genes was present. The observed ultrastructural changes also support the context-dependent role of HGFR inhibition and autophagy on cell survival and proliferation. Further investigation of the influence of the studied signaling pathways and cellular processes can provide a basis for novel, individualized anti-cancer therapies.
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Affiliation(s)
- Bettina Bohusné Barta
- Department of Internal Medicine and Hematology, Semmelweis University, Budapest, Hungary
| | - Ágnes Simon
- Department of Internal Medicine and Hematology, Semmelweis University, Budapest, Hungary
| | - Lőrinc Nagy
- Department of Internal Medicine and Hematology, Semmelweis University, Budapest, Hungary
| | - Titanilla Dankó
- 1st Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - Regina Eszter Raffay
- 1st Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - Gábor Petővári
- 1st Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - Viktória Zsiros
- Department of Anatomy, Histology and Embryology, Semmelweis University, Budapest, Hungary
| | - Anna Sebestyén
- 1st Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - Ferenc Sipos
- Department of Internal Medicine and Hematology, Semmelweis University, Budapest, Hungary
- * E-mail:
| | - Györgyi Műzes
- Department of Internal Medicine and Hematology, Semmelweis University, Budapest, Hungary
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