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Mallick I, Panchal P, Kadam S, Mohite P, Scheele J, Seiz W, Agarwal A, Sharma OP. In-silico identification and prioritization of therapeutic targets of asthma. Sci Rep 2023; 13:15706. [PMID: 37735578 PMCID: PMC10514284 DOI: 10.1038/s41598-023-42803-w] [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: 03/01/2023] [Accepted: 09/14/2023] [Indexed: 09/23/2023] Open
Abstract
Asthma is a "common chronic disorder that affects the lungs causing variable and recurring symptoms like repeated episodes of wheezing, breathlessness, chest tightness and underlying inflammation. The interaction of these features of asthma determines the clinical manifestations and severity of asthma and the response to treatment" [cited from: National Heart, Lung, and Blood Institute. Expert Panel 3 Report. Guidelines for the Diagnosis and Management of Asthma 2007 (EPR-3). Available at: https://www.ncbi.nlm.nih.gov/books/NBK7232/ (accessed on January 3, 2023)]. As per the WHO, 262 million people were affected by asthma in 2019 that leads to 455,000 deaths ( https://www.who.int/news-room/fact-sheets/detail/asthma ). In this current study, our aim was to evaluate thousands of scientific documents and asthma associated omics datasets to identify the most crucial therapeutic target for experimental validation. We leveraged the proprietary tool Ontosight® Discover to annotate asthma associated genes and proteins. Additionally, we also collected and evaluated asthma related patient datasets through bioinformatics and machine learning based approaches to identify most suitable targets. Identified targets were further evaluated based on the various biological parameters to scrutinize their candidature for the ideal therapeutic target. We identified 7237 molecular targets from published scientific documents, 2932 targets from genomic structured databases and 7690 dysregulated genes from the transcriptomics and 560 targets from genomics mutational analysis. In total, 18,419 targets from all the desperate sources were analyzed and evaluated though our approach to identify most promising targets in asthma. Our study revealed IL-13 as one of the most important targets for asthma with approved drugs on the market currently. TNF, VEGFA and IL-18 were the other top targets identified to be explored for therapeutic benefit in asthma but need further clinical testing. HMOX1, ITGAM, DDX58, SFTPD and ADAM17 were the top novel targets identified for asthma which needs to be validated experimentally.
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Affiliation(s)
- Ishita Mallick
- Innoplexus Consulting Pvt. Ltd, 7th Floor, Midas Tower, Next to STPI Building, Phase 1, Hinjewadi Rajiv Gandhi Infotech Park, Hinjawadi, Pune, Maharashtra, 411057, India
| | - Pradnya Panchal
- Innoplexus Consulting Pvt. Ltd, 7th Floor, Midas Tower, Next to STPI Building, Phase 1, Hinjewadi Rajiv Gandhi Infotech Park, Hinjawadi, Pune, Maharashtra, 411057, India
| | - Smita Kadam
- Innoplexus Consulting Pvt. Ltd, 7th Floor, Midas Tower, Next to STPI Building, Phase 1, Hinjewadi Rajiv Gandhi Infotech Park, Hinjawadi, Pune, Maharashtra, 411057, India
| | - Priyanka Mohite
- Innoplexus Consulting Pvt. Ltd, 7th Floor, Midas Tower, Next to STPI Building, Phase 1, Hinjewadi Rajiv Gandhi Infotech Park, Hinjawadi, Pune, Maharashtra, 411057, India
| | - Jürgen Scheele
- Innoplexus AG, Frankfurter Str. 27, 65760, Eschborn, Germany
| | - Werner Seiz
- Innoplexus AG, Frankfurter Str. 27, 65760, Eschborn, Germany
| | - Amit Agarwal
- Innoplexus Consulting Pvt. Ltd, 7th Floor, Midas Tower, Next to STPI Building, Phase 1, Hinjewadi Rajiv Gandhi Infotech Park, Hinjawadi, Pune, Maharashtra, 411057, India
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Piñeiro-Hermida S, Bosso G, Sánchez-Vázquez R, Martínez P, Blasco MA. Telomerase deficiency and dysfunctional telomeres in the lung tumor microenvironment impair tumor progression in NSCLC mouse models and patient-derived xenografts. Cell Death Differ 2023:10.1038/s41418-023-01149-6. [PMID: 37085672 DOI: 10.1038/s41418-023-01149-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 03/02/2023] [Accepted: 03/10/2023] [Indexed: 04/23/2023] Open
Abstract
Non-small cell lung cancer (NSCLC) is a leading cause of cancer death. Tumor progression depends on interactions of cancer cells with the tumor microenvironment. Here, we find increased copy number and mRNA expression of the catalytic subunit of telomerase, TERT, in tumors from NSCLC patients, contributing to a lower survival. Moreover, TERT expression in NSCLC patients from the TCGA cohort is mainly associated to the reduced infiltration of CD8+ T lymphocytes, as well as to increased infiltration of myeloid-derived suppressor cells (MDSCs). We also show that TERT deficiency and dysfunctional telomeres induced by 6-thio-dG treatment in mice reduced lung tumor implantation and vascularization, increased DNA damage response, cell cycle arrest and apoptosis, as well as reduced proliferation, inflammation, lung tumor immunosupression and invasion upon induction of a Lewis lung carcinoma (LLC). Furthermore, 6-thio-dG-treated human NSCLC xenografts exhibited increased telomere damage, cell cycle arrest and apoptosis, as well as reduced proliferation, resulting in a reduced tumor growth. Our results show that targeting telomeres might be an effective therapeutic strategy in NSCLC.
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Affiliation(s)
- Sergio Piñeiro-Hermida
- Telomeres and Telomerase Group, Molecular Oncology Program, Spanish National Cancer Centre (CNIO), Melchor Fernández Almagro 3, Madrid, E-28029, Spain
| | - Giuseppe Bosso
- Telomeres and Telomerase Group, Molecular Oncology Program, Spanish National Cancer Centre (CNIO), Melchor Fernández Almagro 3, Madrid, E-28029, Spain
| | - Raúl Sánchez-Vázquez
- Telomeres and Telomerase Group, Molecular Oncology Program, Spanish National Cancer Centre (CNIO), Melchor Fernández Almagro 3, Madrid, E-28029, Spain
| | - Paula Martínez
- Telomeres and Telomerase Group, Molecular Oncology Program, Spanish National Cancer Centre (CNIO), Melchor Fernández Almagro 3, Madrid, E-28029, Spain
| | - Maria A Blasco
- Telomeres and Telomerase Group, Molecular Oncology Program, Spanish National Cancer Centre (CNIO), Melchor Fernández Almagro 3, Madrid, E-28029, Spain.
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Consequences of telomere dysfunction in fibroblasts, club and basal cells for lung fibrosis development. Nat Commun 2022; 13:5656. [PMID: 36202783 PMCID: PMC9537293 DOI: 10.1038/s41467-022-32771-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 08/16/2022] [Indexed: 11/08/2022] Open
Abstract
TRF1 is an essential component of the telomeric protective complex or shelterin. We previously showed that dysfunctional telomeres in alveolar type II (ATII) cells lead to interstitial lung fibrosis. Here, we study the lung pathologies upon telomere dysfunction in fibroblasts, club and basal cells. TRF1 deficiency in lung fibroblasts, club and basal cells induced telomeric damage, proliferative defects, cell cycle arrest and apoptosis. While Trf1 deletion in fibroblasts does not spontaneously lead to lung pathologies, upon bleomycin challenge exacerbates lung fibrosis. Unlike in females, Trf1 deletion in club and basal cells from male mice resulted in lung inflammation and airway remodeling. Here, we show that depletion of TRF1 in fibroblasts, Club and basal cells does not lead to interstitial lung fibrosis, underscoring ATII cells as the relevant cell type for the origin of interstitial fibrosis. Our findings contribute to a better understanding of proper telomere protection in lung tissue homeostasis.
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IGF1R acts as a cancer-promoting factor in the tumor microenvironment facilitating lung metastasis implantation and progression. Oncogene 2022; 41:3625-3639. [PMID: 35688943 PMCID: PMC9184253 DOI: 10.1038/s41388-022-02376-w] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 05/27/2022] [Accepted: 06/01/2022] [Indexed: 11/08/2022]
Abstract
Given the long-term ineffectiveness of current therapies and late-stage diagnoses, lung cancer is a leading cause of malignant diseases. Tumor progression is influenced by cancer cell interactions with the tumor microenvironment (TME). Insulin-like growth factor 1 receptor (IGF1R) was reported to affect the TME; however, the role of IGF1R in lung TME has not been investigated. First, we assessed IGF1R genomic alterations and expression in NSCLC patient tissue samples, as well as IGF1R serum levels. Next, we performed tumor heterotopic transplantation and pulmonary metastases in IGF1R-deficient mice using melanoma and Lewis lung carcinoma (LLC) cells. Herein we report increased amplification and mRNA expression, as well as increased protein expression (IGF1R/p-IGF1R) and IGF1R levels in tumor samples and serum from NSCLC patients, respectively. Moreover, IGF1R deficiency in mice reduced tumor growth, proliferation, inflammation and vascularization, and increased apoptosis after tumor heterotopic transplantation. Following induction of lung metastasis, IGF1R-deficient lungs also demonstrated a reduced tumor burden, and decreased expression of tumor progression markers, p-IGF1R and p-ERK1/2. Additionally, IGF1R-deficient lungs showed increased apoptosis and diminished proliferation, vascularization, EMT and fibrosis, along with attenuated inflammation and immunosuppression. Accordingly, IGF1R deficiency decreased expression of p-IGF1R in blood vessels, fibroblasts, tumor-associated macrophages and FOXP3+ tumor-infiltrating lymphocytes. Our results demonstrate that IGF1R promotes metastatic tumor initiation and progression in lung TME. Furthermore, our research indicates that IGF1R could be a potential biomarker for early prediction of drug response and clinical evolution in NSCLC patients.
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Correction: Alfaro-Arnedo et al. IGF1R as a Potential Pharmacological Target in Allergic Asthma. Biomedicines 2021, 9, 912. Biomedicines 2022; 10:biomedicines10040733. [PMID: 35453679 PMCID: PMC9030783 DOI: 10.3390/biomedicines10040733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 03/02/2022] [Indexed: 02/01/2023] Open
Abstract
In the original article [...]
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Pérez-Matute P, López IP, Íñiguez M, Recio-Fernández E, Torrens R, Piñeiro-Hermida S, Alfaro-Arnedo E, Chau L, Walz C, Hoeflich A, Oteo JA, Pichel JG. IGF1R is a mediator of sex-specific metabolism in mice: Effects of age and high-fat diet. Front Endocrinol (Lausanne) 2022; 13:1033208. [PMID: 36353242 PMCID: PMC9638844 DOI: 10.3389/fendo.2022.1033208] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 09/29/2022] [Indexed: 11/13/2022] Open
Abstract
OBJECTIVE We aimed to investigate the short and long-term metabolic consequences of IGF1R systemic gene deficiency in mice. METHODS UBC-CreERT2, Igf1rfl/fl mutant mice were used to suppress IGF1R signaling in adult tissues by inducing postnatal generalized Igf1r deletion with tamoxifen. Animals were analyzed at two different ages: i) 13-weeks old young mice, and ii) 12-months old middle-aged mice. In addition, the effects of 10 weeks-long high-fat diet (HFD) were investigated in middle-aged mice. RESULTS Young IGF1R-deficient mice were insulin-resistant, with high IGF1, growth hormone (GH) and IGFBP3, as well as low IGFBP2 circulating levels. Males also presented increased triglycerides in liver. In contrast, middle-aged mice did not clearly show all of these alterations, suggesting possible compensatory effects. Middle-aged IGF1R-deficient male mice were able to counteract the negative effects induced by aging and HFD in adiposity, inflammation and glucose metabolism. A metabolic sexual dimorphism dependent on IGF1R was observed, especially in middle-aged mice. CONCLUSIONS These results demonstrate that IGF1R is involved in metabolic homeostasis, with effects modulated by diet-induced obesity and aging in a sex dependent manner. Thus, IGF1R deficiency in mice is proposed as a useful tool to understand metabolic alterations observed in patients with IGF1R gene deletions.
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Affiliation(s)
- Patricia Pérez-Matute
- Infectious Diseases, Microbiota and Metabolism Unit, Infectious Diseases Department, Center for Biomedical Research of La Rioja (CIBIR) -Hospital Universitario San Pedro, Logroño, Spain
- *Correspondence: Patricia Pérez-Matute,
| | - Icíar P. López
- Lung Cancer and Respiratory Diseases Unit. Fundación Rioja Salud, Center for Biomedical Research of La Rioja (CIBIR), Logroño, Spain
| | - María Íñiguez
- Infectious Diseases, Microbiota and Metabolism Unit, Infectious Diseases Department, Center for Biomedical Research of La Rioja (CIBIR) -Hospital Universitario San Pedro, Logroño, Spain
| | - Emma Recio-Fernández
- Infectious Diseases, Microbiota and Metabolism Unit, Infectious Diseases Department, Center for Biomedical Research of La Rioja (CIBIR) -Hospital Universitario San Pedro, Logroño, Spain
| | - Raquel Torrens
- Lung Cancer and Respiratory Diseases Unit. Fundación Rioja Salud, Center for Biomedical Research of La Rioja (CIBIR), Logroño, Spain
| | - Sergio Piñeiro-Hermida
- Miguel Servet Foundation-Navarra's Health Research Institute (IDISNA), Navarrabiomed Biomedical Research Center, Oncoimmunology Group, Pamplona, Spain
| | - Elvira Alfaro-Arnedo
- Lung Cancer and Respiratory Diseases Unit. Fundación Rioja Salud, Center for Biomedical Research of La Rioja (CIBIR), Logroño, Spain
| | - Luong Chau
- Institute for Genome Biology, Research Institute for Farm Animal Biology (FBN), Dummerstorf, Germany
| | - Christina Walz
- Institute for Genome Biology, Research Institute for Farm Animal Biology (FBN), Dummerstorf, Germany
| | - Andreas Hoeflich
- Institute for Genome Biology, Research Institute for Farm Animal Biology (FBN), Dummerstorf, Germany
| | - José A. Oteo
- Infectious Diseases, Microbiota and Metabolism Unit, Infectious Diseases Department, Center for Biomedical Research of La Rioja (CIBIR) -Hospital Universitario San Pedro, Logroño, Spain
| | - José G. Pichel
- Lung Cancer and Respiratory Diseases Unit. Fundación Rioja Salud, Center for Biomedical Research of La Rioja (CIBIR), Logroño, Spain
- Biomedical Research Networking Center on Respiratory Diseases (CIBERES), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
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