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Pham DT, Tran TD. Drivergene.net: A Cytoscape app for the identification of driver nodes of large-scale complex networks and case studies in discovery of drug target genes. Comput Biol Med 2024; 179:108888. [PMID: 39047507 DOI: 10.1016/j.compbiomed.2024.108888] [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: 02/23/2024] [Revised: 06/15/2024] [Accepted: 07/11/2024] [Indexed: 07/27/2024]
Abstract
There are no tools to identify driver nodes of large-scale networks in approach of competition-based controllability. This study proposed a novel method for this computation of large-scale networks. It implemented the method in a new Cytoscape plug-in app called Drivergene.net. Experiments of the software on large-scale biomolecular networks have shown outstanding speed and computing power. Interestingly, 86.67% of the top 10 driver nodes found on these networks are anticancer drug target genes that reside mostly at the innermost K-cores of the networks. Finally, compared method with those of five other researchers and confirmed that the proposed method outperforms the other methods on identification of anticancer drug target genes. Taken together, Drivergene.net is a reliable tool that efficiently detects not only drug target genes from biomolecular networks but also driver nodes of large-scale complex networks. Drivergene.net with a user manual and example datasets are available https://github.com/tinhpd/Drivergene.git.
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Affiliation(s)
- Duc-Tinh Pham
- Complex Systems and Bioinformatics Lab, Hanoi University of Industry, 298 Cau Dien Street, Bac Tu Liem District, Hanoi, Viet Nam; Graduate University of Science and Technology, Academy of Science and Technology Viet Nam, 18 Hoang Quoc Viet Street, Cau Giay District, Hanoi, Viet Nam
| | - Tien-Dzung Tran
- Complex Systems and Bioinformatics Lab, Hanoi University of Industry, 298 Cau Dien Street, Bac Tu Liem District, Hanoi, Viet Nam; Faculty of Information and Communication Technology, Hanoi University of Industry, 298 Cau Dien Street, Bac Tu Liem District, Hanoi, Viet Nam.
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2
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Rose MM, Espinoza VL, Hoff KJ, Pike LA, Sharma V, Hofmann MC, Tan AC, Pozdeyev N, Schweppe RE. BCL2L11 Induction Mediates Sensitivity to Src and MEK1/2 Inhibition in Thyroid Cancer. Cancers (Basel) 2023; 15:378. [PMID: 36672327 PMCID: PMC9856535 DOI: 10.3390/cancers15020378] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 12/31/2022] [Accepted: 01/03/2023] [Indexed: 01/08/2023] Open
Abstract
Patients with advanced thyroid cancer, including advanced papillary thyroid cancer and anaplastic thyroid cancer (ATC), have low survival rates because of the lack of efficient therapies available that can combat their aggressiveness. A total of 90% of thyroid cancers have identifiable driver mutations, which often are components of the MAPK pathway, including BRAF, RAS, and RET-fusions. In addition, Src is a non-receptor tyrosine kinase that is overexpressed and activated in thyroid cancer, which we and others have shown is a clinically relevant target. We have previously demonstrated that combined inhibition of Src with dasatinib and the MAPK pathway with trametinib synergistically inhibits growth and induces apoptosis in BRAF- and RAS-mutant thyroid cancer cells. Herein, we identified the pro-apoptotic protein BCL2L11 (BIM) as being a key mediator of sensitivity in response to combined dasatinib and trametinib treatment. Specifically, cells that are sensitive to combined dasatinib and trametinib treatment have inhibition of FAK/Src, MEK/ERK, and AKT, resulting in the dramatic upregulation of BIM, while cells that are resistant lack inhibition of AKT and have a dampened induction of BIM. Inhibition of AKT directly sensitizes resistant cells to combined dasatinib and trametinib but will not be clinically feasible. Importantly, targeting BCL-XL with the BH3-mimeitc ABT-263 is sufficient to overcome lack of BIM induction and sensitize resistant cells to combined dasatinib and trametinib treatment. This study provides evidence that combined Src and MEK1/2 inhibition is a promising therapeutic option for patients with advanced thyroid cancer and identifies BIM induction as a potential biomarker of response.
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Affiliation(s)
- Madison M. Rose
- Division of Endocrinology, Metabolism, and Diabetes, School of Medicine, University of Colorado Anschutz Medical Campus, Mail Stop 7103, Aurora, CO 80045, USA
| | - Veronica L. Espinoza
- Division of Endocrinology, Metabolism, and Diabetes, School of Medicine, University of Colorado Anschutz Medical Campus, Mail Stop 7103, Aurora, CO 80045, USA
| | - Katelyn J. Hoff
- Department of Cell and Developmental Biology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Laura A. Pike
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Vibha Sharma
- Division of Endocrinology, Metabolism, and Diabetes, School of Medicine, University of Colorado Anschutz Medical Campus, Mail Stop 7103, Aurora, CO 80045, USA
| | - Marie-Claude Hofmann
- Department of Endocrine Neoplasia & Hormonal Disorders, Division of Internal Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Aik Choon Tan
- Department of Oncological Sciences, Huntsman Cancer Institute, The University of Utah, Salt Lake City, UT 84112, USA
| | - Nikita Pozdeyev
- Division of Endocrinology, Metabolism, and Diabetes, School of Medicine, University of Colorado Anschutz Medical Campus, Mail Stop 7103, Aurora, CO 80045, USA
- Division of Bioinformatics and Personalized Medicine, Department Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
- University of Colorado Cancer Center, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Rebecca E. Schweppe
- Division of Endocrinology, Metabolism, and Diabetes, School of Medicine, University of Colorado Anschutz Medical Campus, Mail Stop 7103, Aurora, CO 80045, USA
- University of Colorado Cancer Center, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
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3
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Zaitseva O, Hoffmann A, Otto C, Wajant H. Targeting fibroblast growth factor (FGF)-inducible 14 (Fn14) for tumor therapy. Front Pharmacol 2022; 13:935086. [PMID: 36339601 PMCID: PMC9634131 DOI: 10.3389/fphar.2022.935086] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 10/10/2022] [Indexed: 11/25/2022] Open
Abstract
Fibroblast growth factor-inducible 14 (Fn14) is a member of the tumor necrosis factor (TNF) receptor superfamily (TNFRSF) and is activated by its ligand TNF-like weak inducer of apoptosis (TWEAK). The latter occurs as a homotrimeric molecule in a soluble and a membrane-bound form. Soluble TWEAK (sTWEAK) activates the weakly inflammatory alternative NF-κB pathway and sensitizes for TNF-induced cell death while membrane TWEAK (memTWEAK) triggers additionally robust activation of the classical NF-κB pathway and various MAP kinase cascades. Fn14 expression is limited in adult organisms but becomes strongly induced in non-hematopoietic cells by a variety of growth factors, cytokines and physical stressors (e.g., hypoxia, irradiation). Since all these Fn14-inducing factors are frequently also present in the tumor microenvironment, Fn14 is regularly found to be expressed by non-hematopoietic cells of the tumor microenvironment and most solid tumor cells. In general, there are three possibilities how the tumor-Fn14 linkage could be taken into consideration for tumor therapy. First, by exploitation of the cancer associated expression of Fn14 to direct cytotoxic activities (antibody-dependent cell-mediated cytotoxicity (ADCC), cytotoxic payloads, CAR T-cells) to the tumor, second by blockade of potential protumoral activities of the TWEAK/Fn14 system, and third, by stimulation of Fn14 which not only triggers proinflammtory activities but also sensitizes cells for apoptotic and necroptotic cell death. Based on a brief description of the biology of the TWEAK/Fn14 system and Fn14 signaling, we discuss the features of the most relevant Fn14-targeting biologicals and review the preclinical data obtained with these reagents. In particular, we address problems and limitations which became evident in the preclinical studies with Fn14-targeting biologicals and debate possibilities how they could be overcome.
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Affiliation(s)
- Olena Zaitseva
- Division of Molecular Internal Medicine, Department of Internal Medicine II, University Hospital Würzburg, Würzburg, Germany
| | - Annett Hoffmann
- Department of General, Visceral, Transplantation,Vascular and Pediatric Surgery, University Hospital Würzburg, Würzburg, Germany
| | - Christoph Otto
- Department of General, Visceral, Transplantation,Vascular and Pediatric Surgery, University Hospital Würzburg, Würzburg, Germany
| | - Harald Wajant
- Division of Molecular Internal Medicine, Department of Internal Medicine II, University Hospital Würzburg, Würzburg, Germany
- *Correspondence: Harald Wajant,
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Lower Expression of TWEAK is Associated with Poor Survival and Dysregulate TIICs in Lung Adenocarcinoma. DISEASE MARKERS 2022; 2022:8661423. [PMID: 35707713 PMCID: PMC9192298 DOI: 10.1155/2022/8661423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 02/22/2022] [Accepted: 05/03/2022] [Indexed: 12/24/2022]
Abstract
Background. Lung cancer remains the leading cause of cancer death worldwide, and the most subtype is lung adenocarcinoma (LUAD). Tumor-infiltrating immune cells (TIICs) greatly impact the prognosis of LUAD. Tumor necrosis factor–like weak inducer of apoptosis (TWEAK), signal via its receptor fibroblast growth factor-inducible 14 (Fn14), dysregulates immune cell recruitment within tumor environment, thus promoting the progression of autoimmune diseases and cancer. We aimed to explore its role in LUAD. Methods. The expression level of TWEAK was explored in Tumor Immune Estimation Resource 2.0 (TIMER2.0) and Oncomine databases. The Tumor Immune Dysfunction and Exclusion (TIDE) and Lung Cancer Explorer (LCE) databases were applied to evaluate the survival in correlation to TWEAK expression. TIICs were assessed with TIMER2.0 and TIDE datasets. The expression of TWEAK protein was detected in LUAD cell lines and also in tissue samples from LUAD patients via western blotting or combination with immunochemistry. Results. Our results showed that TWEAK was downregulated in LUAD tumors compared to normal tissues in TIMER2.0, Oncomine, cell lines, and clinical specimens. Poor survival was uncovered in lower TWEAK expression of LUAD patients in LCE (
[95% CI, 0.76-0.92]) and TCGA (
,
) and GSE13213@PRECOG (
,
) in TIDE. Multiple tumor-infiltrating immune cells (TIICs) were found closely correlated with TWEAK expression in LUAD, especially hematopoietic stem cell (
,
), common lymphoid progenitor (
,
), and myeloid-derived suppressor cells (MDSCs) (
,
). Conclusion. Lower level of TWEAK was linked with poor survival and aberrant recruitment and phenotype of TIICs in LUAD, which might motivate immune escape and weaken the effects of immunotherapy.
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Badia-Villanueva M, Defaus S, Foj R, Andreu D, Oliva B, Sierra A, Fernandez-Fuentes N. Evaluation of Computationally Designed Peptides against TWEAK, a Cytokine of the Tumour Necrosis Factor Ligand Family. Int J Mol Sci 2021; 22:ijms22031066. [PMID: 33494438 PMCID: PMC7866087 DOI: 10.3390/ijms22031066] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 01/12/2021] [Accepted: 01/15/2021] [Indexed: 12/12/2022] Open
Abstract
The tumour necrosis factor-like weak inducer of apoptosis (TWEAK) is a member of the tumour necrosis factor ligand family and has been shown to be overexpressed in tumoral cells together with the fibroblast growth factor–inducible 14 (Fn14) receptor. TWEAK-Fn14 interaction triggers a set of intracellular pathways responsible for tumour cell invasion and migration, as well as proliferation and angiogenesis. Hence, modulation of the TWEAK-Fn14 interaction is an important therapeutic goal. The targeting of protein-protein interactions by external agents, e.g., drugs, remains a substantial challenge. Given their intrinsic features, as well as recent advances that improve their pharmacological profiles, peptides have arisen as promising agents in this regard. Here, we report, by in silico structural design validated by cell-based and in vitro assays, the discovery of four peptides able to target TWEAK. Our results show that, when added to TWEAK-dependent cellular cultures, peptides cause a down-regulation of genes that are part of TWEAK-Fn14 signalling pathway. The direct, physical interaction between the peptides and TWEAK was further elucidated in an in vitro assay which confirmed that the bioactivity shown in cell-based assays was due to the targeting of TWEAK. The results presented here are framed within early pre-clinical drug development and therefore these peptide hits represent a starting point for the development of novel therapeutic agents. Our approach exemplifies the powerful combination of in silico and experimental efforts to quickly identify peptides with desirable traits.
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Affiliation(s)
- Miriam Badia-Villanueva
- Laboratory of Molecular and Translational Oncology, Centre de Recerca Biomèdica CELLEX, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036 Barcelona, Spain; (M.B.-V.); (R.F.)
| | - Sira Defaus
- Proteomics and Protein Chemistry Group, Department of Experimental and Health Science, Pompeu Fabra University, Barcelona, Biomedical Research Park, 08003 Barcelona, Spain; (S.D.); (D.A.)
| | - Ruben Foj
- Laboratory of Molecular and Translational Oncology, Centre de Recerca Biomèdica CELLEX, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036 Barcelona, Spain; (M.B.-V.); (R.F.)
| | - David Andreu
- Proteomics and Protein Chemistry Group, Department of Experimental and Health Science, Pompeu Fabra University, Barcelona, Biomedical Research Park, 08003 Barcelona, Spain; (S.D.); (D.A.)
| | - Baldo Oliva
- Structural Bioinformatics Lab (GRIB-IMIM), Department of Experimental and Health Science, Pompeu Fabra University, Biomedical Research Park, 08003 Barcelona, Spain;
| | - Angels Sierra
- Laboratory of Oncological Neurosurgery, Hospital Clinic de Barcelona—IDIBAPS, 08036 Barcelona, Spain
- Correspondence: (A.S.); (N.F.-F.)
| | - Narcis Fernandez-Fuentes
- Department of Biosciences, U Science Tech, Universitat de Vic-Universitat Central de Catalunya, Vic 08500 Catalonia, Spain
- Correspondence: (A.S.); (N.F.-F.)
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Wang M, Xie Z, Xu J, Feng Z. TWEAK/Fn14 axis in respiratory diseases. Clin Chim Acta 2020; 509:139-148. [PMID: 32526219 DOI: 10.1016/j.cca.2020.06.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 05/31/2020] [Accepted: 06/03/2020] [Indexed: 02/08/2023]
Abstract
Tumor necrosis factor-like weak inducer of apoptosis (TWEAK) is a well known multifunctional cytokine extensively distributed in cell types and tissues. Accumulating evidence has shown that TWEAK binding to the receptor factor-inducible 14 (Fn14) participates in diverse pathologic processes including cell proliferation and death, angiogenesis, carcinogenesis and inflammation. Interestingly, alterations of intracellular signaling cascades are correlated to the development of respiratory disease. Recently, a several lines of evidence suggests that TWEAK in lung tissues are closely associated with these signaling pathways. In this review, we explore if TWEAK could provide a novel therapeutic strategy for managing respiratory disease in general and pulmonary arterial hypertension (PAH), obstructive sleep apnea syndrome (OSAS), asthma, idiopathic pulmonary fibrosis (IPF), chronic obstructive pulmonary disease (COPD) and non-small cell lung cancer (NSCLC), specifically.
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Affiliation(s)
- Min Wang
- Department of Otorhinolaryngology, University of South China Affiliated Nanhua Hospital, Hengyang 421002, China
| | - Zhijuan Xie
- Department of Nephrology, The First Affiliated Hospital of University of South China, Hengyang 421001, China
| | - Jin Xu
- School of Pharmaceutical Sciences, Changsha Medical University, Changsha 410219, Hunan, China.
| | - Zhuyu Feng
- Department of Critical Care Medicine, University of South China Affiliated Nanhua Hospital, Hengyang 421002, China.
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Dong Y, Yang J, Yang L, Li P. Quercetin Inhibits the Proliferation and Metastasis of Human Non-Small Cell Lung Cancer Cell Line: The Key Role of Src-Mediated Fibroblast Growth Factor-Inducible 14 (Fn14)/ Nuclear Factor kappa B (NF-κB) pathway. Med Sci Monit 2020; 26:e920537. [PMID: 32225128 PMCID: PMC7144538 DOI: 10.12659/msm.920537] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Background Quercetin (Que) is reported to induce apoptosis of lung cancer cells. Src is closely related to the progression of non-small cell lung cancer (NSCLC) and can be modulated by Que in macrophages. In the current study, the interaction between Que and Src signaling in NSCLC cells was explored to explain the anti-NSCLC function of Que. Material/Methods NSCLC cell line HCC827 was subjected to the administrations of Que at different concentrations. The effect of Que on tumor cell proliferation was detected using MTT and colony formation assays. Then the effect on the migration and invasion abilities was assessed using scratch and Transwell assays. At molecular level, the changes in Src/Fn14/NF-κB signaling were determined using western blotting assays. The role of Src in the function of Que was further explored by inducing the expression of Src gene in NSCLC cells before Que administration. The results of the in vitro assays were verified using a NSCLC mice model. Results Que inhibited the proliferation and anchorage-independent growth of NSCLC cells. Additionally, Que delayed in the gap closure rate in scratch assays and decreased the membrane-penetrating cell number in Transwell assays. At a molecular level, Que suppressed the expression of Src, which subsequently inhibited Fn14/NF-κB signaling. In in vivo assays, Que inhibited the growth of solid tumors. After the overexpression of Src in NSCLC cells, the anti-NSCLC effect of Que was blocked by inducing NSCLC proliferation and metastasis, and by activating Fn14/NF-κB signaling. Moreover, the induced level of Src promoted the growth and metastasis potential of solid tumors in mice. Conclusions Que exerted the anti-NSCLC effect by inhibiting Src-mediated Fn14/NF-κB pathway both in vitro and in vivo.
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Affiliation(s)
- Yan Dong
- Department of Respiratory Medicine, Xiangyang No. 1 People's Hospital, Hubei University of Medicine, Xiangyang, Hubei, China (mainland)
| | - Jun Yang
- Department of Respiratory Medicine, Xiangyang No. 1 People's Hospital, Hubei University of Medicine, Xiangyang, Hubei, China (mainland)
| | - Liyuan Yang
- Department of Respiratory Medicine, Xiangyang No. 1 People's Hospital, Hubei University of Medicine, Xiangyang, Hubei, China (mainland)
| | - Ping Li
- Department of Respiratory Medicine, Xiangyang No. 1 People's Hospital, Hubei University of Medicine, Xiangyang, Hubei, China (mainland)
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