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Wang Y, Chi Y, Zhu C, Zhang Y, Li K, Chen J, Jiang X, Chen K, Li S. A novel anoikis-related gene signature predicts prognosis in patients with sepsis and reveals immune infiltration. Sci Rep 2024; 14:2313. [PMID: 38281996 PMCID: PMC10822872 DOI: 10.1038/s41598-024-52742-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Accepted: 01/23/2024] [Indexed: 01/30/2024] Open
Abstract
Sepsis is a common acute and severe medical condition with a high mortality rate. Anoikis, an emerging form of cell death, plays a significant role in various diseases. However, the role of anoikis in sepsis remains poorly understood. Based on the datasets from Gene Expression Omnibus and anoikis-related genes from GeneCards, the differentially expressed anoikis-related genes (DEARGs) were identified. Based on hub genes of DEARGs, a novel prognostic risk model was constructed, and the pattern of immune infiltration was investigated by CIBERSORT algorithm. And small molecule compounds targeting anoikis in sepsis were analyzed using Autodock. Of 23 DEARGs, CXCL8, CFLAR, FASLG and TP53 were significantly associated with the prognosis of sepsis (P < 0.05). Based on the prognostic risk model constructed with these four genes, high-risk population of septic patients had significant lower survival probability than low-risk population (HR = 3.30, P < 0.001). And the level of CFLAR was significantly correlated with the number of neutrophils in septic patients (r = 0.54, P < 0.001). Moreover, tozasertib had low binding energy with CXCL8, CFLAR, FASLG and TP53, and would be a potential compound for sepsis. Conclusively, our results identified a new prognostic model and potential therapeutic molecular for sepsis, providing new insights on mechanism and treatment of sepsis.
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Affiliation(s)
- Yonghua Wang
- Department of Emergency, The First Affiliated Hospital of Chengdu Medical College, Chengdu, 610500, Sichuan, People's Republic of China
| | - Yanqi Chi
- School of Public Health, Chengdu Medical College, Chengdu, 610500, Sichuan, People's Republic of China
| | - Cheng Zhu
- Department of Emergency, The First Affiliated Hospital of Chengdu Medical College, Chengdu, 610500, Sichuan, People's Republic of China
| | - Yuxuan Zhang
- Department of Critical Care Medicine, The First Affiliated Hospital of Chengdu Medical College, Chengdu, 610500, Sichuan, People's Republic of China
| | - Ke Li
- Department of Emergency, The First Affiliated Hospital of Chengdu Medical College, Chengdu, 610500, Sichuan, People's Republic of China
| | - Jiajia Chen
- Department of Emergency, The First Affiliated Hospital of Chengdu Medical College, Chengdu, 610500, Sichuan, People's Republic of China
| | - Xiying Jiang
- Department of Emergency, The First Affiliated Hospital of Chengdu Medical College, Chengdu, 610500, Sichuan, People's Republic of China
| | - Kejie Chen
- School of Public Health, Chengdu Medical College, Chengdu, 610500, Sichuan, People's Republic of China.
| | - Shuping Li
- Department of Emergency, The First Affiliated Hospital of Chengdu Medical College, Chengdu, 610500, Sichuan, People's Republic of China.
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Zhai C, Zhang N, Wang J, Cao M, Luan J, Liu H, zhang Q, Zhu Y, Xue Y, Li S. Activation of Autophagy Induces Monocrotaline-Induced Pulmonary Arterial Hypertension by FOXM1-Mediated FAK Phosphorylation. Lung 2022; 200:619-631. [DOI: 10.1007/s00408-022-00569-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 09/01/2022] [Indexed: 11/28/2022]
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Bond KH, Sims-Lucas S, Oxburgh L. Targets for Renal Carcinoma Growth Control Identified by Screening FOXD1 Cell Proliferation Pathways. Cancers (Basel) 2022; 14:cancers14163958. [PMID: 36010951 PMCID: PMC9406217 DOI: 10.3390/cancers14163958] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 08/02/2022] [Accepted: 08/14/2022] [Indexed: 11/24/2022] Open
Abstract
Simple Summary FOXD1 regulates the proliferation of clear cell renal cell carcinoma (ccRCC) cells, and ccRCC cells in which FOXD1 has been inactivated do not form tumors efficiently in an animal model. Reproducing growth inhibition in tumor cells by inhibiting FOXD1 pathways presents a possible therapeutic approach for ccRCC and other cancers. We have established an analysis strategy to identify FOXD1-regulated target pathways that may be therapeutically tractable, and compounds that modulate these pathways were selected for testing. Targets in three pathways were identified: FOXM1, PME1, and TMEM167A, which were inhibited by compounds FDI-6, AMZ-30, and silibinin, respectively. The effects of these compounds on the growth of tumor cells from patients cultured in a novel 3D tumor-replica culture environment revealed that FDI-6 and silibinin had strong growth inhibitory effects. This investigation informs new therapeutic targets to control ccRCC tumor growth, and provides a strategy to compare the responsiveness of individual patient tumor replicas to growth-inhibitory compounds. Abstract Clinical association studies suggest that FOXD1 is a determinant of patient outcome in clear cell renal cell carcinoma (ccRCC), and laboratory investigations have defined a role for this transcription factor in controlling the growth of tumors through regulation of the G2/M cell cycle transition. We hypothesized that the identification of pathways downstream of FOXD1 may define candidates for pharmacological modulation to suppress the G2/M transition in ccRCC. We developed an analysis pipeline that utilizes RNA sequencing, transcription factor binding site analysis, and phenotype validation to identify candidate effectors downstream from FOXD1. Compounds that modulate candidate pathways were tested for their ability to cause growth delay at G2/M. Three targets were identified: FOXM1, PME1, and TMEM167A, which were targeted by compounds FDI-6, AMZ-30, and silibinin, respectively. A 3D ccRCC tumor replica model was used to investigate the effects of these compounds on the growth of primary cells from five patients. While silibinin reduced 3D growth in a subset of tumor replicas, FDI-6 reduced growth in all. This study identifies tractable pathways to target G2/M transition and inhibit ccRCC growth, demonstrates the applicability of these strategies across patient tumor replicas, and provides a platform for individualized patient testing of compounds that inhibit tumor growth.
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Affiliation(s)
- Kyle H. Bond
- Rogosin Institute, Room 2-43, 310 East 67th St., New York, NY 10065, USA
| | - Sunder Sims-Lucas
- Children’s Hospital of Pittsburgh, Rangos Research Building, 4401 Penn Ave, Pittsburgh, PA 15224, USA
| | - Leif Oxburgh
- Rogosin Institute, Room 2-43, 310 East 67th St., New York, NY 10065, USA
- Correspondence:
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Xiao F, Zhang R, Wang L. Inhibitors of Mitochondrial Dynamics Mediated by Dynamin-Related Protein 1 in Pulmonary Arterial Hypertension. Front Cell Dev Biol 2022; 10:913904. [PMID: 35846374 PMCID: PMC9280643 DOI: 10.3389/fcell.2022.913904] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 06/13/2022] [Indexed: 11/13/2022] Open
Abstract
Pulmonary arterial hypertension (PAH) is a chronic, lethal pulmonary disease characterized by pulmonary vascular remodeling. It leads to malignant results, such as rupture of pulmonary arterial dissection, dyspnea, right heart failure, and even death. Previous studies have confirmed that one of the main pathological changes of this disease is abnormal mitochondrial dynamics, which include mitochondrial fission, fusion, and autophagy that keep a dynamic balance under certain physiological state. Dynamin-related protein 1 (Drp1), the key molecule in mitochondrial fission, mediates mitochondrial fission while also affecting mitochondrial fusion and autophagy through numerous pathways. There are various abnormalities of Drp1 in PAH pathophysiology, including Drp1 overexpression and activation as well as an upregulation of its outer mitochondrial membrane ligands. These aberrant alterations will eventually induce the development of PAH. With the process of recent studies, the structure and function of Drp1 have been gradually revealed. Meanwhile, inhibitors targeting this pathway have also been discovered. This review aims to shed more light on the mechanism of Drp1 and its inhibitors in the abnormal mitochondrial dynamics of PAH. Furthermore, it seeks to provide more novel insights to clinical therapy.
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Ferrari R, Cong G, Chattopadhyay A, Xie B, Assaf E, Morder K, Calderon MJ, Watkins SC, Sachdev U. Attenuated cell-cycle division protein 2 and elevated mitotic roles of polo-like kinase 1 characterize deficient myoblast fusion in peripheral arterial disease. Biochem Biophys Res Commun 2022; 609:163-168. [PMID: 35436627 PMCID: PMC10687717 DOI: 10.1016/j.bbrc.2022.03.161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Revised: 03/26/2022] [Accepted: 03/31/2022] [Indexed: 11/02/2022]
Abstract
INTRODUCTION We propose that MuSC-derived myoblasts in PAD have transcriptomic differences that can highlight underlying causes of ischemia-induced myopathy. METHODS Differentiation capacity among perfused and ischemic human myoblasts was compared. Following next generation sequencing of mRNA, Ingenuity Pathway Analysis (IPA) was performed for canonical pathway enrichment. Live cell imaging and immunofluorescence were performed to determine myocyte fusion index and protein expression based on insights from IPA, specifically concerning cell cycle regulators including cell-division cycle protein 2 (CDC2) and polo-like kinase 1 (PLK1). RESULTS Ischemic myoblasts formed attenuated myotubes indicative of reduced fusion. Additionally, myoblasts from ischemic segments showed significant differences in canonical pathways associated with PLK1 (upregulated) and G2/M DNA damage checkpoint regulation (downregulated). PLK1 inhibition with BI2536 did not affect cell viability in any group over 24 h but deterred fusion more significantly in PAD myoblasts. Furthermore, PLK1 inhibition reduced the expression of checkpoint protein CDC2 in perfused but not ischemic cells. CONCLUSION Differentiating myoblasts derived from ischemic muscle have significant differences in gene expression including those essential to DNA-damage checkpoint regulation and cell cycle progress. DNA-damage checkpoint dysregulation may contribute to myopathy in PAD.
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Affiliation(s)
- Ricardo Ferrari
- University of Pittsburgh Medical Center Department of Surgery, Division of Vascular Surgery, USA
| | - Guangzhi Cong
- University of Pittsburgh Medical Center Department of Surgery, Division of Vascular Surgery, USA; Department of Cardiology, Cardiovascular Institute, General Hospital of Ningxia Medical University, Yinchuan, Ningxia, China
| | | | - B Xie
- University of Pittsburgh Medical Center Department of Surgery, Division of Vascular Surgery, USA
| | - E Assaf
- University of Pittsburgh Medical Center Department of Surgery, Division of Vascular Surgery, USA
| | - K Morder
- University of Pittsburgh Medical Center Department of Surgery, Division of Vascular Surgery, USA
| | | | | | - Ulka Sachdev
- University of Pittsburgh Medical Center Department of Surgery, Division of Vascular Surgery, USA.
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Shi Z, Tian L, Qiang T, Li J, Xing Y, Ren X, Liu C, Liang C. From Structure Modification to Drug Launch: A Systematic Review of the Ongoing Development of Cyclin-Dependent Kinase Inhibitors for Multiple Cancer Therapy. J Med Chem 2022; 65:6390-6418. [PMID: 35485642 DOI: 10.1021/acs.jmedchem.1c02064] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Herein, we discuss more than 50 cyclin-dependent kinase (CDK) inhibitors that have been approved or have undergone clinical trials and their therapeutic application in multiple cancers. This review discusses the design strategies, structure-activity relationships, and efficacy performances of these selective or nonselective CDK inhibitors. The theoretical basis of early broad-spectrum CDK inhibitors is similar to the scope of chemotherapy, but because their toxicity is greater than the benefit, there is no clinical therapeutic window. The notion that selective CDK inhibitors have a safer therapeutic potential than pan-CDK inhibitors has been widely recognized during the research process. Four CDK4/6 inhibitors have been approved for the treatment of breast cancer or for prophylactic administration during chemotherapy to protect bone marrow and immune system function. Furthermore, the emerging strategies in the field of CDK inhibitors are summarized briefly, and CDKs continue to be widely pursued as emerging anticancer drug targets for drug discovery.
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Affiliation(s)
- Zhenfeng Shi
- Department of Urology Surgery Center, The People's Hospital of Xinjiang Uyghur Autonomous Region, Urumqi 830002, P. R. China
| | - Lei Tian
- College of Bioresources Chemical and Materials Engineering, Shaanxi University of Science & Technology, Xi'an 710021, P. R. China.,Faculty of Pharmacy, Shaanxi University of Science & Technology, Xi'an 710021, P. R. China
| | - Taotao Qiang
- College of Bioresources Chemical and Materials Engineering, Shaanxi University of Science & Technology, Xi'an 710021, P. R. China
| | - Jingyi Li
- Faculty of Pharmacy, Shaanxi University of Science & Technology, Xi'an 710021, P. R. China
| | - Yue Xing
- Faculty of Pharmacy, Shaanxi University of Science & Technology, Xi'an 710021, P. R. China
| | - Xiaodong Ren
- Medical College, Guizhou University, Guiyang 550025, P. R. China
| | - Chang Liu
- Zhuhai Jinan Selenium Source Nanotechnology Co., Ltd., Zhuhai 519030, P. R. China
| | - Chengyuan Liang
- Faculty of Pharmacy, Shaanxi University of Science & Technology, Xi'an 710021, P. R. China
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Zhang X, Yang Z, Li X, Liu X, Wang X, Qiu T, Wang Y, Li T, Li Q. Bioinformatics Analysis Reveals Cell Cycle-Related Gene Upregulation in Ascending Aortic Tissues From Murine Models. Front Genet 2022; 13:823769. [PMID: 35356426 PMCID: PMC8959095 DOI: 10.3389/fgene.2022.823769] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 02/14/2022] [Indexed: 11/13/2022] Open
Abstract
Thoracic aortic aneurysm and dissection (TAAD) is a high-risk aortic disease. Mouse models are usually used to explore the pathological progression of TAAD. In our studies, we performed bioinformatics analysis on a microarray dataset (GSE36778) and verified experiments to define the integrated hub genes of TAAD in three different mouse models. Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) and protein-protein interaction (PPI) network analyses, and histological and quantitative reverse transcription-PCR (qRT-PCR) experiments were used in our study. First, differentially expressed genes (DEGs) were identified, and twelve common differentially expressed genes were found. Second, genes related to the cell cycle and inflammation were enriched by using GO and PPI. We focused on filtering and validating eighteen hub genes that were upregulated. Then, expression data from human ascending aortic tissues in the GSE153434 dataset were also used to verify our findings. These results indicated that cell cycle-related genes participate in the pathological mechanism of TAAD and provide new insight into the molecular mechanisms of TAAD.
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Affiliation(s)
- Xiaoping Zhang
- Beijing Anzhen Hospital, Capital Medical University, Beijing, China.,Beijing Institute of Heart, Lung and Blood Vessel Disease, Beijing, China
| | - Zuozhen Yang
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Xiaoyan Li
- Beijing Anzhen Hospital, Capital Medical University, Beijing, China.,Beijing Institute of Heart, Lung and Blood Vessel Disease, Beijing, China
| | - Xuxia Liu
- Beijing Anzhen Hospital, Capital Medical University, Beijing, China.,Beijing Institute of Heart, Lung and Blood Vessel Disease, Beijing, China
| | - Xipeng Wang
- Department of Vascular Surgery, Peking University People's Hospital, Beijing, China
| | - Tao Qiu
- The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Yueli Wang
- Beijing Anzhen Hospital, Capital Medical University, Beijing, China
| | - Tongxun Li
- Beijing Anzhen Hospital, Capital Medical University, Beijing, China
| | - Qingle Li
- Department of Vascular Surgery, Peking University People's Hospital, Beijing, China
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