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Du J. Study of Therapeutic Mechanisms of Bupi Yichang Formula against Colon Cancer Based on Network Pharmacology, Machine Learning, and Experimental Verification. Crit Rev Immunol 2024; 44:67-87. [PMID: 38421706 DOI: 10.1615/critrevimmunol.2023051509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2024]
Abstract
Bupi Yichang formula (BPYCF) has shown the anti-cancer potential; however, its effects on colon cancer and the mechanisms remain unknown. This study intended to explore the effects of BPYC on colon cancer and its underlying mechanisms. BPYCF-related and colon cancer-related targets were acquired from public databases, followed by differentially expressed genes (DEG) identification. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed using clusterProfiler. A protein-protein interaction (PPI) network was constructed using STRING database. CytoHubba and MCODE to screen the hub targets. A diagnostic model was built using random forest algorithm. Molecular docking was conducted using PyMOL and AutoDock. High-performance liquid chromatograph-mass spectrometry (HPLC-MS) analysis and in vitro validation were performed. Forty-six overlapping targets of BPYCF-related, colon cancer-related targets, and DEGs were obtained. GO and KEGG analyses showed that the targets were mainly enriched in response to lipopolysaccharide, neuronal cell body, protein serine/threonine/tyrosine, as well as C-type lectin receptor, NOD-like receptor, and TNF signaling pathways. Five targets were identified as the pivotal targets, among which, NOS3, CASP8, RIPK3, and TNFRSF10B were stably docked with the core active component, naringenin. Naringenin was also identified from the BPYCF sample through HPLC-MS analysis. In vitro experiments showed that BPYCF inhibited cell viability, reduced NOS3 expression, and elevated CASP8, RIPK3, and TNFRSF10B expression in colon cancer cells. BPYCF might treat colon cancer mainly by regulating NOS3, CASP8, RIPK3, and TN-FRSF10B. This study first revealed the therapeutic effects and mechanisms of BPYCF against colon cancer, paving the path for the development of targeted therapeutic strategies for this cancer in the clinic.
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Affiliation(s)
- Juan Du
- Beijing Friendship Hospital, Capital Medical University
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2
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Song GQ, Wu HM, Ji KJ, He TL, Duan YM, Zhang JW, Hu GQ. The necroptosis signature and molecular mechanism of lung squamous cell carcinoma. Aging (Albany NY) 2023; 15:12907-12926. [PMID: 37976123 DOI: 10.18632/aging.205210] [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: 04/27/2023] [Accepted: 10/15/2023] [Indexed: 11/19/2023]
Abstract
BACKGROUND Given the poor prognosis of lung squamous cell carcinoma (LUSC), the aim of this study was to screen for new prognostic biomarkers. METHODS The TGCA_LUSC dataset was used as the training set, and GSE73403 was used as the validation set. The genes involved in necroptosis-related pathways were acquired from the KEGG database, and the differential genes between the LUSC and normal samples were identified using the GSEA. A necroptosis signature was constructed by survival analysis, and its correlation with patient prognosis and clinical features was evaluated. The molecular characteristics and drug response associated with the necroptosis signature were also identified. The drug candidates were then validated at the cellular level. RESULTS The TCGA_LUSC dataset included 51 normal samples and 502 LUSC samples. The GSE73403 dataset included 69 samples. 159 genes involved in necroptosis pathways were acquired from the KEGG database, of which most showed significant differences between two groups in terms of genomic, transcriptional and methylation alterations. In particular, CHMP4C, IL1B, JAK1, PYGB and TNFRSF10B were significantly associated with the survival (p < 0.05) and were used to construct the necroptosis signature, which showed significant correlation with patient prognosis and clinical features in univariate and multivariate analyses (p < 0.05). Furthermore, CHMP4C, IL1B, JAK1 and PYGB were identified as potential targets of trametinib, selumetinib, SCH772984, PD 325901 and dasatinib. Finally, knockdown of these genes in LUSC cells increased chemosensitivity to those drugs. CONCLUSION We identified a necroptosis signature in LUSC that can predict prognosis and identify patients who can benefit from targeted therapies.
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Affiliation(s)
- Guo-Qiang Song
- Department of Pulmonary, Changxing County Hospital of Traditional Chinese Medicine, Huzhou, China
| | - Hua-Man Wu
- Department of Pulmonary and Critical Care Medicine, Zigong First People’s Hospital, Zigong, China
| | - Ke-Jie Ji
- Department of Pulmonary, Changxing County Hospital of Traditional Chinese Medicine, Huzhou, China
| | - Tian-Li He
- Department of Radiotherapy, Changxing People’s Hospital, Huzhou, China
| | - Yi-Meng Duan
- Department of Pulmonary, Changxing County Hospital of Traditional Chinese Medicine, Huzhou, China
| | - Jia-Wen Zhang
- Department of Pulmonary, Changxing County Hospital of Traditional Chinese Medicine, Huzhou, China
| | - Guo-Qiang Hu
- Department of Pulmonary, Changxing County Hospital of Traditional Chinese Medicine, Huzhou, China
- Department of Cancer Center, Changxing County Hospital of Traditional Chinese Medicine, Huzhou, China
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3
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Wang Z, Zhang M, Liu L, Yang Y, Qiu J, Yu Y, Li J. Prognostic and immunological role of cancer-associated fibroblasts-derived exosomal protein in esophageal squamous cell carcinoma. Int Immunopharmacol 2023; 124:110837. [PMID: 37634448 DOI: 10.1016/j.intimp.2023.110837] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 08/08/2023] [Accepted: 08/18/2023] [Indexed: 08/29/2023]
Abstract
BACKGROUND Cancer-associated fibroblasts (CAFs) are a crucial component of the tumor microenvironment (TME) and play significant roles in tumor initiation, progression, and immune evasion. Despite this, the specific exosomal proteins derived from CAFs and their functions in esophageal squamous cell carcinoma (ESCC) remain unknown. Therefore, this study aims to investigate the impact and prognostic significance of CAFs-derived exosomal proteins in ESCC. MATERIALS AND METHODS Exosomes obtained from CAFs and normal fibroblasts (NFs) were isolated using ultracentrifugation, and the protein expression profiles of the exosomes were analyzed using liquid chromatography-tandem mass spectrometry (LC-MS/MS). Tumor proliferation was assessed using CCK-8 and colony formation assays, while cell invasion and migration were evaluated using transwell assays. Lasso regression analysis was employed to establish a signature based on CAFs-derived exosomal proteins using the TCGA database. The immunological and prognostic roles of this signature were comprehensively investigated through survival analysis, gene set enrichment analysis (GSEA), immune analysis, immunotherapy response analysis, and drug sensitivity analysis. The GSE160269 dataset was utilized for single-cell transcriptome analysis to further elucidate the role of the signature in the TME. Additionally, cDNA microarray analysis was utilized to validate the prognostic value of the signature. RESULTS Our findings demonstrate that exosomes derived from CAFs significantly enhance the proliferation, invasion, and migration of esophageal cancer cells. We identified 842 differentially expressed exosomal proteins through LC-MS/MS analysis, and two key proteins were utilized to establish a risk signature. Survival analysis revealed a significantly worse prognosis in the high-risk group, with multivariate analysis indicating that the risk score serves as an independent prognostic factor. Moreover, we observed a significant correlation between the risk score and immune cell infiltration, immunotherapy response, and sensitivity to chemotherapeutic treatments in the study population. Lastly, single-cell transcriptome analysis further revealed the expression patterns of TNFRSF10B and ILF3 in different cell subpopulations. CONCLUSION In conclusion, our study has successfully established a robust prognostic signature based on CAFs-derived exosomal proteins, which can serve as a reliable biomarker for predicting prognosis and evaluating the immune microenvironment in ESCC.
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Affiliation(s)
- Zhiping Wang
- Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou, Fujian, China
| | - Mengyan Zhang
- Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou, Fujian, China
| | - Lingyun Liu
- Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou, Fujian, China
| | - Yan Yang
- College of Pharmacy and Food Science, Zhuhai College of Science and Technology, Zhuhai, Guangdong, China
| | - Jianjian Qiu
- Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou, Fujian, China.
| | - Yilin Yu
- Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou, Fujian, China.
| | - Jiancheng Li
- Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou, Fujian, China.
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4
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Cheng KP, Shen WX, Jiang YY, Chen Y, Chen YZ, Tan Y. Deep learning of 2D-Restructured gene expression representations for improved low-sample therapeutic response prediction. Comput Biol Med 2023; 164:107245. [PMID: 37480677 DOI: 10.1016/j.compbiomed.2023.107245] [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: 04/26/2023] [Revised: 06/27/2023] [Accepted: 07/07/2023] [Indexed: 07/24/2023]
Abstract
Clinical outcome prediction is important for stratified therapeutics. Machine learning (ML) and deep learning (DL) methods facilitate therapeutic response prediction from transcriptomic profiles of cells and clinical samples. Clinical transcriptomic DL is challenged by the low-sample sizes (34-286 subjects), high-dimensionality (up to 21,653 genes) and unordered nature of clinical transcriptomic data. The established methods rely on ML algorithms at accuracy levels of 0.6-0.8 AUC/ACC values. Low-sample DL algorithms are needed for enhanced prediction capability. Here, an unsupervised manifold-guided algorithm was employed for restructuring transcriptomic data into ordered image-like 2D-representations, followed by efficient DL of these 2D-representations with deep ConvNets. Our DL models significantly outperformed the state-of-the-art (SOTA) ML models on 82% of 17 low-sample benchmark datasets (53% with >0.05 AUC/ACC improvement). They are more robust than the SOTA models in cross-cohort prediction tasks, and in identifying robust biomarkers and response-dependent variational patterns consistent with experimental indications.
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Affiliation(s)
- Kai Ping Cheng
- The State Key Laboratory of Chemical Oncogenomics, Key Laboratory of Chemical Biology, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, PR China; Institute of Biomedical Health Technology and Engineering, Shenzhen Bay Laboratory, Shenzhen, 518132, PR China
| | - Wan Xiang Shen
- Bioinformatics and Drug Design Group, Department of Pharmacy, Center for Computational Science and Engineering, National University of Singapore, 117543, Singapore
| | - Yu Yang Jiang
- School of Pharmaceutical Sciences, Tsinghua University, Beijing, 100084, PR China
| | - Yan Chen
- The State Key Laboratory of Chemical Oncogenomics, Key Laboratory of Chemical Biology, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, PR China
| | - Yu Zong Chen
- The State Key Laboratory of Chemical Oncogenomics, Key Laboratory of Chemical Biology, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, PR China; Institute of Biomedical Health Technology and Engineering, Shenzhen Bay Laboratory, Shenzhen, 518132, PR China.
| | - Ying Tan
- The State Key Laboratory of Chemical Oncogenomics, Key Laboratory of Chemical Biology, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, PR China; The Institute of Drug Discovery Technology, Ningbo University, Ningbo, 315211, PR China; Shenzhen Kivita Innovative Drug Discovery Institute, Shenzhen, 518110, PR China.
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Wang Y, Worrell GA, Wang HL. It is the Frequency that Matters: Effects of Electromagnetic Fields on the Release and Content of Extracellular Vesicles. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.08.552505. [PMID: 37609326 PMCID: PMC10441284 DOI: 10.1101/2023.08.08.552505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
Extracellular vesicles (EVs) are small membrane-bound structures that originate from various cell types and carry molecular cargo to influence the behavior of recipient cells. The use of EVs as biomarkers and delivery vehicles for diagnosis and treatment in a wide range of human disease is a rapidly growing field of research and clinical practice. Four years ago, we postulated the hypothesis that electromagnetic fields (EMF) will influence the release and content of EVs (1). Since then, we have optimized several technical aspects of our experimental setup. We used a bioreactor system that allows cells to grow in a three-dimensional environment mimicking in-vivo conditions. We designed a custom-made EMF stimulation device that encompasses the bioreactor and delivers uniform EMFs. We established a three-step EV purification protocol that enables high-density production of EVs. We then performed mass spectrometry-based proteomics analysis on EV-related proteins and used high-resolution nanoparticle flowcytometry for single-vesicle analysis. We demonstrate that electrical stimulations of current amplitudes at physiological level that are currently applied in therapeutic deep brain stimulation can modulate EV content in a frequency-dependent manner, which may have important implications for basic biology and medical applications. First, it raises intriguing questions about how the endogenous electrical activity of neuronal and other cellular assemblies influence the production and composition of EVs. Second, it reveals an additional underlying mechanism of how therapeutic electrical stimulations can modulate EVs and treat human brain disorders. Third, it provides a novel approach of utilizing electrical stimulations in generating specific EV cargos.
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Affiliation(s)
- Yihua Wang
- Neurology Department, Mayo Clinic, Rochester, Minnesota
| | - Gregory A. Worrell
- Neurology Department, Mayo Clinic, Rochester, Minnesota
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, Minnesota
| | - Hai-Long Wang
- Neurology Department, Mayo Clinic, Rochester, Minnesota
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, Minnesota
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Esposito R, Polidori T, Meise DF, Pulido-Quetglas C, Chouvardas P, Forster S, Schaerer P, Kobel A, Schlatter J, Kerkhof E, Roemmele M, Rice ES, Zhu L, Lanzós A, Guillen-Ramirez HA, Basile G, Carrozzo I, Vancura A, Ullrich S, Andrades A, Harvey D, Medina PP, Ma PC, Haefliger S, Wang X, Martinez I, Ochsenbein AF, Riether C, Johnson R. Multi-hallmark long noncoding RNA maps reveal non-small cell lung cancer vulnerabilities. CELL GENOMICS 2022; 2:100171. [PMID: 36778670 PMCID: PMC9903773 DOI: 10.1016/j.xgen.2022.100171] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 06/15/2022] [Accepted: 08/01/2022] [Indexed: 12/24/2022]
Abstract
Long noncoding RNAs (lncRNAs) are widely dysregulated in cancer, yet their functional roles in cancer hallmarks remain unclear. We employ pooled CRISPR deletion to perturb 831 lncRNAs detected in KRAS-mutant non-small cell lung cancer (NSCLC) and measure their contribution to proliferation, chemoresistance, and migration across two cell backgrounds. Integrative analysis of these data outperforms conventional "dropout" screens in identifying cancer genes while prioritizing disease-relevant lncRNAs with pleiotropic and background-independent roles. Altogether, 80 high-confidence oncogenic lncRNAs are active in NSCLC, which tend to be amplified and overexpressed in tumors. A follow-up antisense oligonucleotide (ASO) screen shortlisted two candidates, Cancer Hallmarks in Lung LncRNA 1 (CHiLL1) and GCAWKR, whose knockdown consistently suppressed cancer hallmarks in two- and three-dimension tumor models. Molecular phenotyping reveals that CHiLL1 and GCAWKR control cellular-level phenotypes via distinct transcriptional networks. This work reveals a multi-dimensional functional lncRNA landscape underlying NSCLC that contains potential therapeutic vulnerabilities.
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Affiliation(s)
- Roberta Esposito
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, Bern 3010 Switzerland,Department for BioMedical Research, University of Bern, Bern 3008, Switzerland,Institute of Genetics and Biophysics “Adriano Buzzati-Traverso” CNR, Naples 80131, Italy
| | - Taisia Polidori
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, Bern 3010 Switzerland,Department for BioMedical Research, University of Bern, Bern 3008, Switzerland,Graduate School of Cellular and Biomedical Sciences, University of Bern, Bern 3012, Switzerland
| | - Dominik F. Meise
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, Bern 3010 Switzerland,Department for BioMedical Research, University of Bern, Bern 3008, Switzerland
| | - Carlos Pulido-Quetglas
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, Bern 3010 Switzerland,Department for BioMedical Research, University of Bern, Bern 3008, Switzerland,Graduate School of Cellular and Biomedical Sciences, University of Bern, Bern 3012, Switzerland
| | - Panagiotis Chouvardas
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, Bern 3010 Switzerland,Department for BioMedical Research, University of Bern, Bern 3008, Switzerland
| | - Stefan Forster
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, Bern 3010 Switzerland,Department for BioMedical Research, University of Bern, Bern 3008, Switzerland
| | - Paulina Schaerer
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, Bern 3010 Switzerland,Department for BioMedical Research, University of Bern, Bern 3008, Switzerland
| | - Andrea Kobel
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, Bern 3010 Switzerland,Department for BioMedical Research, University of Bern, Bern 3008, Switzerland
| | - Juliette Schlatter
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, Bern 3010 Switzerland,Department for BioMedical Research, University of Bern, Bern 3008, Switzerland
| | - Erik Kerkhof
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, Bern 3010 Switzerland,Department for BioMedical Research, University of Bern, Bern 3008, Switzerland
| | - Michaela Roemmele
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, Bern 3010 Switzerland,Department for BioMedical Research, University of Bern, Bern 3008, Switzerland
| | - Emily S. Rice
- Department of Microbiology, Immunology, and Cell Biology, Morgantown, WV, USA
| | - Lina Zhu
- Department of Surgery, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong,Tung Biomedical Sciences Centre, City University of Hong Kong, Hong Kong,Key Laboratory of Biochip Technology, Biotech and Health Centre, Shenzhen Research Institute, City University of Hong Kong, Shenzhen 518057, China
| | - Andrés Lanzós
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, Bern 3010 Switzerland,Department for BioMedical Research, University of Bern, Bern 3008, Switzerland,Graduate School of Cellular and Biomedical Sciences, University of Bern, Bern 3012, Switzerland
| | - Hugo A. Guillen-Ramirez
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, Bern 3010 Switzerland,Department for BioMedical Research, University of Bern, Bern 3008, Switzerland,School of Biology and Environmental Science, University College Dublin, Dublin D04 V1W8, Ireland,Conway Institute for Biomolecular and Biomedical Research, University College Dublin, Dublin D04 V1W8, Ireland
| | - Giulia Basile
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, Bern 3010 Switzerland,Department for BioMedical Research, University of Bern, Bern 3008, Switzerland
| | - Irene Carrozzo
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, Bern 3010 Switzerland,Department for BioMedical Research, University of Bern, Bern 3008, Switzerland
| | - Adrienne Vancura
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, Bern 3010 Switzerland,Department for BioMedical Research, University of Bern, Bern 3008, Switzerland
| | - Sebastian Ullrich
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology (BIST), Barcelona, Catalonia 08003, Spain
| | - Alvaro Andrades
- GENYO, Centre for Genomics and Oncological Research, Pfizer/University of Granada/Andalusian Regional Government, Granada 18016, Spain,Instituto de Investigación Biosanitaria, Granada 18014, Spain,Department of Biochemistry and Molecular Biology I, University of Granada, Granada 18071, Spain
| | - Dylan Harvey
- School of Biology and Environmental Science, University College Dublin, Dublin D04 V1W8, Ireland
| | - Pedro P. Medina
- GENYO, Centre for Genomics and Oncological Research, Pfizer/University of Granada/Andalusian Regional Government, Granada 18016, Spain,Instituto de Investigación Biosanitaria, Granada 18014, Spain,Department of Biochemistry and Molecular Biology I, University of Granada, Granada 18071, Spain
| | | | - Simon Haefliger
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, Bern 3010 Switzerland,Department for BioMedical Research, University of Bern, Bern 3008, Switzerland
| | - Xin Wang
- Department of Surgery, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong
| | - Ivan Martinez
- Department of Microbiology, Immunology, and Cell Biology, Morgantown, WV, USA
| | - Adrian F. Ochsenbein
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, Bern 3010 Switzerland,Department for BioMedical Research, University of Bern, Bern 3008, Switzerland
| | - Carsten Riether
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, Bern 3010 Switzerland,Department for BioMedical Research, University of Bern, Bern 3008, Switzerland
| | - Rory Johnson
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, Bern 3010 Switzerland,Department for BioMedical Research, University of Bern, Bern 3008, Switzerland,School of Biology and Environmental Science, University College Dublin, Dublin D04 V1W8, Ireland,Conway Institute for Biomolecular and Biomedical Research, University College Dublin, Dublin D04 V1W8, Ireland,Corresponding author
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Angelotti T. Exploring the eukaryotic Yip and REEP/Yop superfamily of membrane-shaping adapter proteins (MSAPs): A cacophony or harmony of structure and function? Front Mol Biosci 2022; 9:912848. [PMID: 36060263 PMCID: PMC9437294 DOI: 10.3389/fmolb.2022.912848] [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: 04/04/2022] [Accepted: 06/27/2022] [Indexed: 11/13/2022] Open
Abstract
Polytopic cargo proteins are synthesized and exported along the secretory pathway from the endoplasmic reticulum (ER), through the Golgi apparatus, with eventual insertion into the plasma membrane (PM). While searching for proteins that could enhance cell surface expression of olfactory receptors, a new family of proteins termed “receptor expression-enhancing proteins” or REEPs were identified. These membrane-shaping hairpin proteins serve as adapters, interacting with intracellular transport machinery, to regulate cargo protein trafficking. However, REEPs belong to a larger family of proteins, the Yip (Ypt-interacting protein) family, conserved in yeast and higher eukaryotes. To date, eighteen mammalian Yip family members, divided into four subfamilies (Yipf, REEP, Yif, and PRAF), have been identified. Yeast research has revealed many intriguing aspects of yeast Yip function, functions that have not completely been explored with mammalian Yip family members. This review and analysis will clarify the different Yip family nomenclature that have encumbered prior comparisons between yeast, plants, and eukaryotic family members, to provide a more complete understanding of their interacting proteins, membrane topology, organelle localization, and role as regulators of cargo trafficking and localization. In addition, the biological role of membrane shaping and sensing hairpin and amphipathic helical domains of various Yip proteins and their potential cellular functions will be described. Lastly, this review will discuss the concept of Yip proteins as members of a larger superfamily of membrane-shaping adapter proteins (MSAPs), proteins that both shape membranes via membrane-sensing and hairpin insertion, and well as act as adapters for protein-protein interactions. MSAPs are defined by their localization to specific membranes, ability to alter membrane structure, interactions with other proteins via specific domains, and specific interactions/effects on cargo proteins.
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Peng F, Liao M, Qin R, Zhu S, Peng C, Fu L, Chen Y, Han B. Regulated cell death (RCD) in cancer: key pathways and targeted therapies. Signal Transduct Target Ther 2022; 7:286. [PMID: 35963853 PMCID: PMC9376115 DOI: 10.1038/s41392-022-01110-y] [Citation(s) in RCA: 180] [Impact Index Per Article: 90.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 07/04/2022] [Accepted: 07/05/2022] [Indexed: 02/07/2023] Open
Abstract
Regulated cell death (RCD), also well-known as programmed cell death (PCD), refers to the form of cell death that can be regulated by a variety of biomacromolecules, which is distinctive from accidental cell death (ACD). Accumulating evidence has revealed that RCD subroutines are the key features of tumorigenesis, which may ultimately lead to the establishment of different potential therapeutic strategies. Hitherto, targeting the subroutines of RCD with pharmacological small-molecule compounds has been emerging as a promising therapeutic avenue, which has rapidly progressed in many types of human cancers. Thus, in this review, we focus on summarizing not only the key apoptotic and autophagy-dependent cell death signaling pathways, but the crucial pathways of other RCD subroutines, including necroptosis, pyroptosis, ferroptosis, parthanatos, entosis, NETosis and lysosome-dependent cell death (LCD) in cancer. Moreover, we further discuss the current situation of several small-molecule compounds targeting the different RCD subroutines to improve cancer treatment, such as single-target, dual or multiple-target small-molecule compounds, drug combinations, and some new emerging therapeutic strategies that would together shed new light on future directions to attack cancer cell vulnerabilities with small-molecule drugs targeting RCD for therapeutic purposes.
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Affiliation(s)
- Fu Peng
- West China School of Pharmacy, State Key Laboratory of Biotherapy and Cancer Center, Department of Gastrointestinal Surgery, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Minru Liao
- West China School of Pharmacy, State Key Laboratory of Biotherapy and Cancer Center, Department of Gastrointestinal Surgery, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Rui Qin
- State Key Laboratory of Southwestern Chinese Medicine Resources, Hospital of Chengdu University of Traditional Chinese Medicine, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Shiou Zhu
- West China School of Pharmacy, State Key Laboratory of Biotherapy and Cancer Center, Department of Gastrointestinal Surgery, West China Hospital, Sichuan University, Chengdu, 610041, China.,Sichuan Engineering Research Center for Biomimetic Synthesis of Natural Drugs, School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, 610031, China
| | - Cheng Peng
- State Key Laboratory of Southwestern Chinese Medicine Resources, Hospital of Chengdu University of Traditional Chinese Medicine, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Leilei Fu
- Sichuan Engineering Research Center for Biomimetic Synthesis of Natural Drugs, School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, 610031, China.
| | - Yi Chen
- West China School of Pharmacy, State Key Laboratory of Biotherapy and Cancer Center, Department of Gastrointestinal Surgery, West China Hospital, Sichuan University, Chengdu, 610041, China.
| | - Bo Han
- State Key Laboratory of Southwestern Chinese Medicine Resources, Hospital of Chengdu University of Traditional Chinese Medicine, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China.
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9
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Ding Y, Ma L, He L, Xu Q, Zhang Z, Zhang Z, Zhang X, Fan R, Ma W, Sun Y, Zhang B, Li W, Zhai Y, Zhang J. A strategy for attenuation of acute radiation-induced lung injury using crocetin from gardenia fruit. Biomed Pharmacother 2022; 149:112899. [PMID: 35366531 DOI: 10.1016/j.biopha.2022.112899] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 03/18/2022] [Accepted: 03/25/2022] [Indexed: 11/29/2022] Open
Abstract
PURPOSE Radiation-induced lung injury limits the implementation of radiotherapy plans and severely impairs the quality of life. Crocetin has the capability to protect against radiation. This study is aimed at estimate the preventive effect and mechanism of crocetin on acute radiation induced lung injury. METHODS AND MATERIALS In this study, we offer a strategy for radiation-induced lung injury by using crocetin, an extract of gardenia fruit. Histopathology, transcriptomics, flow cytometry, and other methods have served to examine the effect and mechanism of crocetin on acute radiation-induced lung injury. RESULTS Crocetin effectively alleviates radiation-induced alveolar wall thickening and alveolar destruction. The number of normal alveoli and lung structure of mice is well protected by the prevention of crocetin. It is found that crocetin inhibits necroptosis to achieve effective radioprotection by down regulating the Tnfrsf10b gene in vitro. CONCLUSION Crocetin inhibits necroptosis through transcriptional regulation of the Tnfrsf10b gene, thereby preventing radiation-induced lung injury. This work may provide a new strategy for the prevention of lung radiation injury by the extract from Chinese herbal medicine.
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Affiliation(s)
- Yan Ding
- Department of Radiation Oncology, Nanyang First People's Hospital Affiliated to Henan University, Nanyang 473000, China
| | - Lei Ma
- Cancer Center, Nanyang First People's Hospital Affiliated to Henan University, Nanyang 473000, China
| | - Limin He
- Cancer Center, Nanyang First People's Hospital Affiliated to Henan University, Nanyang 473000, China
| | - Quanxiao Xu
- Cancer Center, Nanyang First People's Hospital Affiliated to Henan University, Nanyang 473000, China
| | - Zhuang Zhang
- Department of Clinical Medicine, Xinjiang Medical University, Urumqi 830000, China
| | - Zhen Zhang
- Second Ward, Department of Oncology, Nanyang First People's Hospital Affiliated to Henan University, Nanyang 473000, China
| | - Xinping Zhang
- Department of Obstetrics and Gynecology, Nanyang First People's Hospital Affiliated to Henan University, Nanyang 473000, China
| | - Rui Fan
- Department of Pathology, Nanyang First People's Hospital Affiliated to Henan University, Nanyang 473000, China
| | - Wenjun Ma
- Department of Radiation Oncology, Nanyang First People's Hospital Affiliated to Henan University, Nanyang 473000, China
| | - Ya'nan Sun
- Department of Radiation Oncology, Nanyang First People's Hospital Affiliated to Henan University, Nanyang 473000, China
| | - Baile Zhang
- Department of Radiation Oncology, Nanyang First People's Hospital Affiliated to Henan University, Nanyang 473000, China
| | - Wentai Li
- Department of Radiation Oncology, Nanyang First People's Hospital Affiliated to Henan University, Nanyang 473000, China
| | - Yao Zhai
- Department of Radiation Oncology, Nanyang First People's Hospital Affiliated to Henan University, Nanyang 473000, China
| | - Jiandong Zhang
- Department of Radiation Oncology, Nanyang First People's Hospital Affiliated to Henan University, Nanyang 473000, China.
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10
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Liu Y, Zhang Z, Gao X, Ma Q, Yu Z, Huang S. Rab8A promotes breast cancer progression by increasing surface expression of Tropomyosin-related kinase B. Cancer Lett 2022; 535:215629. [PMID: 35278612 DOI: 10.1016/j.canlet.2022.215629] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 03/02/2022] [Accepted: 03/07/2022] [Indexed: 11/17/2022]
Abstract
Ras-related protein in brain (Rab) proteins are dysregulated in cancer cells and affect the proliferation and metastasis of cancer cells, thereby reducing the survival rate of cancer patients. Brain-derived neurotrophic factor (BDNF) and its receptor Tropomyosin-related kinase B (TrkB) play an important role in the occurrence and development of tumors. In this research, we investigate the interaction of Rab8A and TrkB in regulating the progression of breast cancer. Rab8A is upregulated in breast cancer tissues. The knockdown of Rab8A inhibits the proliferation, migration, and invasion of breast cancer cells through inhibiting TrkB. Moreover, the phosphorylation of AKT and ERK1/2 is suppressed by Rab8A knockdown. Rab8A interacts with TrkB, as revealed by co-immunoprecipitation assay to promote the surface expression of TrkB. However, Rab8A induced no significant changes in TrkB internalization. Functionally, BDNF promotes the expression of Rab8A through inhibiting Rab8A degradation. The TrkB inhibitor K252a blocks cell proliferation, migration and invasion as well as the activation of the AKT and ERK1/2 signaling pathway, which is induced by Rab8A in breast cancer cells. Our results reveal that Rab8A is upregulated by BDNF, and that Rab8A increases the surface expression of TrkB to promote the growth of breast cancer through the activation of the AKT and ERK1/2 signaling pathway. These results suggest that inhibiting Rab8A level could inhibit the progression of breast cancer.
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Affiliation(s)
- Yansong Liu
- Department of Breast Disease, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Zhonghua Zhang
- Department of Breast Disease, Dongping County Hospital, Taian, Shandong, China
| | - Xuefeng Gao
- Department of Breast and Thyroid Surgery, Yinan People's Hospital, Linyi, Shandong, China
| | - Qinghua Ma
- Department of Breast Disease, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Zhiyong Yu
- Department of Breast Disease, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China.
| | - Shuhong Huang
- Institute of Basic Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, China.
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11
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Development and Validation of a TNF Family-Based Signature for Predicting Prognosis, Tumor Immune Characteristics, and Immunotherapy Response in Colorectal Cancer Patients. J Immunol Res 2021; 2021:6439975. [PMID: 34541005 PMCID: PMC8448595 DOI: 10.1155/2021/6439975] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 07/10/2021] [Accepted: 08/03/2021] [Indexed: 12/12/2022] Open
Abstract
In this study, a comprehensive analysis of TNF family members in colorectal cancer (CRC) was conducted and a TNF family-based signature (TFS) was generated to predict prognosis and immunotherapy response. Using the expression data of 516 CRC patients from The Cancer Genome Atlas (TCGA) database, TNF family members were screened to construct a TFS by using the univariate Cox proportional hazards regression and the least absolute shrinkage and selection operator- (LASSO-) Cox proportional hazards regression method. The TFS was then validated in a meta-Gene Expression Omnibus (GEO) cohort (n = 1162) from the GEO database. Additionally, the tumor immune characteristics and predicted responses to immune checkpoint blockade in TFS-based risk subgroups were analyzed. Eight genes (TNFRSF11A, TNFRSF10C, TNFRSF10B, TNFSF11, TNFRSF25, TNFRSF19, LTBR, and NGFR) were used to construct the TFS. Compared to the high-risk patients, the low-risk patients had better overall survival, which was verified by the GEO data. In addition, a high TFS risk score was associated with high infiltration of regulatory T cells (Tregs), nonactivated macrophages (M0), natural killer cells, immune escape phenotypes, poor immunotherapy response, and tumorigenic and metastasis-related pathways. Conversely, a low TFS risk score was related to high infiltration of resting CD4 memory T cells and resting dendritic cells, few immune escape phenotypes, and high sensitivity to immunotherapy. Thus, the eight gene-based TFS is a promising index to predict the prognosis, immune characteristics, and immunotherapy response in CRC, and our results also provide new understanding of the role of the TNF family members in the prognosis and treatment of CRC.
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12
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Jin H, Tang Y, Yang L, Peng X, Li B, Fan Q, Wei S, Yang S, Li X, Wu B, Huang M, Tang S, Liu J, Li H. Rab GTPases: Central Coordinators of Membrane Trafficking in Cancer. Front Cell Dev Biol 2021; 9:648384. [PMID: 34141705 PMCID: PMC8204108 DOI: 10.3389/fcell.2021.648384] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Accepted: 05/10/2021] [Indexed: 12/11/2022] Open
Abstract
Tumor progression involves invasion, migration, metabolism, autophagy, exosome secretion, and drug resistance. Cargos transported by membrane vesicle trafficking underlie all of these processes. Rab GTPases, which, through coordinated and dynamic intracellular membrane trafficking alongside cytoskeletal pathways, determine the maintenance of homeostasis and a series of cellular functions. The mechanism of vesicle movement regulated by Rab GTPases plays essential roles in cancers. Therefore, targeting Rab GTPases to adjust membrane trafficking has the potential to become a novel way to adjust cancer treatment. In this review, we describe the characteristics of Rab GTPases; in particular, we discuss the role of their activation in the regulation of membrane transport and provide examples of Rab GTPases regulating membrane transport in tumor progression. Finally, we discuss the clinical implications and the potential as a cancer therapeutic target of Rab GTPases.
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Affiliation(s)
- Hongyuan Jin
- Department of General Surgery, The Fourth Affiliated Hospital of China Medical University, Shenyang, China
| | - Yuanxin Tang
- Department of General Surgery, The Fourth Affiliated Hospital of China Medical University, Shenyang, China
| | - Liang Yang
- Department of General Surgery, The Fourth Affiliated Hospital of China Medical University, Shenyang, China
| | - Xueqiang Peng
- Department of General Surgery, The Fourth Affiliated Hospital of China Medical University, Shenyang, China
| | - Bowen Li
- Department of General Surgery, The Fourth Affiliated Hospital of China Medical University, Shenyang, China
| | - Qin Fan
- Department of General Surgery, The Fourth Affiliated Hospital of China Medical University, Shenyang, China
| | - Shibo Wei
- Department of General Surgery, The Fourth Affiliated Hospital of China Medical University, Shenyang, China
| | - Shuo Yang
- Department of General Surgery, The Fourth Affiliated Hospital of China Medical University, Shenyang, China
| | - Xinyu Li
- Department of General Surgery, The Fourth Affiliated Hospital of China Medical University, Shenyang, China
| | - Bo Wu
- Department of General Surgery, The Fourth Affiliated Hospital of China Medical University, Shenyang, China
| | - Mingyao Huang
- Department of General Surgery, The Fourth Affiliated Hospital of China Medical University, Shenyang, China
| | - Shilei Tang
- Department of General Surgery, The Fourth Affiliated Hospital of China Medical University, Shenyang, China
| | - Jingang Liu
- Department of General Surgery, The Fourth Affiliated Hospital of China Medical University, Shenyang, China
| | - Hangyu Li
- Department of General Surgery, The Fourth Affiliated Hospital of China Medical University, Shenyang, China
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Qi Y, Yang W, Liu S, Han F, Wang H, Zhao Y, Zhou Y, Zhou D. Cisplatin loaded multiwalled carbon nanotubes reverse drug resistance in NSCLC by inhibiting EMT. Cancer Cell Int 2021; 21:74. [PMID: 33494783 PMCID: PMC7836500 DOI: 10.1186/s12935-021-01771-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 01/11/2021] [Indexed: 12/25/2022] Open
Abstract
Background Lung cancer is one of the important health threats worldwide, of which 5-year survival rate is less than 15%. Non-small-cell lung cancer (NSCLC) accounts for about 80% of all lung cancer with high metastasis and mortality. Methods Cisplatin loaded multiwalled carbon nanotubes (Pt-MWNTS) were synthesized and used to evaluate the anticancer effect in our study. The NSCLC cell lines A549 (cisplatin sensitive) and A549/DDP (cisplatin resistant) were used in our in vitro assays. MTT was used to determine Cancer cells viability and invasion were measured by MTT assay and Transwell assay, respectively. Apoptosis and epithelial-mesenchymal transition related marker proteins were measured by western blot. The in vivo anti-cancer effect of Pt-MWNTs were performed in male BALB/c nude mice (4-week old). Results Pt-MWNTS were synthesized and characterized by X-ray diffraction, Raman, FT-IR spectroscopy and scan electron microscopy. No significant cytotoxicity of MWNTS was detected in both A549/DDP and A549 cell lines. However, Pt-MWNTS showed a stronger inhibition effect on cell growth than free cisplatin, especially on A549/DDP. We found Pt-MWNTS showed higher intracellular accumulation of cisplatin in A549/DDP cells than free cisplatin and resulted in enhanced the percent of apoptotic cells. Western blot showed that application of Pt-MWNTS can significantly upregulate the expression level of Bax, Bim, Bid, Caspase-3 and Caspase-9 while downregulate the expression level of Bcl-2, compared with free cisplatin. Moreover, the expression level of mesenchymal markers like Vimentin and N-cadherin was more efficiently reduced by Pt-MWNTS treatment in A549/DDP cells than free cisplatin. In vivo study in nude mice proved that Pt-MWNTS more effectively inhibited tumorigenesis compared with cisplatin, although both of them had no significant effect on body weight. Conclusion Pt-MWNT reverses the drug resistance in the A549/DDP cell line, underlying its possibility of treating NSCLC with cisplatin resistance.
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Affiliation(s)
- Yuxin Qi
- Department of Respiratory Medicine, Jinan People's Hospital Affiliated to Shandong First Medical University, Jinan, 271199, China
| | - Wenping Yang
- Department of Respiratory Medicine, Jinan People's Hospital Affiliated to Shandong First Medical University, Jinan, 271199, China
| | - Shuang Liu
- Department of Respiratory Medicine, Jinan People's Hospital Affiliated to Shandong First Medical University, Jinan, 271199, China
| | - Fanjie Han
- Department of Respiratory Medicine, Jinan People's Hospital Affiliated to Shandong First Medical University, Jinan, 271199, China
| | - Haibin Wang
- Department of Respiratory Medicine, Jinan People's Hospital Affiliated to Shandong First Medical University, Jinan, 271199, China
| | - Yonghong Zhao
- Department of Respiratory Medicine, Jinan People's Hospital Affiliated to Shandong First Medical University, Jinan, 271199, China
| | - Yufa Zhou
- Department of Respiratory Medicine, Jinan People's Hospital Affiliated to Shandong First Medical University, Jinan, 271199, China
| | - Daijun Zhou
- Department of Oncology, General Hospital of Western Theater Command of PLA, Chengdu, 610083, China.
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