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Faulconnier Y, Pawlowski K, Chambon C, Durand D, Pires J, Leroux C. Liver transcriptome and proteome are modulated by nutrient restriction in early lactation cows challenged with intramammary lipopolysaccharide. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2024; 52:101326. [PMID: 39303391 DOI: 10.1016/j.cbd.2024.101326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2024] [Revised: 09/06/2024] [Accepted: 09/09/2024] [Indexed: 09/22/2024]
Abstract
The objective was to evaluate the effects of nutrient restriction on liver function 24 h after an intramammary lipopolysaccharide (LPS) challenge in early lactation cows using transcriptomic and proteomic analyses. Multiparous Holstein cows were fed a lactation diet (CONT, n = 8) throughout the study or were switched to a diet diluted with barley straw (48 % DM) for 96 h (REST, n = 8) starting at 24 (18 to 30) days in milk. At 72 h, a healthy rear mammary quarter was infused with 50 μg of LPS in all cows. Blood and liver biopsies were collected at 96 h, corresponding to 24 h after LPS challenge. Liver transcriptome was analyzed with a 44 K bovine microarray and proteome by LC MS/MS. Transcriptomic and proteomic data were analyzed using GeneSpring (moderated t-test with Westfall-Young correction) and the "between subject design", respectively. Data mining was performed using Panther and Pathway Studio software. By design, the negative energy balance was -68 and -37 MJ/d in REST and CONT, respectively. Plasma non-esterified FAs, and β-hydroxybutyrate were significantly greater in REST compared to CONT, which is consistent with 96 h of nutrient restriction in REST and ketosis induction. We detected 77 and 91 differentially expressed genes at mRNA and protein levels, respectively, between CONT and REST. Genes involved in fatty acid synthesis (e.g.: ACAT, FASN, SCD) were downregulated in REST, whereas those involved in fatty acid oxidation, detoxification, cholesterol synthesis, lipoprotein lipid secretion, and gluconeogenesis (e.g.: ACAD, CPT1A, CPT1B, CPT2) were upregulated. Differentially abundant mRNAs and proteins were consistent with negative energy balance and plasma metabolite concentrations, and reflected a state of intense lipomobilization, glucose deficit and ketogenesis in REST cows. Nutrient restriction did not change in deep liver expression of genes directly involved in immune function 24 h after an intramammary LPS challenge.
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Affiliation(s)
- Yannick Faulconnier
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR Herbivores, F-63122 Saint-Genès-Champanelle, France
| | - Karol Pawlowski
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR Herbivores, F-63122 Saint-Genès-Champanelle, France; Warsaw University of Life Sciences, Faculty of Veterinary Medicine, Department of Pathology and Veterinary Diagnostics, Poland
| | - Christophe Chambon
- INRAE, Plateforme d'Exploration du Métabolisme, composante protéomique PFEMcp, F-63122 Saint-Genès Champanelle, France
| | - Denys Durand
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR Herbivores, F-63122 Saint-Genès-Champanelle, France
| | - José Pires
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR Herbivores, F-63122 Saint-Genès-Champanelle, France
| | - Christine Leroux
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR Herbivores, F-63122 Saint-Genès-Champanelle, France; Department of Food Science and Technology, University of California, Davis, CA, USA.
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Liu T, Kong X, Wei J. Disulfidptosis: A New Target for Parkinson's Disease and Cancer. Curr Issues Mol Biol 2024; 46:10038-10064. [PMID: 39329952 PMCID: PMC11430384 DOI: 10.3390/cimb46090600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2024] [Revised: 09/06/2024] [Accepted: 09/10/2024] [Indexed: 09/28/2024] Open
Abstract
Recent studies have uncovered intriguing connections between Parkinson's disease (PD) and cancer, two seemingly distinct disease categories. Disulfidptosis has garnered attention as a novel form of regulated cell death that is implicated in various pathological conditions, including neurodegenerative disorders and cancer. Disulfidptosis involves the dysregulation of intracellular redox homeostasis, leading to the accumulation of disulfide bonds and subsequent cell demise. This has sparked our interest in exploring common molecular mechanisms and genetic factors that may be involved in the relationship between neurodegenerative diseases and tumorigenesis. The Gene4PD database was used to retrieve PD differentially expressed genes (DEGs), the biological functions of differential expression disulfidptosis-related genes (DEDRGs) were analyzed, the ROCs of DEDRGs were analyzed using the GEO database, and the expression of DEDRGs was verified by an MPTP-induced PD mouse model in vivo. Then, the DEDRGs in more than 9000 samples of more than 30 cancers were comprehensively and systematically characterized by using multi-omics analysis data. In PD, we obtained a total of four DEDRGs, including ACTB, ACTN4, INF2, and MYL6. The enriched biological functions include the regulation of the NF-κB signaling pathway, mitochondrial function, apoptosis, and tumor necrosis factor, and these genes are rich in different brain regions. In the MPTP-induced PD mouse model, the expression of ACTB was decreased, while the expression of ACTN4, INF2, and MYL6 was increased. In pan-cancer, the high expression of ACTB, ACTN4, and MYL6 in GBMLGG, LGG, MESO, and LAML had a poor prognosis, and the high expression of INF2 in LIHC, LUAD, UVM, HNSC, GBM, LAML, and KIPAN had a poor prognosis. Our study showed that these genes were more highly infiltrated in Macrophages, NK cells, Neutrophils, Eosinophils, CD8 T cells, T cells, T helper cells, B cells, dendritic cells, and mast cells in pan-cancer patients. Most substitution mutations were G-to-A transitions and C-to-T transitions. We also found that miR-4298, miR-296-3p, miR-150-3p, miR-493-5p, and miR-6742-5p play important roles in cancer and PD. Cyclophosphamide and ethinyl estradiol may be potential drugs affected by DEDRGs for future research. This study found that ACTB, ACTN4, INF2, and MYL6 are closely related to PD and pan-cancer and can be used as candidate genes for the diagnosis, prognosis, and therapeutic biomarkers of neurodegenerative diseases and cancers.
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Affiliation(s)
- Tingting Liu
- Institute for Brain Sciences Research, School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Xiangrui Kong
- Institute for Brain Sciences Research, School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Jianshe Wei
- Institute for Brain Sciences Research, School of Life Sciences, Henan University, Kaifeng 475004, China
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Qian Y, Li Y, Ji J, Wang Z. Identification of two hub genes and miRNA‑mRNA interactions in chronic obstructive pulmonary disease (COPD) plasma. J Asthma 2024; 61:1058-1067. [PMID: 38411985 DOI: 10.1080/02770903.2024.2324847] [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: 12/02/2023] [Revised: 02/07/2024] [Accepted: 02/25/2024] [Indexed: 02/28/2024]
Abstract
BACKGROUND We aimed to identify hub genes in chronic obstructive pulmonary disease (COPD) plasma through the exploration of a putative miRNA-mRNA regulatory network. METHODS Three datasets (GSE24709, GSE102915, GSE136390) were utilized to discern differentially expressed miRNAs (DEMs) between COPD and normal plasma. miRNET was employed to predict the potential targets of DEMs. Subsequent GO and KEGG analyses were conducted using DAVID. For the construction of the protein-protein interaction (PPI) network and screening of hub genes, STRING and Cytoscape were employed. The expression validation was assessed through GSE56768. RESULTS The results revealed 395 genes targeted by up-regulated DEMs and 234 genes targeted by down-regulated DEMs. The target genes exhibited significant enrichment in the PI3K-Akt signaling pathway and the p53 signaling pathway. Through the validation of hub genes' expression, we proposed two potential miRNA-mRNA interactions: miR-126-5p/miR-495-3p/miR-193b-3p - YWHAZ and miR-937-5p/miR-183-5p/miR-34c-5p/miR-98-5p/miR-525-3p/miR-215-5p - ACTB. CONCLUSIONS In conclusion, our study posits potential miRNA-mRNA interactions in COPD by analyzing datasets from public databases, contributing valuable insights into the understanding of COPD pathogenesis and potential therapeutic avenues.
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Affiliation(s)
- Yuanyuan Qian
- Department of Research and Development, Jilin Ruiguo Technology Co., Ltd, Changchun, China
| | - Yifei Li
- Department of Research and Development, Jilin Ruiguo Technology Co., Ltd, Changchun, China
| | - Jiancheng Ji
- Department of Research and Development, Jilin Ruiguo Technology Co., Ltd, Changchun, China
| | - Zhaojunli Wang
- Department of Research and Development, Jilin Ruiguo Technology Co., Ltd, Changchun, China
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Ramu A, Ak L, Chinnappan J. Identification of prostate cancer associated genes for diagnosis and prognosis: a modernized in silico approach. Mamm Genome 2024:10.1007/s00335-024-10060-5. [PMID: 39153107 DOI: 10.1007/s00335-024-10060-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2024] [Accepted: 08/06/2024] [Indexed: 08/19/2024]
Abstract
Prostate cancer (PCa) ranks as the second leading cause of cancer-related deaths in men. Diagnosing PCa relies on molecular markers known as diagnostic biomarkers, while prognostic biomarkers are used to identify key proteins involved in PCa treatments. This study aims to gather PCa-associated genes and assess their potential as either diagnostic or prognostic biomarkers for PCa. A corpus of 152,064 PCa-related data from PubMed, spanning from May 1936 to December 2020, was compiled. Additionally, 4199 genes associated with PCa terms were collected from the National Center of Biotechnology Information (NCBI) database. The PubMed corpus data was extracted using pubmed.mineR to identify PCa-associated genes. Network and pathway analyses were conducted using various tools, such as STRING, DAVID, KEGG, MCODE 2.0, cytoHubba app, CluePedia, and ClueGO app. Significant marker genes were identified using Random Forest, Support Vector Machines, Neural Network algorithms, and the Cox Proportional Hazard model. This study reports 3062 unique PCa-associated genes along with 2518 corresponding unique PMIDs. Diagnostic markers such as IL6, MAPK3, JUN, FOS, ACTB, MYC, and TGFB1 were identified, while prognostic markers like ACTB and HDAC1 were highlighted in PubMed. This suggests that the potential target genes provided by PubMed data outweigh those in the NCBI database.
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Affiliation(s)
- Akilandeswari Ramu
- Anthropology and Health Informatics Laboratory, Department of Bioinformatics, Bharathiar University, Coimbatore, Tamil Nadu, India.
| | - Lekhashree Ak
- Anthropology and Health Informatics Laboratory, Department of Bioinformatics, Bharathiar University, Coimbatore, Tamil Nadu, India
| | - Jayaprakash Chinnappan
- Anthropology and Health Informatics Laboratory, Department of Bioinformatics, Bharathiar University, Coimbatore, Tamil Nadu, India
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Novais AA, Tamarindo GH, Melo LMM, Balieiro BC, Nóbrega D, dos Santos G, Saldanha SF, de Souza FF, Chuffa LGDA, Bracha S, Zuccari DAPDC. Exploring Canine Mammary Cancer through Liquid Biopsy: Proteomic Profiling of Small Extracellular Vesicles. Cancers (Basel) 2024; 16:2562. [PMID: 39061201 PMCID: PMC11275101 DOI: 10.3390/cancers16142562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2024] [Revised: 07/11/2024] [Accepted: 07/12/2024] [Indexed: 07/28/2024] Open
Abstract
(Background). Canine mammary tumors (CMTs) have emerged as an important model for understanding pathophysiological aspects of human disease. Liquid biopsy (LB), which relies on blood-borne biomarkers and offers minimal invasiveness, holds promise for reflecting the disease status of patients. Small extracellular vesicles (SEVs) and their protein cargo have recently gained attention as potential tools for disease screening and monitoring. (Objectives). This study aimed to isolate SEVs from canine patients and analyze their proteomic profile to assess their diagnostic and prognostic potential. (Methods). Plasma samples were collected from female dogs grouped into CMT (malignant and benign), healthy controls, relapse, and remission groups. SEVs were isolated and characterized using ultracentrifugation (UC), nanoparticle tracking analysis (NTA) and transmission electron microscopy (TEM). Proteomic analysis of circulating SEVs was conducted using liquid chromatography-mass spectrometry (LC-MS). (Results). While no significant differences were observed in the concentration and size of exosomes among the studied groups, proteomic profiling revealed important variations. Mass spectrometry identified exclusive proteins that could serve as potential biomarkers for mammary cancer. These included Inter-alpha-trypsin inhibitor heavy chain (ITIH2 and ITI4), phosphopyruvate hydratase or alpha enolase (ENO1), eukaryotic translation elongation factor 2 (eEF2), actin (ACTB), transthyretin (TTR), beta-2-glycoprotein 1 (APOH) and gelsolin (GSN) found in female dogs with malignant tumors. Additionally, vitamin D-binding protein (VDBP), also known as group-specific component (GC), was identified as a protein present during remission. (Conclusions). The results underscore the potential of proteins found in SEVs as valuable biomarkers in CMTs. Despite the lack of differences in vesicle concentration and size between the groups, the analysis of protein content revealed promising markers with potential applications in CMT diagnosis and monitoring. These findings suggest a novel approach in the development of more precise and effective diagnostic tools for this challenging clinical condition.
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Affiliation(s)
- Adriana Alonso Novais
- Institute of Health Science (ICS), Universidade Federal de Mato Grosso (UFMT), Sinop 78550-728, MT, Brazil; (A.A.N.); (L.M.M.M.)
| | - Guilherme Henrique Tamarindo
- Brazilian Biosciences National Laboratory, Brazilian Center for Research in Energy and Materials (CNPEM), Campinas 13083-100, SP, Brazil;
| | - Luryan Mikaelly Minotti Melo
- Institute of Health Science (ICS), Universidade Federal de Mato Grosso (UFMT), Sinop 78550-728, MT, Brazil; (A.A.N.); (L.M.M.M.)
| | - Beatriz Castilho Balieiro
- Molecular Investigation of Cancer Laboratory (MICL), Department of Molecular Biology, Faculdade de Medicina de São José do Rio Preto/(FAMERP), São José do Rio Preto 15090-000, SP, Brazil;
| | - Daniela Nóbrega
- Pat Animal Laboratory, São José do Rio Preto 15070-000, SP, Brazil;
| | - Gislaine dos Santos
- Laboratory of Molecular Morphophysiology and Development (LMMD/ZMV), University of São Paulo, Pirassununga 13635-900, SP, Brazil; (G.d.S.); (S.F.S.)
| | - Schaienni Fontoura Saldanha
- Laboratory of Molecular Morphophysiology and Development (LMMD/ZMV), University of São Paulo, Pirassununga 13635-900, SP, Brazil; (G.d.S.); (S.F.S.)
| | - Fabiana Ferreira de Souza
- Department of Veterinary Surgery and Animal Reproduction, School of Veterinary Medicine and Animal Science, FMVZ, São Paulo State University (UNESP), Botucatu 18618-681, SP, Brazil;
| | - Luiz Gustavo de Almeida Chuffa
- Department of Structural and Functional Biology, Institute of Biosciences, UNESP—São Paulo State University, Botucatu 18618-689, SP, Brazil;
| | - Shay Bracha
- Department of Veterinary Clinical Sciences, College of Veterinary Medicine, Ohio State University, Columbus, OH 43210, USA;
| | - Debora Aparecida Pires de Campos Zuccari
- Molecular Investigation of Cancer Laboratory (MICL), Department of Molecular Biology, Faculdade de Medicina de São José do Rio Preto/(FAMERP), São José do Rio Preto 15090-000, SP, Brazil;
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Beyer JN, Serebrenik YV, Toy K, Najar MA, Raniszewski NR, Shalem O, Burslem GM. Intracellular Protein Editing to Enable Incorporation of Non-Canonical Residues into Endogenous Proteins. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.08.602493. [PMID: 39026884 PMCID: PMC11257474 DOI: 10.1101/2024.07.08.602493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
The ability to study proteins in a cellular context is crucial to our understanding of biology. Here, we report a new technology for "intracellular protein editing", drawing from intein- mediated protein splicing, genetic code expansion, and endogenous protein tagging. This protein editing approach enables us to rapidly and site specifically install residues and chemical handles into a protein of interest. We demonstrate the power of this protein editing platform to edit cellular proteins, inserting epitope peptides, protein-specific sequences, and non-canonical amino acids (ncAAs). Importantly, we employ an endogenous tagging approach to apply our protein editing technology to endogenous proteins with minimal perturbation. We anticipate that the protein editing technology presented here will be applied to a diverse set of problems, enabling novel experiments in live mammalian cells and therefore provide unique biological insights.
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Jin M, Ni D, Cai J, Yang J. Identification and validation of immunity- and disulfidptosis-related genes signature for predicting prognosis in ovarian cancer. Heliyon 2024; 10:e32273. [PMID: 38952356 PMCID: PMC11215265 DOI: 10.1016/j.heliyon.2024.e32273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Revised: 05/27/2024] [Accepted: 05/30/2024] [Indexed: 07/03/2024] Open
Abstract
Background Ovarian cancer (OC) ranks as the fifth most prevalent neoplasm in women and exhibits an unfavorable prognosis. To improve the OC patient's prognosis, a pioneering risk signature was formulated by amalgamating disulfidptosis-related genes. Methods A comparative analysis of OC tissues and normal tissues was carried out, and differentially expressed disulfidptosis-related genes (DRGs) were found using the criteria of |log2 (fold change) | > 0.585 and adjusted P-value <0.05. Subsequently, the TCGA training set was utilized to create a prognostic risk signature, which was validated by employing both the TCGA testing set and the GEO dataset. Moreover, the immune cell infiltration, mutational load, response to chemotherapy, and response to immunotherapy were analyzed. To further validate these findings, QRT-PCR analysis was conducted on ovarian tumor cell lines. Results A risk signature was created using fourteen differentially expressed genes (DEGs) associated with disulfidptosis, enabling the classification of ovarian cancer (OC) patients into high-risk group (HRG) and low-risk group (LRG). The HRG exhibited a lower overall survival (OS) compared to the LRG. In addition, the risk score remained an independent predictor even after incorporating clinical factors. Furthermore, the LRG displayed lower stromal, immune, and estimated scores compared to the HRG, suggesting a possible connection between the risk signature, immune cell infiltration, and mutational load. Finally, the QRT-PCR experiments revealed that eight genes were upregulated in the human OC cell line SKOV3 compared with the human normal OC line IOSE80, while six genes were down-regulated. Conclusions A fourteen-biomarker signature composed of disulfidptosis-related genes could serve as a valuable risk stratification tool in OC, facilitating the identification of patients who may benefit from individualized treatment and follow-up management.
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Affiliation(s)
- Miaojia Jin
- Nursing Department, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, 310016, China
| | - Dan Ni
- Department of Obstetrics and Gynecology, Jinhua Jindong District Maternal and Child Health Hospital, Jinhua, 321000, China
| | - Jianshu Cai
- Nursing Department, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, 310016, China
| | - Jianhua Yang
- Department of Obstetrics and Gynecology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Key Laboratory of Reproductive Dysfunction Management of Zhejiang Province, Hangzhou, 310016, China
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Zareinejad M, Faghih Z, Ramezani A, Safaei A, Ghaderi A. Exploring heterogeneous expression of beta-actin (ACTB) in bladder cancer by producing a monoclonal antibody 6D6. BMC Urol 2024; 24:124. [PMID: 38867273 PMCID: PMC11167769 DOI: 10.1186/s12894-024-01489-6] [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: 08/13/2023] [Accepted: 04/22/2024] [Indexed: 06/14/2024] Open
Abstract
BACKGROUND To predict outcomes and identify potential therapeutic targets for cancers, it is critical to find novel specific biomarkers. The objective of this study was to search for and explore novel bladder cancer-associated protein biomarkers. METHODS A library of monoclonal antibodies (mAbs) against the JAM-ICR cell line was first generated, and clones with high affinity were selected. Hybridomas were screened using bladder cancer (BLCA) cell lines and normal cells. The target of the selected mAb was then characterized through immunoaffinity purification, western blotting, and mass spectrometry analysis. Expression of the target antigen was assessed by flow cytometry and IHC methods. Several databases were also used to evaluate the target antigen in BLCA and other types of cancers. RESULTS Based on screenings, a 6D6 clone was selected that recognized an isoform of beta-actin (ACTB). Our data showed that ACTB expression on different cell lines was heterogeneous and varied significantly from low to high intensity. 6D6 bound strongly to epithelial cells while showing weak to no reactivity to stromal, endothelial, and smooth muscle cells. There was no association between ACTB intensity and related prognostic factors in BLCA. In silico evaluations revealed a significant correlation between ACTB and overexpressed genes and biomarkers in BLCA. Additionally, the differential expression of ACTB in tumor and healthy tissue as well as its correlation with survival time in a number of cancers were shown. CONCLUSIONS The heterogeneous expression of ACTB may suggest the potential value of this marker in the diagnosis or prognosis of cancer.
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Affiliation(s)
- Mohammadrasul Zareinejad
- Shiraz Institute for Cancer Research, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
- Department of Immunology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Zahra Faghih
- Shiraz Institute for Cancer Research, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Amin Ramezani
- Shiraz Institute for Cancer Research, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
- Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Akbar Safaei
- Department of Pathology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Abbas Ghaderi
- Shiraz Institute for Cancer Research, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran.
- Department of Immunology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran.
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Xiao H, Chen H, Zhang L, Duolikun M, Zhen B, Kuerban S, Li X, Wang Y, Chen L, Lin J. Cytoskeletal gene alterations linked to sorafenib resistance in hepatocellular carcinoma. World J Surg Oncol 2024; 22:152. [PMID: 38849867 PMCID: PMC11157844 DOI: 10.1186/s12957-024-03417-2] [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: 02/28/2024] [Accepted: 05/20/2024] [Indexed: 06/09/2024] Open
Abstract
BACKGROUND Although sorafenib has been consistently used as a first-line treatment for advanced hepatocellular carcinoma (HCC), most patients will develop resistance, and the mechanism of resistance to sorafenib needs further study. METHODS Using KAS-seq technology, we obtained the ssDNA profiles within the whole genome range of SMMC-7721 cells treated with sorafenib for differential analysis. We then intersected the differential genes obtained from the analysis of hepatocellular carcinoma patients in GSE109211 who were ineffective and effective with sorafenib treatment, constructed a PPI network, and obtained hub genes. We then analyzed the relationship between the expression of these genes and the prognosis of hepatocellular carcinoma patients. RESULTS In this study, we identified 7 hub ERGs (ACTB, CFL1, ACTG1, ACTN1, WDR1, TAGLN2, HSPA8) related to drug resistance, and these genes are associated with the cytoskeleton. CONCLUSIONS The cytoskeleton is associated with sorafenib resistance in hepatocellular carcinoma. Using KAS-seq to analyze the early changes in tumor cells treated with drugs is feasible for studying the drug resistance of tumors, which provides reference significance for future research.
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Affiliation(s)
- Hong Xiao
- Key Laboratory of Tropical Biological Resources of Ministry of Education, School of Pharmaceutical Sciences, Hainan University, Hainan, China
| | - Hangyu Chen
- Department of Pharmacy, Peking University Third Hospital, 49 Huayuan North Rd, Haidian District, Beijing, 100191, China
| | - Lei Zhang
- Department of Pharmacy, Peking University Third Hospital, 49 Huayuan North Rd, Haidian District, Beijing, 100191, China
| | - Maimaitiyasen Duolikun
- Key Laboratory of Tropical Biological Resources of Ministry of Education, School of Pharmaceutical Sciences, Hainan University, Hainan, China
| | - Baixin Zhen
- Department of Pharmacology, Xinjiang Medical University, Urumqi, China
| | - Subinuer Kuerban
- Department of Pharmacology, Xinjiang Medical University, Urumqi, China
| | - Xuehui Li
- Department of Pharmacology, Xinjiang Medical University, Urumqi, China
| | - Yuxi Wang
- Department of Pharmacy, Peking University Third Hospital, 49 Huayuan North Rd, Haidian District, Beijing, 100191, China
| | - Long Chen
- Department of Pharmacy, Peking University Third Hospital, 49 Huayuan North Rd, Haidian District, Beijing, 100191, China.
- Peking University, Third Hospital Cancer Center, 49 Huayuan North Rd, Haidian District, Beijing, 100191, China.
| | - Jian Lin
- Key Laboratory of Tropical Biological Resources of Ministry of Education, School of Pharmaceutical Sciences, Hainan University, Hainan, China.
- Department of Pharmacy, Peking University Third Hospital, 49 Huayuan North Rd, Haidian District, Beijing, 100191, China.
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Peking University, 49 Huayuan North Rd, Haidian District, Beijing, 100191, China.
- Peking University, Third Hospital Cancer Center, 49 Huayuan North Rd, Haidian District, Beijing, 100191, China.
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Heissler SM, Chinthalapudi K. Structural and functional mechanisms of actin isoforms. FEBS J 2024. [PMID: 38779987 DOI: 10.1111/febs.17153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2024] [Revised: 04/01/2024] [Accepted: 04/23/2024] [Indexed: 05/25/2024]
Abstract
Actin is a highly conserved and fundamental protein in eukaryotes and participates in a broad spectrum of cellular functions. Cells maintain a conserved ratio of actin isoforms, with muscle and non-muscle actins representing the main actin isoforms in muscle and non-muscle cells, respectively. Actin isoforms have specific and redundant functional roles and display different biochemistries, cellular localization, and interactions with myosins and actin-binding proteins. Understanding the specific roles of actin isoforms from the structural and functional perspective is crucial for elucidating the intricacies of cytoskeletal dynamics and regulation and their implications in health and disease. Here, we review how the structure contributes to the functional mechanisms of actin isoforms with a special emphasis on the questions of how post-translational modifications and disease-linked mutations affect actin isoforms biochemistry, function, and interaction with actin-binding proteins and myosin motors.
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Affiliation(s)
- Sarah M Heissler
- Department of Physiology and Cell Biology, Dorothy M. Davis Heart & Lung Research Institute, The Ohio State University, Columbus, OH, USA
| | - Krishna Chinthalapudi
- Department of Physiology and Cell Biology, Dorothy M. Davis Heart & Lung Research Institute, The Ohio State University, Columbus, OH, USA
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Gu Q, An Y, Xu M, Huang X, Chen X, Li X, Shan H, Zhang M. Disulfidptosis, A Novel Cell Death Pathway: Molecular Landscape and Therapeutic Implications. Aging Dis 2024:AD.2024.0083. [PMID: 38739940 DOI: 10.14336/ad.2024.0083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 05/02/2024] [Indexed: 05/16/2024] Open
Abstract
Programmed cell death is pivotal for several physiological processes, including immune defense. Further, it has been implicated in the pathogenesis of developmental disorders and the onset of numerous diseases. Multiple modes of programmed cell death, including apoptosis, pyroptosis, necroptosis, and ferroptosis, have been identified, each with their own unique characteristics and biological implications. In February 2023, Liu Xiaoguang and his team discovered "disulfidptosis," a novel pathway of programmed cell death. Their findings demonstrated that disulfidptosis is triggered in glucose-starved cells exhibiting high expression of a protein called SLC7A11. Furthermore, disulfidptosis is marked by a drastic imbalance in the NADPH/NADP+ ratio and the abnormal accumulation of disulfides like cystine. These changes ultimately lead to the destabilization of the F-actin network, causing cell death. Given that high SLC7A11 expression is a key feature of certain cancers, these findings indicate that disulfidptosis could serve as the basis of innovative anti-cancer therapies. Hence, this review delves into the discovery of disulfidptosis, its underlying molecular mechanisms and metabolic regulation, and its prospective applications in disease treatment.
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Affiliation(s)
- Qiuyang Gu
- Institute of Forensic Sciences, Suzhou Medical College, Soochow University, Suzhou, China
| | - Yumei An
- Institute of Forensic Sciences, Suzhou Medical College, Soochow University, Suzhou, China
| | - Mingyuan Xu
- Institute of Forensic Sciences, Suzhou Medical College, Soochow University, Suzhou, China
| | - Xinqi Huang
- Institute of Forensic Sciences, Suzhou Medical College, Soochow University, Suzhou, China
| | - Xueshi Chen
- Institute of Forensic Sciences, Suzhou Medical College, Soochow University, Suzhou, China
| | - Xianzhe Li
- Institute of Forensic Sciences, Suzhou Medical College, Soochow University, Suzhou, China
| | - Haiyan Shan
- Department of Obstetrics and Gynecology, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China
| | - Mingyang Zhang
- Institute of Forensic Sciences, Suzhou Medical College, Soochow University, Suzhou, China
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12
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Guo N, Han X, Han G, Dai M, Han Z, Li Q. Bioinformation Analysis of Differential Expression Proteins in Different Processes of COVID-19. Viral Immunol 2024; 37:194-201. [PMID: 38717820 DOI: 10.1089/vim.2023.0094] [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] [Indexed: 05/14/2024] Open
Abstract
COVID-19 is a highly infectious respiratory disease whose progression has been associated with multiple factors. From SARS-CoV-2 infection to death, biomarkers capable of predicting different disease processes are needed to help us further understand the molecular progression of COVID-19 disease. The aim is to find differentially expressed proteins that are associated with the progression of COVID-19 disease or can be potential biomarkers, and to provide a reference for further understanding of the molecular mechanisms of COVID-19 occurrence, progression, and treatment. Data-independent Acquisition (DIA) proteomics to obtain sample protein expression data, using R language screening differentially expressed proteins. Gene Ontology and Kyoto Encyclopedia for Genes and Genomes analysis was performed on differential proteins and protein-protein interaction (PPI) network was constructed to screen key proteins. A total of 47 differentially expressed proteins were obtained from COVID-19 incubation patients and healthy population (L/H), mainly enriched in platelet-related functions, and complement and coagulation cascade reaction pathways, such as platelet degranulation and platelet aggregation. A total of 42 differential proteins were obtained in clinical and latent phase patients (C/L), also mainly enriched in platelet-related functions and in complement and coagulation cascade reactions, platelet activation pathways. A total of 10 differential proteins were screened in recovery and clinical phase patients (R/C), mostly immune-related proteins. The differentially expressed proteins in different stages of COVID-19 are mostly closely associated with coagulation, and key differential proteins, such as FGA, FGB, FGG, ACTB, PFN1, VCL, SERPZNCL, APOC3, LTF, and DEFA1, have the potential to be used as early diagnostic markers.
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Affiliation(s)
- Nana Guo
- Hebei Province Center for Disease Control and Prevention, Shijiazhuang, China
| | - Xu Han
- Hebei Province Center for Disease Control and Prevention, Shijiazhuang, China
| | - Guangyue Han
- Hebei Province Center for Disease Control and Prevention, Shijiazhuang, China
| | - Mingyan Dai
- Hebei Medical University, Shijiazhuang, China
| | - Zhanying Han
- Hebei Province Center for Disease Control and Prevention, Shijiazhuang, China
| | - Qi Li
- Hebei Province Center for Disease Control and Prevention, Shijiazhuang, China
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13
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Hidmi O, Oster S, Monin J, Aqeilan RI. TOP1 and R-loops facilitate transcriptional DSBs at hypertranscribed cancer driver genes. iScience 2024; 27:109082. [PMID: 38375218 PMCID: PMC10875566 DOI: 10.1016/j.isci.2024.109082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 12/26/2023] [Accepted: 01/28/2024] [Indexed: 02/21/2024] Open
Abstract
DNA double-stranded breaks (DSBs) pose a significant threat to genomic integrity, and their generation during essential cellular processes like transcription remains poorly understood. In this study, we employ several techniques to map DSBs, R-loops, and topoisomerase 1 cleavage complex (TOP1cc) to comprehensively investigate the interplay between transcription, DSBs, topoisomerase 1 (TOP1), and R-loops. Our findings reveal the presence of DSBs at highly expressed genes enriched with TOP1 and R-loops. Remarkably, transcription-associated DSBs at these loci are significantly reduced upon depletion of R-loops and TOP1, uncovering the pivotal roles of TOP1 and R-loops in transcriptional DSB formation. By elucidating the intricate interplay between TOP1cc trapping, R-loops, and DSBs, our study provides insights into the mechanisms underlying transcription-associated genomic instability. Moreover, we establish a link between transcriptional DSBs and early molecular changes driving cancer development, highlighting the distinct etiology and molecular characteristics of driver mutations compared to passenger mutations.
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Affiliation(s)
- Osama Hidmi
- The Concern Foundation Laboratories, The Lautenberg Center for Immunology and Cancer Research, Department of Immunology and Cancer Research-IMRIC, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Sara Oster
- The Concern Foundation Laboratories, The Lautenberg Center for Immunology and Cancer Research, Department of Immunology and Cancer Research-IMRIC, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Jonathan Monin
- The Concern Foundation Laboratories, The Lautenberg Center for Immunology and Cancer Research, Department of Immunology and Cancer Research-IMRIC, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Rami I. Aqeilan
- The Concern Foundation Laboratories, The Lautenberg Center for Immunology and Cancer Research, Department of Immunology and Cancer Research-IMRIC, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
- Cyprus Cancer Research Institute (CCRI), Nicosia, Cyprus
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14
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Díaz-Campos MÁ, Vasquez-Arriaga J, Ochoa S, Hernández-Lemus E. Functional impact of multi-omic interactions in lung cancer. Front Genet 2024; 15:1282241. [PMID: 38389572 PMCID: PMC10881857 DOI: 10.3389/fgene.2024.1282241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 01/23/2024] [Indexed: 02/24/2024] Open
Abstract
Lung tumors are a leading cause of cancer-related death worldwide. Lung cancers are highly heterogeneous on their phenotypes, both at the cellular and molecular levels. Efforts to better understand the biological origins and outcomes of lung cancer in terms of this enormous variability often require of high-throughput experimental techniques paired with advanced data analytics. Anticipated advancements in multi-omic methodologies hold potential to reveal a broader molecular perspective of these tumors. This study introduces a theoretical and computational framework for generating network models depicting regulatory constraints on biological functions in a semi-automated way. The approach successfully identifies enriched functions in analyzed omics data, focusing on Adenocarcinoma (LUAD) and Squamous cell carcinoma (LUSC, a type of NSCLC) in the lung. Valuable information about novel regulatory characteristics, supported by robust biological reasoning, is illustrated, for instance by considering the role of genes, miRNAs and CpG sites associated with NSCLC, both novel and previously reported. Utilizing multi-omic regulatory networks, we constructed robust models elucidating omics data interconnectedness, enabling systematic generation of mechanistic hypotheses. These findings offer insights into complex regulatory mechanisms underlying these cancer types, paving the way for further exploring their molecular complexity.
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Affiliation(s)
| | - Jorge Vasquez-Arriaga
- Computational Genomics Division, National Institute of Genomic Medicine, Mexico City, Mexico
| | - Soledad Ochoa
- Computational Genomics Division, National Institute of Genomic Medicine, Mexico City, Mexico
- Department of Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA, United States
| | - Enrique Hernández-Lemus
- Computational Genomics Division, National Institute of Genomic Medicine, Mexico City, Mexico
- Center for Complexity Sciences, Universidad Nacional Autónoma de México, Mexico City, Mexico
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15
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Pessoa FMCDP, Viana VBDJ, de Oliveira MB, Nogueira BMD, Ribeiro RM, Oliveira DDS, Lopes GS, Vieira RPG, de Moraes Filho MO, de Moraes MEA, Khayat AS, Moreira FC, Moreira-Nunes CA. Validation of Endogenous Control Genes by Real-Time Quantitative Reverse Transcriptase Polymerase Chain Reaction for Acute Leukemia Gene Expression Studies. Genes (Basel) 2024; 15:151. [PMID: 38397141 PMCID: PMC10887733 DOI: 10.3390/genes15020151] [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: 12/07/2023] [Revised: 01/09/2024] [Accepted: 01/22/2024] [Indexed: 02/25/2024] Open
Abstract
Reference genes are used as internal reaction controls for gene expression analysis, and for this reason, they are considered reliable and must meet several important criteria. In view of the absence of studies regarding the best reference gene for the analysis of acute leukemia patients, a panel of genes commonly used as endogenous controls was selected from the literature for stability analysis: Glyceraldehyde-3-phosphate dehydrogenase (GAPDH), Abelson murine leukemia viral oncogene human homolog 1 (ABL), Hypoxanthine phosphoribosyl-transferase 1 (HPRT1), Ribosomal protein lateral stalk subunit P0 (RPLP0), β-actin (ACTB) and TATA box binding protein (TBP). The stability of candidate reference genes was analyzed according to three statistical methods of assessment, namely, NormFinder, GeNorm and R software (version 4.0.3). From this study's analysis, it was possible to identify that the endogenous set composed of ACTB, ABL, TBP and RPLP0 demonstrated good performances and stable expressions between the analyzed groups. In addition to that, the GAPDH and HPRT genes could not be classified as good reference genes, considering that they presented a high standard deviation and great variability between groups, indicating low stability. Given these findings, this study suggests the main endogenous gene set for use as a control/reference for the gene expression in peripheral blood and bone marrow samples from patients with acute leukemias is composed of the ACTB, ABL, TBP and RPLP0 genes. Researchers may choose two to three of these housekeeping genes to perform data normalization.
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Affiliation(s)
- Flávia Melo Cunha de Pinho Pessoa
- Department of Medicine, Pharmacogenetics Laboratory, Drug Research and Development Center (NPDM), Federal University of Ceará, Fortaleza 60430-275, CE, Brazil; (F.M.C.d.P.P.); (B.M.D.N.); (D.d.S.O.); (M.O.d.M.F.)
| | - Vitória Beatriz de Jesus Viana
- Department of Biological Sciences, Oncology Research Center, Federal University of Pará, Belém 66073-005, PA, Brazil; (V.B.d.J.V.); (M.B.d.O.); (F.C.M.)
| | - Marcelo Braga de Oliveira
- Department of Biological Sciences, Oncology Research Center, Federal University of Pará, Belém 66073-005, PA, Brazil; (V.B.d.J.V.); (M.B.d.O.); (F.C.M.)
| | - Beatriz Maria Dias Nogueira
- Department of Medicine, Pharmacogenetics Laboratory, Drug Research and Development Center (NPDM), Federal University of Ceará, Fortaleza 60430-275, CE, Brazil; (F.M.C.d.P.P.); (B.M.D.N.); (D.d.S.O.); (M.O.d.M.F.)
| | | | - Deivide de Sousa Oliveira
- Department of Medicine, Pharmacogenetics Laboratory, Drug Research and Development Center (NPDM), Federal University of Ceará, Fortaleza 60430-275, CE, Brazil; (F.M.C.d.P.P.); (B.M.D.N.); (D.d.S.O.); (M.O.d.M.F.)
- Department of Hematology, Fortaleza General Hospital (HGF), Fortaleza 60150-160, CE, Brazil
| | - Germison Silva Lopes
- Department of Hematology, César Cals General Hospital, Fortaleza 60015-152, CE, Brazil;
| | | | - Manoel Odorico de Moraes Filho
- Department of Medicine, Pharmacogenetics Laboratory, Drug Research and Development Center (NPDM), Federal University of Ceará, Fortaleza 60430-275, CE, Brazil; (F.M.C.d.P.P.); (B.M.D.N.); (D.d.S.O.); (M.O.d.M.F.)
| | - Maria Elisabete Amaral de Moraes
- Department of Medicine, Pharmacogenetics Laboratory, Drug Research and Development Center (NPDM), Federal University of Ceará, Fortaleza 60430-275, CE, Brazil; (F.M.C.d.P.P.); (B.M.D.N.); (D.d.S.O.); (M.O.d.M.F.)
| | - André Salim Khayat
- Department of Biological Sciences, Oncology Research Center, Federal University of Pará, Belém 66073-005, PA, Brazil; (V.B.d.J.V.); (M.B.d.O.); (F.C.M.)
| | - Fabiano Cordeiro Moreira
- Department of Biological Sciences, Oncology Research Center, Federal University of Pará, Belém 66073-005, PA, Brazil; (V.B.d.J.V.); (M.B.d.O.); (F.C.M.)
| | - Caroline Aquino Moreira-Nunes
- Department of Medicine, Pharmacogenetics Laboratory, Drug Research and Development Center (NPDM), Federal University of Ceará, Fortaleza 60430-275, CE, Brazil; (F.M.C.d.P.P.); (B.M.D.N.); (D.d.S.O.); (M.O.d.M.F.)
- Department of Biological Sciences, Oncology Research Center, Federal University of Pará, Belém 66073-005, PA, Brazil; (V.B.d.J.V.); (M.B.d.O.); (F.C.M.)
- Central Unity, Molecular Biology Laboratory, Clementino Fraga Group, Fortaleza 60115-170, CE, Brazil
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16
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Nathani A, Sun L, Khan I, Aare M, Bagde A, Li Y, Singh M. Combined Role of Interleukin-15 Stimulated Natural Killer Cell-Derived Extracellular Vesicles and Carboplatin in Osimertinib-Resistant H1975 Lung Cancer Cells with EGFR Mutations. Pharmaceutics 2024; 16:83. [PMID: 38258094 PMCID: PMC10821370 DOI: 10.3390/pharmaceutics16010083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 01/05/2024] [Accepted: 01/06/2024] [Indexed: 01/24/2024] Open
Abstract
In this study, we evaluated IL-15 stimulated natural killer cell-derived EVs (NK-EVs) as therapeutic agents in vitro and in vivo in Osimertinib-resistant lung cancer (H1975R) with EGFR mutations (L858R) in combination with carboplatin (CBP). NK-EVs were isolated by ultracentrifugation and characterized by nanoparticle tracking analysis, and atomic force microscopy imaging revealed vesicles with a spherical form and sizes meeting the criteria of exosomal EVs. Further, Western blot studies demonstrated the presence of regular EV markers along with specific NK markers (perforin and granzyme). EVs were also characterized by proteomic analysis, which demonstrated that EVs had proteins for natural killer cell-mediated cytotoxicity (Granzyme B) and T cell activation (perforin and plastin-2). Gene oncology analysis showed that these differentially expressed proteins are involved in programmed cell death and positive regulation of cell death. Further, isolated NK-EVs were cytotoxic to H1975R cells in vitro in 2D and 3D cell cultures. CBP's IC50 was reduced by approximately in 2D and 3D cell cultures when combined with NK-EVs. The EVs were then combined with CBP and administered by i.p. route to H1975R tumor xenografts, and a significant reduction in tumor volume in vivo was observed. Our findings show for the first time that NK-EVs target the PD-L1/PD-1 immunological checkpoint to induce apoptosis and anti-inflammatory response by downregulation of SOD2, PARP, BCL2, SET, NF-κB, and TGF-ß. The ability to isolate functional NK-EVs on a large scale and use them with platinum-based drugs may lead to new clinical applications. The results of the present study suggest the possibility of the combination of NK-cell-derived EVs and CBP as a viable immunochemotherapeutic strategy for resistant cancers.
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Affiliation(s)
- Aakash Nathani
- College of Pharmacy and Pharmaceutical Sciences, Florida A&M University, Tallahassee, FL 32307, USA; (A.N.); (I.K.); (M.A.); (A.B.)
| | - Li Sun
- Department of Chemical and Biomedical Engineering, FAMU-FSU College of Engineering, Florida State University, Tallahassee, FL 32310, USA;
- Department of Biomedical Sciences, College of Medicine, Florida State University, Tallahassee, FL 32304, USA
| | - Islauddin Khan
- College of Pharmacy and Pharmaceutical Sciences, Florida A&M University, Tallahassee, FL 32307, USA; (A.N.); (I.K.); (M.A.); (A.B.)
| | - Mounika Aare
- College of Pharmacy and Pharmaceutical Sciences, Florida A&M University, Tallahassee, FL 32307, USA; (A.N.); (I.K.); (M.A.); (A.B.)
| | - Arvind Bagde
- College of Pharmacy and Pharmaceutical Sciences, Florida A&M University, Tallahassee, FL 32307, USA; (A.N.); (I.K.); (M.A.); (A.B.)
| | - Yan Li
- Department of Chemical and Biomedical Engineering, FAMU-FSU College of Engineering, Florida State University, Tallahassee, FL 32310, USA;
| | - Mandip Singh
- College of Pharmacy and Pharmaceutical Sciences, Florida A&M University, Tallahassee, FL 32307, USA; (A.N.); (I.K.); (M.A.); (A.B.)
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17
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Yang R, Lu Y, Yin N, Faiola F. Transcriptomic Integration Analyses Uncover Common Bisphenol A Effects Across Species and Tissues Primarily Mediated by Disruption of JUN/FOS, EGFR, ER, PPARG, and P53 Pathways. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:19156-19168. [PMID: 37978927 DOI: 10.1021/acs.est.3c02016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2023]
Abstract
Bisphenol A (BPA) is a common endocrine disruptor widely used in the production of electronic, sports, and medical equipment, as well as consumer products like milk bottles, dental sealants, and thermal paper. Despite its widespread use, current assessments of BPA exposure risks remain limited due to the lack of comprehensive cross-species comparative analyses. To address this gap, we conducted a study aimed at identifying genes and fundamental molecular processes consistently affected by BPA in various species and tissues, employing an effective data integration method and bioinformatic analyses. Our findings revealed that exposure to BPA led to significant changes in processes like lipid metabolism, proliferation, and apoptosis in the tissues/cells of mammals, fish, and nematodes. These processes were found to be commonly affected in adipose, liver, mammary, uterus, testes, and ovary tissues. Additionally, through an in-depth analysis of signaling pathways influenced by BPA in different species and tissues, we observed that the JUN/FOS, EGFR, ER, PPARG, and P53 pathways, along with their downstream key transcription factors and kinases, were all impacted by BPA. Our study provides compelling evidence that BPA indeed induces similar toxic effects across different species and tissues. Furthermore, our investigation sheds light on the underlying molecular mechanisms responsible for these toxic effects. By uncovering these mechanisms, we gain valuable insights into the potential health implications associated with BPA exposure, highlighting the importance of comprehensive assessments and awareness of this widespread endocrine disruptor.
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Affiliation(s)
- Renjun Yang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuanping Lu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Nuoya Yin
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Francesco Faiola
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
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18
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Ghalehno AD, Abdi H, Boustan A, Jamialahmadi K, Mosaffa F. Tamoxifen resistance induction results in the upregulation of ABCG2 expression and mitoxantrone resistance in MCF-7 breast cancer cells. NAUNYN-SCHMIEDEBERG'S ARCHIVES OF PHARMACOLOGY 2023; 396:3723-3732. [PMID: 37310508 DOI: 10.1007/s00210-023-02567-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Accepted: 05/31/2023] [Indexed: 06/14/2023]
Abstract
Cancer endocrine therapy can promote evolutionary dynamics and lead to changes in the gene expression profile of tumor cells. We aimed to assess the effect of tamoxifen (TAM)-resistance induction on ABCG2 pump mRNA, protein, and activity in ER + MCF-7 breast cancer cells. We also evaluated if the resistance to TAM leads to the cross-resistance toward mitoxantrone (MX), a well-known substrate of the ABCG2 pump. The ABCG2 mRNA and protein expression were compared in MCF-7 and its TAM-resistant derivative MCF-7/TAMR cells using RT-qPCR and western blot methods, respectively. Cross-resistance of MCF-7/TAMR cells toward MX was evaluated by the MTT method. Flow cytometry was applied to compare ABCG2 function between cell lines using MX accumulation assay. ABCG2 mRNA expression was also analyzed in tamoxifen-sensitive (TAM-S) and tamoxifen-resistant (TAM-R) breast tumor tissues. The levels of ABCG2 mRNA, protein, and activity were significantly higher in MCF-7/TAMR cells compared to TAM-sensitive MCF-7 cells. MX was also less toxic in MCF-7/TAMR compared to MCF-7 cells. ABCG2 was also upregulated in tissue samples obtained from TAM-R cancer patients compared to TAM-S patients. Prolonged exposure of ER + breast cancer cells to the active form of TAM and clonal evolution imposed by the selective pressure of the drug can lead to higher expression of the ABCG2 pump in the emerged TAM-resistant cells. Therefore, in choosing a sequential therapy for a patient who develops resistance to TAM, the possibility of the cross-resistance of the evolved tumor to chemotherapy drugs that are ABCG2 substrates should be considered. Prolonged exposure of MCF-7 breast cancer cells to tamoxifen can cause resistance to it and an increase in the expression of the ABCG2 mRNA and protein levels in the cells. Tamoxifen resistance can lead to cross-resistance to mitoxantrone.
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Affiliation(s)
- Asefeh Dahmardeh Ghalehno
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Hakimeh Abdi
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Arad Boustan
- Department of Medical Biotechnology and Nanotechnology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Khadijeh Jamialahmadi
- Biotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran.
| | - Fatemeh Mosaffa
- Biotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran.
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19
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Das S, Srivastava DK. ioSearch: An approach for identifying interacting multiomics biomarkers using a novel algorithm with application on breast cancer data sets. Genet Epidemiol 2023; 47:600-616. [PMID: 37795815 DOI: 10.1002/gepi.22536] [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: 01/20/2023] [Revised: 08/04/2023] [Accepted: 09/18/2023] [Indexed: 10/06/2023]
Abstract
Identification of biomarkers by integrating multiple omics together is important because complex diseases occur due to an intricate interplay of various genetic materials. Traditional single-omics association tests neither explore this crucial interomics dependence nor identify moderately weak signals due to the multiple-testing burden. Conversely, multiomics data integration imparts complementary information but suffers from an increased multiple-testing burden, data diversity inherent with different omics features, high-dimensionality, and so forth. Most of the available methods address subtype classification using dimension-reduction techniques to circumvent the sample size issue but interacting multiomics biomarker identification methods are unavailable. We propose a two-step model that first investigates phenotype-omics association using logistic regression. Then, selects disease-associated omics using sparse principal components which explores the interrelationship of multiple variables from two omics in a multivariate multiple regression framework. On the basis of this model, we developed a multiomics biomarker identification algorithm, interacting omics search (ioSearch), that jointly tests the effect of multiple omics with disease and between-omics associations by using pathway information that subsequently reduces the multiple-testing burden. Further, inference in terms of p values potentially makes it an easily interpretable biomarker identification tool. Extensive simulation demonstrates ioSearch as statistically powerful with a controlled Type-I error rate. Its application to publicly available breast cancer data sets identified relevant omics features in important pathways.
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Affiliation(s)
- Sarmistha Das
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Deo Kumar Srivastava
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
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20
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Klemt I, Varzatskii O, Selin R, Vakarov S, Kovalska V, Bila G, Bilyy R, Voloshin Y, Cuartero IC, Hidalgo A, Frey B, Becker I, Friedrich B, Tietze R, Friedrich RP, Alexiou C, Ursu EL, Rotaru A, Solymosi I, Pérez-Ojeda ME, Mokhir A. 3D-Shaped Binders of Unfolded Proteins Inducing Cancer Cell-Specific Endoplasmic Reticulum Stress In Vitro and In Vivo. J Am Chem Soc 2023; 145:22252-22264. [PMID: 37773090 DOI: 10.1021/jacs.3c08827] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/30/2023]
Abstract
The amount of unfolded proteins is increased in cancer cells, leading to endoplasmic reticulum (ER) stress. Therefore, cancer cells are sensitive to drugs capable of further enhancing ER stress. Examples of such drugs include the clinically approved proteosome inhibitors bortezomib and carfilzomib. Unfortunately, the known ER stress inducers exhibit dose-limiting side effects that justify the search for better, more cancer-specific drugs of this type. Herein, we report on FeC 2, which binds to unfolded proteins prevents their further processing, thereby leading to ER stress and ROS increase in cancer cells, but not in normal cells. FeC 2 exhibits low micromolar toxicity toward human acute promyelocytic leukemia HL-60, Burkitt's lymphoma BL-2, T-cell leukemia Jurkat, ovarian carcinoma A2780, lung cancer SK-MES-1, and murine lung cancer LLC1 cells. Due to the cancer-specific mode of action, 2 is not toxic in vivo up to the dose of 147 mg/kg, does not affect normal blood and bone marrow cells at the therapeutically active dose, but strongly suppresses both primary tumor growth (confirmed in Nemeth-Kellner lymphoma and LLC1 lung cancer models of murine tumor) and spreading of metastases (LLC1).
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Affiliation(s)
- Insa Klemt
- Department of Chemistry and Pharmacy, Organic Chemistry II, Friedrich-Alexander-University of Erlangen-Nürnberg (FAU), 91058 Erlangen, Germany
| | - Oleg Varzatskii
- Princeton Biomolecular Research Laboratories, 26A Saperne Pole Street, 01042 Kyiv, Ukraine
- V.I. Vernadsky Institute of General and Inorganic Chemistry, NASU, 32/34 Palladin Av., 03142 Kyiv, Ukraine
| | - Roman Selin
- Department of Chemistry and Pharmacy, Organic Chemistry II, Friedrich-Alexander-University of Erlangen-Nürnberg (FAU), 91058 Erlangen, Germany
| | - Serhii Vakarov
- Princeton Biomolecular Research Laboratories, 26A Saperne Pole Street, 01042 Kyiv, Ukraine
- V.I. Vernadsky Institute of General and Inorganic Chemistry, NASU, 32/34 Palladin Av., 03142 Kyiv, Ukraine
| | - Vladyslava Kovalska
- Princeton Biomolecular Research Laboratories, 26A Saperne Pole Street, 01042 Kyiv, Ukraine
- Institute of Molecular Biology and Genetics, NASU, 150 Zabolotnogo Street, 03143 Kyiv, Ukraine
| | - Galyna Bila
- Department of Histology, Cytology and Embryology, Danylo Halytsky Lviv National Medical University, Pekarska Street 69, 79010 Lviv, Ukraine
- Lectinotest R&D, Mechanichna Street 2, 79024 Lviv, Ukraine
| | - Rostyslav Bilyy
- Department of Histology, Cytology and Embryology, Danylo Halytsky Lviv National Medical University, Pekarska Street 69, 79010 Lviv, Ukraine
- Lectinotest R&D, Mechanichna Street 2, 79024 Lviv, Ukraine
| | - Yan Voloshin
- Nesmeyanov Institute of Organoelement Compounds, RAS, 28 Vavilova Street, 119334 Moscow, Russia
| | - Itziar Cossío Cuartero
- Program of Cardiovascular Regeneration, Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), C. Melchor Fernández Almagro, 3, 28029 Madrid, Spain
| | - Andrés Hidalgo
- Program of Cardiovascular Regeneration, Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), C. Melchor Fernández Almagro, 3, 28029 Madrid, Spain
| | - Benjamin Frey
- Department of Radiation Oncology, Translational Radiobiology, Universitaetsklinikum Erlangen, Friedrich-Alexander-University of Erlangen-Nürnberg (FAU), Glueckstrasse 4A, 91054 Erlangen, Germany
| | - Ina Becker
- Department of Radiation Oncology, Translational Radiobiology, Universitaetsklinikum Erlangen, Friedrich-Alexander-University of Erlangen-Nürnberg (FAU), Glueckstrasse 4A, 91054 Erlangen, Germany
| | - Bernhard Friedrich
- Department of Otorhinolaryngology, Head and Neck Surgery, Section of Experimental Oncology and Nanomedicine (SEON), University Hospital, Friedrich-Alexander-University of Erlangen-Nürnberg (FAU), Glückstraße 10a, 91054 Erlangen, Germany
| | - Rainer Tietze
- Department of Otorhinolaryngology, Head and Neck Surgery, Section of Experimental Oncology and Nanomedicine (SEON), University Hospital, Friedrich-Alexander-University of Erlangen-Nürnberg (FAU), Glückstraße 10a, 91054 Erlangen, Germany
| | - Ralf P Friedrich
- Department of Otorhinolaryngology, Head and Neck Surgery, Section of Experimental Oncology and Nanomedicine (SEON), University Hospital, Friedrich-Alexander-University of Erlangen-Nürnberg (FAU), Glückstraße 10a, 91054 Erlangen, Germany
| | - Christoph Alexiou
- Department of Otorhinolaryngology, Head and Neck Surgery, Section of Experimental Oncology and Nanomedicine (SEON), University Hospital, Friedrich-Alexander-University of Erlangen-Nürnberg (FAU), Glückstraße 10a, 91054 Erlangen, Germany
| | - Elena-Laura Ursu
- "Petru Poni" Institute of Macromolecular Chemistry, Romanian Academy, Centre of Advanced Research in Bionanoconjugates and Biopolymers, Grigore Ghica Voda Alley 41 A, 700487 Iasi, Romania
| | - Alexandru Rotaru
- "Petru Poni" Institute of Macromolecular Chemistry, Romanian Academy, Centre of Advanced Research in Bionanoconjugates and Biopolymers, Grigore Ghica Voda Alley 41 A, 700487 Iasi, Romania
| | - Iris Solymosi
- Department of Chemistry and Pharmacy, Organic Chemistry II, Friedrich-Alexander-University of Erlangen-Nürnberg (FAU), 91058 Erlangen, Germany
| | - M Eugenia Pérez-Ojeda
- Department of Chemistry and Pharmacy, Organic Chemistry II, Friedrich-Alexander-University of Erlangen-Nürnberg (FAU), 91058 Erlangen, Germany
| | - Andriy Mokhir
- Department of Chemistry and Pharmacy, Organic Chemistry II, Friedrich-Alexander-University of Erlangen-Nürnberg (FAU), 91058 Erlangen, Germany
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21
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Xia Q, Yan Q, Wang Z, Huang Q, Zheng X, Shen J, Du L, Li H, Duan S. Disulfidptosis-associated lncRNAs predict breast cancer subtypes. Sci Rep 2023; 13:16268. [PMID: 37758759 PMCID: PMC10533517 DOI: 10.1038/s41598-023-43414-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 09/23/2023] [Indexed: 09/29/2023] Open
Abstract
Disulfidptosis is a newly discovered mode of cell death. However, its relationship with breast cancer subtypes remains unclear. In this study, we aimed to construct a disulfidptosis-associated breast cancer subtype prediction model. We obtained 19 disulfidptosis-related genes from published articles and performed correlation analysis with lncRNAs differentially expressed in breast cancer. We then used the random forest algorithm to select important lncRNAs and establish a breast cancer subtype prediction model. We identified 132 lncRNAs significantly associated with disulfidptosis (FDR < 0.01, |R|> 0.15) and selected the first four important lncRNAs to build a prediction model (training set AUC = 0.992). The model accurately predicted breast cancer subtypes (test set AUC = 0.842). Among the key lncRNAs, LINC02188 had the highest expression in the Basal subtype, while LINC01488 and GATA3-AS1 had the lowest expression in Basal. In the Her2 subtype, LINC00511 had the highest expression level compared to other key lncRNAs. GATA3-AS1 had the highest expression in LumA and LumB subtypes, while LINC00511 had the lowest expression in these subtypes. In the Normal subtype, GATA3-AS1 had the highest expression level compared to other key lncRNAs. Our study also found that key lncRNAs were closely related to RNA methylation modification and angiogenesis (FDR < 0.05, |R|> 0.1), as well as immune infiltrating cells (P.adj < 0.01, |R|> 0.1). Our random forest model based on disulfidptosis-related lncRNAs can accurately predict breast cancer subtypes and provide a new direction for research on clinical therapeutic targets for breast cancer.
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Affiliation(s)
- Qing Xia
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, School of Medicine, Hangzhou City University, Hangzhou, 310015, Zhejiang, China
- College of Pharmacy, Zhejiang University of Technology, Hangzhou, 310014, Zhejiang, China
| | - Qibin Yan
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, School of Medicine, Hangzhou City University, Hangzhou, 310015, Zhejiang, China
- College of Pharmacy, Zhejiang University of Technology, Hangzhou, 310014, Zhejiang, China
| | - Zehua Wang
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, School of Medicine, Hangzhou City University, Hangzhou, 310015, Zhejiang, China
| | - Qinyuan Huang
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, School of Medicine, Hangzhou City University, Hangzhou, 310015, Zhejiang, China
| | - Xinying Zheng
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, School of Medicine, Hangzhou City University, Hangzhou, 310015, Zhejiang, China
- College of Pharmacy, Zhejiang University of Technology, Hangzhou, 310014, Zhejiang, China
| | - Jinze Shen
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, School of Medicine, Hangzhou City University, Hangzhou, 310015, Zhejiang, China
| | - Lihua Du
- College of Pharmacy, Zhejiang University of Technology, Hangzhou, 310014, Zhejiang, China
| | - Hanbing Li
- College of Pharmacy, Zhejiang University of Technology, Hangzhou, 310014, Zhejiang, China.
| | - Shiwei Duan
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, School of Medicine, Hangzhou City University, Hangzhou, 310015, Zhejiang, China.
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22
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Batten DJ, Crofts JJ, Chuzhanova N. Towards In Silico Identification of Genes Contributing to Similarity of Patients' Multi-Omics Profiles: A Case Study of Acute Myeloid Leukemia. Genes (Basel) 2023; 14:1795. [PMID: 37761935 PMCID: PMC10531350 DOI: 10.3390/genes14091795] [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: 08/06/2023] [Revised: 09/09/2023] [Accepted: 09/11/2023] [Indexed: 09/29/2023] Open
Abstract
We propose a computational framework for selecting biologically plausible genes identified by clustering of multi-omics data that reveal patients' similarity, thus giving researchers a more comprehensive view on any given disease. We employ spectral clustering of a similarity network created by fusion of three similarity networks, based on mRNA expression of immune genes, miRNA expression and DNA methylation data, using SNF_v2.1 software. For each cluster, we rank multi-omics features, ensuring the best separation between clusters, and select the top-ranked features that preserve clustering. To find genes targeted by DNA methylation and miRNAs found in the top-ranked features, we use chromosome-conformation capture data and miRNet2.0 software, respectively. To identify informative genes, these combined sets of target genes are analyzed in terms of their enrichment in somatic/germline mutations, GO biological processes/pathways terms and known sets of genes considered to be important in relation to a given disease, as recorded in the Molecular Signature Database from GSEA. The protein-protein interaction (PPI) networks were analyzed to identify genes that are hubs of PPI networks. We used data recorded in The Cancer Genome Atlas for patients with acute myeloid leukemia to demonstrate our approach, and discuss our findings in the context of results in the literature.
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Affiliation(s)
| | | | - Nadia Chuzhanova
- School of Science and Technology, Nottingham Trent University, Clifton Lane, Nottingham NG11 8NS, UK; (D.J.B.); (J.J.C.)
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23
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Liu Y, Wu Z, Fu Z, Han Y, Wang J, Zhang Y, Liang B, Tao Y, Zhang Y, Shen C, Xu Y, Yin S, Chen B, Liu Y, Pan H, Liang Z, Wu K. A predictive model of immune infiltration and prognosis of head and neck squamous cell carcinoma based on cell adhesion-related genes: including molecular biological validation. Front Immunol 2023; 14:1190678. [PMID: 37691922 PMCID: PMC10484396 DOI: 10.3389/fimmu.2023.1190678] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 08/10/2023] [Indexed: 09/12/2023] Open
Abstract
Background Focal adhesion serves as a bridge between tumour cells and the extracellular matrix (ECM) and has multiple roles in tumour invasion, migration, and therapeutic resistance. However, studies on focal adhesion-related genes (FARGs) in head and neck squamous cell carcinoma (HNSCC) are limited. Methods Data on HNSCC samples were obtained from The Cancer Genome Atlas and GSE41613 datasets, and 199 FARGs were obtained from the Molecular Signatures database. The integrated datasets' dimensions were reduced by the use of cluster analysis, which was also used to classify patients with HNSCC into subclusters. A FARG signature model was developed and utilized to calculate each patient's risk score using least extreme shrinkage and selection operator regression analysis. The risk score was done to quantify the subgroups of all patients. We evaluated the model's value for prognostic prediction, immune infiltration status, and therapeutic response in HNSCC. Preliminary molecular and biological experiments were performed to verify these results. Results Two different HNSCC molecular subtypes were identified according to FARGs, and patients with C2 had a shorter overall survival (OS) than those with C1. We constructed an FARG signature comprising nine genes. We constructed a FARG signature consisting of nine genes. Patients with higher risk scores calculated from the FARG signature had a lower OS, and the FARG signature was considered an independent prognostic factor for HNSCC in univariate and multivariate analyses. FARGs are associated with immune cell invasion, gene mutation status, and chemosensitivity. Finally, we observed an abnormal overexpression of MAPK9 in HNSCC tissues, and MAPK9 knockdown greatly impeded the proliferation, migration, and invasion of HNSCC cells. Conclusion The FARG signature can provide reliable prognostic prediction for patients with HNSCC. Apart from that, the genes in this model were related to immune invasion, gene mutation status, and chemosensitivity, which may provide new ideas for targeted therapies for HNSCC.
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Affiliation(s)
- Yuchen Liu
- Department of Otolaryngology, Head and Neck Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
- Anhui Medical University, Hefei, Anhui, China
| | - Zhechen Wu
- Department of Otolaryngology, Head and Neck Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
- Anhui Medical University, Hefei, Anhui, China
| | - Ziyue Fu
- Anhui Medical University, Hefei, Anhui, China
| | - Yanxun Han
- Department of Otolaryngology, Head and Neck Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
- Anhui Medical University, Hefei, Anhui, China
| | | | - Yanqiang Zhang
- Department of Otolaryngology, Head and Neck Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
- Anhui Medical University, Hefei, Anhui, China
| | - Bingyu Liang
- Department of Otolaryngology, Head and Neck Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
- Anhui Medical University, Hefei, Anhui, China
| | - Ye Tao
- Department of Otolaryngology, Head and Neck Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
- Anhui Medical University, Hefei, Anhui, China
| | - Yuchen Zhang
- Department of Otolaryngology, Head and Neck Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
- Anhui Medical University, Hefei, Anhui, China
| | | | - Yidan Xu
- Anhui Medical University, Hefei, Anhui, China
- Department of Oncology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Siyue Yin
- Anhui Medical University, Hefei, Anhui, China
- Department of Oncology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Bangjie Chen
- Anhui Medical University, Hefei, Anhui, China
- Department of Oncology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Yehai Liu
- Department of Otolaryngology, Head and Neck Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
- Anhui Medical University, Hefei, Anhui, China
| | - Haifeng Pan
- Anhui Medical University, Hefei, Anhui, China
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, China
| | - Zhang Liang
- Department of Otolaryngology, Head and Neck Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
- Anhui Medical University, Hefei, Anhui, China
| | - Kaile Wu
- Department of Otolaryngology, Head and Neck Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
- Anhui Medical University, Hefei, Anhui, China
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24
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Xi Y, Zhang Y, Zheng K, Zou J, Gui L, Zou X, Chen L, Hao J, Zhang Y. A chemotherapy response prediction model derived from tumor-promoting B and Tregs and proinflammatory macrophages in HGSOC. Front Oncol 2023; 13:1171582. [PMID: 37519793 PMCID: PMC10382026 DOI: 10.3389/fonc.2023.1171582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 06/27/2023] [Indexed: 08/01/2023] Open
Abstract
Background Most patients with high-grade serous ovarian cancer (HGSOC) experienced disease recurrence with cumulative chemoresistance, leading to treatment failure. However, few biomarkers are currently available in clinical practice that can accurately predict chemotherapy response. The tumor immune microenvironment is critical for cancer development, and its transcriptomic profile may be associated with treatment response and differential outcomes. The aim of this study was to develop a new predictive signature for chemotherapy in patients with HGSOC. Methods Two HGSOC single-cell RNA sequencing datasets from patients receiving chemotherapy were reinvestigated. The subtypes of endoplasmic reticulum stress-related XBP1+ B cells, invasive metastasis-related ACTB+ Tregs, and proinflammatory-related macrophage subtypes with good predictive power and associated with chemotherapy response were identified. These results were verified in an independent HGSOC bulk RNA-seq dataset for chemotherapy. Further validation in clinical cohorts used quantitative real-time PCR (qRT-PCR). Results By combining cluster-specific genes for the aforementioned cell subtypes, we constructed a chemotherapy response prediction model containing 43 signature genes that achieved an area under the receiver operator curve (AUC) of 0.97 (p = 2.1e-07) for the GSE156699 cohort (88 samples). A huge improvement was achieved compared to existing prediction models with a maximum AUC of 0.74. In addition, its predictive capability was validated in multiple independent bulk RNA-seq datasets. The qRT-PCR results demonstrate that the expression of the six genes has the highest diagnostic value, consistent with the trend observed in the analysis of public data. Conclusions The developed chemotherapy response prediction model can be used as a valuable clinical decision tool to guide chemotherapy in HGSOC patients.
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Affiliation(s)
- Yue Xi
- Department of Reproductive Medicine, Central Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, China
| | - Yingchun Zhang
- Department of Reproductive Medicine, Central Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, China
| | - Kun Zheng
- Department of Urology, Shanghai Sixth People’s Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jiawei Zou
- Institute of Clinical Science, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Lv Gui
- Department of Pathology, Jinshan Hospital, Fudan University, Shanghai, China
| | - Xin Zou
- Jinshan Hospital Center for Tumor Diagnosis & Therapy, Jinshan Hospital, Fudan University, Shanghai, China
| | - Liang Chen
- Department of Gynecological Oncology, Shandong Cancer Hospital Affiliated to Shandong University, Shandong Academy of Medical Sciences, Jinan, China
| | - Jie Hao
- Institute of Clinical Science, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yiming Zhang
- Department of Reproductive Medicine, Central Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, China
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25
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Banaee M, Sagvand S, Sureda A, Amini M, Haghi BN, Sopjani M, Faggio C. Evaluation of single and combined effects of mancozeb and metalaxyl on the transcriptional and biochemical response of zebrafish (Danio rerio). Comp Biochem Physiol C Toxicol Pharmacol 2023; 268:109597. [PMID: 36889533 DOI: 10.1016/j.cbpc.2023.109597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 02/23/2023] [Accepted: 03/01/2023] [Indexed: 03/08/2023]
Abstract
Mancozeb and metalaxyl are fungicidal agents frequently used in combination to control fungi in crops that may affect non-target organisms when entering ecosystems. This study aims to evaluate the environmental effects of Mancozeb (MAN) and Metalaxyl (MET), alone and in combination, on zebrafish (Danio rerio) as an experimental model. The oxidative stress biomarkers and the transcription of genes involved in detoxification in zebrafish (Danio rerio) were assessed after co-exposure to MAN (0, 5.5, and 11 μg L-1) and MET (0, 6.5, and 13 mg L-1) for 21 days. Exposure to MAN and MET induced a significant increase in the expression of genes related to detoxification mechanisms (Ces2, Cyp1a, and Mt2). Although Mt1 gene expression increased in fish exposed to 11 μg L-1 of MAN combined with 13 mg L-1 of MET, Mt1 expression was down-regulated significantly in other experimental groups (p < 0.05). The combined exposure to both fungicides showed synergistic effects in the expression levels that are manifested mainly at the highest concentration. Although a significant (p < 0.05) increase in alkaline phosphatase (ALP) and transaminases (AST and ALT), catalase activities, the total antioxidant capacity, and malondialdehyde (MDA) contents in the hepatocytes of fish exposed to MAN and MET alone and in combination was detected, lactate dehydrogenase (LDH), gamma-glutamyl transferase (GGT) activities, and hepatic glycogen content decreased significantly (p < 0.05). Overall, these results emphasize that combined exposure to MET and MAN can synergistically affect the transcription of genes involved in detoxification (except Mt1 and Mt2) and biochemical indicators in zebrafish.
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Affiliation(s)
- Mahdi Banaee
- Aquaculture Department, Faculty of Natural Resources and the Environment, Behbahan Khatam Alanbia University of Technology, Behbahan, Iran.
| | - Shiva Sagvand
- Aquaculture Department, Faculty of Natural Resources and the Environment, Behbahan Khatam Alanbia University of Technology, Behbahan, Iran
| | - Antoni Sureda
- Research Group on Community Nutrition and Oxidative Stress, Health Research Institute of the Balearic Islands (IdISBa), and CIBEROBN Fisiopatología de la Obesidad la Nutrición, University of Balearic Islands, 07122 Palma de Mallorca, Spain.
| | - Mohammad Amini
- Aquaculture Department, Faculty of Natural Resources and the Environment, Behbahan Khatam Alanbia University of Technology, Behbahan, Iran
| | - Behzad Nematdoost Haghi
- Aquaculture Department, Faculty of Natural Resources and the Environment, Behbahan Khatam Alanbia University of Technology, Behbahan, Iran
| | - Mentor Sopjani
- Faculty of Medicine of the University of Prishtina, Prishtina, Kosovo.
| | - Caterina Faggio
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Messina, Italy.
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26
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Gu W, Wang Y, Xu R, Li J, Jin J, Zhao J, Chen Y, Lu Y, Zhang G. Experimental assessment of robust reference genes for qRT-PCR in lung cancer studies. Front Oncol 2023; 13:1178629. [PMID: 37274277 PMCID: PMC10233025 DOI: 10.3389/fonc.2023.1178629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 05/05/2023] [Indexed: 06/06/2023] Open
Abstract
Stable internal reference genes are crucial for quantitative real-time PCR (qRT-PCR) analyses in lung cancer studies. Widely used reference genes are mostly chosen by intuition or from pan-cancer transcriptome data and lack experimental validation by qRT-PCR in the context of lung cancer. This study evaluated the stability of candidate reference genes in lung cancer cell lines under normal homeostasis, hypoxia, and serum deprivation to screen for robust reference genes for qRT-PCR in lung cancer studies. The stability of reference gene combinations was also assessed. We found that most of the stably expressed genes from pan-cancer transcriptome analyses were not sufficiently stable under some of the tested conditions. CIAO1, CNOT4, and SNW1 were found to be the most stable reference genes under various conditions. Greater stability was achieved by combining more reference genes. We further used the hypoxia biomarker hypoxia-inducible factor (HIF)-2α to demonstrate that choosing inappropriate reference genes can lead to incorrect qRT-PCR results. We also found that the stable reference genes were irrelevant to malignancy, which may explain their stability under various conditions that cancer cells often encounter. This study provides a list of validated and stable qRT-PCR reference genes and reference gene combinations for lung cancer that may standardize qRT-PCR experiments in future lung cancer studies.
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Affiliation(s)
- Wei Gu
- Department of Pathology, First Affiliated Hospital of Jinan University, Jinan University, Guangzhou, China
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes and MOE Key Laboratory of Tumor Molecular Biology, Institute of Life and Health Engineering, Jinan University, Guangzhou, China
| | - Yubin Wang
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes and MOE Key Laboratory of Tumor Molecular Biology, Institute of Life and Health Engineering, Jinan University, Guangzhou, China
| | - Ran Xu
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes and MOE Key Laboratory of Tumor Molecular Biology, Institute of Life and Health Engineering, Jinan University, Guangzhou, China
| | - Jiamin Li
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes and MOE Key Laboratory of Tumor Molecular Biology, Institute of Life and Health Engineering, Jinan University, Guangzhou, China
| | - Jingjie Jin
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes and MOE Key Laboratory of Tumor Molecular Biology, Institute of Life and Health Engineering, Jinan University, Guangzhou, China
| | - Jing Zhao
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes and MOE Key Laboratory of Tumor Molecular Biology, Institute of Life and Health Engineering, Jinan University, Guangzhou, China
| | - Yang Chen
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes and MOE Key Laboratory of Tumor Molecular Biology, Institute of Life and Health Engineering, Jinan University, Guangzhou, China
| | - Yuanzhi Lu
- Department of Pathology, First Affiliated Hospital of Jinan University, Jinan University, Guangzhou, China
| | - Gong Zhang
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes and MOE Key Laboratory of Tumor Molecular Biology, Institute of Life and Health Engineering, Jinan University, Guangzhou, China
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27
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Jeruzalska E, Mazur AJ. The Role of non-muscle actin paralogs in cell cycle progression and proliferation. Eur J Cell Biol 2023; 102:151315. [PMID: 37099935 DOI: 10.1016/j.ejcb.2023.151315] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 04/14/2023] [Accepted: 04/17/2023] [Indexed: 04/28/2023] Open
Abstract
Uncontrolled cell proliferation leads to several pathologies, including cancer. Thus, this process must be tightly regulated. The cell cycle accounts for cell proliferation, and its progression is coordinated with changes in cell shape, for which cytoskeleton reorganization is responsible. Rearrangement of the cytoskeleton allows for its participation in the precise division of genetic material and cytokinesis. One of the main cytoskeletal components is filamentous actin-based structures. Mammalian cells have at least six actin paralogs, four of which are muscle-specific, while two, named β- and γ-actin, are abundantly present in all types of cells. This review summarizes the findings that establish the role of non-muscle actin paralogs in regulating cell cycle progression and proliferation. We discuss studies showing that the level of a given non-muscle actin paralog in a cell influences the cell's ability to progress through the cell cycle and, thus, proliferation. Moreover, we elaborate on the non-muscle actins' role in regulating gene transcription, interactions of actin paralogs with proteins involved in controlling cell proliferation, and the contribution of non-muscle actins to different structures in a dividing cell. The data cited in this review show that non-muscle actins regulate the cell cycle and proliferation through varying mechanisms. We point to the need for further studies addressing these mechanisms.
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Affiliation(s)
- Estera Jeruzalska
- Department of Cell Pathology, Faculty of Biotechnology, University of Wroclaw, Poland
| | - Antonina J Mazur
- Department of Cell Pathology, Faculty of Biotechnology, University of Wroclaw, Poland.
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28
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Sun R, Yang Y, Lü W, Yang Y, Li Y, Liu Z, Diao D, Wang Y, Chang S, Lu M, Jiang Q, Dai B, Ma X, Zhao C, Lü M, Zhang J, Ding C, Li N, Zhang J, Xiao Z, Zhou D, Huang C. Single-cell transcriptomic analysis of normal and pathological tissues from the same patient uncovers colon cancer progression. Cell Biosci 2023; 13:62. [PMID: 36944972 PMCID: PMC10031920 DOI: 10.1186/s13578-023-01002-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 03/01/2023] [Indexed: 03/23/2023] Open
Abstract
The aim of the present study was to elucidate the evolutionary trajectory of colon cells from normal colon mucosa, to adenoma, then to carcinoma in the same microenvironment. Normal colon, adenoma and carcinoma tissues from the same patient were analyzed by single-cell sequencing, which perfectly simulated the process of time-dependent colon cancer due to the same microenvironment. A total of 22 cell types were identified. Results suggest the presence of dominant clones of same cells including C2 goblet cell, epithelial cell subtype 1 (Epi1), enterocyte cell subset 0 (Entero0), and Entero5 in carcinoma. Epi1 and Entero0 were Co-enriched in antibacterial and IL-17 signaling, Entero5 was enriched in immune response and mucin-type O-glycan biosynthesis. We discovered new colon cancer related genes including AC007952.4, NEK8, CHRM3, ANO7, B3GNT6, NEURL1, ODC1 and KCNMA1. The function of TBC1D4, LTB, C2CD4A, AND GBP4/5 in T cells needs to be clarified. We used colon samples from the same person, which provide new information for colon cancer therapy.
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Affiliation(s)
- Ruifang Sun
- Department of Oncology Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, 277 Yanta West Road, Xi'an, Shaanxi, People's Republic of China
- Department of Pathology, School of Basic Medical Sciences, Health Science Center, Xi'an Jiaotong University, 76 Yanta West Road, Xi'an, Shaanxi, People's Republic of China
| | - Yang Yang
- School of Public Health, Shaanxi University of Chinese Medicine, Middle Section of Century Avenue, Xianyang, Shaanxi, People's Republic of China.
| | - Weidong Lü
- Department of Thoracic Surgery, Shaanxi Provincial Tumor Hospital, Xi'an Jiaotong University, 309 Yanta West Road, Xi'an, Shaanxi, People's Republic of China
| | - Yanqi Yang
- Department of Pathology, School of Basic Medical Sciences, Health Science Center, Xi'an Jiaotong University, 76 Yanta West Road, Xi'an, Shaanxi, People's Republic of China
| | - Yulong Li
- Department of Gastroenterology, Shaanxi Provincial People's Hospital, 256 Youyi West Road, Xi'an, Shaanxi, People's Republic of China
| | - Zhigang Liu
- Department of Thoracic Surgery, Shaanxi Provincial Tumor Hospital, Xi'an Jiaotong University, 309 Yanta West Road, Xi'an, Shaanxi, People's Republic of China
| | - Dongmei Diao
- Department of Oncology Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, 277 Yanta West Road, Xi'an, Shaanxi, People's Republic of China
| | - Yang Wang
- Department of Oncology Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, 277 Yanta West Road, Xi'an, Shaanxi, People's Republic of China
| | - Su'e Chang
- Department of Orthopedics, The Second Affiliated Hospital of Xi'an Jiaotong University, 157 Xiwu Road, Xi'an, Shaanxi, People's Republic of China
| | - Mengnan Lu
- Department of Pediatrics, The Second Affiliated Hospital of Xi'an Jiaotong University, 157 Xiwu Road, Xi'an, Shaanxi, People's Republic of China
| | - Qiuyu Jiang
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Health Science Center, Xi'an Jiaotong University, 76 Yanta West Road, Xi'an, Shaanxi, People's Republic of China
| | - Bingling Dai
- School of Pharmacy, Health Science Center, Xi'an Jiaotong University, 76 Yanta West Road, Xi'an, Shaanxi, People's Republic of China
| | - Xiaobin Ma
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, 157 Xiwu Road, Xi'an, Shaanxi, People's Republic of China
| | - Chang'an Zhao
- Department of Pathology, School of Basic Medical Sciences, Health Science Center, Xi'an Jiaotong University, 76 Yanta West Road, Xi'an, Shaanxi, People's Republic of China
| | - Moqi Lü
- Department of Pathology, School of Basic Medical Sciences, Health Science Center, Xi'an Jiaotong University, 76 Yanta West Road, Xi'an, Shaanxi, People's Republic of China
| | - Juan Zhang
- Department of Pathology, Shaanxi Provincial Tumor Hospital, Xi'an Jiaotong University, 309 Yanta West Road, Xi'an, Shaanxi, People's Republic of China
| | - Caixia Ding
- Department of Pathology, Shaanxi Provincial Tumor Hospital, Xi'an Jiaotong University, 309 Yanta West Road, Xi'an, Shaanxi, People's Republic of China
| | - Na Li
- School of Pharmacy, Xinxiang Medical University, 601 Jinsui Avenue, Xinxiang, Henan, People's Republic of China
| | - Jian Zhang
- Department of Pathology, School of Basic Medical Sciences, Health Science Center, Xi'an Jiaotong University, 76 Yanta West Road, Xi'an, Shaanxi, People's Republic of China
| | - Zhengtao Xiao
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Health Science Center, Xi'an Jiaotong University, 76 Yanta West Road, Xi'an, Shaanxi, People's Republic of China.
| | - Dangxia Zhou
- Department of Pathology, School of Basic Medical Sciences, Health Science Center, Xi'an Jiaotong University, 76 Yanta West Road, Xi'an, Shaanxi, People's Republic of China.
| | - Chen Huang
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Health Science Center, Xi'an Jiaotong University, 76 Yanta West Road, Xi'an, Shaanxi, People's Republic of China.
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Li J, Dai F, Kou X, Wu B, Xu J, He S. β-Actin: An Emerging Biomarker in Ischemic Stroke. Cell Mol Neurobiol 2023; 43:683-696. [PMID: 35556192 DOI: 10.1007/s10571-022-01225-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 04/10/2022] [Indexed: 11/03/2022]
Abstract
At present, the diagnosis of ischemic stroke mainly depends on neuroimaging technology, but it still has many limitations. Therefore, it is very important to find new biomarkers of ischemic stroke. Recently, β-actin has attracted extensive attention as a biomarker of a variety of cancers. Although several recent studies have been investigating its role in ischemic stroke and other cerebrovascular diseases, the understanding of this emerging biomarker in neurology is still limited. We examined human and preclinical studies to gain a comprehensive understanding of the literature on the subject. Most relevant literatures focus on preclinical research, and pay more attention to the role of β-actin in the process of cerebral ischemia, but some recent literatures reported that in human studies, serum β-actin increased significantly in the early stage of acute cerebral ischemia. This review will investigate the basic biology of β-actin, pay attention to the potential role of serum β-actin as an early diagnostic blood biomarker of ischemic stroke, and explore its potential mechanism in ischemic stroke and new strategies for stroke treatment in the future.
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Affiliation(s)
- Jiaqian Li
- Department of Neurology, School of Medicine, Zhoushan Hospital, Zhejiang University, Zhoushan, 316000, Zhejiang Province, China
| | - Fangyu Dai
- Department of Neurology, School of Medicine, Zhoushan Hospital, Zhejiang University, Zhoushan, 316000, Zhejiang Province, China
| | - Xuelian Kou
- Department of Neurology, School of Medicine, Zhoushan Hospital, Zhejiang University, Zhoushan, 316000, Zhejiang Province, China
| | - Bin Wu
- Department of Neurology, School of Medicine, Zhoushan Hospital, Zhejiang University, Zhoushan, 316000, Zhejiang Province, China
| | - Jie Xu
- Department of Neurology, School of Medicine, Zhoushan Hospital, Zhejiang University, Zhoushan, 316000, Zhejiang Province, China
| | - Songbin He
- Department of Neurology, School of Medicine, Zhoushan Hospital, Zhejiang University, Zhoushan, 316000, Zhejiang Province, China.
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30
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Meng L, Zhan Y, Wei M, Yang R, Wang J, Weng S, Chen L, Zheng S, Dong K, Dong R. Single-cell RNA sequencing of solid pseudopapillary neoplasms of the pancreas in children. Cancer Sci 2023; 114:1986-2000. [PMID: 36721980 PMCID: PMC10154873 DOI: 10.1111/cas.15744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 01/05/2023] [Accepted: 01/23/2023] [Indexed: 02/02/2023] Open
Abstract
Solid pseudopapillary neoplasm (SPN) of the pancreas is a rare pancreatic tumor in children. Its origin remains elusive, along with its pathogenesis. Heterogeneity within SPN has not been previously described. In addition, low malignant but recurrent cases have occasionally been reported. To comprehensively unravel these profiles, single-cell RNA sequencing was performed using surgical specimens. We identified the cell types and suggested the origin of pancreatic endocrine progenitors. The Wnt/β-catenin pathway may be involved in tumorigenesis, while the epithelial-to-mesenchymal transition may be responsible for SPN recurrence. Furthermore, NOV, DCN were nominated as primary and S100A10, MGP as recurrent SPN marker genes, respectively. Our results provide insight into the pathogenesis of SPN.
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Affiliation(s)
- Lingdu Meng
- Department of Pediatric Surgery, Children's Hospital of Fudan University, Shanghai Key Laboratory of Birth Defect, Shanghai, China
| | - Yong Zhan
- Department of Pediatric Surgery, Children's Hospital of Fudan University, Shanghai Key Laboratory of Birth Defect, Shanghai, China
| | - Meng Wei
- Department of Pediatric Surgery, Children's Hospital of Fudan University, Shanghai Key Laboratory of Birth Defect, Shanghai, China.,Department of Hematology, Shanghai Children's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ran Yang
- Department of Pediatric Surgery, Children's Hospital of Fudan University, Shanghai Key Laboratory of Birth Defect, Shanghai, China
| | - Junfeng Wang
- Department of Pediatric Surgery, Children's Hospital of Fudan University, Shanghai Key Laboratory of Birth Defect, Shanghai, China
| | - Shuting Weng
- Department of Pediatric Surgery, Children's Hospital of Fudan University, Shanghai Key Laboratory of Birth Defect, Shanghai, China
| | - Lian Chen
- Department of Pathology, Children's Hospital of Fudan University, Shanghai, China
| | - Shan Zheng
- Department of Pediatric Surgery, Children's Hospital of Fudan University, Shanghai Key Laboratory of Birth Defect, Shanghai, China
| | - Kuiran Dong
- Department of Pediatric Surgery, Children's Hospital of Fudan University, Shanghai Key Laboratory of Birth Defect, Shanghai, China
| | - Rui Dong
- Department of Pediatric Surgery, Children's Hospital of Fudan University, Shanghai Key Laboratory of Birth Defect, Shanghai, China
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31
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Chen Y, Zhang XF, Ou-Yang L. Inferring cancer common and specific gene networks via multi-layer joint graphical model. Comput Struct Biotechnol J 2023; 21:974-990. [PMID: 36733706 PMCID: PMC9873583 DOI: 10.1016/j.csbj.2023.01.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 01/08/2023] [Accepted: 01/14/2023] [Indexed: 01/19/2023] Open
Abstract
Cancer is a complex disease caused primarily by genetic variants. Reconstructing gene networks within tumors is essential for understanding the functional regulatory mechanisms of carcinogenesis. Advances in high-throughput sequencing technologies have provided tremendous opportunities for inferring gene networks via computational approaches. However, due to the heterogeneity of the same cancer type and the similarities between different cancer types, it remains a challenge to systematically investigate the commonalities and specificities between gene networks of different cancer types, which is a crucial step towards precision cancer diagnosis and treatment. In this study, we propose a new sparse regularized multi-layer decomposition graphical model to jointly estimate the gene networks of multiple cancer types. Our model can handle various types of gene expression data and decomposes each cancer-type-specific network into three components, i.e., globally shared, partially shared and cancer-type-unique components. By identifying the globally and partially shared gene network components, our model can explore the heterogeneous similarities between different cancer types, and our identified cancer-type-unique components can help to reveal the regulatory mechanisms unique to each cancer type. Extensive experiments on synthetic data illustrate the effectiveness of our model in joint estimation of multiple gene networks. We also apply our model to two real data sets to infer the gene networks of multiple cancer subtypes or cell lines. By analyzing our estimated globally shared, partially shared, and cancer-type-unique components, we identified a number of important genes associated with common and specific regulatory mechanisms across different cancer types.
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Affiliation(s)
- Yuanxiao Chen
- Guangdong Key Laboratory of Intelligent Information Processing, Shenzhen Key Laboratory of Media Security, and Guangdong Laboratory of Artificial Intelligence and Digital Economy(SZ), Shenzhen University, Shenzhen, China
| | - Xiao-Fei Zhang
- School of Mathematics and Statistics & Hubei Key Laboratory of Mathematical Sciences, Central China Normal University, Wuhan, China
| | - Le Ou-Yang
- Guangdong Key Laboratory of Intelligent Information Processing, Shenzhen Key Laboratory of Media Security, and Guangdong Laboratory of Artificial Intelligence and Digital Economy(SZ), Shenzhen University, Shenzhen, China,Corresponding author.
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32
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Long-Term Simulation of Microgravity Induces Changes in Gene Expression in Breast Cancer Cells. Int J Mol Sci 2023; 24:ijms24021181. [PMID: 36674696 PMCID: PMC9864731 DOI: 10.3390/ijms24021181] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 12/21/2022] [Accepted: 01/03/2023] [Indexed: 01/11/2023] Open
Abstract
Microgravity changes the gene expression pattern in various cell types. This study focuses on the breast cancer cell lines MCF-7 (less invasive) and MDA-MB-231 (triple-negative, highly invasive). The cells were cultured for 14 days under simulated microgravity (s-µg) conditions using a random positioning machine (RPM). We investigated cytoskeletal and extracellular matrix (ECM) factors as well as focal adhesion (FA) and the transmembrane proteins involved in different cellular signaling pathways (MAPK, PAM and VEGF). The mRNA expressions of 24 genes of interest (TUBB, ACTB, COL1A1, COL4A5, LAMA3, ITGB1, CD44, VEGF, FLK1, EGFR, SRC, FAK1, RAF1, AKT1, ERK1, MAPK14, MAP2K1, MTOR, RICTOR, VCL, PXN, CDKN1, CTNNA1 and CTNNB1) were determined by quantitative real-time PCR (qPCR) and studied using STRING interaction analysis. Histochemical staining was carried out to investigate the morphology of the adherent cells (ADs) and the multicellular spheroids (MCSs) after RPM exposure. To better understand this experimental model in the context of breast cancer patients, a weighted gene co-expression network analysis (WGCNA) was conducted to obtain the expression profiles of 35 breast cell lines from the HMS LINCS Database. The qPCR-verified genes were searched in the mammalian phenotype database and the human genome-wide association studies (GWAS) Catalog. The results demonstrated the positive association between the real metastatic microtumor environment and MCSs with respect to the extracellular matrix, cytoskeleton, morphology, different cellular signaling pathway key proteins and several other components. In summary, the microgravity-engineered three-dimensional MCS model can be utilized to study breast cancer cell behavior and to assess the therapeutic efficacies of drugs against breast cancer in the future.
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Xu J, Yang M, Shao AZ, Pan HW, Fan YX, Chen KP. Identification and Validation of Common Reference Genes for Normalization of Esophageal Squamous Cell Carcinoma Gene Expression Profiles. BIOMED RESEARCH INTERNATIONAL 2022; 2022:9125242. [PMID: 36467891 PMCID: PMC9711964 DOI: 10.1155/2022/9125242] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 09/29/2022] [Accepted: 09/30/2022] [Indexed: 09/04/2024]
Abstract
Esophageal squamous cell carcinoma (ESCC) is one of the subtypes of esophageal cancer with Chinese characteristics, and its five-year survival rate is less than 20%. Early diagnosis is beneficial to improving the survival rate of ESCC significantly. Quantitative Real-Time Polymerase Chain Reaction is a high-throughput technique that can quantify tumor-related genes for early diagnosis. Its accuracy largely depends on the stability of the reference gene. There is no systematic scientific basis to demonstrate which reference gene expression is stable in ESCC and no consensus on the selection of internal reference. Therefore, this research used four software programs (The comparative delta-Ct method, GeNorm, NormFinder, and BestKeeper) to evaluate the expression stability of eight candidate reference genes commonly used in other tumor tissues and generated a comprehensive analysis by RefFinder. Randomly selected transcriptome sequencing analysis confirmed the SPP1 gene is closely related to ESCC. It was found that the expression trend of SPP1 obtained by RPS18 and PPIA as internal reference genes were the same as that of sequencing. The results show that RPS18 and PPIA are stable reference genes, and PPIA + RPS18 are a suitable reference gene combination. This is a reference gene report that combines transcriptome sequencing analysis and only focuses on ESCC, which makes the quantification more precise, systematic, and standardized, and promotes gene regulation research and the early diagnosis of ESCC in the future.
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Affiliation(s)
- Jia Xu
- School of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Ming Yang
- Department of General Surgery, Fifth People's Hospital of Huaian City, Huaian, China
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, China
| | - Ai-zhong Shao
- Department of Cardiothorac Surgery, Affiliated People's Hospital of Jiangsu University, Zhenjiang, China
| | - Hui-wen Pan
- Department of Cardiothoracic Surgery, Affiliated People's Hospital of Jiangsu University, Zhenjiang, Jiangsu Province, China
| | - Yi-xuan Fan
- School of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Ke-ping Chen
- School of Life Sciences, Jiangsu University, Zhenjiang, China
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Ishimoto T, Mori H. Control of actin polymerization via reactive oxygen species generation using light or radiation. Front Cell Dev Biol 2022; 10:1014008. [PMID: 36211457 PMCID: PMC9538341 DOI: 10.3389/fcell.2022.1014008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 09/07/2022] [Indexed: 11/25/2022] Open
Abstract
Actin is one of the most prevalent proteins in cells, and its amino acid sequence is remarkably conserved from protozoa to humans. The polymerization-depolymerization cycle of actin immediately below the plasma membrane regulates cell function, motility, and morphology. It is known that actin and other actin-binding proteins are targets for reactive oxygen species (ROS), indicating that ROS affects cells through actin reorganization. Several researchers have attempted to control actin polymerization from outside the cell to mimic or inhibit actin reorganization. To modify the polymerization state of actin, ultraviolet, visible, and near-infrared light, ionizing radiation, and chromophore-assisted light inactivation have all been reported to induce ROS. Additionally, a combination of the fluorescent protein KillerRed and the luminescent protein luciferase can generate ROS on actin fibers and promote actin polymerization. These techniques are very useful tools for analyzing the relationship between ROS and cell function, movement, and morphology, and are also expected to be used in therapeutics. In this mini review, we offer an overview of the advancements in this field, with a particular focus on how to control intracellular actin polymerization using such optical approaches, and discuss future challenges.
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Affiliation(s)
- Tetsuya Ishimoto
- Department of Molecular Neuroscience, Faculty of Medicine, University of Toyama, Toyama, Japan
- Research Center for Idling Brain Science, University of Toyama, Toyama, Japan
- *Correspondence: Tetsuya Ishimoto,
| | - Hisashi Mori
- Department of Molecular Neuroscience, Faculty of Medicine, University of Toyama, Toyama, Japan
- Research Center for Idling Brain Science, University of Toyama, Toyama, Japan
- Research Center for Pre-Disease Science, University of Toyama, Toyama, Japan
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35
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Liu Q, Zhang P, Yuan X, Ya O, Li Q, Li J, Long Q. Investigate the stemness of adult adipose-derived stromal cells based on single-cell RNA-sequencing. Cell Biol Int 2022; 46:2118-2131. [PMID: 36150081 DOI: 10.1002/cbin.11898] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 08/15/2022] [Accepted: 08/20/2022] [Indexed: 11/06/2022]
Abstract
The cellular heterogeneity and genetic features of stemness of adipose-derived stromal cells (ADSCs) remain unclear. Using single-cell RNA sequencing (scRNA-seq), we investigated the genomic features of the stemness gene in ADSCs with genetic variability. We cultured the ADSCs isolated from the fat waste of a healthy adult volunteers undergoing cosmetic plastic surgery to the third generation, used the BD Rhapsody platform to perform scRNA-seq, then used Monocle2 to analyze the growth and development trajectory of ADSCs, Cellular Trajectory Reconstruction Analysis Using Gene Counts and Expression (CytoTRACE) to evaluate the stemness gene characteristics in ADSCs clusters, and Beam to analyze the expression change characteristics of the main stemness related genes of ADSCs. According to the scRNA-seq data of 5325 ADSCs, they could be classified into nine cell clusters. According to CytoTRACE analysis, Cluster 3 of ADSCs had the highest stemness, whereas Cluster 8 had the lowest stemness. Pseudotime analysis revealed that Cluster 3 of ADSCs was primarily dispersed in the middle part of the growth and development trajectory, whereas Cluster 8 was primarily distributed at the end. We summarized the stemness of Cluster 3 in ADSCs with high expression of TPM1 and CCND1 genes in the metaphase of growth and development is the strongest, whereas the stemness of Cluster 8 with high expression of FICD, CREBRF, SDF2L1, HERPUD1, and HYOU1 genes in the telophase of growth and development is the weakest, providing a theoretical basis for screening and improving the therapeutic effect of ADSCs in cell transplantation research.
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Affiliation(s)
- Qing Liu
- Department of Neurology, Kailuan General Hospital, Affiliated North China University of Science and Technology, Tangshan
| | - Pingshu Zhang
- Department of Neurology, Kailuan General Hospital, Affiliated North China University of Science and Technology, Tangshan
| | - Xiaodong Yuan
- Department of Neurology, Kailuan General Hospital, Affiliated North China University of Science and Technology, Tangshan
| | - Ou Ya
- Department of Neurology, Kailuan General Hospital, Affiliated North China University of Science and Technology, Tangshan
| | - Qi Li
- Hebei Provincial Key Laboratory of Neurobiological Function, Tangshan, China
| | - Jing Li
- Radiology Department, Tangshan Maternal and Child Health Hospital, Tangshan, China
| | - Qingxi Long
- Department of Neurology, Kailuan General Hospital, Affiliated North China University of Science and Technology, Tangshan
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36
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Szychowski KA, Skóra B, Pomianek T. Effect of the elastin-derived peptides (VGVAPG and VVGPGA) on breast (MCF-7) and lung (A549) cancer cell lines in vitro. Biomed Pharmacother 2022; 151:113149. [PMID: 35598370 DOI: 10.1016/j.biopha.2022.113149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 05/11/2022] [Accepted: 05/15/2022] [Indexed: 11/29/2022] Open
Abstract
Tissues are subjected to dynamic communication between cells and the extracellular matrix (ECM), resulting in ECM remodeling. One of the ECM components is elastin, which releases elastin-derived peptides (EDPs) during the aging process. Therefore, the aim of the present study was to evaluate the impact of the VGVAPG hexapeptide and elastin-like peptide VVGPGA (control) on certain metabolism parameters in human breast adenocarcinoma (MCF-7) and human lung carcinoma (A549) cell lines. The results did not show a significant effect of the peptides on metabolic activity and caspase-3 activity. However, more specific analysis revealed that VGVAPG and VVGPGA were able to increase KI67 protein expression in both tested cell lines after 24-h treatment. Moreover, the same correlation was observed at the KI67 gene level. VGVAPG also increased the P53, ATM and SHH gene expression in the A549 cells up to 19.08%, 20.74%, and 28.77%, respectively. Interestingly, the VGVAPG peptide exerted an effect on the expression of antioxidant enzymes SOD2 and CAT in the A549 and MCF-7 cells, especially after the 24-h treatment. Lastly, both peptides influenced the CAV1 and CLTC1 expression. Our results show that the tested EDPs have an effect on both A549 and MCF-7 cells at the cellular level. This may be correlated with the multidrug-resistance (MDR) phenotype in these cancer cells, which is an emerging problem in the current anticancer treatment. However, more research is needed in this field.
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Affiliation(s)
- Konrad A Szychowski
- Department of Biotechnology and Cell Biology, Medical College, University of Information Technology and Management in Rzeszow, Sucharskiego 2, 35-225 Rzeszow, Poland.
| | - Bartosz Skóra
- Department of Biotechnology and Cell Biology, Medical College, University of Information Technology and Management in Rzeszow, Sucharskiego 2, 35-225 Rzeszow, Poland
| | - Tadeusz Pomianek
- Department of Management, Management College, University of Information Technology and Management in Rzeszow, Sucharskiego 2, Rzeszow 35-225, Poland
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37
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Feng S, Lou K, Zou X, Zou J, Zhang G. The Potential Role of Exosomal Proteins in Prostate Cancer. Front Oncol 2022; 12:873296. [PMID: 35747825 PMCID: PMC9209716 DOI: 10.3389/fonc.2022.873296] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 05/16/2022] [Indexed: 01/10/2023] Open
Abstract
Prostate cancer is the most prevalent malignant tumor in men across developed countries. Traditional diagnostic and therapeutic methods for this tumor have become increasingly difficult to adapt to today’s medical philosophy, thus compromising early detection, diagnosis, and treatment. Prospecting for new diagnostic markers and therapeutic targets has become a hot topic in today’s research. Notably, exosomes, small vesicles characterized by a phospholipid bilayer structure released by cells that is capable of delivering different types of cargo that target specific cells to regulate biological properties, have been extensively studied. Exosomes composition, coupled with their interactions with cells make them multifaceted regulators in cancer development. Numerous studies have described the role of prostate cancer-derived exosomal proteins in diagnosis and treatment of prostate cancer. However, so far, there is no relevant literature to systematically summarize its role in tumors, which brings obstacles to the later research of related proteins. In this review, we summarize exosomal proteins derived from prostate cancer from different sources and summarize their roles in tumor development and drug resistance.
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Affiliation(s)
- Shangzhi Feng
- The First Clinical College, Gannan Medical University, Ganzhou, Jiangxi, China
- Department of Urology, The First Affiliated hospital of Gannan Medical University, Ganzhou, China
| | - Kecheng Lou
- The First Clinical College, Gannan Medical University, Ganzhou, Jiangxi, China
- Department of Urology, The First Affiliated hospital of Gannan Medical University, Ganzhou, China
| | - Xiaofeng Zou
- Department of Urology, The First Affiliated hospital of Gannan Medical University, Ganzhou, China
- Institute of Urology, The First Affiliated Hospital of Ganna Medical University, Ganzhou, China
- Department of Jiangxi Engineering Technology Research Center of Calculi Prevention, Gannan Medical University, Ganzhou, Jiangxi, China
| | - Junrong Zou
- Department of Urology, The First Affiliated hospital of Gannan Medical University, Ganzhou, China
- Institute of Urology, The First Affiliated Hospital of Ganna Medical University, Ganzhou, China
- Department of Jiangxi Engineering Technology Research Center of Calculi Prevention, Gannan Medical University, Ganzhou, Jiangxi, China
- *Correspondence: Junrong Zou, ; Guoxi Zhang,
| | - Guoxi Zhang
- Department of Urology, The First Affiliated hospital of Gannan Medical University, Ganzhou, China
- Institute of Urology, The First Affiliated Hospital of Ganna Medical University, Ganzhou, China
- Department of Jiangxi Engineering Technology Research Center of Calculi Prevention, Gannan Medical University, Ganzhou, Jiangxi, China
- *Correspondence: Junrong Zou, ; Guoxi Zhang,
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38
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Malhan D, Basti A, Relógio A. Transcriptome analysis of clock disrupted cancer cells reveals differential alternative splicing of cancer hallmarks genes. NPJ Syst Biol Appl 2022; 8:17. [PMID: 35552415 PMCID: PMC9098426 DOI: 10.1038/s41540-022-00225-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 04/04/2022] [Indexed: 12/13/2022] Open
Abstract
Emerging evidence points towards a regulatory role of the circadian clock in alternative splicing (AS). Whether alterations in core-clock components may contribute to differential AS events is largely unknown. To address this, we carried out a computational analysis on recently generated time-series RNA-seq datasets from three core-clock knockout (KO) genes (ARNTL, NR1D1, PER2) and WT of a colorectal cancer (CRC) cell line, and time-series RNA-seq datasets for additional CRC and Hodgkin’s lymphoma (HL) cells, murine WT, Arntl KO, and Nr1d1/2 KO, and murine SCN WT tissue. The deletion of individual core-clock genes resulted in the loss of circadian expression in crucial spliceosome components such as SF3A1 (in ARNTLKO), SNW1 (in NR1D1KO), and HNRNPC (in PER2KO), which led to a differential pattern of KO-specific AS events. All HCT116KO cells showed a rhythmicity loss of a crucial spliceosome gene U2AF1, which was also not rhythmic in higher progression stage CRC and HL cancer cells. AS analysis revealed an increase in alternative first exon events specific to PER2 and NR1D1 KO in HCT116 cells, and a KO-specific change in expression and rhythmicity pattern of AS transcripts related to cancer hallmarks genes including FGFR2 in HCT116_ARNTLKO, CD44 in HCT116_NR1D1KO, and MET in HCT116_PER2KO. KO-specific changes in rhythmic properties of known spliced variants of these genes (e.g. FGFR2 IIIb/FGFR2 IIIc) correlated with epithelial-mesenchymal-transition signalling. Altogether, our bioinformatic analysis highlights a role for the circadian clock in the regulation of AS, and reveals a potential impact of clock disruption in aberrant splicing in cancer hallmark genes.
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Affiliation(s)
- Deeksha Malhan
- Institute for Theoretical Biology (ITB), Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt - Universität zu Berlin, and Berlin Institute of Health, Berlin, 10117, Germany.,Molecular Cancer Research Center (MKFZ), Medical Department of Hematology, Oncology, and Tumor Immunology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin Humboldt - Universität zu Berlin, and Berlin Institute of Health, Berlin, 10117, Germany.,Institute for Systems Medicine, Faculty of Human Medicine, MSH Medical School Hamburg, Hamburg, 20457, Germany
| | - Alireza Basti
- Institute for Theoretical Biology (ITB), Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt - Universität zu Berlin, and Berlin Institute of Health, Berlin, 10117, Germany.,Molecular Cancer Research Center (MKFZ), Medical Department of Hematology, Oncology, and Tumor Immunology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin Humboldt - Universität zu Berlin, and Berlin Institute of Health, Berlin, 10117, Germany.,Institute for Systems Medicine, Faculty of Human Medicine, MSH Medical School Hamburg, Hamburg, 20457, Germany
| | - Angela Relógio
- Institute for Theoretical Biology (ITB), Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt - Universität zu Berlin, and Berlin Institute of Health, Berlin, 10117, Germany. .,Molecular Cancer Research Center (MKFZ), Medical Department of Hematology, Oncology, and Tumor Immunology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin Humboldt - Universität zu Berlin, and Berlin Institute of Health, Berlin, 10117, Germany. .,Institute for Systems Medicine, Faculty of Human Medicine, MSH Medical School Hamburg, Hamburg, 20457, Germany.
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Gu Y, Tang S, Wang Z, Cai L, Lian H, Shen Y, Zhou Y. A pan-cancer analysis of the prognostic and immunological role of β-actin (ACTB) in human cancers. Bioengineered 2021; 12:6166-6185. [PMID: 34486492 PMCID: PMC8806805 DOI: 10.1080/21655979.2021.1973220] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 08/18/2021] [Indexed: 02/08/2023] Open
Abstract
Beta-actin (ACTB), a highly conserved cytoskeleton structural protein, has been regarded as a common housekeep gene and used as a reference gene for years. However, accumulating evidence indicates that ACTB is abnormally expressed in multiple cancers and hence changes the cytoskeleton to affect the invasiveness and metastasis of tumors. This study aimed to investigate the function and clinical significance of ACTB in pan-cancer. The role of ACTB for prognosis and immune regulation across 33 tumors was explored based on the datasets of gene expression omnibus and the cancer genome atlas. Differential expression of ACTB was found between cancer and adjacent normal tissues, and significant associations was found between ACTB expression and prognosis of tumor patients. In most cancers, ACTB expression was associated with immune cells infiltration, immune checkpoints and other immune modulators. Relevance between ACTB and metastasis and invasion was identified in various types of cancers by CancerSEA. Moreover, focal adhesion and actin regulation-associated pathways were included in the functional mechanisms of ACTB. The expression of ACTB was verified by quantitative real-time polymerase chain reaction. Knockdown of ACTB inhibited head and neck squamous carcinoma cell migration and invasion by NF-κB and Wnt/β-catenin pathways. Our first pan-cancer study of ACTB offers insight into the prognostic and immunological roles of ACTB across different tumors, indicating ACTB may be a potential biomarker for poor prognosis and immune infiltration in cancers, and the role of ACTB as a reference gene in cancers was challenged.
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Affiliation(s)
- Yuxi Gu
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Shouyi Tang
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Zhen Wang
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Luyao Cai
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Haosen Lian
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Yingqiang Shen
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Yu Zhou
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, West China Hospital of Stomatology, Sichuan University, Chengdu, China
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40
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García-Pérez O, Melgar-Vilaplana L, Córdoba-Lanús E, Fernández-de-Misa R. Gene Expression Studies in Formalin-Fixed Paraffin-Embedded Samples of Cutaneous Cancer: The Need for Reference Genes. Curr Issues Mol Biol 2021; 43:2167-2176. [PMID: 34940125 PMCID: PMC8928935 DOI: 10.3390/cimb43030151] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 11/27/2021] [Accepted: 11/29/2021] [Indexed: 01/02/2023] Open
Abstract
Formalin-fixed paraffin-embedded (FFPE) tumour samples may provide crucial data regarding biomarkers for neoplasm progression. Analysis of gene expression is frequently used for this purpose. Therefore, mRNA expression needs to be normalized through comparison to reference genes. In this study, we establish which of the usually reported reference genes is the most reliable one in cutaneous malignant melanoma (MM) and cutaneous squamous cell carcinoma (CSCC). ACTB, TFRC, HPRT1 and TBP expression was quantified in 123 FFPE samples (74 MM and 49 CSCC biopsies) using qPCR. Expression stability was analysed by NormFinder and Bestkeeper softwares, and the direct comparison method between means and SD. The in-silico analysis with BestKeeper indicated that HPRT1 was more stable than ACTB and TFRC in MM (1.85 vs. 2.15) and CSCC tissues (2.09 vs. 2.33). The best option to NormFinder was ACTB gene (0.56) in MM and TFRC (0.26) in CSCC. The direct comparison method showed lower SD means of ACTB expression in MM (1.17) and TFRC expression in CSCC samples (1.00). When analysing the combination of two reference genes for improving stability, NormFinder indicated HPRT1 and ACTB to be the best for MM samples, and HPRT1 and TFRC genes for CSCC. In conclusion, HPRT1 and ACTB genes in combination are the most appropriate choice for normalization in gene expression studies in MM FFPE tissue, while the combination of HPRT1 and TFRC genes are the best option in analysing CSCC FFPE samples. These may be used consistently in forthcoming studies on gene expression in both tumours.
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Affiliation(s)
- Omar García-Pérez
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, Ctra. Gral. del Rosario, 145, 38010 Santa Cruz de Tenerife, Spain;
- Universidad de La Laguna, Calle Padre Herrera, s/n, 38200 San Cristóbal de La Laguna, Spain
- Instituto Universitario de Enfermedades Tropicales y Salud Pública de Canarias (IUETSPC), 38296 San Cristóbal de La Laguna, Spain
| | - Leticia Melgar-Vilaplana
- Pathology Department, Hospital Universitario Nuestra Señora de Candelaria, Ctra. Gral. del Rosario, 145, 38010 Santa Cruz de Tenerife, Spain;
| | - Elizabeth Córdoba-Lanús
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, Ctra. Gral. del Rosario, 145, 38010 Santa Cruz de Tenerife, Spain;
- Universidad de La Laguna, Calle Padre Herrera, s/n, 38200 San Cristóbal de La Laguna, Spain
- Instituto Universitario de Enfermedades Tropicales y Salud Pública de Canarias (IUETSPC), 38296 San Cristóbal de La Laguna, Spain
- Correspondence: (E.C.-L.); (R.F.-d.-M.)
| | - Ricardo Fernández-de-Misa
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, Ctra. Gral. del Rosario, 145, 38010 Santa Cruz de Tenerife, Spain;
- Universidad de La Laguna, Calle Padre Herrera, s/n, 38200 San Cristóbal de La Laguna, Spain
- Dermatology Department, Hospital Universitario Nuestra Señora de Candelaria, Ctra. Gral. del Rosario, 145, 38010 Santa Cruz de Tenerife, Spain
- Correspondence: (E.C.-L.); (R.F.-d.-M.)
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Gonda A, Zhao N, Shah JV, Siebert JN, Gunda S, Inan B, Kwon M, Libutti SK, Moghe PV, Francis NL, Ganapathy V. Extracellular Vesicle Molecular Signatures Characterize Metastatic Dynamicity in Ovarian Cancer. Front Oncol 2021; 11:718408. [PMID: 34868914 PMCID: PMC8637407 DOI: 10.3389/fonc.2021.718408] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 10/29/2021] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND Late-stage diagnosis of ovarian cancer, a disease that originates in the ovaries and spreads to the peritoneal cavity, lowers 5-year survival rate from 90% to 30%. Early screening tools that can: i) detect with high specificity and sensitivity before conventional tools such as transvaginal ultrasound and CA-125, ii) use non-invasive sampling methods and iii) longitudinally significantly increase survival rates in ovarian cancer are needed. Studies that employ blood-based screening tools using circulating tumor-cells, -DNA, and most recently tumor-derived small extracellular vesicles (sEVs) have shown promise in non-invasive detection of cancer before standard of care. Our findings in this study show the promise of a sEV-derived signature as a non-invasive longitudinal screening tool in ovarian cancer. METHODS Human serum samples as well as plasma and ascites from a mouse model of ovarian cancer were collected at various disease stages. Small extracellular vesicles (sEVs) were extracted using a commercially available kit. RNA was isolated from lysed sEVs, and quantitative RT-PCR was performed to identify specific metastatic gene expression. CONCLUSION This paper highlights the potential of sEVs in monitoring ovarian cancer progression and metastatic development. We identified a 7-gene panel in sEVs derived from plasma, serum, and ascites that overlapped with an established metastatic ovarian carcinoma signature. We found the 7-gene panel to be differentially expressed with tumor development and metastatic spread in a mouse model of ovarian cancer. The most notable finding was a significant change in the ascites-derived sEV gene signature that overlapped with that of the plasma-derived sEV signature at varying stages of disease progression. While there were quantifiable changes in genes from the 7-gene panel in serum-derived sEVs from ovarian cancer patients, we were unable to establish a definitive signature due to low sample number. Taken together our findings show that differential expression of metastatic genes derived from circulating sEVs present a minimally invasive screening tool for ovarian cancer detection and longitudinal monitoring of molecular changes associated with progression and metastatic spread.
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Affiliation(s)
- Amber Gonda
- Department of Biomedical Engineering, Rutgers University, Piscataway, NJ, United States
| | - Nanxia Zhao
- Department of Chemical and Biochemical Engineering, Rutgers University, Piscataway, NJ, United States
| | - Jay V. Shah
- Department of Biomedical Engineering, Rutgers University, Piscataway, NJ, United States
| | - Jake N. Siebert
- Department of Biomedical Engineering, Rutgers University, Piscataway, NJ, United States
- Rutgers-Robert Wood Johnson Medical School, Rutgers University, New Brunswick, NJ, United States
| | - Srujanesh Gunda
- School of Environmental and Biological Sciences, Rutgers University, New Brunswick, NJ, United States
| | - Berk Inan
- School of Environmental and Biological Sciences, Rutgers University, New Brunswick, NJ, United States
| | - Mijung Kwon
- Rutgers Cancer Institute of New Jersey, Rutgers University, New Brunswick, NJ, United States
| | - Steven K. Libutti
- Rutgers Cancer Institute of New Jersey, Rutgers University, New Brunswick, NJ, United States
| | - Prabhas V. Moghe
- Department of Biomedical Engineering, Rutgers University, Piscataway, NJ, United States
- Department of Chemical and Biochemical Engineering, Rutgers University, Piscataway, NJ, United States
| | - Nicola L. Francis
- Department of Biomedical Engineering, Rutgers University, Piscataway, NJ, United States
| | - Vidya Ganapathy
- Department of Biomedical Engineering, Rutgers University, Piscataway, NJ, United States
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Saha S, Soliman A, Rajasekaran S. A robust and stable gene selection algorithm based on graph theory and machine learning. Hum Genomics 2021; 15:66. [PMID: 34753514 PMCID: PMC8579680 DOI: 10.1186/s40246-021-00366-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 10/25/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Nowadays we are observing an explosion of gene expression data with phenotypes. It enables us to accurately identify genes responsible for certain medical condition as well as classify them for drug target. Like any other phenotype data in medical domain, gene expression data with phenotypes also suffer from being a very underdetermined system. In a very large set of features but a very small sample size domain (e.g. DNA microarray, RNA-seq data, GWAS data, etc.), it is often reported that several contrasting feature subsets may yield near equally optimal results. This phenomenon is known as instability. Considering these facts, we have developed a robust and stable supervised gene selection algorithm to select a set of robust and stable genes having a better prediction ability from the gene expression datasets with phenotypes. Stability and robustness is ensured by class and instance level perturbations, respectively. RESULTS We have performed rigorous experimental evaluations using 10 real gene expression microarray datasets with phenotypes. They reveal that our algorithm outperforms the state-of-the-art algorithms with respect to stability and classification accuracy. We have also performed biological enrichment analysis based on gene ontology-biological processes (GO-BP) terms, disease ontology (DO) terms, and biological pathways. CONCLUSIONS It is indisputable from the results of the performance evaluations that our proposed method is indeed an effective and efficient supervised gene selection algorithm.
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Affiliation(s)
- Subrata Saha
- Irving Medical Center, Columbia University, New York, NY, 10032, USA
| | - Ahmed Soliman
- Department of Computer Science and Engineering, University of Connecticut, Storrs, CT, 06269, USA
| | - Sanguthevar Rajasekaran
- Department of Computer Science and Engineering, University of Connecticut, Storrs, CT, 06269, USA.
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43
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Loch FN, Klein O, Beyer K, Klauschen F, Schineis C, Lauscher JC, Margonis GA, Degro CE, Rayya W, Kamphues C. Peptide Signatures for Prognostic Markers of Pancreatic Cancer by MALDI Mass Spectrometry Imaging. BIOLOGY 2021; 10:1033. [PMID: 34681132 PMCID: PMC8533220 DOI: 10.3390/biology10101033] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 10/07/2021] [Accepted: 10/08/2021] [Indexed: 12/23/2022]
Abstract
Despite the overall poor prognosis of pancreatic cancer there is heterogeneity in clinical courses of tumors not assessed by conventional risk stratification. This yields the need of additional markers for proper assessment of prognosis and multimodal clinical management. We provide a proof of concept study evaluating the feasibility of Matrix-assisted laser desorption/ionization (MALDI) mass spectrometry imaging (MSI) to identify specific peptide signatures linked to prognostic parameters of pancreatic cancer. On 18 patients with exocrine pancreatic cancer after tumor resection, MALDI imaging analysis was performed additional to histopathological assessment. Principal component analysis (PCA) was used to explore discrimination of peptide signatures of prognostic histopathological features and receiver operator characteristic (ROC) to identify which specific m/z values are the most discriminative between the prognostic subgroups of patients. Out of 557 aligned m/z values discriminate peptide signatures for the prognostic histopathological features lymphatic vessel invasion (pL, 16 m/z values, eight proteins), nodal metastasis (pN, two m/z values, one protein) and angioinvasion (pV, 4 m/z values, two proteins) were identified. These results yield proof of concept that MALDI-MSI of pancreatic cancer tissue is feasible to identify peptide signatures of prognostic relevance and can augment risk assessment.
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Affiliation(s)
- Florian N. Loch
- Department of Surgery, Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Hindenburgdamm 30, 12203 Berlin, Germany; (K.B.); (C.S.); (J.C.L.); (C.E.D.); (W.R.); (C.K.)
| | - Oliver Klein
- Berlin Institute of Health, Charité—Universitätsmedizin Berlin, Center for Regenerative Therapies BCRT, Charitéplatz 1, 10117 Berlin, Germany;
| | - Katharina Beyer
- Department of Surgery, Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Hindenburgdamm 30, 12203 Berlin, Germany; (K.B.); (C.S.); (J.C.L.); (C.E.D.); (W.R.); (C.K.)
| | - Frederick Klauschen
- Institute for Pathology, Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Charitéplatz 1, 10117 Berlin, Germany;
- Institute for Pathology, Ludwig-Maximilians-Universität München, 80337 München, Germany
| | - Christian Schineis
- Department of Surgery, Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Hindenburgdamm 30, 12203 Berlin, Germany; (K.B.); (C.S.); (J.C.L.); (C.E.D.); (W.R.); (C.K.)
| | - Johannes C. Lauscher
- Department of Surgery, Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Hindenburgdamm 30, 12203 Berlin, Germany; (K.B.); (C.S.); (J.C.L.); (C.E.D.); (W.R.); (C.K.)
| | - Georgios A. Margonis
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA;
| | - Claudius E. Degro
- Department of Surgery, Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Hindenburgdamm 30, 12203 Berlin, Germany; (K.B.); (C.S.); (J.C.L.); (C.E.D.); (W.R.); (C.K.)
| | - Wael Rayya
- Department of Surgery, Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Hindenburgdamm 30, 12203 Berlin, Germany; (K.B.); (C.S.); (J.C.L.); (C.E.D.); (W.R.); (C.K.)
| | - Carsten Kamphues
- Department of Surgery, Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Hindenburgdamm 30, 12203 Berlin, Germany; (K.B.); (C.S.); (J.C.L.); (C.E.D.); (W.R.); (C.K.)
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Ahn HR, Baek GO, Yoon MG, Son JA, You D, Yoon JH, Cho HJ, Kim SS, Cheong JY, Eun JW. HMBS is the most suitable reference gene for RT-qPCR in human HCC tissues and blood samples. Oncol Lett 2021; 22:791. [PMID: 34584568 PMCID: PMC8461756 DOI: 10.3892/ol.2021.13052] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 08/17/2021] [Indexed: 12/15/2022] Open
Abstract
Reverse transcription-quantitative (RT-q) PCR is the most feasible and useful technique for identifying and evaluating cancer biomarkers; however, the method requires suitable reference genes for gene expression analysis. The aim of the present study was to identify the most suitable reference gene for the normalization of relative gene expression in human hepatocellular carcinoma (HCC) tissue and blood samples. First, 14 candidate reference genes were selected through a systematic literature search. The expression levels of these genes (ACTB, B2M, GAPDH, GUSB, HMBS, HPRT1, PGK1, PPIA, RPLP0, RPL13A, SDHA, TBP, TFRC and YWHAZ) were evaluated using human multistage HCC transcriptome data (dataset GSE114564), which included normal liver (n=15), chronic hepatitis (n=20), liver cirrhosis (n=10), and early (n=18) and advanced HCC (n=45). From the 14 selected genes, five genes, whose expression levels were stable in all liver disease statuses (ACTB, GAPDH, HMBS, PPIA and RPLP0), were further assessed using RT-qPCR in 40 tissues (20 paired healthy tissues and 20 tissues from patients with HCC) and 40 blood samples (20 healthy controls and 20 samples from patients with HCC). BestKeeper statistical algorithms were used to identify the most stable reference genes, of which HMBS was found to be the most stable in both HCC tissues and blood samples. Therefore, the results of the present study suggest HMBS as a promising reference gene for the normalization of relative RT-qPCR techniques in HCC-related studies.
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Affiliation(s)
- Hye Ri Ahn
- Department of Gastroenterology, Ajou University School of Medicine, Suwon 16499, Republic of Korea.,Department of Biomedical Sciences, Ajou University Graduate School of Medicine, Suwon 16499, Republic of Korea
| | - Geum Ok Baek
- Department of Gastroenterology, Ajou University School of Medicine, Suwon 16499, Republic of Korea
| | - Moon Gyeong Yoon
- Department of Gastroenterology, Ajou University School of Medicine, Suwon 16499, Republic of Korea
| | - Ju A Son
- Department of Gastroenterology, Ajou University School of Medicine, Suwon 16499, Republic of Korea.,Department of Biomedical Sciences, Ajou University Graduate School of Medicine, Suwon 16499, Republic of Korea
| | - Donglim You
- Department of Gastroenterology, Ajou University School of Medicine, Suwon 16499, Republic of Korea.,Department of Biomedical Sciences, Ajou University Graduate School of Medicine, Suwon 16499, Republic of Korea
| | - Jung Hwan Yoon
- Department of Pathology, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea
| | - Hyo Jung Cho
- Department of Gastroenterology, Ajou University School of Medicine, Suwon 16499, Republic of Korea
| | - Soon Sun Kim
- Department of Gastroenterology, Ajou University School of Medicine, Suwon 16499, Republic of Korea
| | - Jae Yeon Cheong
- Department of Gastroenterology, Ajou University School of Medicine, Suwon 16499, Republic of Korea
| | - Jung Woo Eun
- Department of Gastroenterology, Ajou University School of Medicine, Suwon 16499, Republic of Korea
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Boustan A, Mosaffa F, Jahangiri R, Heidarian-Miri H, Dahmardeh-Ghalehno A, Jamialahmadi K. Role of SALL4 and Nodal in the prognosis and tamoxifen resistance of estrogen receptor-positive breast cancer. MOLECULAR BIOLOGY RESEARCH COMMUNICATIONS 2021; 10:109-119. [PMID: 34476264 PMCID: PMC8340312 DOI: 10.22099/mbrc.2021.39878.1597] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Despite the discovery of a number of different mechanisms underlying tamoxifen resistance, its molecular pathway is not completely clear. The upregulation of SALL4 and Nodal has been reported in breast cancer. Nevertheless, their role in tamoxifen resistance has not been investigated. In the present study, we compared Nodal and SALL4 expression in 72 tamoxifen sensitive (TAMS) and tamoxifen-resistant (TAMR) patients. Afterward, the correlation of expression data with clinicopathological features and survival of patients was studied. Results showed that both SALL4 and Nodal were significantly upregulated in TAMR compared to TAMS patients. Besides, there was a positive association between Nodal and SALL4 expression. Furthermore, we evaluated their correlation with the expression of Oct4, Nanog and Sox2 stemness markers. The results demonstrated that in most tissue samples there was a positive correlation between Nodal and SALL4 expression with these stemness markers. Besides, the overexpression of SALL4 and Nodal significantly correlated with the N stage. Moreover, the overexpression of SALL4 was associated with extracapsular invasion and lymphatic invasion. High level expressions of SALL4 and Nodal had a significant association with worse disease-free survival (DFS) rates. In addition, increased level of Nodal expression provides a superior predictor factor for DFS. The multivariate Cox regression analysis also revealed that for DFS, perineural invasion (PNI) was independently an unfavorable prognostic value. These findings suggest that the high expression of SALL4 and Nodal could contribute to tamoxifen resistance and worse survival rates in tamoxifen-treated ER+ breast cancer patients.
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Affiliation(s)
- Arad Boustan
- Department of Medical Biotechnology and Nanotechnology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Fatemeh Mosaffa
- Biotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran.,Department of Pharmaceutical Biotechnology, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Rosa Jahangiri
- Department of Medical Biotechnology and Nanotechnology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Hamid Heidarian-Miri
- Department of Epidemiology, School of Health, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Asefeh Dahmardeh-Ghalehno
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Khadijeh Jamialahmadi
- Biotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
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Bayat Z, Farhadi Z, Taherkhani A. Identification of potential biomarkers associated with poor prognosis in oral squamous cell carcinoma through integrated bioinformatics analysis: A pilot study. GENE REPORTS 2021. [DOI: 10.1016/j.genrep.2021.101243] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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47
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Cavalloni G, Peraldo-Neia C, Massa A, Bergamini C, Trentini A, De Rosa G, Daniele L, Ciccosanti F, Cervellati C, Leone F, Aglietta M. Proteomic analysis identifies deregulated metabolic and oxidative-associated proteins in Italian intrahepatic cholangiocarcinoma patients. BMC Cancer 2021; 21:865. [PMID: 34320944 PMCID: PMC8317365 DOI: 10.1186/s12885-021-08576-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 07/09/2021] [Indexed: 12/14/2022] Open
Abstract
Background Cholangiocarcinoma (CCA) is an aggressive disease with poor prognosis. A molecular classification based on mutational, methylation and transcriptomic features could allow identifying tailored therapies to improve CCA patient outcome. Proteomic remains partially unexplored; here, we analyzed the proteomic profile of five intrahepatic cholangiocarcinoma (ICC) derived from Italian patients undergone surgery and one normal bile duct cell line. Methods Proteome profile was investigated by using 2D electrophoresis followed by Mass Spectrometry (MS). To validate proteomic data, the expression of four overexpressed proteins (CAT, SOD, PRDX6, DBI/ACBP) was evaluated by immunohistochemistry in an independent cohort of formalin fixed, paraffin-embedded (FFPE) ICC tissues. We also compared proteomic data with those obtained by transcriptomic profile evaluated by microarray analysis of the same tissues. Results We identified 19 differentially expressed protein spots, which were further characterized by MS; 13 of them were up- and 6 were down-regulated in ICC. These proteins are mainly involved in redox processes (CAT, SODM, PRDX2, PRDX6), in metabolism (ACBP, ACY1, UCRI, FTCD, HCMS2), and cell structure and organization (TUB2, ACTB). CAT is overexpressed in 86% of patients, PRDX6 in 73%, SODM in 100%, and DBI/ACBP in 81% compared to normal adjacent tissues. A concordance of 50% between proteomic and transcriptomic data was observed. Conclusions This study pointed out that the impairment of the metabolic and antioxidant systems, with a subsequent accumulation of free radicals, might be a key step in CCA development and progression. Supplementary Information The online version contains supplementary material available at 10.1186/s12885-021-08576-z.
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Affiliation(s)
- Giuliana Cavalloni
- Division of Medical Oncology, Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Torino, Italy.
| | | | - Annamaria Massa
- Division of Medical Oncology, Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Torino, Italy
| | - Carlo Bergamini
- Department of Chemistry and Pharmaceutical Sciences, University of Ferrara, Ferrara, Italy
| | - Alessandro Trentini
- Department of Chemistry and Pharmaceutical Sciences, University of Ferrara, Ferrara, Italy
| | | | | | - Fabiola Ciccosanti
- Department of Epidemiology, Preclinical Research, and Advanced Diagnostics, National Institute for Infectious Diseases, IRCCS 'Lazzaro Spallanzani', Rome, Italy
| | - Carlo Cervellati
- Department of Morphology, Surgery & Experimental Medicine, University of Ferrara, Ferrara, Italy
| | - Francesco Leone
- Department of Oncology, ASL BI, Ospedale degli Infermi di Biella, Ponderano, BI, Italy
| | - Massimo Aglietta
- Division of Medical Oncology, Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Torino, Italy.,Department of Oncology, University of Turin, Torino, Italy
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48
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Transcriptomic analysis of castration, chemo-resistant and metastatic prostate cancer elucidates complex genetic crosstalk leading to disease progression. Funct Integr Genomics 2021; 21:451-472. [PMID: 34184132 DOI: 10.1007/s10142-021-00789-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 06/05/2020] [Accepted: 05/06/2021] [Indexed: 12/22/2022]
Abstract
Prostate adenocarcinoma, with its rising numbers and high fatality rate, is a daunting healthcare challenge to clinicians and researchers alike. The mainstay of our meta-analysis was to decipher differentially expressed genes (DEGs), their corresponding transcription factors (TFs), miRNAs (microRNA) and interacting pathways underlying the progression of prostate cancer (PCa). We have chosen multiple datasets from primary, castration-resistant, chemo-resistant and metastatic prostate cancer stages for investigation. From our tissue-specific and disease-specific co-expression networks, fifteen hub genes such as ACTB, ACTN1, CDH1, CDKN1A, DDX21, ELF3, FLNA, FLNC, IKZF1, ILK, KRT13, KRT18, KRT19, SVIL and TRIM29 were identified and validated by molecular complex detection analysis as well as survival analysis. In our attempt to highlight hub gene-associated mutations and drug interactions, FLNC was found to be most commonly mutated and CDKN1A gene was found to have highest druggability. Moreover, from DAVID and gene set enrichment analysis, the focal adhesion and oestrogen signalling pathways were found enriched which indicates the involvement of hub genes in tumour invasiveness and metastasis. Finally by Enrichr tool and miRNet, we identified transcriptional factors SNAI2, TP63, CEBPB and KLF11 and microRNAs, namely hsa-mir-1-3p, hsa-mir-145-5p, hsa-mir-124-3p and hsa-mir-218-5p significantly controlling the hub gene expressions. In a nutshell, our report will help to gain a deeper insight into complex molecular intricacies and thereby unveil the probable biomarkers and therapeutic targets involved with PCa progression.
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Mahmood RI, Abbass AK, Razali N, Al-Saffar AZ, Al-Obaidi JR. Protein profile of MCF-7 breast cancer cell line treated with lectin delivered by CaCO 3NPs revealed changes in molecular chaperones, cytoskeleton, and membrane-associated proteins. Int J Biol Macromol 2021; 184:636-647. [PMID: 34174302 DOI: 10.1016/j.ijbiomac.2021.06.144] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 06/16/2021] [Accepted: 06/21/2021] [Indexed: 02/09/2023]
Abstract
The second most predominant cancer in the world and the first among women is breast cancer. We aimed to study the protein abundance profiles induced by lectin purified from the Agaricus bisporus mushroom (ABL) and conjugated with CaCO3NPs in the MCF-7 breast cancer cell line. Two-dimensional electrophoresis (2-DE) and orbitrap mass spectrometry techniques were used to reveal the protein abundance pattern induced by lectin. Flow cytometric analysis showed the accumulation of ABL-CaCO3NPs treated cells in the G1 phase than the positive control. Thirteen proteins were found different in their abundance in breast cancer cells after 24 h exposure to lectin conjugated with CaCO3NPs. Most of the identified proteins were showing a low abundance in ABL-CaCO3NPs treated cells in comparison to the positive and negative controls, including V-set and immunoglobulin domain, serum albumin, actin cytoplasmic 1, triosephosphate isomerase, tropomyosin alpha-4 chain, and endoplasmic reticulum chaperone BiP. Hornerin, tropomyosin alpha-1 chain, annexin A2, and protein disulfide-isomerase were up-regulated in comparison to the positive. Bioinformatic analyses revealed the regulation changes of these proteins mainly affected the pathways of 'Bcl-2-associated athanogene 2 signalling pathway', 'Unfolded protein response', 'Caveolar-mediated endocytosis signalling', 'Clathrin-mediated endocytosis signalling', 'Calcium signalling' and 'Sucrose degradation V', which are associated with breast cancer. We concluded that lectin altered the abundance in molecular chaperones/heat shock proteins, cytoskeletal, and metabolic proteins. Additionally, lectin induced a low abundance of MCF-7 cancer cell proteins in comparison to the positive and negative controls, including; V-set and immunoglobulin domain, serum albumin, actin cytoplasmic 1, triosephosphate isomerase, tropomyosin alpha-4 chain, and endoplasmic reticulum chaperone BiP.
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Affiliation(s)
- Rana I Mahmood
- Department of Biology, College of Science, Baghdad University, Baghdad, Iraq; Department of Biomedical Engineering, College of Engineering, Al-Nahrain University, Baghdad, Iraq
| | - Amal Kh Abbass
- Department of Biology, College of Science, Baghdad University, Baghdad, Iraq
| | - Nurhanani Razali
- Department of Hygienic Sciences, Kobe Pharmaceutical University, Motoyamakita-machi, Higashinada-ku, 658-8558, Kobe, Japan; Membranology Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Kunigami-gun, Okinawa, Japan, 904-0495
| | - Ali Z Al-Saffar
- Department of Molecular and Medical Biotechnology, College of Biotechnology, Al-Nahrain University, Baghdad, Iraq
| | - Jameel R Al-Obaidi
- Department of Biology, Faculty of Science and Mathematics, Universiti Pendidikan Sultan Idris, 35900 Tanjong Malim, Perak, Malaysia.
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50
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Suresh R, Diaz RJ. The remodelling of actin composition as a hallmark of cancer. Transl Oncol 2021; 14:101051. [PMID: 33761369 PMCID: PMC8008238 DOI: 10.1016/j.tranon.2021.101051] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 02/01/2021] [Accepted: 02/17/2021] [Indexed: 02/06/2023] Open
Abstract
Actin is a key structural protein that makes up the cytoskeleton of cells, and plays a role in functions such as division, migration, and vesicle trafficking. It comprises six different cell-type specific isoforms: ACTA1, ACTA2, ACTB, ACTC1, ACTG1, and ACTG2. Abnormal actin isoform expression has been reported in many cancers, which led us to hypothesize that it may serve as an early biomarker of cancer. We show an overview of the different actin isoforms and highlight mechanisms by which they may contribute to tumorigenicity. Furthermore, we suggest how the aberrant expression of actin subunits can confer cells with greater proliferation ability, increased migratory capability, and chemoresistance through incorporation into the normal cellular F-actin network and altered actin binding protein interaction. Studying this fundamental change that takes place within cancer cells can further our understanding of neoplastic transformation in multiple tissue types, which can ultimately aid in the early-detection, diagnosis and treatment of cancer.
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Affiliation(s)
- Rahul Suresh
- Montreal Neurological Institute, Integrated Program in Neuroscience, McGill University, Montreal, Canada
| | - Roberto J Diaz
- Department of Neurology and Neurosurgery, Montreal Neurological Institute and Hospital, Faculty of Medicine, McGill University, Montreal, Canada.
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