1
|
Liu M, Li H, Huo Z, Chen H, Kang X, Xu B. Bioinformatics Research and qRT-PCR Verify Hub Genes and a Transcription Factor-MicroRNA Feedback Network in Intervertebral Disc Degeneration. Appl Biochem Biotechnol 2024; 196:3184-3198. [PMID: 37632659 DOI: 10.1007/s12010-023-04699-0] [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] [Accepted: 08/16/2023] [Indexed: 08/28/2023]
Abstract
The present study explores the potentials of bioinformatics analysis to identify hub genes linked to intervertebral disc degeneration (IDD) and explored the potential molecular mechanism of transcription factor-microRNA regulatory network. Furthermore, the hub genes were identified through quantitative reverse transcriptase PCR (qRT-PCR). GEO database expression profile datasets for candidate genes (GSE124272) were downloaded. Genes that were differentially expressed (DEGs) were detected utilizing limma technique in the R programming language. Search Tool for the Retrieval of Interacting Genes/Proteins and NetworkAnalyst software identified hub genes. The Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis as well as Gene Ontology annotation of the DEGs were performed using Metascape. Using Bioinformatics data from the TRRUST, StarBase, and TransmiR databases, a TF-miRNA-hub genes network was constructed. qRT-PCR was utilized to confirm the result. As compared to healthy persons, 521 DEGs, comprising 203 down-regulated and 318 up-regulated genes, as well as 7 core genes, were found in people with IDD. Analysis revealed that all seven essential genes were under-expressed. qRT-PCR further confirmed the low expression of these seven important genes. Based on the TRRUST database, 16 TFs that could target five junction genes were then predicted. According to the StarBase database, four miRNAs were linked to crucial genes, while the TransmiR database predicted regulatory connections between four miRNAs and five TFs. The expression of the TP53-(hsa-miR-183-5p)-CCNB1 TF-miRNA-mRNA interaction network was discovered to be correlated with IDD. Throughout this investigation, a network of TF-miRNA-mRNA connections was built for investigation of the probable molecular mechanisms responsible for IDD. The identification of hub genes associated with IDD may reveal promising IDD treatment strategies.
Collapse
Affiliation(s)
- Mingli Liu
- Graduate School, Tianjin Medical University, No. 22 Qixiangtai Road, Heping District, Tianjin, 300211, China
| | - Hao Li
- Graduate School, Tianjin Medical University, No. 22 Qixiangtai Road, Heping District, Tianjin, 300211, China
| | - Zhenxin Huo
- Graduate School, Tianjin Medical University, No. 22 Qixiangtai Road, Heping District, Tianjin, 300211, China
| | - Houcong Chen
- Graduate School, Tianjin Medical University, No. 22 Qixiangtai Road, Heping District, Tianjin, 300211, China
| | - Xinjian Kang
- Graduate School, Tianjin Medical University, No. 22 Qixiangtai Road, Heping District, Tianjin, 300211, China
| | - Baoshan Xu
- Department of Minimally Invasive Spine Surgery, Tianjin Hospital, No. 406 Jiefangnan Road, Hexi District, Tianjin, 300211, China.
| |
Collapse
|
2
|
Gong X, Gong Y, Wu G, Ke H. Bioinformatics analysis highlights CCNB1 as a potential prognostic biomarker and an anti-kidney renal papillary cell carcinoma drug target. Medicine (Baltimore) 2024; 103:e37609. [PMID: 38518000 PMCID: PMC10956941 DOI: 10.1097/md.0000000000037609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 02/23/2024] [Indexed: 03/24/2024] Open
Abstract
Kidney renal papillary cell carcinoma (KIRP) is a common urinary tumor that causes lymph node invasion. Once metastatic, the prognosis is poor and there is a lack of effective early diagnostic markers for this tumor. The expression of CCNB1 in KIRP tumor tissues was significantly higher than that in normal tissues in The Cancer Genome Atlas database with or without the genotype-tissue expression database, and a consistent result was obtained in 32 paired tissues. In addition, CCNB1 expression increased remarkably with the progression of the T and M stages. Moreover, using the online HPA database, we verified that the immunohistochemical scores of CCNB1 in KIRP were higher than those in the normal kidney tissues. The higher expression group of CCNB1 showed a worse prognosis in KIRP. Moreover, the receiver operating characteristic curve, univariate and multivariate analyses, and construction of the column diagram further illustrated that CCNB1 was an independent prognostic factor for KIRP. Meanwhile, CCNB1 could better predict the 1- and 3-year survival rates of KIRP. Six genes were significantly and positively co-expressed with CCNB1. We also found that the CCNB1 high-expression group was enriched in the ECM_RECEPTOR_INTERACTION and FOCAL_ADHESION pathways. Finally, drug sensitivity analysis combined with molecular docking identified 5 targeting drugs with the strongest binding activity to CCNB1. CCNB1 is a potential and reliable biomarker for KIRP diagnosis and can be used to predict the survival of patients with KIRP. The 5 selected drugs targeting CCNB1 may provide new hopes for patients with KIRP metastasis.
Collapse
Affiliation(s)
- Xiaoming Gong
- Department of Infectious Disease, Hubei AIDS Clinical Training Center, Zhongnan Hospital of Wuhan University, Wuhan, China
- Department of Radiology, Xianning Central Hospital, The First Affiliate Hospital of Hubei University of Science and Technology, Xianning, China
| | - Yahong Gong
- Department of Radiology, Xianning Central Hospital, The First Affiliate Hospital of Hubei University of Science and Technology, Xianning, China
| | - GuiFang Wu
- Department of Infectious Disease, Hubei AIDS Clinical Training Center, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Hengning Ke
- Department of Infectious Disease, Hubei AIDS Clinical Training Center, Zhongnan Hospital of Wuhan University, Wuhan, China
- Wuhan Research Center for Infectious Diseases and Cancer, Chinese Academy of Medical Sciences, Wuhan, China
- Cancer Research Institute, General Hospital, Ningxia Medical University, Yinchuan, China
| |
Collapse
|
3
|
Nemtsova MV, Kuznetsova EB, Bure IV. Chromosomal Instability in Gastric Cancer: Role in Tumor Development, Progression, and Therapy. Int J Mol Sci 2023; 24:16961. [PMID: 38069284 PMCID: PMC10707305 DOI: 10.3390/ijms242316961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 11/23/2023] [Accepted: 11/29/2023] [Indexed: 12/18/2023] Open
Abstract
According to the Cancer Genome Atlas (TCGA), gastric cancers are classified into four molecular subtypes: Epstein-Barr virus-positive (EBV+), tumors with microsatellite instability (MSI), tumors with chromosomal instability (CIN), and genomically stable (GS) tumors. However, the gastric cancer (GC) with chromosomal instability remains insufficiently described and does not have effective markers for molecular and histological verification and diagnosis. The CIN subtype of GC is characterized by chromosomal instability, which is manifested by an increased frequency of aneuploidies and/or structural chromosomal rearrangements in tumor cells. Structural rearrangements in the CIN subtype of GC are not accidental and are commonly detected in chromosomal loci, being abnormal because of specific structural organization. The causes of CIN are still being discussed; however, according to recent data, aberrations in the TP53 gene may cause CIN development or worsen its phenotype. Clinically, patients with the CIN subtype of GC demonstrate poor survival, but receive the maximum benefit from adjuvant chemotherapy. In the review, we consider the molecular mechanisms and possible causes of chromosomal instability in GC, the common rearrangements of chromosomal loci and their impact on the development and clinical course of the disease, as well as the driver genes, their functions, and perspectives on their targeting in the CIN subtype of GC.
Collapse
Affiliation(s)
- Marina V. Nemtsova
- Laboratory of Medical Genetics, I.M. Sechenov First Moscow State Medical University (Sechenov University), 119991 Moscow, Russia; (M.V.N.); (E.B.K.)
- Laboratory of Epigenetics, Research Centre for Medical Genetics, 115522 Moscow, Russia
| | - Ekaterina B. Kuznetsova
- Laboratory of Medical Genetics, I.M. Sechenov First Moscow State Medical University (Sechenov University), 119991 Moscow, Russia; (M.V.N.); (E.B.K.)
- Laboratory of Epigenetics, Research Centre for Medical Genetics, 115522 Moscow, Russia
| | - Irina V. Bure
- Laboratory of Medical Genetics, I.M. Sechenov First Moscow State Medical University (Sechenov University), 119991 Moscow, Russia; (M.V.N.); (E.B.K.)
- Russian Medical Academy of Continuous Professional Education, 125993 Moscow, Russia
| |
Collapse
|
4
|
Ersoz NS, Bakir-Gungor B, Yousef M. GeNetOntology: identifying affected gene ontology terms via grouping, scoring, and modeling of gene expression data utilizing biological knowledge-based machine learning. Front Genet 2023; 14:1139082. [PMID: 37671046 PMCID: PMC10476493 DOI: 10.3389/fgene.2023.1139082] [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: 01/06/2023] [Accepted: 07/05/2023] [Indexed: 09/07/2023] Open
Abstract
Introduction: Identifying significant sets of genes that are up/downregulated under specific conditions is vital to understand disease development mechanisms at the molecular level. Along this line, in order to analyze transcriptomic data, several computational feature selection (i.e., gene selection) methods have been proposed. On the other hand, uncovering the core functions of the selected genes provides a deep understanding of diseases. In order to address this problem, biological domain knowledge-based feature selection methods have been proposed. Unlike computational gene selection approaches, these domain knowledge-based methods take the underlying biology into account and integrate knowledge from external biological resources. Gene Ontology (GO) is one such biological resource that provides ontology terms for defining the molecular function, cellular component, and biological process of the gene product. Methods: In this study, we developed a tool named GeNetOntology which performs GO-based feature selection for gene expression data analysis. In the proposed approach, the process of Grouping, Scoring, and Modeling (G-S-M) is used to identify significant GO terms. GO information has been used as the grouping information, which has been embedded into a machine learning (ML) algorithm to select informative ontology terms. The genes annotated with the selected ontology terms have been used in the training part to carry out the classification task of the ML model. The output is an important set of ontologies for the two-class classification task applied to gene expression data for a given phenotype. Results: Our approach has been tested on 11 different gene expression datasets, and the results showed that GeNetOntology successfully identified important disease-related ontology terms to be used in the classification model. Discussion: GeNetOntology will assist geneticists and scientists to identify a range of disease-related genes and ontologies in transcriptomic data analysis, and it will also help doctors design diagnosis platforms and improve patient treatment plans.
Collapse
Affiliation(s)
- Nur Sebnem Ersoz
- Department of Bioengineering, Graduate School of Engineering and Science, Abdullah Gul University, Kayseri, Türkiye
| | - Burcu Bakir-Gungor
- Department of Computer Engineering, Faculty of Engineering, Abdullah Gul University, Kayseri, Türkiye
- Department of Bioengineering, Faculty of Life and Natural Sciences, Abdullah Gul University, Kayseri, Türkiye
| | - Malik Yousef
- Department of Information Systems, Zefat Academic College, Zefat, Israel
- Galilee Digital Health Research Center (GDH), Zefat Academic College, Zefat, Israel
| |
Collapse
|
5
|
Mehdizadeh R, Madjid Ansari A, Forouzesh F, Shahriari F, Shariatpanahi SP, Salaritabar A, Javidi MA. P53 status, and G2/M cell cycle arrest, are determining factors in cell-death induction mediated by ELF-EMF in glioblastoma. Sci Rep 2023; 13:10845. [PMID: 37407632 DOI: 10.1038/s41598-023-38021-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 06/30/2023] [Indexed: 07/07/2023] Open
Abstract
The average survival of patients with glioblastoma is 12-15 months. Therefore, finding a new treatment method is important, especially in cases that show resistance to treatment. Extremely low-frequency electromagnetic fields (ELF-EMF) have characteristics and capabilities that can be proposed as a new cancer treatment method with low side effects. This research examines the antitumor effect of ELF-EMF on U87 and U251 glioblastoma cell lines. Flowcytometry determined the viability/apoptosis and distribution of cells in different phases of the cell cycle. The size of cells was assessed by TEM. Important cell cycle regulation genes mRNA expression levels were investigated by real-time PCR. ELF-EMF induced apoptosis in U87cells much more than U251 (15% against 2.43%) and increased G2/M cell population in U87 (2.56%, p value < 0.05), and S phase in U251 (2.4%) (data are normalized to their sham exposure). The size of U87 cells increased significantly after ELF-EMF exposure (overexpressing P53 in U251 cells increased the apoptosis induction by ELF-EMF). The expression level of P53, P21, and MDM2 increased and CCNB1 decreased in U87. Among the studied genes, MCM6 expression decreased in U251. Increasing expression of P53, P21 and decreasing CCNB1, induction of cell G2/M cycle arrest, and consequently increase in the cell size can be suggested as one of the main mechanisms of apoptosis induction by ELF-EMF; furthermore, our results demonstrate the possible footprint of P53 in the apoptosis induction by ELF-EMF, as U87 carry the wild type of P53 and U251 has the mutated form of this gene.
Collapse
Affiliation(s)
- Romina Mehdizadeh
- Department of Genetics, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Alireza Madjid Ansari
- Department of Integrative Oncology, Breast Cancer Research Center, Motamed Cancer Institute, ACECR, Tehran, Iran
| | - Flora Forouzesh
- Department of Genetics, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Fatemeh Shahriari
- Department of Molecular Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | | | - Ali Salaritabar
- Department of Integrative Oncology, Breast Cancer Research Center, Motamed Cancer Institute, ACECR, Tehran, Iran
| | - Mohammad Amin Javidi
- Department of Integrative Oncology, Breast Cancer Research Center, Motamed Cancer Institute, ACECR, Tehran, Iran.
- Department of Genetics, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran.
| |
Collapse
|
6
|
King AC, Zenker AK. Sex blind: bridging the gap between drug exposure and sex-related gene expression in Danio rerio using next-generation sequencing (NGS) data and a literature review to find the missing links in pharmaceutical and environmental toxicology studies. FRONTIERS IN TOXICOLOGY 2023; 5:1187302. [PMID: 37398910 PMCID: PMC10312089 DOI: 10.3389/ftox.2023.1187302] [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: 03/15/2023] [Accepted: 06/01/2023] [Indexed: 07/04/2023] Open
Abstract
The sex of both humans and Danio rerio has previously been shown to affect the way individuals respond to drug exposure. Genes which allow identification of sex in juvenile zebrafish show potential to reveal these confounding variables between sex in toxicological and preclinical trials but the link between these is so far missing. These sex-specific, early expressed genes where expression is not altered by drug exposure must be carefully selected for this purpose. We aimed to discover genes which can be used in pharmaceutical trials and environmental toxicology studies to uncover sex-related variations in gene expression with drug application using the model organism Danio rerio. Previously published early sex determining genes from King et al. were evaluated as well as additional genes selected from our zebrafish Next-generation sequencing (NGS) data which are known from previously published works not to be susceptible to changes in expression with drug exposure. NGS revealed a further ten female-specific genes (vtg1, cyp17a1, cyp19a1a, igf3, ftz-f1, gdf9, foxl2a, Nr0b1, ipo4, lhcgr) and five male related candidate genes (FKBP5, apobb1, hbaa1, dmrt1, spata6) which are also expressed in juvenile zebrafish, 28 days post fertilisation (dpf). Following this, a literature review was performed to classify which of these early-expressed sex specific genes are already known to be affected by drug exposure in order to determine candidate genes to be used in pharmaceutical trials or environmental toxicology testing studies. Discovery of these early sex-determining genes in Danio rerio will allow identification of sex-related responses to drug testing to improve sex-specific healthcare and the medical treatment of human patients.
Collapse
Affiliation(s)
| | - Armin K. Zenker
- University of Applied Sciences and Arts North-Western Switzerland (FHNW), Muttenz, Switzerland
| |
Collapse
|
7
|
Olszańska J, Pietraszek-Gremplewicz K, Domagalski M, Nowak D. Mutual impact of adipocytes and colorectal cancer cells growing in co-culture conditions. Cell Commun Signal 2023; 21:130. [PMID: 37316878 DOI: 10.1186/s12964-023-01155-8] [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: 03/12/2023] [Accepted: 04/29/2023] [Indexed: 06/16/2023] Open
Abstract
BACKGROUND Colorectal cancer (CRC) is the third most common malignancy worldwide. CRC cells are situated in an adipocyte-rich microenvironment, which leads to interactions between adipocytes and CRC cells. Upon exposure to cancer cells, adipocytes transform into cancer-associated adipocytes (CAAs), and as a result, they gain features that promote tumor progression. The aim of this research was to shed more light on the detailed role of interactions between adipocytes and CRC cells associated with cancer progression in the context of these alterations. METHODS To implement adipocyte-CRC cell interaction, a co-culture model was applied. The analyses mainly focused on the metabolic modifications within CAAs and CRC cells, as well as the proliferation and migration potential of CRC cells. The impact of CRC on adipocytes was investigated by qRT-PCR analysis and Oil Red O staining. Proliferation and migration of CRC cells upon co-culture were tested with videomicroscopy, XTT, and a wound healing assay. Metabolic changes within CAAs and CRC cells were investigated based on lipid droplet formation, cell cycle analysis, gene and protein expression by qRT-PCR, and western blotting techniques. RESULTS CRC cells induced reprogramming of adipocytes into CAAs, which was connected with downregulation of lipid droplet formation in CAAs and alteration in adipocyte features. CAAs showed decreased metabolism-related gene expression, phosphorylation of Akt, ERK kinases, STAT3, and lactate secretion in comparison to the control. CAAs also promoted the migration, proliferation, and lipid droplet accumulation of CRC cells. After co-culturing with adipocytes, there was a shift to the G2/M phase of the cell cycle according to the differences in cyclin expression. CONCLUSION There are complex bidirectional interactions between adipocytes and CRC cells that may be connected with the induction of CRC cell progression. Video Abstract.
Collapse
Affiliation(s)
- Joanna Olszańska
- Department of Cell Pathology, Faculty of Biotechnology, University of Wroclaw, Joliot-Curie 14a, 50-383, Wroclaw, Poland
| | | | - Mikołaj Domagalski
- Department of Cell Pathology, Faculty of Biotechnology, University of Wroclaw, Joliot-Curie 14a, 50-383, Wroclaw, Poland
| | - Dorota Nowak
- Department of Cell Pathology, Faculty of Biotechnology, University of Wroclaw, Joliot-Curie 14a, 50-383, Wroclaw, Poland
| |
Collapse
|
8
|
Aljohani AI, Toss MS, Green AR, Rakha EA. The clinical significance of cyclin B1 (CCNB1) in invasive breast cancer with emphasis on its contribution to lymphovascular invasion development. Breast Cancer Res Treat 2023; 198:423-435. [PMID: 36418517 PMCID: PMC10036284 DOI: 10.1007/s10549-022-06801-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Accepted: 11/03/2022] [Indexed: 11/25/2022]
Abstract
BACKGROUND Lymphovascular invasion (LVI) is regulated through complex molecular mechanisms. Cyclin B1 (CCNB1) was previously determined as being associated with LVI using large cohorts of breast cancer (BC) and artificial neural network (ANN) technique. In this study, we aimed to assess the association between CCNB1 and LVI, other clinicopathological and other LVI-related biomarkers at the molecular (RNA transcriptomic) and proteomic levels in BC. METHODS Two transcriptomic BC cohorts (n = 2834) were used to assess the association between the expression of CCNB1 at the mRNA level and clinicopathological characteristics and patient outcome. Tissue microarrays (TMAs) from a well-characterised BC cohort (n = 2480) with long-term outcome were also used to assess the clinical significance of CCNB1 protein expression using immunohistochemistry. RESULTS High CCNB1 mRNA expression was associated with aggressive tumour behaviour, including LVI, larger size, higher tumour grade, high lymph nodal stage, hormonal receptor negativity, HER2 positivity and poor clinical outcome (all p < 0.0001). Similarly, high CCNB1 protein expression was associated with higher tumour grade, hormonal receptor negativity and HER2 positivity (all p < 0.0001). Additionally, there was a significant association between CCNB1- and LVI-related biomarkers including N-cadherin, P-cadherin and TWIST2 at the transcriptomic and proteomic level. Multivariate analysis revealed that CCNB1 was an independent predictor of shorter BC-specific survival (HR = 1.3; 95% CI 1.2-1.5; p = 0.010). CONCLUSION CCNB1 is a key gene associated with LVI in BC and has prognostic value. More functional studies are warranted to unravel the mechanistic role of CCNB1 in the development of LVI.
Collapse
Affiliation(s)
- Abrar I Aljohani
- Academic Unit for Translational Medical Sciences, School of Medicine, Nottingham Breast Cancer Research Centre, University of Nottingham Biodiscovery Institute, University Park, Nottingham, NG7 2RD, UK
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, Taif 21944, Saudi Arabia
| | - Michael S Toss
- Academic Unit for Translational Medical Sciences, School of Medicine, Nottingham Breast Cancer Research Centre, University of Nottingham Biodiscovery Institute, University Park, Nottingham, NG7 2RD, UK
| | - Andrew R Green
- Academic Unit for Translational Medical Sciences, School of Medicine, Nottingham Breast Cancer Research Centre, University of Nottingham Biodiscovery Institute, University Park, Nottingham, NG7 2RD, UK
| | - Emad A Rakha
- Academic Unit for Translational Medical Sciences, School of Medicine, Nottingham Breast Cancer Research Centre, University of Nottingham Biodiscovery Institute, University Park, Nottingham, NG7 2RD, UK.
- Histopathology Department, Faculty of Medicine, Menoufia University, Shebeen El-Kom, Egypt.
- Department of Histopathology, Nottingham University Hospital NHS Trust, City Hospital Campus, Hucknall Road, Nottingham, NG5 1PB, UK.
| |
Collapse
|
9
|
Barzaghini B, Carelli S, Messa L, Rey F, Avanzini MA, Jacchetti E, Maghraby E, Berardo C, Zuccotti G, Raimondi MT, Cereda C, Calcaterra V, Pelizzo G. Bone Marrow Mesenchymal Stem Cells Expanded Inside the Nichoid Micro-Scaffold: a Focus on Anti-Inflammatory Response. REGENERATIVE ENGINEERING AND TRANSLATIONAL MEDICINE 2023:1-12. [PMID: 37363698 PMCID: PMC10027280 DOI: 10.1007/s40883-023-00296-z] [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: 10/19/2022] [Revised: 02/08/2023] [Accepted: 02/19/2023] [Indexed: 03/28/2023]
Abstract
Purpose Mesenchymal stem cells (MSCs) represent a promising source for stem cell therapies in numerous diseases, including pediatric respiratory system diseases. Characterized by low immunogenicity, high anti-inflammatory, and immunoregulatory features, MSCs demonstrated an excellent therapeutic profile in numerous in vitro and preclinical models. MSCs reside in a specialized physiologic microenvironment, characterized by a unique combination of biophysical, biochemical, and cellular properties. The exploitation of the 3D micro-scaffold Nichoid, which simulates the native niche, enhanced the anti-inflammatory potential of stem cells through mechanical stimulation only, overcoming the limitation of biochemical and xenogenic growth factors application. Materials and Methods In this work, we expanded pediatric bone marrow MSCs (BM-MSCs) inside the Nichoid and performed a complete cellular characterization with different approaches including viability assays, immunofluorescence analyses, RNA sequencing, and gene expression analysis. Results We demonstrated that BM-MSCs inside the scaffold remain in a stem cell quiescent state mimicking the condition of the in vivo environment. Moreover, the gene expression profile of these cells shows a significant up-regulation of genes involved in immune response when compared with the flat control. Conclusion The significant changes in the expression profile of anti-inflammatory genes could potentiate the therapeutic effect of BM-MSCs, encouraging the possible clinical translation for the treatment of pediatric congenital and acquired pulmonary disorders, including post-COVID lung manifestations. Lay Summary Regenerative medicine is the research field integrating medicine, biology, and biomedical engineering. In this context, stem cells, which are a fundamental cell source able to regenerate tissues and restore damage in the body, are the key component for a regenerative therapeutic approach. When expanded outside the body, stem cells tend to differentiate spontaneously and lose regenerative potential due to external stimuli. For this reason, we exploit the scaffold named Nichoid, which mimics the in vivo cell niche architecture. In this scaffold, mesenchymal stem cells "feel at home" due to the three-dimensional mechanical stimuli, and our findings could be considered as an innovative culture system for the in vitro expansion of stem cells for clinical translation. Future Perspective The increasing demand of safe and effective cell therapies projects our findings toward the possibility of improving cell therapies based on the use of BM-MSCs, particularly for their clinical translation in lung diseases. Graphical Abstract
Collapse
Affiliation(s)
- Bianca Barzaghini
- Department of Chemistry, Materials, and Chemical Engineering “Giulio Natta,” Politecnico Di Milano, Milan, Italy
| | - Stephana Carelli
- Pediatric Research Center “Romeo Ed Enrica Invernizzi,” Department of Biomedical and Clinical Sciences, University of Milan, Milan, Italy
- Center of Functional Genomics and Rare Diseases, Department of Pediatrics, Buzzi Children’s Hospital, Milan, Italy
| | - Letizia Messa
- Center of Functional Genomics and Rare Diseases, Department of Pediatrics, Buzzi Children’s Hospital, Milan, Italy
- Department of Electronic, Information and Bioengineering, Politecnico di Milano, Milan, Italy
| | - Federica Rey
- Pediatric Research Center “Romeo Ed Enrica Invernizzi,” Department of Biomedical and Clinical Sciences, University of Milan, Milan, Italy
- Center of Functional Genomics and Rare Diseases, Department of Pediatrics, Buzzi Children’s Hospital, Milan, Italy
| | - Maria Antonietta Avanzini
- Immunology and Transplantation Laboratory, Cell Factory, Pediatric Hematology Oncology, Fondazione IRCCS Policlinico S. Matteo, Pavia, Italy
| | - Emanuela Jacchetti
- Department of Chemistry, Materials, and Chemical Engineering “Giulio Natta,” Politecnico Di Milano, Milan, Italy
| | - Erika Maghraby
- Pediatric Research Center “Romeo Ed Enrica Invernizzi,” Department of Biomedical and Clinical Sciences, University of Milan, Milan, Italy
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, Pavia, Italy
| | - Clarissa Berardo
- Pediatric Research Center “Romeo Ed Enrica Invernizzi,” Department of Biomedical and Clinical Sciences, University of Milan, Milan, Italy
- Center of Functional Genomics and Rare Diseases, Department of Pediatrics, Buzzi Children’s Hospital, Milan, Italy
| | - Gianvincenzo Zuccotti
- Pediatric Research Center “Romeo Ed Enrica Invernizzi,” Department of Biomedical and Clinical Sciences, University of Milan, Milan, Italy
- Department of Pediatrics, Buzzi Children’s Hospital, Milan, Italy
| | - Manuela Teresa Raimondi
- Department of Chemistry, Materials, and Chemical Engineering “Giulio Natta,” Politecnico Di Milano, Milan, Italy
| | - Cristina Cereda
- Center of Functional Genomics and Rare Diseases, Department of Pediatrics, Buzzi Children’s Hospital, Milan, Italy
| | - Valeria Calcaterra
- Department of Pediatrics, Buzzi Children’s Hospital, Milan, Italy
- Department of Internal Medicine, University of Pavia, Pavia, Italy
| | - Gloria Pelizzo
- Pediatric Surgery Unit, Buzzi Children’s Hospital, Milan, Italy
- Department of Biomedical and Clinical Science, University of Milan, Milan, Italy
| |
Collapse
|
10
|
Ampelopsin induces MDA-MB-231 cell cycle arrest through cyclin B1-mediated PI3K/AKT/mTOR pathway in vitro and in vivo. ACTA PHARMACEUTICA (ZAGREB, CROATIA) 2023; 73:75-90. [PMID: 36692465 DOI: 10.2478/acph-2023-0005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 07/31/2022] [Indexed: 01/25/2023]
Abstract
Breast cancer is one of the most common malignant tumors in women and it is the most frequently diagnosed cancer in the world. Ampelopsin (AMP) is a purified component from the root of Ampelopsis grossedentata. It is reported that AMP could significantly inhibit the proliferation of breast cancer cells. However, the antitumor mechanism against breast cancer has not yet been fully elucidated. The purpose of this work was to study the role of AMP against breast cancer MDA-MB-231 cells and to further investigate the underlying mechanism. PI3K/AKT/mTOR plays a very important role in tumor cell growth and proliferation and we hypothesize that AMP may inhibit this pathway. In the present work, the results showed that AMP could significantly inhibit the growth of breast cancer MDA-MB-231 cells in vitro and in vivo. In addition, treatment with AMP decreased the levels of PI3K, AKT and mTOR, as well as cyclin B1 expression, followed by p53/p21 pathway activation to arrest the cell cycle at G2/M. Moreover, it demonstrated a positive association between cyclin B1 and PI3K/AKT/mTOR levels. Importantly, this pathway was found to be regulated by cyclin B1 in MDA-MB-231 cells treated with AMP. Also, it was observed that cyclin B1 overexpression attenuated cell apoptosis and weakened the inhibitory effects of AMP on cell proliferation. Together, AMP could inhibit breast cancer MDA-MB-231 cell proliferation in vitro and in vivo, due to cell cycle arrest at G2/M by inactivating PI3K/AKT/mTOR pathway regulated by cyclin B1.
Collapse
|
11
|
Setiwalidi K, Fu J, Hei H, Nuer S, Zhang F, Chen S, Liu Y, Chen F, Li S, Wang C, Wu Y, Gong Y, Hu M, Huang R, Liu J, Zhang T, Ning Y, Zhao H, Guo X, Wang X. Differential expression of cyclins CCNB1 and CCNG1 is involved in the chondrocyte damage of kashin-beck disease. Front Genet 2022; 13:1053685. [PMID: 36588792 PMCID: PMC9794764 DOI: 10.3389/fgene.2022.1053685] [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: 09/28/2022] [Accepted: 11/29/2022] [Indexed: 12/15/2022] Open
Abstract
The purpose of this study was clarify the relationship between the differential expression of cyclins CCNB1 and CCNG1 and chondrocyte damage in Kashin-Beck disease. Systematic review and high-throughput sequencing of chondrocytes derived from Kashin-Beck disease patients were combined to identify the differentially expressed cyclins and cyclin-dependent kinase genes. In parallel, weaned SD rats were treated with low selenium for 4 weeks and then T-2 toxin for 4 weeks. Knee cartilage was collected to harvest chondrocytes for gene expression profiling. Finally, the protein expression levels of CCNB1 and CCNG1 were verified in knee cartilage tissue of Kashin-Beck disease patients and normal controls by immunohistochemical staining. The systematic review found 52 cartilage disease-related cyclins and cyclin-dependent kinase genes, 23 of which were coexpressed in Kashin-Beck disease, including 15 upregulated and 8 downregulated genes. Under the intervention of a low selenium diet and T-2 toxin exposure, CCNB1 (FC = 0.36) and CCNG1 (FC = 0.73) showed a downward expression trend in rat articular cartilage. Furthermore, compared to normal controls, CCNB1 protein in Kashin-Beck disease articular cartilage was 71.98% and 66.27% downregulated in the superficial and middle zones, respectively, and 12.06% upregulated in the deep zone. CCNG1 protein was 45.66% downregulated in the superficial zone and 12.19% and 9.13% upregulated in the middle and deep zones, respectively. The differential expression of cyclins CCNB1 and CCNG1 may be related to articular cartilage damage in Kashin-Beck disease.
Collapse
Affiliation(s)
- Kaidiriye Setiwalidi
- School of Public Health, Xi’an Jiaotong University Health Science Center, Key Laboratory of Trace Elements and Endemic Diseases, Collaborative Innovation Center of Endemic Disease and Health Promotion for Silk Road Region, Xi’an, China
| | - Jialei Fu
- School of Public Health, Xi’an Jiaotong University Health Science Center, Key Laboratory of Trace Elements and Endemic Diseases, Collaborative Innovation Center of Endemic Disease and Health Promotion for Silk Road Region, Xi’an, China
| | - He Hei
- School of Public Health, Xi’an Jiaotong University Health Science Center, Key Laboratory of Trace Elements and Endemic Diseases, Collaborative Innovation Center of Endemic Disease and Health Promotion for Silk Road Region, Xi’an, China
| | - Shaniya Nuer
- School of Public Health, Xi’an Jiaotong University Health Science Center, Key Laboratory of Trace Elements and Endemic Diseases, Collaborative Innovation Center of Endemic Disease and Health Promotion for Silk Road Region, Xi’an, China
| | - Feiyu Zhang
- School of Public Health, Xi’an Jiaotong University Health Science Center, Key Laboratory of Trace Elements and Endemic Diseases, Collaborative Innovation Center of Endemic Disease and Health Promotion for Silk Road Region, Xi’an, China
| | - Sijie Chen
- School of Public Health, Xi’an Jiaotong University Health Science Center, Key Laboratory of Trace Elements and Endemic Diseases, Collaborative Innovation Center of Endemic Disease and Health Promotion for Silk Road Region, Xi’an, China
| | - Yanli Liu
- Department of Occupational and Environmental Health, School of Public Health, Xi’an Jiaotong University Health Science Center, Xi’an, China
| | - Feihong Chen
- Department of Occupational and Environmental Health, School of Public Health, Xi’an Jiaotong University Health Science Center, Xi’an, China
| | - Shujin Li
- School of Public Health, Xi’an Jiaotong University Health Science Center, Key Laboratory of Trace Elements and Endemic Diseases, Collaborative Innovation Center of Endemic Disease and Health Promotion for Silk Road Region, Xi’an, China
| | - Chaowei Wang
- School of Public Health, Xi’an Jiaotong University Health Science Center, Key Laboratory of Trace Elements and Endemic Diseases, Collaborative Innovation Center of Endemic Disease and Health Promotion for Silk Road Region, Xi’an, China
| | - Yifan Wu
- Department of Occupational and Environmental Health, School of Public Health, Xi’an Jiaotong University Health Science Center, Xi’an, China
| | - Yi Gong
- Department of Occupational and Environmental Health, School of Public Health, Xi’an Jiaotong University Health Science Center, Xi’an, China
| | - Minhan Hu
- School of Public Health, Xi’an Jiaotong University Health Science Center, Key Laboratory of Trace Elements and Endemic Diseases, Collaborative Innovation Center of Endemic Disease and Health Promotion for Silk Road Region, Xi’an, China
| | - Ruitian Huang
- Department of Occupational and Environmental Health, School of Public Health, Xi’an Jiaotong University Health Science Center, Xi’an, China
| | - Junyi Liu
- School of Public Health, Xi’an Jiaotong University Health Science Center, Key Laboratory of Trace Elements and Endemic Diseases, Collaborative Innovation Center of Endemic Disease and Health Promotion for Silk Road Region, Xi’an, China
| | - Tianxiao Zhang
- Department of Epidemiology and Health Statistics, School of Public Health, Xi’an Jiaotong University Health Science Center, Xi’an, China
| | - Yujie Ning
- School of Public Health, Xi’an Jiaotong University Health Science Center, Key Laboratory of Trace Elements and Endemic Diseases, Collaborative Innovation Center of Endemic Disease and Health Promotion for Silk Road Region, Xi’an, China,*Correspondence: Yujie Ning, ; Hongmou Zhao,
| | - Hongmou Zhao
- Foot and Ankle Surgery Department, Honghui Hospital of Xi’an Jiaotong University, Xi’an, China,*Correspondence: Yujie Ning, ; Hongmou Zhao,
| | - Xiong Guo
- School of Public Health, Xi’an Jiaotong University Health Science Center, Key Laboratory of Trace Elements and Endemic Diseases, Collaborative Innovation Center of Endemic Disease and Health Promotion for Silk Road Region, Xi’an, China,Clinical Research Center for Endemic Disease of Shaanxi Province, The Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Xi Wang
- Department of Occupational and Environmental Health, School of Public Health, Xi’an Jiaotong University Health Science Center, Xi’an, China
| |
Collapse
|
12
|
Xu Z, Zhou T, Wang Y, Zhu L, Tu J, Xu Z, Li L, Li Y. Integrated PPI- and WGCNA-retrieval of hub gene signatures for soft substrates inhibition of human fibroblasts proliferation and differentiation. Aging (Albany NY) 2022; 14:6957-6974. [PMID: 36057261 PMCID: PMC9512501 DOI: 10.18632/aging.204258] [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: 05/13/2022] [Accepted: 08/23/2022] [Indexed: 11/25/2022]
Abstract
Fibroblasts (FBs) are the most important functional cells in the process of wound repair, and their functions can be activated by different signals at the pathological site. Although wound repair is associated with microenvironmental stiffness, the effect of matrix stiffness on FBs remains elusive. In this study, TGF-β1 was used to mimic the fibrotic environment under pathological conditions. We found that the soft substrates made FBs slender compared with tissue culture plastic, and the main altered biological function was the inhibition of proliferation and differentiation ability. Through PPI and WGCNA analysis, 63 hub genes were found, including GADD45A, CDKN3, HIST2H3PS2, ACTB, etc., which may be the main targets of soft substrates affecting the proliferation and differentiation of FBs. Our findings not only provide a more detailed report on the effect of matrix stiffness on the function of human skin FBs, but also may provide new intervention ideas for improving scars and other diseases caused by excessive cell proliferation, with potential clinical application prospects.
Collapse
Affiliation(s)
- Ziran Xu
- The Key Laboratory of Pathobiology, Ministry of Education, College of Basic Medical Sciences, Jilin University, Changchun 130021, China
| | - Tian Zhou
- The First Norman Bethune Clinical Medical College, Jilin University, Changchun 130021, China
| | - Yin Wang
- The Key Laboratory of Pathobiology, Ministry of Education, College of Basic Medical Sciences, Jilin University, Changchun 130021, China
| | - Leijie Zhu
- The Third Norman Bethune Clinical Medical College, Jilin University, Changchun 130021, China
| | - Jihao Tu
- Department of Hand and Foot Surgery, The First Hospital of Jilin University, Changchun 130021, China
| | - Zhixiang Xu
- The Key Laboratory of Pathobiology, Ministry of Education, College of Basic Medical Sciences, Jilin University, Changchun 130021, China
| | - Lisha Li
- The Key Laboratory of Pathobiology, Ministry of Education, College of Basic Medical Sciences, Jilin University, Changchun 130021, China
| | - Yulin Li
- The Key Laboratory of Pathobiology, Ministry of Education, College of Basic Medical Sciences, Jilin University, Changchun 130021, China
| |
Collapse
|
13
|
Hosseinkhan N, Honardoost M, Emami Z, Cheraghi S, Hashemi-Madani N, Khamseh ME. A systematic review of molecular alterations in invasive non-functioning pituitary adenoma. Endocrine 2022; 77:500-509. [PMID: 35711030 DOI: 10.1007/s12020-022-03105-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 06/03/2022] [Indexed: 11/03/2022]
Abstract
PURPOSE Invasive non-functional pituitary adenomas (NFPAs) constitute 35% of NFPAs. Despite a relatively large body of molecular investigations on the invasiveness of NFPA, the underlying molecular mechanisms of invasiveness are yet to be determined. Herein, we aimed to provide an overview of gene/microRNA(miRNAs) expression alterations in invasive NFPA. METHODS This article describes a systematic literature review of articles published up to March 23, 2021, on the transcriptional alterations of invasive NFPA. Five digital libraries were searched, and 42 articles in total fulfilled the eligibility criteria. Pathway enrichment was conducted, and protein interactions among the identified deregulated genes were inferred. RESULTS In total 133 gene/protein transcriptional alterations, comprising 87 increased and 46 decreased expressions, were detected in a collective number of 1001 invasive compared with 1007 non-invasive patients with NFPA. Deregulation of CDH1, PTTG1, CCNB1, SNAI1, SLUG, EZR, and PRKACB, which are associated with epidermal-mesenchymal transition (EMT), was identified. Moreover, six members of the angiogenesis pathway, i.e., VEGFA, FLT1, CCND1, CTNNB1, MYC(c-MYC), and PTTG1, were detected. SLC2A1, FLT1, and VEGFA were also recognized in the hypoxia pathway. Physical interactions of CTNNB1 with FLT1, CCND1, and EZR as well as its indirect interactions with VEGFA, MYC, CCNB1, and PCNA indicate the tight interplay between EMT, angiogenesis, and hypoxia pathways in invasive NFPAs. In addition, Hippo, JAK-STAT, MAPK, Wnt, PI3K-Akt, Ras, TGF-b, VEGF, and ErbB were identified as interwoven signaling pathways. CONCLUSION In conclusion, invasive NFPA shares very common deregulated signaling pathways with invasive cancers. A large amount of heterogeneity in the reported deregulations in different studies necessitates the validation of the expressional changes of the suggested biomarkers in a large number of patients with invasive NFPA.
Collapse
Affiliation(s)
- Nazanin Hosseinkhan
- Endocrine Research Center, Institute of Endocrinology and Metabolism, Iran University of Medical Sciences, Tehran, Iran
| | - Maryam Honardoost
- Endocrine Research Center, Institute of Endocrinology and Metabolism, Iran University of Medical Sciences, Tehran, Iran
| | - Zahra Emami
- Endocrine Research Center, Institute of Endocrinology and Metabolism, Iran University of Medical Sciences, Tehran, Iran
| | - Sara Cheraghi
- Endocrine Research Center, Institute of Endocrinology and Metabolism, Iran University of Medical Sciences, Tehran, Iran
| | - Nahid Hashemi-Madani
- Endocrine Research Center, Institute of Endocrinology and Metabolism, Iran University of Medical Sciences, Tehran, Iran
| | - Mohammad E Khamseh
- Endocrine Research Center, Institute of Endocrinology and Metabolism, Iran University of Medical Sciences, Tehran, Iran.
| |
Collapse
|
14
|
Arowolo A, Malebana M, Sunda F, Rhoda C. Proposed Cellular Function of the Human FAM111B Protein and Dysregulation in Fibrosis and Cancer. Front Oncol 2022; 12:932167. [PMID: 35860584 PMCID: PMC9293052 DOI: 10.3389/fonc.2022.932167] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 05/24/2022] [Indexed: 11/13/2022] Open
Abstract
FAM111B gene mutations are associated with a hereditary fibrosing poikiloderma known to cause poikiloderma, tendon contracture, myopathy, and pulmonary fibrosis (POIKTMP). In addition, the overexpression of FAM111B has been associated with cancer progression and poor prognosis. This review inferred the molecular function of this gene's protein product and mutational dysfunction in fibrosis and cancer based on recent findings from studies on this gene. In conclusion, FAM111B represents an uncharacterized protease involved in DNA repair, cell cycle regulation, and apoptosis. The dysregulation of this protein ultimately leads to fibrotic diseases like POIKTMP and cancers via the disruption of these cellular processes by the mutation of the FAM111B gene. Hence, it should be studied in the context of these diseases as a possible therapeutic target.
Collapse
Affiliation(s)
- Afolake Arowolo
- Hair and Skin Research Laboratory, Division of Dermatology, Groote Schuur Hospital, Cape Town, South Africa
- Department of Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Moses Malebana
- Hair and Skin Research Laboratory, Division of Dermatology, Groote Schuur Hospital, Cape Town, South Africa
- Department of Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Falone Sunda
- Hair and Skin Research Laboratory, Division of Dermatology, Groote Schuur Hospital, Cape Town, South Africa
- Department of Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Cenza Rhoda
- Hair and Skin Research Laboratory, Division of Dermatology, Groote Schuur Hospital, Cape Town, South Africa
- Department of Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| |
Collapse
|
15
|
Sunitha P, Arya KR, Nair AS, Oommen OV, Sudhakaran PR. Metabolite Effect on Angiogenesis: Insights from Transcriptome Analysis. Cell Biochem Biophys 2022; 80:519-536. [PMID: 35701692 DOI: 10.1007/s12013-022-01078-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 06/06/2022] [Indexed: 12/26/2022]
Abstract
Metabolic status of the cells is important in the expression of the angiogenic phenotype in endothelial cells. Our earlier studies demonstrated the effects of metabolites such as lactate, citrate and lipoxygenase products, on VEGFA-VEGFR2 signaling pathway. Though this link between metabolite status and molecular mechanisms of angiogenesis is becoming evident, it is not clear how it affects genome-level expression in endothelial cells, critical to angiogenesis. In the present study, computational analysis was carried out on the transcriptome data of 4 different datasets where HUVECs were exposed to low and high glucose, both in vitro and in vivo, and the expression of a key enzyme involved in glucose metabolism is altered. The differentially expressed genes belonging to both VEGFA-VEGFR2 signaling pathway, as well as several VEGF signature genes as hub genes were also identified. These findings suggest the metabolite dependence, particularly glucose dependence, of angiogenesis, involving modulation of genome-level expression of angiogenesis- functional genome. This is important in tumor angiogenesis where reprogramming of metabolism is critical.
Collapse
Affiliation(s)
- P Sunitha
- Department of Computational Biology and Bioinformatics, University of Kerala, Kariavattom, Thiruvananthapuram, 695581, Kerala, India
| | - Kesavan R Arya
- Department of Computational Biology and Bioinformatics, University of Kerala, Kariavattom, Thiruvananthapuram, 695581, Kerala, India
| | - Achuthsankar S Nair
- Department of Computational Biology and Bioinformatics, University of Kerala, Kariavattom, Thiruvananthapuram, 695581, Kerala, India
| | - Oommen V Oommen
- Department of Computational Biology and Bioinformatics, University of Kerala, Kariavattom, Thiruvananthapuram, 695581, Kerala, India
| | - Perumana R Sudhakaran
- Department of Computational Biology and Bioinformatics, University of Kerala, Kariavattom, Thiruvananthapuram, 695581, Kerala, India.
| |
Collapse
|
16
|
Khayer N, Jalessi M, Jahanbakhshi A, Tabib Khooei A, Mirzaie M. Nkx3-1 and Fech genes might be switch genes involved in pituitary non-functioning adenoma invasiveness. Sci Rep 2021; 11:20943. [PMID: 34686726 PMCID: PMC8536755 DOI: 10.1038/s41598-021-00431-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 10/12/2021] [Indexed: 12/12/2022] Open
Abstract
Non-functioning pituitary adenomas (NFPAs) are typical pituitary macroadenomas in adults associated with increased mortality and morbidity. Although pituitary adenomas are commonly considered slow-growing benign brain tumors, numerous of them possess an invasive nature. Such tumors destroy sella turcica and invade the adjacent tissues such as the cavernous sinus and sphenoid sinus. In these cases, the most critical obstacle for complete surgical removal is the high risk of damaging adjacent vital structures. Therefore, the development of novel therapeutic strategies for either early diagnosis through biomarkers or medical therapies to reduce the recurrence rate of NFPAs is imperative. Identification of gene interactions has paved the way for decoding complex molecular mechanisms, including disease-related pathways, and identifying the most momentous genes involved in a specific disease. Currently, our knowledge of the invasion of the pituitary adenoma at the molecular level is not sufficient. The current study aimed to identify critical biomarkers and biological pathways associated with invasiveness in the NFPAs using a three-way interaction model for the first time. In the current study, the Liquid association method was applied to capture the statistically significant triplets involved in NFPAs invasiveness. Subsequently, Random Forest analysis was applied to select the most important switch genes. Finally, gene set enrichment (GSE) and gene regulatory network (GRN) analyses were applied to trace the biological relevance of the statistically significant triplets. The results of this study suggest that "mRNA processing" and "spindle organization" biological processes are important in NFAPs invasiveness. Specifically, our results suggest Nkx3-1 and Fech as two switch genes in NFAPs invasiveness that may be potential biomarkers or target genes in this pathology.
Collapse
Affiliation(s)
- Nasibeh Khayer
- Skull Base Research Center, The Five Senses Health Institute, Iran University of Medical Sciences, Tehran, Iran
| | - Maryam Jalessi
- Skull Base Research Center, The Five Senses Health Institute, Iran University of Medical Sciences, Tehran, Iran.
- ENT and Head & Neck Research Center and Department, Hazrat Rasoul Hospital, Iran University of Medical Sciences, Tehran, Iran.
| | - Amin Jahanbakhshi
- Skull Base Research Center, The Five Senses Health Institute, Iran University of Medical Sciences, Tehran, Iran
- Neurology Department, Hazrat Rasoul Hospital, Iran University of Medical Sciences, Tehran, Iran
| | - Alireza Tabib Khooei
- Neurology Department, Hazrat Rasoul Hospital, Iran University of Medical Sciences, Tehran, Iran
| | - Mehdi Mirzaie
- Department of Applied Mathematics, Faculty of Mathematical Sciences, Tarbiat Modares University, Tehran, Iran.
| |
Collapse
|
17
|
Suski JM, Braun M, Strmiska V, Sicinski P. Targeting cell-cycle machinery in cancer. Cancer Cell 2021; 39:759-778. [PMID: 33891890 PMCID: PMC8206013 DOI: 10.1016/j.ccell.2021.03.010] [Citation(s) in RCA: 201] [Impact Index Per Article: 67.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 02/09/2021] [Accepted: 03/26/2021] [Indexed: 12/19/2022]
Abstract
Abnormal activity of the core cell-cycle machinery is seen in essentially all tumor types and represents a driving force of tumorigenesis. Recent studies revealed that cell-cycle proteins regulate a wide range of cellular functions, in addition to promoting cell division. With the clinical success of CDK4/6 inhibitors, it is becoming increasingly clear that targeting individual cell-cycle components may represent an effective anti-cancer strategy. Here, we discuss the potential of inhibiting different cell-cycle proteins for cancer therapy.
Collapse
Affiliation(s)
- Jan M Suski
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Marcin Braun
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA; Department of Pathology, Chair of Oncology, Medical University of Lodz, 92-213 Lodz, Poland
| | - Vladislav Strmiska
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Piotr Sicinski
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA.
| |
Collapse
|
18
|
You H, Xu J, Qin X, Qian G, Wang Y, Chen F, Shen X, Zhao D, Liu Q. Fascin promotes the invasion of pituitary adenoma through partial dependence on epithelial-mesenchymal transition. J Mol Histol 2021; 52:823-838. [PMID: 34097178 DOI: 10.1007/s10735-021-09995-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 06/03/2021] [Indexed: 11/30/2022]
Abstract
The aim of the present study was to investigate the role and potential regulatory mechanisms of fascin in the invasion and epithelial-to-mesenchymal transition of pituitary adenoma cells. A total of 30 specimens were assessed in the present study. The expression levels of fascin in the invasive pituitary adenoma group and non-invasive pituitary adenoma group were determined by immunochemistry. Fascin was downregulated via small interfering RNA in mouse pituitary AtT-20 cells. The proliferation, cell cycle and apoptosis of AtT-20 cells were assessed using Cell Counting Kit‑8 and flow cytometry. The invasion of AtT-20 cells was detected using a Transwell assay. Transmission electron microscopy was utilized to observe the ultrastructure of AtT-20 cells. Real-time quantitative PCR, Western blotting and immunofluorescence staining were utilized to detect the expression levels of fascin and EMT markers. In the present study, fascin expression and clinical characteristics were not significantly correlated in pituitary adenoma. The protein expression level of fascin in invasive pituitary adenoma was higher than that in non-invasive pituitary adenoma, as assessed by immunochemistry. Downregulation of fascin resulted in significant decreases in cell viability, proliferation and invasion, arrested the cell cycle at the G1 phase and increased apoptosis. In addition, downregulation of fascin significantly decreased the expression levels of N-cadherin, the mesenchymal cell marker vimentin and the transcription factor Twist but significantly increased the expression levels of the epithelial cell marker E-cadherin. Further experiments revealed that overexpression of E-cadherin resulted in significant decreases in cell viability, proliferation, invasion, and the expression of fascin and transcription factor Twist and also arrested the cell cycle at the G2 phase. The results of the present study suggest that suppressing the expression level of fascin could regulate the invasion, proliferation and apoptosis of pituitary tumour cells and alter the expression level of various EMT markers. The present study identified that fascin effectively promotes the invasion, proliferation and apoptosis of pituitary tumour cells partially via the EMT pathway.
Collapse
Affiliation(s)
- Hong You
- Department of Neurosurgery, The First Affiliated Hospital, Shihezi University School of Medicine, North 2 Road, Shihezi, 832000, Xinjiang, China
| | - Jian Xu
- Department of Neurosurgery, The First Affiliated Hospital, Shihezi University School of Medicine, North 2 Road, Shihezi, 832000, Xinjiang, China
| | - Xiaochun Qin
- Department of Neurosurgery, The First Affiliated Hospital, Shihezi University School of Medicine, North 2 Road, Shihezi, 832000, Xinjiang, China
| | - Guodong Qian
- Department of Neurosurgery, The First Affiliated Hospital, Shihezi University School of Medicine, North 2 Road, Shihezi, 832000, Xinjiang, China
| | - Yang Wang
- Department of Neurosurgery, The First Affiliated Hospital, Shihezi University School of Medicine, North 2 Road, Shihezi, 832000, Xinjiang, China
| | - Fulei Chen
- Department of Neurosurgery, The First Affiliated Hospital, Shihezi University School of Medicine, North 2 Road, Shihezi, 832000, Xinjiang, China
| | - Xiaoxu Shen
- Department of Neurosurgery, The First Affiliated Hospital, Shihezi University School of Medicine, North 2 Road, Shihezi, 832000, Xinjiang, China
| | - Dong Zhao
- Department of Neurosurgery, The First Affiliated Hospital, Shihezi University School of Medicine, North 2 Road, Shihezi, 832000, Xinjiang, China
| | - Qi Liu
- Department of Neurosurgery, The First Affiliated Hospital, Shihezi University School of Medicine, North 2 Road, Shihezi, 832000, Xinjiang, China.
| |
Collapse
|
19
|
Guo K, Feng Y, Zheng X, Sun L, Wasan HS, Ruan S, Shen M. Resveratrol and Its Analogs: Potent Agents to Reverse Epithelial-to-Mesenchymal Transition in Tumors. Front Oncol 2021; 11:644134. [PMID: 33937049 PMCID: PMC8085503 DOI: 10.3389/fonc.2021.644134] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Accepted: 03/17/2021] [Indexed: 02/06/2023] Open
Abstract
Epithelial-to-mesenchymal transition (EMT), a complicated program through which polarized epithelial cells acquire motile mesothelial traits, is regulated by tumor microenvironment. EMT is involved in tumor progression, invasion and metastasis via reconstructing the cytoskeleton and degrading the tumor basement membrane. Accumulating evidence shows that resveratrol, as a non-flavonoid polyphenol, can reverse EMT and inhibit invasion and migration of human tumors via diverse mechanisms and signaling pathways. In the present review, we will summarize the detailed mechanisms and pathways by which resveratrol and its analogs (e.g. Triacetyl resveratrol, 3,5,4'-Trimethoxystilbene) might regulate the EMT process in cancer cells to better understand their potential as novel anti-tumor agents. Resveratrol can also reverse chemoresistance via EMT inhibition and improvement of the antiproliferative effects of conventional treatments. Therefore, resveratrol and its analogs have the potential to become novel adjunctive agents to inhibit cancer metastasis, which might be partly related to their blocking of the EMT process.
Collapse
Affiliation(s)
- Kaibo Guo
- The First Clinical Medical College of Zhejiang Chinese Medical University, Hangzhou, China
| | - Yuqian Feng
- The First Clinical Medical College of Zhejiang Chinese Medical University, Hangzhou, China
| | - Xueer Zheng
- The First Clinical Medical College of Zhejiang Chinese Medical University, Hangzhou, China
| | - Leitao Sun
- The First Clinical Medical College of Zhejiang Chinese Medical University, Hangzhou, China
- Department of Medical Oncology, The First Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, China
| | - Harpreet S. Wasan
- Department of Cancer Medicine, Hammersmith Hospital, Imperial College Healthcare NHS Trust, London, United Kingdom
| | - Shanming Ruan
- The First Clinical Medical College of Zhejiang Chinese Medical University, Hangzhou, China
- Department of Medical Oncology, The First Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, China
| | - Minhe Shen
- The First Clinical Medical College of Zhejiang Chinese Medical University, Hangzhou, China
- Department of Medical Oncology, The First Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, China
| |
Collapse
|
20
|
Gil J, Jordà M, Soldevila B, Puig-Domingo M. Epithelial-Mesenchymal Transition in the Resistance to Somatostatin Receptor Ligands in Acromegaly. Front Endocrinol (Lausanne) 2021; 12:646210. [PMID: 33790868 PMCID: PMC8006574 DOI: 10.3389/fendo.2021.646210] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/25/2020] [Accepted: 02/22/2021] [Indexed: 01/06/2023] Open
Abstract
Epithelial-mesenchymal transition (EMT) is a dynamic process by which epithelial cells loss their phenotype and acquire mesenchymal traits, including increased migratory and invasive capacities. EMT is involved in physiological processes, such as embryogenesis and wound healing, and in pathological processes such as cancer, playing a pivotal role in tumor progression and metastasis. Pituitary tumors, although typically benign, can be locally invasive. Different studies have shown the association of EMT with increased tumor size and invasion in pituitary tumors, and in particular with a poor response to Somatostatin Receptor Ligands (SRLs) treatment in GH-producing pituitary tumors, the main cause of acromegaly. This review will summarize the current knowledge regarding EMT and SRLs resistance in acromegaly and, based on this relation, will suggest new biomarkers and possible therapies to SRLs resistant tumors.
Collapse
Affiliation(s)
- Joan Gil
- Endocrine Tumours Lab, Program of Predictive and Personalized Medicine of Cancer (PMPPC), Germans Trias i Pujol Research Institute (IGTP), Badalona, Spain
| | - Mireia Jordà
- Endocrine Tumours Lab, Program of Predictive and Personalized Medicine of Cancer (PMPPC), Germans Trias i Pujol Research Institute (IGTP), Badalona, Spain
- *Correspondence: Manel Puig-Domingo, ; Mireia Jordà,
| | - Berta Soldevila
- Department of Endocrinology and Nutrition, Germans Trias i Pujol University Hospital, Badalona, Spain
| | - Manel Puig-Domingo
- Endocrine Tumours Lab, Program of Predictive and Personalized Medicine of Cancer (PMPPC), Germans Trias i Pujol Research Institute (IGTP), Badalona, Spain
- Department of Endocrinology and Nutrition, Germans Trias i Pujol University Hospital, Badalona, Spain
- Department of Medicine, Autonomous University of Barcelona, Bellaterra, Spain
- *Correspondence: Manel Puig-Domingo, ; Mireia Jordà,
| |
Collapse
|
21
|
Rosmarinic Acid Methyl Ester Regulates Ovarian Cancer Cell Migration and Reverses Cisplatin Resistance by Inhibiting the Expression of Forkhead Box M1. Pharmaceuticals (Basel) 2020; 13:ph13100302. [PMID: 33053721 PMCID: PMC7601071 DOI: 10.3390/ph13100302] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 09/29/2020] [Accepted: 10/08/2020] [Indexed: 12/15/2022] Open
Abstract
Rosmarinic acid methyl ester (RAME), a derivative of rosmarinic acid (RA), is reported to have several therapeutic effects, including anti-tumor effects against cervical cancer. However, its anti-tumor effects in ovarian cancer is unclear. In this study, we studied the molecular pathways associated with the anti-tumor effects of RAME in ovarian cancer. To identify the effects of RAME in ovarian cancer, RNA sequencing was performed in RAME-treated ovarian cancer cells; we found that RAME treatment downregulated the genes closely involved with the target genes of the transcription factor Forkhead box M1 (FOXM1). It was reported that FOXM1 is overexpressed in a variety of cancer cells and is associated with cell proliferation and tumorigenesis. Therefore, we hypothesized that FOXM1 is a key target of RAME; this could result in its anti-tumor effects. Treatment of ovarian cancer cells with RAME-inhibited cell migration and invasion, as shown by wound healing and transwell migration assays. To examine whether RAME represses the action of FOXM1, we performed quantitative RT-PCR and ChIP-qPCR. Treatment of ovarian cancer cells with RAME decreased the mRNA expression of FOXM1 target genes and the binding of FOXM1 to its target genes. Moreover, FOXM1 expression was increased in cisplatin-resistant ovarian cancer cells, and combination treatment with RAME and cisplatin sensitized the cisplatin-resistant ovarian cancer cells, which was likely due to FOXM1 inhibition. Our research suggests that RAME is a promising option in treating ovarian cancer patients, as it revealed a novel molecular pathway underlying its anti-tumor effects.
Collapse
|
22
|
Li XZ, Wang ZC, Qiu Y, Ma SX, Meng LB, Wu WH, Zhang P, Yang W, Song WP, Huang L. Bioinformatics analysis and verification of gene targets for benign tracheal stenosis. Mol Genet Genomic Med 2020; 8:e1245. [PMID: 32309912 PMCID: PMC7284051 DOI: 10.1002/mgg3.1245] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Revised: 03/10/2020] [Accepted: 03/20/2020] [Indexed: 12/15/2022] Open
Abstract
Background Tracheal injury could cause intratracheal scar hyperplasia which in turn causes benign tracheal stenosis (TS). With the increasing use of mechanical ventilation and ventilator, the incidence of TS is increasing. However, the molecular mechanisms of TS have not been elucidated. It is significant to further explore the molecular mechanisms of TS. Methods The repeatability of public data was verified. Differently expressed genes (DEGs) and most significant genes were identified between TS and normal samples. Enrichment analysis of Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) were analyzed. The comparative toxicogenomics database were analyzed. TS patients were recruited and RT‐qPCR were performed to verify the most significant genes. Results There exist strong correlations among samples of TS and normal group. There was a total of 194 DEGs, including 61 downregulated DEGs and 133 upregulated DEGs. GO were significantly enriched in mitotic nuclear division, cell cycle, and cell division. Analysis of KEGG indicated that the top pathways were cell cycle, and p53 pathway. MKI67(OMIM:176741), CCNB1(OMIM:123836), and CCNB2(OMIM:602755) were identified as the most significant genes of TS, and validated by the clinical samples. Conclusion Bioinformatics methods might be useful method to explore the mechanisms of TS. In addition, MKI67, CCNB1, and CCNB2 might be the most significant genes of TS.
Collapse
Affiliation(s)
- Xu-Ze Li
- Department of Anesthesiology, The Second Hospital of Hebei Medical University, Shijiazhuang, China
| | - Zi-Chen Wang
- Department of Anesthesiology, The Second Hospital of Hebei Medical University, Shijiazhuang, China
| | - Yong Qiu
- Anesthesiology Department, Beijing Hospital, National Center of Gerontology, Beijing, P. R. China
| | - Shu-Xian Ma
- Department of Anesthesiology, The Second Hospital of Hebei Medical University, Shijiazhuang, China
| | - Ling-Bing Meng
- Neurology Department, Beijing Hospital, National Center of Gerontology, Beijing, P. R. China
| | - Wen-Hao Wu
- Department of Anesthesiology, The Second Hospital of Hebei Medical University, Shijiazhuang, China
| | - Pei Zhang
- Department of Anesthesiology, The Second Hospital of Hebei Medical University, Shijiazhuang, China
| | - Wei Yang
- Shandong Weigao Group National Engineering Lab, Weihai, China
| | - Wen-Ping Song
- Shandong Weigao Group National Engineering Lab, Weihai, China
| | - Lining Huang
- Department of Anesthesiology, The Second Hospital of Hebei Medical University, Shijiazhuang, China
| |
Collapse
|