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Imran K, Iqbal MJ, Abid R, Ahmad MM, Calina D, Sharifi-Rad J, Cho WC. Cellular signaling modulated by miRNA-3652 in ovarian cancer: unveiling mechanistic pathways for future therapeutic strategies. Cell Commun Signal 2023; 21:289. [PMID: 37845675 PMCID: PMC10577948 DOI: 10.1186/s12964-023-01330-x] [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: 07/06/2023] [Accepted: 09/21/2023] [Indexed: 10/18/2023] Open
Abstract
MicroRNAs (miRNAs) are small non-coding RNA molecules that play pivotal roles in regulating gene expression and have been implicated in the pathogenesis of numerous cancers. miRNA-3652, though relatively less explored, has recently emerged as a potential key player in ovarian cancer's molecular landscape. This review aims to delineate the functional significance and tumor progression role of miRNA-3652 in ovarian cancer, shedding light on its potential as both a diagnostic biomarker and therapeutic target. A comprehensive literature search was carried out using established databases, the focus was on articles that reported the role of miRNA-3652 in ovarian cancer, encompassing mechanistic insights, functional studies, and its association with clinical outcomes. This updated review highlighted that miRNA-3652 is intricately involved in ovarian cancer cell proliferation, migration, and invasion, its dysregulation was linked to altered expression of critical genes involved in tumor growth and metastasis; furthermore, miRNA-3652 expression levels were found to correlate with clinical stages, prognosis, and response to therapy in ovarian cancer patients. miRNA-3652 holds significant promise as a vital molecular player in ovarian cancer's pathophysiology. Its functional role and impact on tumor progression make it a potential candidate for diagnostic and therapeutic applications in ovarian cancer. Given the pivotal role of miRNA-3652 in ovarian cancer, future studies should emphasize in-depth mechanistic explorations, utilizing advanced genomic and proteomic tools. Collaboration between basic scientists and clinicians will be vital to translating these findings into innovative diagnostic and therapeutic strategies, ultimately benefiting ovarian cancer patients. Video Abstract.
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Affiliation(s)
- Komal Imran
- Department of Biotechnology, Faculty of Sciences, University of Sialkot, Sialkot, Pakistan
| | - Muhammad Javed Iqbal
- Department of Biotechnology, Faculty of Sciences, University of Sialkot, Sialkot, Pakistan
| | - Rameesha Abid
- Department of Microbiology, Quaid-i-Azam University, Islamabad, Pakistan
| | - Muhammad Mushtaq Ahmad
- Department of Allied Health Sciences, International Institute of Science, Art and Technology, Gujranwala, Pakistan
| | - Daniela Calina
- Department of Clinical Pharmacy, University of Medicine and Pharmacy of Craiova, 200349, Craiova, Romania.
| | | | - William C Cho
- Department of Clinical Oncology, Queen Elizabeth Hospital, Kowloon, Hong Kong.
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102
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Peralta S, Marcinczyk MM, Katt WP, Duhamel GE. Confirmation of canine acanthomatous ameloblastoma using RAS Q61R immunohistochemical staining of formalin-fixed paraffin-embedded tissues. Front Vet Sci 2023; 10:1281022. [PMID: 37901104 PMCID: PMC10611472 DOI: 10.3389/fvets.2023.1281022] [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: 08/21/2023] [Accepted: 10/03/2023] [Indexed: 10/31/2023] Open
Abstract
Differentiating canine acanthomatous ameloblastoma (CAA) from oral squamous cell carcinoma (OSCC) based on routine histopathology can be challenging. We have previously shown that more than 95% of CAAs harbor an HRAS p.Q61R somatic mutation, while OSCCs carry either wild-type alleles or other MAPK pathway activating mutations (e.g., HRAS p.Q61L, BRAF p.V595E). Given that HRAS p.Q61R mutations are highly prevalent in CAA, we hypothesized that a RAS Q61R-specific rabbit monoclonal antibody may be a useful tool for confirmation of CAA by immunohistochemical (IHC) staining. In the present study, we assessed IHC staining of archived formalin-fixed and paraffin-embedded biopsy samples with a diagnosis of CAA (n = 23), using a RAS Q61R-specific rabbit monoclonal antibody (SP174) and an automated IHC stainer. Negative control samples consisted of HRAS p.Q61R mutation-negative OSCC tumors with either a known HRAS p.Q61L mutation (n = 1), BRAF p.V595E mutation (n = 4), or wild-type corresponding alleles (n = 3). We found that all 23 CAAs showed diffuse and strong membranous RAS Q61R immunoreactivity (100% sensitivity), while none of the 8 OSCCs showed immunoreactivity (100% specificity). The data supports the use of RAS Q61R-specific rabbit monoclonal antibody for diagnostic IHC confirmation of CAA and ruling out OSCC in dogs.
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Affiliation(s)
- Santiago Peralta
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, United States
| | - Magdalena M. Marcinczyk
- Department of Biomedical Sciences and New York Animal Health Diagnostic Center, College of Veterinary Medicine, Cornell University, Ithaca, NY, United States
| | - William P. Katt
- Department of Molecular Medicine, College of Veterinary Medicine, Cornell University, Ithaca, NY, United States
| | - Gerald E. Duhamel
- Department of Biomedical Sciences and New York Animal Health Diagnostic Center, College of Veterinary Medicine, Cornell University, Ithaca, NY, United States
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Liang K, Guo Z, Zhang S, Chen D, Zou R, Weng Y, Peng C, Xu Z, Zhang J, Liu X, Pang X, Ji Y, Liao D, Lai M, Peng H, Ke Y, Wang Z, Wang Y. GPR37 expression as a prognostic marker in gliomas: a bioinformatics-based analysis. Aging (Albany NY) 2023; 15:10146-10167. [PMID: 37837549 PMCID: PMC10599758 DOI: 10.18632/aging.205063] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 08/21/2023] [Indexed: 10/16/2023]
Abstract
BACKGROUND Gliomas are the most frequently diagnosed primary brain tumors, and are associated with multiple molecular aberrations during their development and progression. GPR37 is an orphan G protein-coupled receptor (GPCR) that is implicated in different physiological pathways in the brain, and has been linked to various malignancies. The aim of this study was to explore the relationship between GPR37 gene expression and the clinicopathological factors, patient prognosis, tumor-infiltrating immune cell signature GSEA and methylation levels in glioma. METHODS We explored the diagnostic value, clinical relevance, and molecular function of GPR37 in glioma using TCGA, STRING, cBioPortal, Tumor Immunity Estimation Resource (TIMER) database and MethSurv databases. Besides, the "ssGSEA" algorithm was conducted to estimate immune cells infiltration abundance, with 'ggplot2' package visualizing the results. Immunohistochemical staining of clinical samples were used to verify the speculations of bioinformatics analysis. RESULTS GPR37 expression was significantly higher in the glioma tissues compared to the normal brain tissues, and was linked to poor prognosis. Functional annotation of GPR37 showed enrichment of ether lipid metabolism, fat digestion and absorption, and histidine metabolism. In addition, GSEA showed that GPR37 was positively correlated to the positive regulation of macrophage derived foam cell differentiation, negative regulation of T cell receptor signaling pathway, neuroactive ligand receptor interaction, calcium signaling pathway, and negatively associated with immunoglobulin complex, immunoglobulin complex circulating, ribosome and spliceosome mediated by circulating immunoglobulin etc. TIMER2.0 and ssGSEA showed that GPR37 expression was significantly associated with the infiltration of T cells, CD8 T cell, eosinophils, macrophages, neutrophils, NK CD56dim cells, NK cells, plasmacytoid DCs (pDCs), T helper cells and T effector memory (Tem) cells. In addition, high GPR37 expression was positively correlated with increased infiltration of M2 macrophages, which in turn was associated with poor prognosis. Furthermore, GPR37 was positively correlated with various immune checkpoints (ICPs). Finally, hypomethylation of the GPR37 promoter was associated with its high expression levels and poor prognosis in glioma. CONCLUSION GPR37 had diagnostic and prognostic value in glioma. The possible biological mechanisms of GPR37 provide novel insights into the clinical diagnosis and treatment of glioma.
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Affiliation(s)
- Kairong Liang
- Institute of Neuroscience, Department of Neurosurgery, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou 510260, China
| | - Zhaoxiong Guo
- Science and Technology Innovation Center, Institute of Clinical Pharmacology, Guangzhou University of Chinese Medicine, Guangzhou 510405, China
| | - Shizhen Zhang
- Institute of Neuroscience, Department of Neurosurgery, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou 510260, China
| | - Danmin Chen
- Institute of Neuroscience, Department of Neurosurgery, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou 510260, China
| | - Renheng Zou
- Institute of Neuroscience, Department of Neurosurgery, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou 510260, China
| | - Yuhao Weng
- Institute of Neuroscience, Department of Neurosurgery, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou 510260, China
| | - Chengxiang Peng
- Institute of Neuroscience, Department of Neurosurgery, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou 510260, China
| | - Zhichao Xu
- Institute of Neuroscience, Department of Neurosurgery, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou 510260, China
| | - Jingbai Zhang
- Institute of Neuroscience, Department of Neurosurgery, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou 510260, China
| | - Xiaorui Liu
- Department of Pharmacy, Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou 510095, China
| | - Xiao Pang
- Institute of Neuroscience, Department of Neurosurgery, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou 510260, China
| | - Yunxiang Ji
- Institute of Neuroscience, Department of Neurosurgery, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou 510260, China
| | - Degui Liao
- Institute of Neuroscience, Department of Neurosurgery, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou 510260, China
| | - Miaoling Lai
- Institute of Neuroscience, Department of Neurosurgery, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou 510260, China
| | - Huaidong Peng
- Department of Pharmacy, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou 510260, China
| | - Yanbin Ke
- Institute of Neuroscience, Department of Neurosurgery, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou 510260, China
| | - Zhaotao Wang
- Institute of Neuroscience, Department of Neurosurgery, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou 510260, China
| | - Yezhong Wang
- Institute of Neuroscience, Department of Neurosurgery, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou 510260, China
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Peng J, Li P, Li Y, Quan J, Yao Y, Duan J, Liu X, Li H, Yuan D, Wang X. PFKP is a prospective prognostic, diagnostic, immunological and drug sensitivity predictor across pan-cancer. Sci Rep 2023; 13:17399. [PMID: 37833332 PMCID: PMC10576092 DOI: 10.1038/s41598-023-43982-2] [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: 06/20/2023] [Accepted: 10/01/2023] [Indexed: 10/15/2023] Open
Abstract
Phosphofructokinase, platelet (PFKP) is a rate-limiting enzyme of glycolysis that plays a decisive role in various human physio-pathological processes. PFKP has been reported to have multiple functions in different cancer types, including lung cancer and breast cancer. However, no systematic pancancer analysis of PFKP has been performed; this type of analysis could elucidate the clinical value of PFKP in terms of diagnosis, prognosis, drug sensitivity, and immunological correlation. Systematic bioinformation analysis of PFKP was performed based on several public datasets, including The Cancer Genome Atlas (TCGA), Cancer Cell Line Encyclopedia (CCLE), Genotype-Tissue Expression Project (GTEx), and Human Protein Atlas (HPA). Prospective carcinogenesis of PFKP across cancers was estimated by expression analysis, effect on patient prognosis, diagnosis significance evaluation, and immunity regulation estimation. Then, pancancer functional enrichment of PFKP was also assessed through its effect on the signaling score and gene expression profile. Finally, upstream expression regulation of PFKP was explored by promoter DNA methylation and transcription factor (TF) prediction. Our analysis revealed that high expression of PFKP was found in most cancer types. Additionally, a high level of PFKP displayed a significant correlation with poor prognosis in patients across cancers. The diagnostic value of PFKP was performed based on its positive correlation with programmed cell death-ligand 1 (PD-L1). We also found an obvious immune-regulating effect of PFKP in most cancer types. PFKP also had a strong negative correlation with several cancer drugs. Finally, ectopic expression of PFKP may depend on DNA methylation and several predicated transcription factors, including the KLF (KLF transcription factor) and Sp (Sp transcription factor) families. This pancancer analysis revealed that a high expression level of PFKP might be a useful biomarker and predictor in most cancer types. Additionally, the performance of PFKP across cancers also suggested its meaningful role in cancer immunity regulation, even in immunotherapy and drug resistance. Overall, PFKP might be explored as an auxiliary monitor for pancancer early prognosis and diagnosis.
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Affiliation(s)
- Jian Peng
- Department of Critical Care Medicine, Second Hospital of Shanxi Medical University, Taiyuan, 030001, Shanxi, China
| | - Pingping Li
- Comprehensive Liver Cancer Center, The Fifth Medical Center of the PLA General Hospital, Beijing, 100039, China
| | - Yuan Li
- Department of Critical Care Medicine, Second Hospital of Shanxi Medical University, Taiyuan, 030001, Shanxi, China
| | - Jichuan Quan
- Department of Colorectal Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100020, China
| | - Yanwei Yao
- Department of Critical Care Medicine, Second Hospital of Shanxi Medical University, Taiyuan, 030001, Shanxi, China
| | - Junfang Duan
- Department of Critical Care Medicine, Second Hospital of Shanxi Medical University, Taiyuan, 030001, Shanxi, China
| | - Xuemei Liu
- Department of Respiratory and Critical Care Medicine, Second People's Hospital of Taiyuan, Taiyuan, 030002, Shanxi, China
| | - Hao Li
- Department of Critical Care Medicine, Second Hospital of Shanxi Medical University, Taiyuan, 030001, Shanxi, China.
| | - Dajiang Yuan
- Department of Critical Care Medicine, Second Hospital of Shanxi Medical University, Taiyuan, 030001, Shanxi, China.
| | - Xiaoru Wang
- Department of Critical Care Medicine, Second Hospital of Shanxi Medical University, Taiyuan, 030001, Shanxi, China.
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105
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Honar YS, Javaher S, Soleimani M, Zarebkohan A, Farhadihosseinabadi B, Tohidfar M, Abdollahpour-Alitappeh M. Advanced stage, high-grade primary tumor ovarian cancer: a multi-omics dissection and biomarker prediction process. Sci Rep 2023; 13:17265. [PMID: 37828118 PMCID: PMC10570268 DOI: 10.1038/s41598-023-44246-9] [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: 11/25/2022] [Accepted: 10/05/2023] [Indexed: 10/14/2023] Open
Abstract
Ovarian cancer (OC) incidence and mortality rates continue to escalate globally. Early detection of OC is challenging due to extensive metastases and the ambiguity of biomarkers in advanced High-Grade Primary Tumors (HGPTs). In the present study, we conducted an in-depth in silico analysis in OC cell lines using the Gene Expression Omnibus (GEO) microarray dataset with 53 HGPT and 10 normal samples. Differentially-Expressed Genes (DEGs) were also identified by GEO2r. A variety of analyses, including gene set enrichment analysis (GSEA), ChIP enrichment analysis (ChEA), eXpression2Kinases (X2K) and Human Protein Atlas (HPA), elucidated signaling pathways, transcription factors (TFs), kinases, and proteome, respectively. Protein-Protein Interaction (PPI) networks were generated using STRING and Cytoscape, in which co-expression and hub genes were pinpointed by the cytoHubba plug-in. Validity of DEG analysis was achieved via Gene Expression Profiling Interactive Analysis (GEPIA). Of note, KIAA0101, RAD51AP1, FAM83D, CEP55, PRC1, CKS2, CDCA5, NUSAP1, ECT2, and TRIP13 were found as top 10 hub genes; SIN3A, VDR, TCF7L2, NFYA, and FOXM1 were detected as predominant TFs in HGPTs; CEP55, PRC1, CKS2, CDCA5, and NUSAP1 were identified as potential biomarkers from hub gene clustering. Further analysis indicated hsa-miR-215-5p, hsa-miR-193b-3p, and hsa-miR-192-5p as key miRNAs targeting HGPT genes. Collectively, our findings spotlighted HGPT-associated genes, TFs, miRNAs, and pathways as prospective biomarkers, offering new avenues for OC diagnostic and therapeutic approaches.
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Affiliation(s)
- Yousof Saeedi Honar
- Department of Plant Biotechnology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, 1983963113, Iran
| | - Saleh Javaher
- Department of Plant Biotechnology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, 1983963113, Iran
| | - Marziye Soleimani
- Department of Cell and Molecular Biology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, 1983969411, Iran
| | - Amir Zarebkohan
- Department of Medical Nanotechnology, Drug Applied Research Center, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, 516661-4733, Iran
| | | | - Masoud Tohidfar
- Department of Cell and Molecular Biology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, 1983969411, Iran.
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Rivest F, Eroglu D, Pelz B, Kowal J, Kehren A, Navikas V, Procopio MG, Bordignon P, Pérès E, Ammann M, Dorel E, Scalmazzi S, Bruno L, Ruegg M, Campargue G, Casqueiro G, Arn L, Fischer J, Brajkovic S, Joris P, Cassano M, Dupouy D. Fully automated sequential immunofluorescence (seqIF) for hyperplex spatial proteomics. Sci Rep 2023; 13:16994. [PMID: 37813886 PMCID: PMC10562446 DOI: 10.1038/s41598-023-43435-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 09/23/2023] [Indexed: 10/11/2023] Open
Abstract
Tissues are complex environments where different cell types are in constant interaction with each other and with non-cellular components. Preserving the spatial context during proteomics analyses of tissue samples has become an important objective for different applications, one of the most important being the investigation of the tumor microenvironment. Here, we describe a multiplexed protein biomarker detection method on the COMET instrument, coined sequential ImmunoFluorescence (seqIF). The fully automated method uses successive applications of antibody incubation and elution, and in-situ imaging enabled by an integrated microscope and a microfluidic chip that provides optimized optical access to the sample. We show seqIF data on different sample types such as tumor and healthy tissue, including 40-plex on a single tissue section that is obtained in less than 24 h, using off-the-shelf antibodies. We also present extensive characterization of the developed method, including elution efficiency, epitope stability, repeatability and reproducibility, signal uniformity, and dynamic range, in addition to marker and panel optimization strategies. The streamlined workflow using off-the-shelf antibodies, data quality enabling downstream analysis, and ease of reaching hyperplex levels make seqIF suitable for immune-oncology research and other disciplines requiring spatial analysis, paving the way for its adoption in clinical settings.
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Affiliation(s)
| | - Deniz Eroglu
- Lunaphore Technologies SA, Tolochenaz, Switzerland
| | | | - Joanna Kowal
- Lunaphore Technologies SA, Tolochenaz, Switzerland
| | | | | | | | | | - Emilie Pérès
- Lunaphore Technologies SA, Tolochenaz, Switzerland
| | - Marco Ammann
- Lunaphore Technologies SA, Tolochenaz, Switzerland
| | | | | | | | | | | | | | - Lionel Arn
- Lunaphore Technologies SA, Tolochenaz, Switzerland
| | | | | | - Pierre Joris
- Lunaphore Technologies SA, Tolochenaz, Switzerland
| | | | - Diego Dupouy
- Lunaphore Technologies SA, Tolochenaz, Switzerland.
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107
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Rehman A, Fatima I, Wang Y, Tong J, Noor F, Qasim M, Peng Y, Liao M. Unveiling the multi-target compounds of Rhazya stricta: Discovery and inhibition of novel target genes for the treatment of clear cell renal cell carcinoma. Comput Biol Med 2023; 165:107424. [PMID: 37717527 DOI: 10.1016/j.compbiomed.2023.107424] [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: 06/02/2023] [Revised: 07/24/2023] [Accepted: 08/28/2023] [Indexed: 09/19/2023]
Abstract
Clear cell renal cell carcinoma (ccRCC) is a prevalent kidney malignancy with a pressing need for innovative therapeutic strategies. In this context, emerging research has focused on exploring the medicinal potential of plants such as Rhazya stricta. Nevertheless, the complex molecular mechanisms underlying its potential therapeutic efficacy remain largely elusive. Our study employed an integrative approach comprising data mining,network pharmacology,tissue cell type analysis, and molecular modelling approaches to identify potent phytochemicals from R. stricta, with potential relevance for ccRCC treatments. Initially, we collected data on R. stricta's phytochemical from public databases. Subsequently, we integrated this information with differentially expressed genes (DEGs) in ccRCC, which were derived from microarray datasets(GSE16441,GSE66270, and GSE76351). We identified potential intersections between R. stricta and ccRCC targets, which enabled us to construct a compound-genes-pathway network using Cytoscape software. This helped illuminate R. stricta's multi-target pharmacological effects on ccRCC. Moreover, tissue cell type analysis added another layer of insight into the cellular specificity of potential therapeutic targets in the kidney. Through further Kaplan-Meier survival analysis, we pinpointed MMP9,ACE,ERBB2, and HSP90AA1 as prospective diagnostic and prognostic biomarkers for ccRCC. Notably, our study underscores the potential of R. stricta derived compounds-namely quebrachamine,corynan-17-ol, stemmadenine,strictanol,rhazinilam, and rhazimolare-to impede ccRCC progression by modulating the activity of MMP9,ACE,ERBB2, and HSP90AA1 genes. Further, molecular docking and dynamic simulations confirmed the plausible binding affinities of these compounds. Despite these promising findings, we recognize the need for comprehensive in vivo and in vitro studies to further investigate the pharmacokinetics and biosafety profiles of these compounds.
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Affiliation(s)
- Abdur Rehman
- Center of Bioinformatics, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Israr Fatima
- Center of Bioinformatics, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Yinuo Wang
- Center of Bioinformatics, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Jiapei Tong
- College of Information Engineering, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Fatima Noor
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, 38000, Pakistan
| | - Muhammad Qasim
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, 38000, Pakistan
| | - Yuzhong Peng
- Key Lab of Scientific Computing and Intelligent Information Processing in Universities of Guangxi, Nanning Normal University, Nanning, 530001, China.
| | - Mingzhi Liao
- Center of Bioinformatics, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China.
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108
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Yuan K, Zhang Y, Yu Y, Xu Y, Xian S. Anchoring Filament Protein Ladinin-1 is an Immunosuppressive Microenvironment and Cold Tumor Correlated Prognosticator in Lung Adenocarcinoma. Biochem Genet 2023; 61:2173-2202. [PMID: 37005975 DOI: 10.1007/s10528-023-10370-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 03/19/2023] [Indexed: 04/04/2023]
Abstract
Anchoring filament protein ladinin-1 (LAD1) codes for an anchor filament protein in the basement membrane. Here, we have aimed to determine its potential role in LUAD. According to the comprehensive analyses conducted in this study, we studied the expression, prognostic significance, function, methylation, copy number variations, and the immune cell infiltration of LAD1 in LUAD. A higher level of LAD1 gene expression was observed in the LUAD tumor tissues compared to the normal lung tissues (p < 0.001). Furthermore, the multivariate analysis indicated that a higher LAD1 gene expression level was the independent prognostic factor. Additionally, the DNA methylation level of the LAD1 was inversely linked to its expression (p < 0.001). We noted that the patients affected due to LAD1 hypomethylation showed a very low overall survival rate compared to the patients with a higher LAD1 methylation score (p < 0.05). Moreover, the results of the immunity analysis indicated that the LAD1 expression might be inversely linked to the immune cell infiltration degree, expression of the infiltrated immune cells, and the PD-L1 levels. Lastly, we supplemented some verification to increase the rigor of the study. The results suggested that high expression of LAD1 may be related to cold tumors. Hence, this indirectly reflects that the immunotherapy effect of LUAD patients with high LAD1 expression might be worse. Based on the role played by the LAD1 in the tumor immune microenvironment, it can be considered a potential biomarker for predicting the immunotherapy response to LUAD.
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Affiliation(s)
- Kun Yuan
- Department of Respiratory and Critical Care Medicine, Chengdu First People's Hospital, Chengdu, 610095, China
| | - Yiping Zhang
- Department of Radiation Oncology, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou, 350014, China
| | - Yilin Yu
- Department of Radiation Oncology, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou, 350014, China
| | - Yuanji Xu
- Department of Radiation Oncology, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou, 350014, China
| | - Shuang Xian
- China Drug Development and Medical Affairs Center, Eli Lilly and Company, Shanghai, 20040, China.
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Rydland A, Heinicke F, Flåm ST, Mjaavatten MD, Lie BA. Small extracellular vesicles have distinct CD81 and CD9 tetraspanin expression profiles in plasma from rheumatoid arthritis patients. Clin Exp Med 2023; 23:2867-2875. [PMID: 36826611 PMCID: PMC10543154 DOI: 10.1007/s10238-023-01024-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 02/06/2023] [Indexed: 02/25/2023]
Abstract
Extracellular vesicles (EVs) are implicated in the pathogenesis of rheumatoid arthritis (RA) but little is known about the composition of specific small EV (sEV) subpopulations. This study aimed to characterize the CD63, CD81 and CD9 tetraspanin profile in the membrane of single EVs in plasma from treatment naïve RA patients and assess potential discrepancies between methotrexate (MTX) responder groups. EVs isolated from plasma were characterized using transmission electron microscopy, and detection of surface markers (CD63, CD81 and CD9) on single EVs was performed on the ExoView platform. All RA patients (N = 8) were newly diagnosed, treatment naïve, females, ACPA positive and former smokers. The controls (N = 5) were matched for age and gender. After three months of MTX treatment, responders (N = 4) were defined as those with ΔDAS28 > 1.2 and DAS28 ≤ 3.2 post-treatment. The isolated EVs were 50-200 nm in size. The RA patients had a higher proportion of both CD9 and CD81 single positive sEVs compared to healthy controls, while there was a decrease in CD81/CD9 double positive sEVs in patients. Stratification of RA patients into MTX responders and non-responders revealed a distinctly higher proportion of CD81 single positive sEVs in the responder group. The proportion of CD81/CD9 double positive sEVs (anti-CD9 captured) was lower in the non-responders, but increased upon 3 months of MTX treatment. Our exploratory study revealed distinct tetraspanin profiles in RA patients suggesting their implication in RA pathophysiology and MTX treatment response.
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Affiliation(s)
- Anne Rydland
- Department of Medical Genetics, University of Oslo and Oslo University Hospital, Oslo, Norway.
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway.
- Center for Treatment of Rheumatic and Musculoskeletal Diseases (REMEDY), Diakonhjemmet Hospital, Oslo, Norway.
| | - Fatima Heinicke
- Department of Medical Genetics, University of Oslo and Oslo University Hospital, Oslo, Norway
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Center for Treatment of Rheumatic and Musculoskeletal Diseases (REMEDY), Diakonhjemmet Hospital, Oslo, Norway
| | - Siri T Flåm
- Department of Medical Genetics, University of Oslo and Oslo University Hospital, Oslo, Norway
- Center for Treatment of Rheumatic and Musculoskeletal Diseases (REMEDY), Diakonhjemmet Hospital, Oslo, Norway
| | - Maria D Mjaavatten
- Division of Rheumatology, Diakonhjemmet Hospital, Oslo, Norway
- Center for Treatment of Rheumatic and Musculoskeletal Diseases (REMEDY), Diakonhjemmet Hospital, Oslo, Norway
| | - Benedicte A Lie
- Department of Medical Genetics, University of Oslo and Oslo University Hospital, Oslo, Norway.
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway.
- Department of Immunology, Oslo University Hospital, Oslo, Norway.
- Center for Treatment of Rheumatic and Musculoskeletal Diseases (REMEDY), Diakonhjemmet Hospital, Oslo, Norway.
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Choi W, Kim YH, Woo SM, Yu Y, Lee MR, Lee WJ, Chun JW, Sim SH, Chae H, Shim H, Lee KS, Kong SY. Establishment of Patient-Derived Organoids Using Ascitic or Pleural Fluid from Cancer Patients. Cancer Res Treat 2023; 55:1077-1086. [PMID: 37309112 PMCID: PMC10582554 DOI: 10.4143/crt.2022.1630] [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: 12/20/2022] [Accepted: 06/07/2023] [Indexed: 06/14/2023] Open
Abstract
PURPOSE Patient-derived tumor cells can be a powerful resource for studying pathophysiological mechanisms and developing robust strategies for precision medicine. However, establishing organoids from patient-derived cells is challenging because of limited access to tissue specimens. Therefore, we aimed to establish organoids from malignant ascites and pleural effusions. MATERIALS AND METHODS Ascitic or pleural fluid from pancreatic, gastric, and breast cancer patients was collected and concentrated to culture tumor cells ex vivo. Organoids were considered to be successfully cultured when maintained for five or more passages. Immunohistochemical staining was performed to compare the molecular features, and drug sensitivity was assayed to analyze the clinical responses of original patients. RESULTS We collected 70 fluid samples from 58 patients (pancreatic cancer, n=39; gastric cancer, n=21; and breast cancer, n=10). The overall success rate was 40%; however, it differed with types of malignancy, with pancreatic, gastric, and breast cancers showing 48.7%, 33.3%, and 20%, respectively. Cytopathological results significantly differed between successful and failed cases (p=0.014). Immunohistochemical staining of breast cancer organoids showed molecular features identical to those of tumor tissues. In drug sensitivity assays, pancreatic cancer organoids recapitulated the clinical responses of the original patients. CONCLUSION Tumor organoids established from malignant ascites or pleural effusion of pancreatic, gastric, and breast cancers reflect the molecular characteristics and drug sensitivity profiles. Our organoid platform could be used as a testbed for patients with pleural and peritoneal metastases to guide precision oncology and drug discovery.
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Affiliation(s)
- Wonyoung Choi
- Center for Clinical Trials, National Cancer Center, Goyang, Korea
- Division of Cancer Biology, Cancer Molecular Biology Branch, Research Institute of National Cancer Center, Goyang, Korea
- Department of Cancer Biomedical Science, National Cancer Center Graduate School of Cancer Science and Policy, Goyang, Korea
| | - Yun-Hee Kim
- Department of Cancer Biomedical Science, National Cancer Center Graduate School of Cancer Science and Policy, Goyang, Korea
- Division of Technology Convergence, Cancer Molecular Imaging Branch, Research Institute of National Cancer Center, Goyang, Korea
| | - Sang Myung Woo
- Division of Rare and Refractory Cancer, Immuno-oncology Branch, Research Institute of National Cancer Center, Goyang, Korea
- Center for Liver and Pancreatobiliary Cancer, Hospital, National Cancer Center, Goyang, Korea
| | - Yebeen Yu
- Division of Rare and Refractory Cancer, Targeted Therapy Branch of Research Institute, National Cancer Center, Goyang, Korea
| | - Mi Rim Lee
- Division of Technology Convergence, Cancer Molecular Imaging Branch, Research Institute of National Cancer Center, Goyang, Korea
| | - Woo Jin Lee
- Center for Liver and Pancreatobiliary Cancer, Hospital, National Cancer Center, Goyang, Korea
- Division of Clinical Research, Cancer Outcome & Quality Improvement Branch, Research Institute of National Cancer Center, Goyang, Korea
| | - Jung Won Chun
- Center for Liver and Pancreatobiliary Cancer, Hospital, National Cancer Center, Goyang, Korea
- Division of Clinical Research, Interventional Medicine Branch, Research Institute of National Cancer Center, Goyang, Korea
| | - Sung Hoon Sim
- Center for Breast Cancer, National Cancer Center, Goyang, Korea
- Division of Rare and Refractory Cancer, Anticancer Resistance Branch, Research Institute of National Cancer Center, Goyang, Korea
| | - Heejung Chae
- Center for Breast Cancer, National Cancer Center, Goyang, Korea
- Center for Cancer Data Center, National Cancer Control Institute of National Cancer Center, Goyang, Korea
| | - Hyoeun Shim
- Department of Laboratory Medicine, National Cancer Center, Goyang, Korea
| | - Keun Seok Lee
- Center for Clinical Trials, National Cancer Center, Goyang, Korea
- Center for Breast Cancer, National Cancer Center, Goyang, Korea
| | - Sun-Young Kong
- Department of Cancer Biomedical Science, National Cancer Center Graduate School of Cancer Science and Policy, Goyang, Korea
- Division of Rare and Refractory Cancer, Targeted Therapy Branch of Research Institute, National Cancer Center, Goyang, Korea
- Department of Laboratory Medicine, National Cancer Center, Goyang, Korea
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Yang D, Han F, Cai J, Sun H, Wang F, Jiang M, Zhang M, Yuan M, Zhou W, Li H, Yang L, Bai Y, Xiao L, Dong H, Cheng Q, Mao H, Zhou L, Wang R, Li Y, Nie H. N-glycosylation by N-acetylglucosaminyltransferase IVa enhances the interaction of integrin β1 with vimentin and promotes hepatocellular carcinoma cell motility. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2023; 1870:119513. [PMID: 37295747 DOI: 10.1016/j.bbamcr.2023.119513] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 06/02/2023] [Accepted: 06/05/2023] [Indexed: 06/12/2023]
Abstract
N-glycosylation has been revealed to be tightly associated with cancer metastasis. As a key transferase that catalyzes the formation of β1,4 N-acetylglucosamine (β1,4GlcNAc) branches on the mannose core of N-glycans, N-acetylglucosaminyltransferase IVa (GnT-IVa) has been reported to be involved in hepatocellular carcinoma (HCC) metastasis by forming N-glycans; however, the underlying mechanisms are largely unknown. In the current study, we found that GnT-IVa was upregulated in HCC tissues and positively correlated with worse outcomes in HCC patients. We found that GnT-IVa could promote tumor growth in mice; notably, this effect was attenuated after mutating the enzymatic site (D445A) of GnT-IVa, suggesting that GnT-IVa regulated HCC progression by forming β1,4GlcNAc branches. To mechanistically investigate the role of GnT-IVa in HCC, we conducted GSEA and GO functional analysis as well as in vitro experiments. The results showed that GnT-IVa could enhance HCC cell migration, invasion and adhesion ability and increase β1,4GlcNAc branch glycans on integrin β1 (ITGB1), a tumor-associated glycoprotein that is closely involved in cell motility by interacting with vimentin. Interruption of β1,4GlcNAc branch glycan modification on ITGB1 could suppress the interaction of ITGB1 with vimentin and inhibit cell motility. These results revealed that GnT-IVa could promote HCC cell motility by affecting the biological functions of ITGB1 through N-glycosylation. In summary, our results revealed that GnT-IVa is highly expressed in HCC and can form β1,4GlcNAc branches on ITGB1, which are essential for interactions with vimentin to promote HCC cell motility. These findings not only proposed a novel mechanism for GnT-IVa in HCC progression but also revealed the significance of N-glycosylation on ITGB1 during the process, which may provide a novel target for future HCC therapy.
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Affiliation(s)
- Depeng Yang
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, Heilongjiang 150001, China
| | - Fang Han
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, Heilongjiang 150001, China
| | - Jialing Cai
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, Heilongjiang 150001, China
| | - Handi Sun
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, Heilongjiang 150001, China
| | - Fengyou Wang
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, Heilongjiang 150001, China
| | - Meiyi Jiang
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, Heilongjiang 150001, China
| | - Mengmeng Zhang
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, Heilongjiang 150001, China
| | - Mengfan Yuan
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, Heilongjiang 150001, China
| | - Wenyang Zhou
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, Heilongjiang 150001, China
| | - Huaxin Li
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, Heilongjiang 150001, China
| | - Lijun Yang
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, Heilongjiang 150001, China
| | - Yan Bai
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, Heilongjiang 150001, China
| | - Lixing Xiao
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, Heilongjiang 150001, China
| | - Haiyang Dong
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, Heilongjiang 150001, China
| | - Qixiang Cheng
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, Heilongjiang 150001, China
| | - Haoyu Mao
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, Heilongjiang 150001, China
| | - Lu Zhou
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, Heilongjiang 150001, China
| | - Ruonan Wang
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, Heilongjiang 150001, China
| | - Yu Li
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, Heilongjiang 150001, China.
| | - Huan Nie
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, Heilongjiang 150001, China.
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Ma L, Zhang S, Liang Q, Huang W, Wang H, Pan E, Xu P, Zhang S, Tao F, Tang J, Qing R. CrMP-Sol database: classification, bioinformatic analyses and comparison of cancer-related membrane proteins and their water-soluble variant designs. BMC Bioinformatics 2023; 24:360. [PMID: 37743473 PMCID: PMC10518928 DOI: 10.1186/s12859-023-05477-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 09/12/2023] [Indexed: 09/26/2023] Open
Abstract
Membrane proteins are critical mediators for tumor progression and present enormous therapeutic potentials. Although gene profiling can identify their cancer-specific signatures, systematic correlations between protein functions and tumor-related mechanisms are still unclear. We present here the CrMP-Sol database ( https://bio-gateway.aigene.org.cn/g/CrMP ), which aims to breach the gap between the two. Machine learning was used to extract key functional descriptions for protein visualization in the 3D-space, where spatial distributions provide function-based predictive connections between proteins and cancer types. CrMP-Sol also presents QTY-enabled water-soluble designs to facilitate native membrane protein studies despite natural hydrophobicity. Five examples with varying transmembrane helices in different categories were used to demonstrate the feasibility. Native and redesigned proteins exhibited highly similar characteristics, predicted structures and binding pockets, and slightly different docking poses against known ligands, although task-specific designs are still required for proteins more susceptible to internal hydrogen bond formations. The database can accelerate therapeutic developments and biotechnological applications of cancer-related membrane proteins.
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Affiliation(s)
- Lina Ma
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Sitao Zhang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Qi Liang
- Zhejiang Lab, Research Center for Intelligent Computing Platforms, Hangzhou, 311121, Zhejiang, China
| | - Wenting Huang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Hui Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Emily Pan
- The Lawrenceville School, 2500 Main Street, Lawrenceville, NJ, 08648, USA
| | - Ping Xu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Shuguang Zhang
- Media Lab, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - Fei Tao
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.
| | - Jin Tang
- Zhejiang Lab, Research Center for Intelligent Computing Platforms, Hangzhou, 311121, Zhejiang, China.
| | - Rui Qing
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.
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Dixit N, Motwani H, Patel SK, Rawal RM, Solanki HA. Decoding the mechanism of andrographolide to combat hepatocellular carcinoma: a network pharmacology integrated molecular docking and dynamics approach. J Biomol Struct Dyn 2023:1-19. [PMID: 37728545 DOI: 10.1080/07391102.2023.2256866] [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: 06/14/2023] [Accepted: 09/02/2023] [Indexed: 09/21/2023]
Abstract
HepatoCellular Carcinoma, being one of the most mortally convoluted malignancy with mounting number of occurrences across the world and being classified as the third most prevalent cause of cancer-associated mortalities and sixth most prevalent neoplasia. The active phytoconstituent andrographolide, derived from Andrographis paniculata is conveyed to reconcile a number of human ailments including various oncologies. However, the molecular mechanism underlying the anti-oncogenic effects of Andrographolide on HCC remains skeptical and unclear, emerging as a budding challenge for researchers and oncologists. The present study intends to analyze the underlying pharmacological mechanism of Andrographolide over HCC, established via assimilated approach of network pharmacology. Herein, the Network pharmacology stratagem was instigated to investigate potential HCC targets. The Andrographolide targets along with HCC targets were extracted from multiple databases. A total of 162 potential overlapping targets among HCC and Andrographolide were obtained and further subjected to gene ontology and Pathway enrichment analysis by employing OmicsBox and DAVID database, respectively. Subsequently, Protein-protein interaction network construction by Cytoscape software identified the top 10 hub nodes which were validated by survival and expression analysis. Further, the results derived from molecular docking and dynamic simulations by CB-Dock2 server and Desmond module (Schrodinger software) indicate ALB, CCND1, HIF1A, TNF, and VEGFA as potential Andrographolide related targets with high binding affinity and promising complex stability. Our findings not only reveal the antioncogenic role of andrographolide but also provide novel insights illuminating the identified targets as scientific foundation for anti-oncogenic clinical application of andrographolide in HCC therapeutics.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Nandan Dixit
- Department of Botany, Bioinformatics and Climate Change Impacts Management, Gujarat University, Ahmedabad, Gujarat, India
| | - Harsha Motwani
- Department of Botany, Bioinformatics and Climate Change Impacts Management, Gujarat University, Ahmedabad, Gujarat, India
| | - Saumya K Patel
- Department of Botany, Bioinformatics and Climate Change Impacts Management, Gujarat University, Ahmedabad, Gujarat, India
| | - Rakesh M Rawal
- Department of Life Science, School of Sciences, Gujarat University, Ahmedabad, Gujarat, India
| | - Hiteshkumar A Solanki
- Department of Botany, Bioinformatics and Climate Change Impacts Management, Gujarat University, Ahmedabad, Gujarat, India
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114
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Xu Z, Ma D, Su H, Jia X, Li Y, Lu Y, Xie Z. Explore the dominant factor in prime editing via a view of DNA processing. Synth Syst Biotechnol 2023; 8:371-377. [PMID: 37325180 PMCID: PMC10265487 DOI: 10.1016/j.synbio.2023.05.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 05/23/2023] [Accepted: 05/25/2023] [Indexed: 06/17/2023] Open
Abstract
Prime editing is a revolutionary gene-editing method that is capable of introducing insertions, deletions and base substitutions into the genome. However, the editing efficiency of Prime Editor (PE) is limited by the DNA repair process. Here, we show that overexpression of the flap structure-specific endonuclease 1 (FEN1) and the DNA ligase 1 (LIG1) increases the efficiency of prime editing, which is similar to the dominant negative mutL homolog 1 (MLH1dn). In addition, MLH1 is still the dominant factor over FEN1 and LIG1 in prime editing. Our results help to further understand the relationship of proteins involved in prime editing and envisage future directions for the development of PE.
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Affiliation(s)
- Zhimeng Xu
- MOE Key Laboratory of Bioinformatics and Bioinformatics Division, Center for Synthetic and System Biology, Department of Automation, Beijing National Research Center for Information Science and Technology, Tsinghua University, Beijing, 100084, China
| | - Dacheng Ma
- Research Center for Biological Computation, Zhejiang Laboratory, Hangzhou, 311100, China
| | - Houzhen Su
- MOE Key Laboratory of Bioinformatics and Bioinformatics Division, Center for Synthetic and System Biology, Department of Automation, Beijing National Research Center for Information Science and Technology, Tsinghua University, Beijing, 100084, China
| | - Xiaodong Jia
- Comprehensive Liver Cancer Centre, The Fifth Medical Center of PLA General Hospital, Beijing, China
| | - Yinqing Li
- School of Pharmaceutical Sciences, IDG/McGovern Institute for Brain Research, Tsinghua University, Beijing, China
| | - Yinying Lu
- Comprehensive Liver Cancer Centre, The Fifth Medical Center of PLA General Hospital, Beijing, China
| | - Zhen Xie
- MOE Key Laboratory of Bioinformatics and Bioinformatics Division, Center for Synthetic and System Biology, Department of Automation, Beijing National Research Center for Information Science and Technology, Tsinghua University, Beijing, 100084, China
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115
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Peralta S, Grenier JK, Webb SM, Miller AD, Miranda IC, Parker JSL. Transcriptomic signatures of feline chronic gingivostomatitis are influenced by upregulated IL6. Sci Rep 2023; 13:13437. [PMID: 37596310 PMCID: PMC10439118 DOI: 10.1038/s41598-023-40679-4] [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: 04/23/2023] [Accepted: 08/16/2023] [Indexed: 08/20/2023] Open
Abstract
Feline chronic gingivostomatitis (FCGS) is a relatively common and debilitating disease characterized by bilateral inflammation and ulceration of the caudal oral mucosa, alveolar and buccal mucosa, and varying degrees of periodontal disease. The etiopathogenesis of FCGS remains unresolved. In this study, we performed bulk RNA-seq molecular profiling of affected tissues derived from a cohort of client-owned cats with FCGS compared to tissues from unaffected animals, to identify candidate genes and pathways that can help guide future exploration of novel clinical solutions. We complemented transcriptomic findings with immunohistochemistry and in situ hybridization assays to better understand the biological significance of the results and performed RNA-seq validation of biologically relevant differentially expressed genes using qPCR assays to demonstrate technical reproducibility. Transcriptomic profiles of oral mucosal tissues in cats with FCGS are enriched with immune- and inflammation-related genes and pathways that appear to be largely influenced by IL6, and include NFKB, JAK/STAT, IL-17 and IFN type I and II signaling, offering new opportunities to develop novel clinical applications based on a more rational understanding of the disease.
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Affiliation(s)
- Santiago Peralta
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA.
- Clinical Programs Center, College of Veterinary Medicine, Cornell University, Box 31, Ithaca, NY, 14853, USA.
| | - Jennifer K Grenier
- Transcriptional Regulation and Expression Facility, Biotechnology Resource Center, Institute of Biotechnology, Cornell University, Ithaca, NY, 14853, USA
| | - Suzin M Webb
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| | - Andrew D Miller
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| | - Ileana C Miranda
- Laboratory of Comparative Pathology, Memorial Sloan Kettering Cancer Center, Weill Cornell Medical College, and The Rockefeller University, New York, NY, 10065, USA
| | - John S L Parker
- Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
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116
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Faber ML, Oldham RAA, Thakur A, Rademacher MJ, Kubicka E, Dlugi TA, Gifford SA, McKillop WM, Schloemer NJ, Lum LG, Medin JA. Novel anti-CD30/CD3 bispecific antibodies activate human T cells and mediate potent anti-tumor activity. Front Immunol 2023; 14:1225610. [PMID: 37646042 PMCID: PMC10461807 DOI: 10.3389/fimmu.2023.1225610] [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: 05/19/2023] [Accepted: 07/12/2023] [Indexed: 09/01/2023] Open
Abstract
CD30 is expressed on Hodgkin lymphomas (HL), many non-Hodgkin lymphomas (NHLs), and non-lymphoid malignancies in children and adults. Tumor expression, combined with restricted expression in healthy tissues, identifies CD30 as a promising immunotherapy target. An anti-CD30 antibody-drug conjugate (ADC) has been approved by the FDA for HL. While anti-CD30 ADCs and chimeric antigen receptors (CARs) have shown promise, their shortcomings and toxicities suggest that alternative treatments are needed. We developed novel anti-CD30 x anti-CD3 bispecific antibodies (biAbs) to coat activated patient T cells (ATCs) ex vivo prior to autologous re-infusions. Our goal is to harness the dual specificity of the biAb, the power of cellular therapy, and the safety of non-genetically modified autologous T cell infusions. We present a comprehensive characterization of the CD30 binding and tumor cell killing properties of these biAbs. Five unique murine monoclonal antibodies (mAbs) were generated against the extracellular domain of human CD30. Resultant anti-CD30 mAbs were purified and screened for binding specificity, affinity, and epitope recognition. Two lead mAb candidates with unique sequences and CD30 binding clusters that differ from the ADC in clinical use were identified. These mAbs were chemically conjugated with OKT3 (an anti-CD3 mAb). ATCs were armed and evaluated in vitro for binding, cytokine production, and cytotoxicity against tumor lines and then in vivo for tumor cell killing. Our lead mAb was subcloned to make a Master Cell Bank (MCB) and screened for binding against a library of human cell surface proteins. Only huCD30 was bound. These studies support a clinical trial in development employing ex vivo-loading of autologous T cells with this novel biAb.
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Affiliation(s)
- Mary L. Faber
- Department of Pediatrics, Medical College of Wisconsin (MCW), Milwaukee, WI, United States
| | - Robyn A. A. Oldham
- Department of Pediatrics, Medical College of Wisconsin (MCW), Milwaukee, WI, United States
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Archana Thakur
- Department of Medicine, Division of Hematology/Oncology, University of Virginia Cancer Center, Charlottesville, VA, United States
| | - Mary Jo Rademacher
- Department of Pediatrics, Medical College of Wisconsin (MCW), Milwaukee, WI, United States
| | - Ewa Kubicka
- Department of Medicine, Division of Hematology/Oncology, University of Virginia Cancer Center, Charlottesville, VA, United States
| | - Theresa A. Dlugi
- Department of Pediatrics, Medical College of Wisconsin (MCW), Milwaukee, WI, United States
| | - Steven A. Gifford
- Department of Pediatrics, Medical College of Wisconsin (MCW), Milwaukee, WI, United States
| | - William M. McKillop
- Department of Pediatrics, Medical College of Wisconsin (MCW), Milwaukee, WI, United States
| | - Nathan J. Schloemer
- Department of Pediatrics, Medical College of Wisconsin (MCW), Milwaukee, WI, United States
| | - Lawrence G. Lum
- Department of Medicine, Division of Hematology/Oncology, University of Virginia Cancer Center, Charlottesville, VA, United States
| | - Jeffrey A. Medin
- Department of Pediatrics, Medical College of Wisconsin (MCW), Milwaukee, WI, United States
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
- Department of Biochemistry, MCW, Milwaukee, WI, United States
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117
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Li XY, He XY, Zhao H, Qi L, Lu JJ. Identification of a novel therapeutic target for lung cancer: Mitochondrial ribosome protein L9. Pathol Res Pract 2023; 248:154625. [PMID: 37343379 DOI: 10.1016/j.prp.2023.154625] [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: 03/23/2023] [Revised: 06/13/2023] [Accepted: 06/14/2023] [Indexed: 06/23/2023]
Abstract
Lung cancer has a high fatality rate and incidence rate. At present, the initial and progress mechanism of lung cancer has not been completely elucidated and new therapeutic targets still need to be developed. In this study, the screening process was based on lung cancer expression profile data and survival analysis. Mitochondrial ribosome protein L9 (MRPL9) was upregulated in lung cancer tissues and related to the poor overall survival rate and recurrence-free survival rate of lung cancer patients. Knockdown of MRPL9 inhibited the proliferation, sphere-formation, and migration ability of lung cancer cells. MRPL9 was associated with the c-MYC signaling pathway, and lung cancer patients with high expression of both MRPL9 and MYC had a poor prognosis. Furthermore, c-MYC was associated with the epithelial-mesenchymal transition (EMT) regulatory protein zinc finger E-box binding homeobox 1 (ZEB1) by bioinformatics analysis. The relationship between ZEB1 and c-MYC was further confirmed by interfering with c-MYC expression. MRPL9 is a potential therapeutic target for lung cancer and exerts its biological functions by affecting the transcription factor c-MYC thereby regulating the EMT regulator ZEB1.
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Affiliation(s)
- Xin-Yuan Li
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao, China
| | - Xin-Yu He
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao, China
| | - Hong Zhao
- The First Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou 310006, China
| | - Lu Qi
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao, China; Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China.
| | - Jin-Jian Lu
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao, China; Department of Pharmaceutical Sciences, Faculty of Health Sciences, University of Macau, Macao, China; Guangdong-Hong Kong-Macau Joint Lab on Chinese Medicine and Immune Disease Research, University of Macau, Macao, China.
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118
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Choi W, Wu H, Yserentant K, Huang B, Cheng Y. Efficient tagging of endogenous proteins in human cell lines for structural studies by single-particle cryo-EM. Proc Natl Acad Sci U S A 2023; 120:e2302471120. [PMID: 37487103 PMCID: PMC10401002 DOI: 10.1073/pnas.2302471120] [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: 02/12/2023] [Accepted: 06/21/2023] [Indexed: 07/26/2023] Open
Abstract
CRISPR/Cas9-based genome engineering has revolutionized our ability to manipulate biological systems, particularly in higher organisms. Here, we designed a set of homology-directed repair donor templates that enable efficient tagging of endogenous proteins with affinity tags by transient transfection and selection of genome-edited cells in various human cell lines. Combined with technological advancements in single-particle cryogenic electron microscopy, this strategy allows efficient structural studies of endogenous proteins captured in their native cellular environment and during different cellular processes. We demonstrated this strategy by tagging six different human proteins in both HEK293T and Jurkat cells. Moreover, analysis of endogenous glyceraldehyde 3-phosphate dehydrogenase (GAPDH) in HEK293T cells allowed us to follow its behavior spatially and temporally in response to prolonged oxidative stress, correlating the increased number of oxidation-induced inactive catalytic sites in GAPDH with its translocation from cytosol to nucleus.
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Affiliation(s)
- Wooyoung Choi
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA94143
| | - Hao Wu
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA94143
| | - Klaus Yserentant
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA94143
| | - Bo Huang
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA94143
- Chan Zuckerberg Biohub-San Francisco, San Francisco, CA94158
| | - Yifan Cheng
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA94143
- HHMI, University of California, San Francisco, CA94143
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Liu SC, Gong LL, Huang FC, Xu N, Yang KX, Liu XH, Li WL. RNF114 facilitates the proliferation, stemness, and metastasis of colorectal cancer. Pathol Res Pract 2023; 248:154716. [PMID: 37523804 DOI: 10.1016/j.prp.2023.154716] [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: 11/29/2022] [Revised: 07/17/2023] [Accepted: 07/25/2023] [Indexed: 08/02/2023]
Abstract
BACKGROUND Colorectal cancer (CRC), the fourth of the world's major common malignancy, poses a serious threat to the physical and mental health of the population. Nevertheless, the prognosis of CRC patients remains unsatisfactory. Consequently, it is still imperative to continuously discover the CRC mechanisms. METHODS The expression profiles of mRNAs were recognized by whole transcriptome sequencing to identity differentially expressed mRNA (DE-mRNA). TCGA COAD cohort, PPOGgene and Kaplan-Meier Plotter databases were utilized to validate RNF114 relevance to CRC prognosis. The effect of RNF114 on the malignant biological behavior of CRC was explored in CRC cells and subcutaneous tumor models and lung metastasis model after exogenous regulation of RNF114. RESULTS A total of 1358 DE-mRNAs were identified, including 617 up-regulated and 741 down-regulated DE-mRNAs, and they were mainly involved in the term of receptor ligand activity, Wnt signaling pathway and pathway in cancer. Notably, RNF114 was hyper-expressed in tissues and cell of CRC, and significantly correlated with tumor invasion depth and TNM stage of CRC patients. RNF114 expression were significantly associated with overall survival, and had superior diagnostic value in CRC. In vitro, knockdown of RNF114 statistically diminished the proliferation, stemness, invasion and wound healing of CRC cells and facilitated their apoptosis, and the opposite result was observed for overexpression of RNF114. In vivo, knockdown of RNF114 effectively diminished the mass and volume of tumors, and lung metastasis in animal model. CONCLUSIONS In summary, we identified DE-mRNAs in CRC, and elucidated that RNF114 facilitates CRC process. The discovery will contribute to theoretical foundation for RNF114 as a potential therapeutic target and biomarker, and offer new perspectives for CRC research.
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Affiliation(s)
- Shi-Cheng Liu
- Department of Colorectal Surgery, the Third Affiliated Hospital of Kunming Medical University (the Tumor Hospital of Yunnan), China
| | - Le-Lan Gong
- Department of Colorectal Surgery, the Third Affiliated Hospital of Kunming Medical University (the Tumor Hospital of Yunnan), China
| | - Feng-Chang Huang
- Department of Oncology, the First Affiliated Hospital of Kunming Medical University, China
| | - Ning Xu
- Department of Oncology, the First Affiliated Hospital of Kunming Medical University, China
| | - Ke-Xin Yang
- Department of Colorectal Surgery, the Third Affiliated Hospital of Kunming Medical University (the Tumor Hospital of Yunnan), China
| | - Xi-Hong Liu
- Department of Oncology, the First Affiliated Hospital of Kunming Medical University, China
| | - Wen-Liang Li
- Department of Colorectal Surgery, the Third Affiliated Hospital of Kunming Medical University (the Tumor Hospital of Yunnan), China.
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Petell CJ, Burkholder NT, Ruiz PA, Skela J, Foreman JR, Southwell LE, Temple BR, Krajewski K, Strahl BD. The bromo-adjacent homology domains of PBRM1 associate with histone tails and contribute to PBAF-mediated gene regulation. J Biol Chem 2023; 299:104996. [PMID: 37394010 PMCID: PMC10425938 DOI: 10.1016/j.jbc.2023.104996] [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: 01/31/2023] [Revised: 06/14/2023] [Accepted: 06/16/2023] [Indexed: 07/04/2023] Open
Abstract
A critical component of gene regulation is recognition of histones and their post-translational modifications by transcription-associated proteins or complexes. Although many histone-binding reader modules have been characterized, the bromo-adjacent homology (BAH) domain family of readers is still poorly characterized. A pre-eminent member of this family is PBRM1 (BAF180), a component of the PBAF chromatin-remodeling complex. PBRM1 contains two adjacent BAH domains of unknown histone-binding potential. We evaluated the tandem BAH domains for their capacity to associate with histones and to contribute to PBAF-mediated gene regulation. The BAH1 and BAH2 domains of human PBRM1 broadly interacted with histone tails, but they showed a preference for unmodified N-termini of histones H3 and H4. Molecular modeling and comparison of the BAH1 and BAH2 domains with other BAH readers pointed to a conserved binding mode via an extended open pocket and, in general, an aromatic cage for histone lysine binding. Point mutants that were predicted to disrupt the interaction between the BAH domains and histones reduced histone binding in vitro and resulted in dysregulation of genes targeted by PBAF in cellulo. Although the BAH domains in PBRM1 were important for PBAF-mediated gene regulation, we found that overall chromatin targeting of PBRM1 was not dependent on BAH-histone interaction. Our findings identify a function of the PBRM1 BAH domains in PBAF activity that is likely mediated by histone tail interaction.
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Affiliation(s)
- Christopher J Petell
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA; UNC Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Nathaniel T Burkholder
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA; UNC Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Paloma A Ruiz
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Jessica Skela
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Jake R Foreman
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Lauren E Southwell
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Brenda R Temple
- UNC Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA; R L Juliano Structural Bioinformatics Core Facility, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Krzysztof Krajewski
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA; UNC Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Brian D Strahl
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA; UNC Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.
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Guo J, Huang S, Yi Q, Liu N, Cui T, Duan S, Chen J, Li J, Li J, Wang L, Gao Y, Nie G. Hepatic Clstn3 Ameliorates Lipid Metabolism Disorders in High Fat Diet-Induced NAFLD through Activation of FXR. ACS OMEGA 2023; 8:26158-26169. [PMID: 37521618 PMCID: PMC10373204 DOI: 10.1021/acsomega.3c02347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 06/22/2023] [Indexed: 08/01/2023]
Abstract
Non-alcoholic fatty liver disease (NAFLD) has become serious liver disease all over the world. At present, NAFLD caused by high calorie and fat diet is increasing. Calsyntenin-3 (Clstn3) is a transmembrane protein that has recently been found to participate in lipid energy metabolism. But whether Clstn3 affects NAFLD lipid metabolism has not been analyzed. We stimulate the mice primary hepatocytes (MPHs) with oleic acid and palmitic acid (OA&PA) to establish a cell model. Then, potential targets, including Clstn3 gene, were validated for improving lipid metabolism disorder in NAFLD model mice (HFD and db/db) by silencing and overexpressing hepatic Clstn3. Moreover, the effects of Clstn3 on lipid homeostasis were determined by functional determination, triglyceride (TG) levels, total cholesterol (TC) levels, ELISA, and qRT-PCR detection. Our results displayed that Clstn3 was decreased in the NAFLD mice model. Also, overexpression of Clstn3 improved lipid metabolism disorders, gluconeogenesis, and energy homeostasis and reduced liver injury, inflammation, and oxidative stress injury. However, opposite results were obtained in Clstn3-silencing mice, suggesting that the Clstn3 gene is closely related to lipid metabolism disorder in NAFLD. RNAseq expression demonstrated that Farnesoid X Receptor (FXR) expression was increased after overexpression of Clstn3. Clstn3 supplementation in FXRKO mice can improve the dysfunction caused by insufficient FXR, suggesting that Clstn3 can improve the NAFLD lipid metabolism disorder to some extent through FXR, which may provide a new method for the treatment of NAFLD.
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Affiliation(s)
- Jingyi Guo
- Science
and Technology Innovation Center, Guangzhou
University of Chinese Medicine, Guangzhou, Guangdong 510080, China
- State
Key Laboratory of Dampness Syndrome of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University
of Chinese Medicine, Guangzhou, Guangdong 510120, China
| | - Shangyi Huang
- Science
and Technology Innovation Center, Guangzhou
University of Chinese Medicine, Guangzhou, Guangdong 510080, China
| | - Qincheng Yi
- State
Key Laboratory of Dampness Syndrome of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University
of Chinese Medicine, Guangzhou, Guangdong 510120, China
| | - Naihua Liu
- Science
and Technology Innovation Center, Guangzhou
University of Chinese Medicine, Guangzhou, Guangdong 510080, China
| | - Tianqi Cui
- Science
and Technology Innovation Center, Guangzhou
University of Chinese Medicine, Guangzhou, Guangdong 510080, China
| | - Siwei Duan
- Science
and Technology Innovation Center, Guangzhou
University of Chinese Medicine, Guangzhou, Guangdong 510080, China
| | - Jiabing Chen
- Science
and Technology Innovation Center, Guangzhou
University of Chinese Medicine, Guangzhou, Guangdong 510080, China
| | - Jiayu Li
- Science
and Technology Innovation Center, Guangzhou
University of Chinese Medicine, Guangzhou, Guangdong 510080, China
| | - Jun Li
- State
Key Laboratory of Dampness Syndrome of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University
of Chinese Medicine, Guangzhou, Guangdong 510120, China
| | - Lei Wang
- State
Key Laboratory of Dampness Syndrome of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University
of Chinese Medicine, Guangzhou, Guangdong 510120, China
- Department
of Cardiovascular Medicine, The Second Affiliated
Hospital of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong 510120, China
| | - Yong Gao
- Science
and Technology Innovation Center, Guangzhou
University of Chinese Medicine, Guangzhou, Guangdong 510080, China
| | - Guangning Nie
- State
Key Laboratory of Dampness Syndrome of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University
of Chinese Medicine, Guangzhou, Guangdong 510120, China
- Department
of Gynecology, The Second Affiliated Hospital
of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong 510120, China
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Ye J, Tang H, Xie C, Han W, Shen G, Qian Y, Xu J. Identification of sterile a-motif domain-containing 9-like as a potential biomarker in patients with cutaneous melanoma. PeerJ 2023; 11:e15634. [PMID: 37426410 PMCID: PMC10329423 DOI: 10.7717/peerj.15634] [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: 03/10/2023] [Accepted: 06/05/2023] [Indexed: 07/11/2023] Open
Abstract
Skin cutaneous melanoma (SKCM) is one of the most aggressive malignancies, accounting for approximately 75% of skin cancer-related fatalities annually. Sterile a-motif domain-containing 9-like (SAMD9L) has been found to regulate cell proliferation and suppress the neoplastic phenotype, but its specific role in SKCM remains unknown. To investigate the cancer-associated immunology of SKCM and the role of SAMD9L in tumor progression, we conducted an integrative bioinformatics analysis that revealed elevated expression levels of SAMD9L in SKCM. ROC curves and survival analyses confirmed the considerable diagnostic and prognostic abilities of SAMD9L. Moreover, a real-world cohort of 35 SKCM patients from the First Affiliated Hospital of Soochow University showed that higher expression levels of SAMD9L were associated with better prognosis. We performed validation experiments, including cell culture, generation of lentiviral-transfected SKCM cell lines, cell proliferation assay, and transwell assay, which demonstrated that down-regulation of SAMD9L significantly promoted proliferation and migration capacities of SKCM cells. Additionally, SAMD9L expression was found to be strongly linked to immune infiltration. Our results revealed a positive correlation between SAMD9L and XAF1 expression, suggesting that SAMD9L may serve as a prospective prognostic indicator of SKCM with co-expressed XAF1 gene. In summary, our findings indicate that SAMD9L may serve as a promising prognostic and therapeutic biomarker and play a critical role in tumor-immune interactions in SKCM.
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Affiliation(s)
- Junsen Ye
- The Department of Scientific Education, The First People’s Hospital of Jiande, Hangzhou, China
| | - Haidan Tang
- Affiliated Hospital of Youjiang Medical University for Nationalities, Guangxi, China
| | - Chuanrui Xie
- The Department of Surgery, The People’s Hospital of Rongcheng, Rongcheng, China
| | - Wei Han
- Institute of Regenerative Biology and Medicine, Helmholtz Centre for Environmental Research–UFZ, Munich, Germany
| | - Guoliang Shen
- Department of Burn and Plastic Surgery, First Affiliated Hospital of Soochow University, Suzhou, China
| | - Ying Qian
- Department of Burn and Plastic Surgery, First Affiliated Hospital of Soochow University, Suzhou, China
| | - Jin Xu
- Institute of Regenerative Biology and Medicine, Helmholtz Centre for Environmental Research–UFZ, Munich, Germany
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Zhao S, Ye B, Chi H, Cheng C, Liu J. Identification of peripheral blood immune infiltration signatures and construction of monocyte-associated signatures in ovarian cancer and Alzheimer's disease using single-cell sequencing. Heliyon 2023; 9:e17454. [PMID: 37449151 PMCID: PMC10336450 DOI: 10.1016/j.heliyon.2023.e17454] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 06/12/2023] [Accepted: 06/18/2023] [Indexed: 07/18/2023] Open
Abstract
Background Ovarian cancer (OC) is a common tumor of the female reproductive system, while Alzheimer's disease (AD) is a prevalent neurodegenerative disease that primarily affects cognitive function in the elderly. Monocytes are immune cells in the blood that can enter tissues and transform into macrophages, thus participating in immune and inflammatory responses. Overall, monocytes may play an important role in Alzheimer's disease and ovarian cancer. Methods The CIBERSORT algorithm results indicate a potential crucial role of monocytes/macrophages in OC and AD. To identify monocyte marker genes, single-cell RNA-seq data of peripheral blood mononuclear cells (PBMCs) from OC and AD patients were analyzed. Enrichment analysis of various cell subpopulations was performed using the "irGSEA" R package. The estimation of cell cycle was conducted with the "tricycle" R package, and intercellular communication networks were analyzed using "CellChat". For 134 monocyte-associated genes (MRGs), bulk RNA-seq data from two diseased tissues were obtained. Cox regression analysis was employed to develop risk models, categorizing patients into high-risk (HR) and low-risk (LR) groups. The model's accuracy was validated using an external GEO cohort. The different risk groups were evaluated in terms of immune cell infiltration, mutational status, signaling pathways, immune checkpoint expression, and immunotherapy. To identify characteristic MRGs in AD, two machine learning algorithms, namely random forest and support vector machine (SVM), were utilized. Results Based on Cox regression analysis, a risk model consisting of seven genes was developed in OC, indicating a better prognosis for patients in the LR group. The LR group had a higher tumor mutation burden, immune cell infiltration abundance, and immune checkpoint expression. The results of the TIDE algorithm and the IMvigor210 cohort showed that the LR group was more likely to benefit from immunotherapy. Finally, ZFP36L1 and AP1S2 were identified as characteristic MRGs affecting OC and AD progression. Conclusion The risk profile containing seven genes identified in this study may help further guide clinical management and targeted therapy for OC. ZFP36L1 and AP1S2 may serve as biomarkers and new therapeutic targets for patients with OC and AD.
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Affiliation(s)
- Songyun Zhao
- Department of Neurosurgery, Wuxi People's Hospital Affiliated to Nanjing Medical University, Wuxi, 214000, China
| | - Bicheng Ye
- School of Clinical Medicine, Yangzhou Polytechnic College, Yangzhou, 225000, China
| | - Hao Chi
- Clinical Medical College, Southwest Medical University, Luzhou, 646000, China
| | - Chao Cheng
- Department of Neurosurgery, Wuxi People's Hospital Affiliated to Nanjing Medical University, Wuxi, 214000, China
| | - Jinhui Liu
- Department of Gynecology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210000, China
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He E, Jiang Y, Wei D, Wang Y, Sun W, Jia M, Shi B, Cui H. The potential effects and mechanism of echinacoside powder in the treatment of Hirschsprung's Disease. MATHEMATICAL BIOSCIENCES AND ENGINEERING : MBE 2023; 20:14222-14240. [PMID: 37679133 DOI: 10.3934/mbe.2023636] [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: 09/09/2023]
Abstract
Possible complications, such as intestinal obstruction and inflammation of the intestinal tract, can have a detrimental effect on the prognosis after surgery for Hirschsprung disease. The aim of this study was to investigate the potential targets and mechanisms of action of echinacoside to improve the prognosis of Hirschsprung disease. Genes related to the disease were obtained through analysis of the GSE96854 dataset and four databases: OMIM, DisGeNET, Genecard and NCBI. The targets of echinacoside were obtained from three databases: PharmMapper, Drugbank and TargetNet. The intersection of disease genes and drug targets was validated by molecular docking. The valid docked targets were further explored for their expression by using immunohistochemistry. In this study, enrichment analysis was used to explore the mechanistic pathways involved in the genes. Finally, we identified CA1, CA2, CA9, CA12, DNMT1, RIMS2, RPGRIP1L and ZEB2 as the core targets. Except for ZEB2, which is predominantly expressed in brain tissue, the remaining seven genes show tissue specificity and high expression in the gastrointestinal tract. RIMS2 possesses a high mutation phenomenon in pan-cancer, while a validated ceRNA network of eight genes was constructed. The core genes are involved in several signaling pathways, including the one-carbon metabolic process, carbonate dehydratase activity and others. This study may help us to further understand the pharmacological mechanisms of echinacoside and provide new guidance and ideas to guide the treatment of Hirschsprung disease.
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Affiliation(s)
- Enyang He
- Tianjin Medical University of Pediatric Surgery, Tianjin, China
| | - Yuhang Jiang
- Tianjin Medical University of Clinical Medicine, Tianjin, China
| | - Diwei Wei
- Tianjin Medical University of Pediatrics, Tianjin, China
| | - Yifan Wang
- Tianjin Medical University of Pediatrics, Tianjin, China
| | - Wenjing Sun
- Tianjin Medical University of Pediatric Surgery, Tianjin, China
| | - Miao Jia
- Tianjin Medical University of Pediatric Surgery, Tianjin, China
| | - Bowen Shi
- Tianjin Medical University of Pediatric Surgery, Tianjin, China
| | - Hualei Cui
- Tianjin Children's Hospital of Minimally Invasive Surgery, Tianjin, China
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Lu J, Liang K, Zou R, Peng Y, Wang H, Huang R, Zeng Z, Feng Z, Fan Y, Zhang S, Ji Y, Pang X, Wang Y, Zhang H, Wang Z. Comprehensive analysis of the prognostic and immunological signature of eight Tripartitemotif (TRIM) family molecules in human gliomas. Aging (Albany NY) 2023; 15:5798-5825. [PMID: 37367937 PMCID: PMC10333093 DOI: 10.18632/aging.204841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 06/09/2023] [Indexed: 06/28/2023]
Abstract
BACKGROUND TRIM family molecules have been identified as being involved in the tumor progression of various cancer types. Increasingly, experimental evidence indicates that some of TRIM family molecules are implicated in glioma tumorigenesis. However, the diverse genomic changes, prognostic values and immunological landscapes of TRIM family of molecules have yet to be fully determined in glioma. METHODS In our study, employing the comprehensive bioinformatics tools, we evaluated the unique functions of 8 TRIM members including TRIM5/17/21/22/24/28/34/47 in gliomas. RESULTS The expression levels of 7 TRIM members (TRIM5/21/22/24/28/34/47) were higher in glioma as well as its diverse cancer subtypes than in normal tissues, whereas the expression level of TRIM17 was the opposite, lower in the former than in the latter. In addition, survival analysis revealed that the high expression profiles of TRIM5/21/22/24/28/34/47 were associated with poor overall survival (OS), disease-specific survival (DSS) and progress-free interval (PFI) in glioma patients, whereas TRIM17 displayed adverse outcomes. Moreover, the 8 TRIM molecules expression as well as methylation profiles remarkably correlated with different WHO grades. And genetic alterations, including mutations and copy number alterations (CNAs), in the TRIM family were correlated with longer OS, DSS and progress-free survival (PFS) in glioma patients. Furthermore, through Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis results of these 8 molecules and their related genes, we found that these molecules may change the immune infiltration of the tumor microenvironment and regulate the expression of immune checkpoint molecules (ICMs), affecting the occurrence and development of gliomas. The correlation analyses between the 8 TRIM molecules and TMB (tumor mutational burden)/MSI (microsatellite instability)/ICMs discovered that as the expression level of TRIM5/21/22/24/28/34/47 increased, the TMB score also increased significantly, while TRIM17 showed an opposite outcome. Further, a 6-gene signature (TRIM 5/17/21/28/34/47) for predicting overall survival (OS) in gliomas was built by using the least absolute shrinkage and selection operator (LASSO) regression, and the survival and time-dependent ROC analyses all were found to perform well in testing and validation cohorts. Results of multivariate COX regression analysis showed that TRIM5/28 are both expected to become independent risk predictors to guide clinical treatment. CONCLUSION In general, the results indicate that TRIM5/17/21/22/24/28/34/47 might exert a crucial influence on gliomas tumorigenesis and might be putative prognostic markers and therapeutic targets for glioma patients.
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Affiliation(s)
- Jiajie Lu
- Institute of Neuroscience, Department of Neurosurgery, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou 510260, China
- Department of Clinical Medicine, The Second Clinical School of Guangzhou Medical University, Guangzhou 510182, China
| | - Kairong Liang
- Institute of Neuroscience, Department of Neurosurgery, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou 510260, China
| | - Renheng Zou
- Institute of Neuroscience, Department of Neurosurgery, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou 510260, China
| | - Yuecheng Peng
- Institute of Neuroscience, Department of Neurosurgery, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou 510260, China
- Department of Clinical Medicine, The Second Clinical School of Guangzhou Medical University, Guangzhou 510182, China
| | - Haojian Wang
- Institute of Neuroscience, Department of Neurosurgery, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou 510260, China
- Department of Clinical Medicine, The Second Clinical School of Guangzhou Medical University, Guangzhou 510182, China
| | - Rihong Huang
- Institute of Neuroscience, Department of Neurosurgery, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou 510260, China
- Department of Clinical Medicine, The Second Clinical School of Guangzhou Medical University, Guangzhou 510182, China
| | - Zhaorong Zeng
- Institute of Neuroscience, Department of Neurosurgery, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou 510260, China
- Department of Clinical Medicine, The Second Clinical School of Guangzhou Medical University, Guangzhou 510182, China
| | - Zejia Feng
- Institute of Neuroscience, Department of Neurosurgery, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou 510260, China
- Department of Clinical Medicine, The Second Clinical School of Guangzhou Medical University, Guangzhou 510182, China
| | - Yongyang Fan
- Institute of Neuroscience, Department of Neurosurgery, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou 510260, China
- Department of Clinical Medicine, The Second Clinical School of Guangzhou Medical University, Guangzhou 510182, China
| | - Shizhen Zhang
- Institute of Neuroscience, Department of Neurosurgery, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou 510260, China
| | - Yunxiang Ji
- Institute of Neuroscience, Department of Neurosurgery, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou 510260, China
| | - Xiao Pang
- Institute of Neuroscience, Department of Neurosurgery, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou 510260, China
| | - Yezhong Wang
- Institute of Neuroscience, Department of Neurosurgery, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou 510260, China
| | - Hongri Zhang
- Department of Neurosurgery, The First Affiliated Hospital and College of Clinical Medicine of Henan University of Science and Technology, Luoyang, Henan 471003, China
| | - Zhaotao Wang
- Institute of Neuroscience, Department of Neurosurgery, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou 510260, China
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He XL, Lyu WY, Li XY, Zhao H, Qi L, Lu JJ. Identification of glycogen phosphorylase L as a potential target for lung cancer. Med Oncol 2023; 40:211. [PMID: 37347364 DOI: 10.1007/s12032-023-02069-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 05/29/2023] [Indexed: 06/23/2023]
Abstract
Traditional Chinese medicine (TCM) has been widely used for cancer treatment. Identification of anti-cancer targets of TCM is the first and principal step in discovering molecular mechanisms of TCM as well as obtaining novel targets for cancer therapy. In this study, glycogen phosphorylase L (PYGL) was identified as one of the targeted proteins for several TCMs and was upregulated in various cancer types. The expression level of PYGL was positively correlated with the stage of lung cancer and the poor prognosis of patients. Meanwhile, knockdown of PYGL significantly inhibited proliferation and migration in lung cancer cells. In addition, PYGL was associated with spindle, kinetochore, and microtubule, the cellular components that are closely related to mitosis, in lung cancer. Moreover, PYGL was more susceptible to be upregulated by 144 mutated genes. Taken together, PYGL is a potential target for lung cancer treatment and its molecular mechanism probably influences the mitotic function of cells by regulating energy metabolism.
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Affiliation(s)
- Xin-Ling He
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao, China
| | - Wen-Yu Lyu
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao, China
| | - Xin-Yuan Li
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao, China
| | - Hong Zhao
- The First Affiliated Hospital of Zhejiang, Chinese Medical University, Hangzhou, 310006, China
| | - Lu Qi
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao, China.
- Department of Pathology, School of Basic Medical Sciences, Southern Medical University, No.1023 Shatai Road Baiyun District, Guangzhou, 510515, Guangdong, China.
| | - Jin-Jian Lu
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao, China.
- Department of Pharmaceutical Sciences, Faculty of Health Sciences, University of Macau, Macao, China.
- Guangdong-Hong Kong-Macau Joint Lab on Chinese Medicine and Immune Disease Research, University of Macau, Macao, China.
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García-Cárdenas JM, Armendáriz-Castillo I, García-Cárdenas N, Pesantez-Coronel D, López-Cortés A, Indacochea A, Guerrero S. Data mining identifies novel RNA-binding proteins involved in colon and rectal carcinomas. Front Cell Dev Biol 2023; 11:1088057. [PMID: 37384253 PMCID: PMC10293682 DOI: 10.3389/fcell.2023.1088057] [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: 11/03/2022] [Accepted: 02/13/2023] [Indexed: 06/30/2023] Open
Abstract
Colorectal adenocarcinoma (COREAD) is the second most deadly cancer and third most frequently encountered malignancy worldwide. Despite efforts in molecular subtyping and subsequent personalized COREAD treatments, multidisciplinary evidence suggests separating COREAD into colon cancer (COAD) and rectal cancer (READ). This new perspective could improve diagnosis and treatment of both carcinomas. RNA-binding proteins (RBPs), as critical regulators of every hallmark of cancer, could fulfill the need to identify sensitive biomarkers for COAD and READ separately. To detect new RBPs involved in COAD and READ progression, here we used a multidata integration strategy to prioritize tumorigenic RBPs. We analyzed and integrated 1) RBPs genomic and transcriptomic alterations from 488 COAD and 155 READ patients, 2) ∼ 10,000 raw associations between RBPs and cancer genes, 3) ∼ 15,000 immunostainings, and 4) loss-of-function screens performed in 102 COREAD cell lines. Thus, we unraveled new putative roles of NOP56, RBM12, NAT10, FKBP1A, EMG1, and CSE1L in COAD and READ progression. Interestingly, FKBP1A and EMG1 have never been related with any of these carcinomas but presented tumorigenic features in other cancer types. Subsequent survival analyses highlighted the clinical relevance of FKBP1A, NOP56, and NAT10 mRNA expression to predict poor prognosis in COREAD and COAD patients. Further research should be performed to validate their clinical potential and to elucidate their molecular mechanisms underlying these malignancies.
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Affiliation(s)
- Jennyfer M. García-Cárdenas
- Laboratorio de Ciencia de Datos Biomédicos, Escuela de Medicina, Facultad de Ciencias Médicas de la Salud y de la Vida, Universidad Internacional del Ecuador, Quito, Ecuador
- Latin American Network for the Implementation and Validation of Clinical Pharmacogenomics Guidelines (RELIVAF-CYTED), Madrid, Spain
| | - Isaac Armendáriz-Castillo
- Laboratorio de Ciencia de Datos Biomédicos, Escuela de Medicina, Facultad de Ciencias Médicas de la Salud y de la Vida, Universidad Internacional del Ecuador, Quito, Ecuador
- Latin American Network for the Implementation and Validation of Clinical Pharmacogenomics Guidelines (RELIVAF-CYTED), Madrid, Spain
- Facultad de Ingenierías y Ciencias Aplicadas, Universidad Internacional SEK, Quito, Ecuador
| | | | - David Pesantez-Coronel
- Medical Oncology Department Hospital Clinic and Translational Genomics and Targeted Therapies in Solid Tumors, IDIBAPS, Barcelona, Spain
| | - Andrés López-Cortés
- Latin American Network for the Implementation and Validation of Clinical Pharmacogenomics Guidelines (RELIVAF-CYTED), Madrid, Spain
- Cancer Research Group (CRG), Faculty of Medicine, Universidad de Las Américas, Quito, Ecuador
| | - Alberto Indacochea
- Medical Oncology Department Hospital Clinic and Translational Genomics and Targeted Therapies in Solid Tumors, IDIBAPS, Barcelona, Spain
| | - Santiago Guerrero
- Laboratorio de Ciencia de Datos Biomédicos, Escuela de Medicina, Facultad de Ciencias Médicas de la Salud y de la Vida, Universidad Internacional del Ecuador, Quito, Ecuador
- Latin American Network for the Implementation and Validation of Clinical Pharmacogenomics Guidelines (RELIVAF-CYTED), Madrid, Spain
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Wannowius M, Karakus E, Aktürk Z, Breuer J, Geyer J. Role of the Sodium-Dependent Organic Anion Transporter (SOAT/SLC10A6) in Physiology and Pathophysiology. Int J Mol Sci 2023; 24:9926. [PMID: 37373074 DOI: 10.3390/ijms24129926] [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: 04/24/2023] [Revised: 06/02/2023] [Accepted: 06/03/2023] [Indexed: 06/29/2023] Open
Abstract
The sodium-dependent organic anion transporter (SOAT, gene symbol SLC10A6) specifically transports 3'- and 17'-monosulfated steroid hormones, such as estrone sulfate and dehydroepiandrosterone sulfate, into specific target cells. These biologically inactive sulfo-conjugated steroids occur in high concentrations in the blood circulation and serve as precursors for the intracrine formation of active estrogens and androgens that contribute to the overall regulation of steroids in many peripheral tissues. Although SOAT expression has been detected in several hormone-responsive peripheral tissues, its quantitative contribution to steroid sulfate uptake in different organs is still not completely clear. Given this fact, the present review provides a comprehensive overview of the current knowledge about the SOAT by summarizing all experimental findings obtained since its first cloning in 2004 and by processing SOAT/SLC10A6-related data from genome-wide protein and mRNA expression databases. In conclusion, despite a significantly increased understanding of the function and physiological significance of the SOAT over the past 20 years, further studies are needed to finally establish it as a potential drug target for endocrine-based therapy of steroid-responsive diseases such as hormone-dependent breast cancer.
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Affiliation(s)
- Marie Wannowius
- Institute of Pharmacology and Toxicology, Faculty of Veterinary Medicine, Biomedical Research Center Seltersberg (BFS), Justus Liebig University of Giessen, Schubertstr. 81, 35392 Giessen, Germany
| | - Emre Karakus
- Institute of Pharmacology and Toxicology, Faculty of Veterinary Medicine, Biomedical Research Center Seltersberg (BFS), Justus Liebig University of Giessen, Schubertstr. 81, 35392 Giessen, Germany
| | - Zekeriya Aktürk
- General Practice, Faculty of Medicine, University of Augsburg, 86159 Augsburg, Germany
| | - Janina Breuer
- Institute of Pharmacology and Toxicology, Faculty of Veterinary Medicine, Biomedical Research Center Seltersberg (BFS), Justus Liebig University of Giessen, Schubertstr. 81, 35392 Giessen, Germany
| | - Joachim Geyer
- Institute of Pharmacology and Toxicology, Faculty of Veterinary Medicine, Biomedical Research Center Seltersberg (BFS), Justus Liebig University of Giessen, Schubertstr. 81, 35392 Giessen, Germany
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Ma Q, Chang L, Wang W, Che L, Song X, Li G, Zhang Y, Chen Y, Gu Z, Ge X. Leucyl and Cystinyl Aminopeptidase as a Prognostic-Related Biomarker in OV Correlating with Immune Infiltrates. Pharmgenomics Pers Med 2023; 16:551-568. [PMID: 37293607 PMCID: PMC10244028 DOI: 10.2147/pgpm.s400145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Accepted: 05/03/2023] [Indexed: 06/10/2023] Open
Abstract
Background It was indicated that tumor intrinsic heterogeneity and the tumor microenvironment (TME) of ovarian cancer (OV) influence immunotherapy efficacy and patient outcomes. Leucyl and cystinyl aminopeptidase (LNPEP) encodes a zinc-dependent aminopeptidase, which has been proved to participant in the vesicle-mediated transport and class I MHC mediated antigen processing and presentation. However, the function of LNPEP in TME of OV and its potential molecular mechanisms have not been determined. Therefore, we aimed to investigate a prognostic biomarker which may be helpful in identifying TME heterogeneity of ovarian cancer. Methods In this study, bioinformatics databases were used to explore the expression profile and immune infiltration of LNPEP. Bioinformatics analyses of survival data and interactors of LNPEP were conducted to predict the prognostic value of LNPEP in OV. The protein levels of LNPEP were validated by Western blot and immunohistochemistry. Results Based on the TCGA data, our data displayed that the mRNA expression of LNPEP was markedly down-regulated in ovarian cancer than that in para-cancer tissues, contrary to the protein level. Importantly, high LNPEP expression was associated with poor prognosis in patients with OV. Furthermore, Cox regression analysis showed that LNPEP was an independent prognostic factor in OV. GO and KEGG pathway analyses indicated the co-expressed genes of LNPEP were mainly related to a variety of immune-related pathways, including Th1 and Th2 cell differentiation, Th17 cell differentiation, and immunoregulatory interaction. Our data also demonstrated that the expression of LNPEP was strongly correlated with immune infiltration levels, immunomodulators, chemokines and chemokine receptors. Conclusion In our study, we identified and established a prognostic signature of immune-related LNPEP in OV, which will be of great value in predicting the prognosis of clinical trials and may become a new therapeutic target for immunological research and potential prognostic biomarker in OV.
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Affiliation(s)
- Qian Ma
- Genetics and Prenatal Diagnosis Center, First Affiliated Hospital, Zhengzhou University, Zhengzhou, 450052, People’s Republic of China
| | - Lei Chang
- Department of Gynecology and Obstetrics, First Affiliated Hospital, Zhengzhou University, Zhengzhou, 450052, People’s Republic of China
| | - Wenwen Wang
- Department of Gynecology and Obstetrics, First Affiliated Hospital, Zhengzhou University, Zhengzhou, 450052, People’s Republic of China
| | - Lingyi Che
- Genetics and Prenatal Diagnosis Center, First Affiliated Hospital, Zhengzhou University, Zhengzhou, 450052, People’s Republic of China
| | - Xiaoqin Song
- Physical Examination Center, First Affiliated Hospital, Zhengzhou University, Zhengzhou, 450052, People’s Republic of China
| | - Gailing Li
- Department of Gynecology and Obstetrics, First Affiliated Hospital, Zhengzhou University, Zhengzhou, 450052, People’s Republic of China
| | - Ying Zhang
- Department of Gynecology and Obstetrics, First Affiliated Hospital, Zhengzhou University, Zhengzhou, 450052, People’s Republic of China
| | - Yibing Chen
- Genetics and Prenatal Diagnosis Center, First Affiliated Hospital, Zhengzhou University, Zhengzhou, 450052, People’s Republic of China
| | - Zhuoyu Gu
- Department of Thoracic Surgery, First Affiliated Hospital, Zhengzhou University, Zhengzhou, 450052, People’s Republic of China
| | - Xin Ge
- Department of Breast Surgery, First Affiliated Hospital, Zhengzhou University, Zhengzhou, 450052, People’s Republic of China
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Somsuan K, Aluksanasuwan S. Bioinformatic analyses reveal the prognostic significance and potential role of ankyrin 3 (ANK3) in kidney renal clear cell carcinoma. Genomics Inform 2023; 21:e22. [PMID: 37423640 PMCID: PMC10326534 DOI: 10.5808/gi.23013] [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: 02/13/2023] [Revised: 04/14/2023] [Accepted: 04/20/2023] [Indexed: 07/08/2023] Open
Abstract
Kidney renal clear cell carcinoma (KIRC) is one of the most aggressive cancer type of the urinary system. Metastatic KIRC patients have poor prognosis and limited therapeutic options. Ankyrin 3 (ANK3) is a scaffold protein that plays important roles in maintaining physiological function of the kidney and its alteration is implicated in many cancers. In this study, we investigated differential expression of ANK3 in KIRC using GEPIA2, UALCAN, and HPA databases. Survival analysis was performed by GEPIA2, Kaplan-Meier plotter, and OSkirc databases. Genetic alterations of ANK3 in KIRC were assessed using cBioPortal database. Interaction network and functional enrichment analyses of ANK3-correlated genes in KIRC were performed using GeneMANIA and Shiny GO, respectively. Finally, the TIMER2.0 database was used to assess correlation between ANK3 expression and immune infiltration in KIRC. We found that ANK3 expression was significantly decreased in KIRC compared to normal tissues. The KIRC patients with low ANK3 expression had poorer survival outcomes than those with high ANK3 expression. ANK3 mutations were found in 2.4% of KIRC patients and were frequently co-mutated with several genes with a prognostic significance. ANK3-correlated genes were significantly enriched in various biological processes, mainly involved in peroxisome proliferator-activated receptor (PPAR) signaling pathway, in which positive correlations of ANK3 with PPARA and PPARG expressions were confirmed. Expression of ANK3 in KIRC was significantly correlated with infiltration level of B cell, CD8+ T cell, macrophage, and neutrophil. These findings suggested that ANK3 could serve as a prognostic biomarker and promising therapeutic target for KIRC.
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Affiliation(s)
- Keerakarn Somsuan
- School of Medicine, Mae Fah Luang University, Chiang Rai 57100, Thailand
- Cancer and Immunology Research Unit (CIRU), Mae Fah Luang University, Chiang Rai 57100, Thailand
| | - Siripat Aluksanasuwan
- School of Medicine, Mae Fah Luang University, Chiang Rai 57100, Thailand
- Cancer and Immunology Research Unit (CIRU), Mae Fah Luang University, Chiang Rai 57100, Thailand
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131
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Jiang S, Xiao M, Shi Y, Wang Y, Xu Z, Wang K. Identification of m7G-Related miRNA Signatures Associated with Prognosis, Oxidative Stress, and Immune Landscape in Lung Adenocarcinoma. Biomedicines 2023; 11:1569. [PMID: 37371664 DOI: 10.3390/biomedicines11061569] [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: 04/20/2023] [Revised: 05/13/2023] [Accepted: 05/24/2023] [Indexed: 06/29/2023] Open
Abstract
The role of N7-methylguanosine(m7G)-related miRNAs in lung adenocarcinoma (LUAD) remains unclear. We used LUAD data from The Cancer Genome Atlas (TCGA) to establish a risk model based on the m7G-related miRNAs, and divided patients into high-risk or low-risk subgroups. A nomogram for predicting overall survival (OS) was then constructed based on the independent risk factors. In addition, we performed a functional enrichment analysis and defined the oxidative stress-related genes, immune landscape as well as a drug response profile in the high-risk and low-risk subgroups. This study incorporated 28 m7G-related miRNAs into the risk model. The data showed a significant difference in the OS between the high-risk and low-risk subgroups. The receiver operating characteristic curve (ROC) predicted that the area under the curve (AUC) of one-year, three-year and five-year OS was 0.781, 0.804 and 0.853, respectively. The C-index of the prognostic nomogram for predicting OS was 0.739. We then analyzed the oxidative stress-related genes and immune landscape in the high-risk and low-risk subgroups. The data demonstrated significant differences in the expression of albumin (ALB), estimated score, immune score, stromal score, immune cell infiltration and functions between the high-risk and low-risk subgroups. In addition, the drug response analysis showed that low-risk subgroups may be more sensitive to tyrosine kinase inhibitor (TKI) and histone deacetylase (HDAC) inhibitors. We successfully developed a novel risk model based on m7G-related miRNAs in this study. The model can predict clinical prognosis and guide therapeutic regimens in patients with LUAD. Our data also provided new insights into the molecular mechanisms of m7G in LUAD.
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Affiliation(s)
- Sujing Jiang
- Department of Respiratory and Critical Care Medicine, The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu 322000, China
| | - Mingshu Xiao
- Department of Respiratory and Critical Care Medicine, The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu 322000, China
| | - Yueli Shi
- Department of Respiratory and Critical Care Medicine, The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu 322000, China
| | - Yongfang Wang
- Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310009, China
| | - Zhiyong Xu
- Department of Respiratory and Critical Care Medicine, The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu 322000, China
| | - Kai Wang
- Department of Respiratory and Critical Care Medicine, The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu 322000, China
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Huang AS, Tong BCK, Hung HCH, Wu AJ, Ho OKY, Kong AHY, Leung MMK, Bai J, Fu X, Yu Z, Li M, Leung TF, Mak JCW, Leung GPH, Cheung KH. Targeting calcium signaling by inositol trisphosphate receptors: A novel mechanism for the anti-asthmatic effects of Houttuynia cordata. Biomed Pharmacother 2023; 164:114935. [PMID: 37245337 DOI: 10.1016/j.biopha.2023.114935] [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: 03/01/2023] [Revised: 05/09/2023] [Accepted: 05/22/2023] [Indexed: 05/30/2023] Open
Abstract
Asthma is a chronic inflammatory disease characterized by airway hypersensitivity and remodeling. The current treatments provide only short-term benefits and may have undesirable side effects; thus, alternative or supplementary therapy is needed. Because intracellular calcium (Ca2+) signaling plays an essential role in regulating the contractility and remodeling of airway smooth muscle cells, the targeting of Ca2+ signaling is a potential therapeutic strategy for asthma. Houttuynia cordata is a traditional Chinese herb that is used to treat asthma due to its anti-allergic and anti-inflammatory properties. We hypothesized that H. cordata might modulate intracellular Ca2+ signaling and could help relieve asthmatic airway remodeling. We found that the mRNA and protein levels of inositol trisphosphate receptors (IP3Rs) were elevated in interleukin-stimulated primary human bronchial smooth muscle cells and a house dust mite-sensitized model of asthma. The upregulation of IP3R expression enhanced intracellular Ca2+ release upon stimulation and contributed to airway remodeling in asthma. Intriguingly, pretreatment with H. cordata essential oil rectified the disruption of Ca2+ signaling, mitigated asthma development, and prevented airway narrowing. Furthermore, our analysis suggested that houttuynin/2-undecanone could be the bioactive component in H. cordata essential oil because we found similar IP3R suppression in response to the commercially available derivative sodium houttuyfonate. An in silico analysis showed that houttuynin, which downregulates IP3R expression, binds to the IP3 binding domain of IP3R and may mediate a direct inhibitory effect. In summary, our findings suggest that H. cordata is a potential alternative treatment choice that may reduce asthma severity by targeting the dysregulation of Ca2+ signaling.
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Affiliation(s)
- Alexis Shiying Huang
- Teaching and Research Division, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong Special Administrative Region of China
| | - Benjamin Chun-Kit Tong
- Teaching and Research Division, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong Special Administrative Region of China
| | - Harry Chun-Hin Hung
- Teaching and Research Division, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong Special Administrative Region of China
| | - Aston Jiaxi Wu
- Teaching and Research Division, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong Special Administrative Region of China
| | - Olivia Ka-Yi Ho
- Teaching and Research Division, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong Special Administrative Region of China
| | - Anna Hau-Yee Kong
- Teaching and Research Division, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong Special Administrative Region of China
| | - Maggie Ming-Ki Leung
- Teaching and Research Division, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong Special Administrative Region of China
| | - Jingxuan Bai
- Teaching and Research Division, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong Special Administrative Region of China
| | - Xiuqiong Fu
- Teaching and Research Division, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong Special Administrative Region of China
| | - Zhiling Yu
- Teaching and Research Division, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong Special Administrative Region of China
| | - Min Li
- Teaching and Research Division, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong Special Administrative Region of China
| | - Ting Fan Leung
- Department of Paediatrics, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong Special Administrative Region of China
| | - Judith Choi-Wo Mak
- Department of Pharmacology and Pharmacy, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region of China
| | - George Pak-Heng Leung
- Department of Pharmacology and Pharmacy, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region of China
| | - King-Ho Cheung
- Teaching and Research Division, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong Special Administrative Region of China.
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Yoshikawa N, Yoshida K, Liu W, Matsukawa T, Hattori S, Yoshihara M, Tamauchi S, Ikeda Y, Yokoi A, Shimizu Y, Niimi K, Kajiyama H. The prognostic significance of DDIT4 in endometrial cancer. Cancer Biomark 2023:CBM220368. [PMID: 37302026 DOI: 10.3233/cbm-220368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
BACKGROUND Despite extensive research on endometrial cancer and tumor hypoxic microenvironment, there are no reports exploring the role of DDIT4 in endometrial cancer. OBJECTIVE This study aimed to elucidate the significance of DDIT4, as a prognostic biomarker for endometrial cancer by immunohistochemical staining and statistical analysis. METHODS Four endometrial cancer cells were cultured under normoxia and hypoxia, and the differentially expressed genes were examined using RNA-seq. Immunohistochemical staining for DDIT4 and HIF1A was performed in 86 patients with type II endometrial cancer treated at our hospital, and their correlation with other clinicopathological factors and the prognostic role was analyzed using statistical methods. RESULTS The expression analysis of hypoxia-inducible genes using four types of endometrial cancer cells revealed that DDIT4 was among the 28 genes that were upregulated in all cells. Based on our results of immunohistochemistry of DDIT4 expression in endometrial cancer tissues, univariate and multivariate analyses based on COX regression analysis showed that high DDIT4 expression significantly correlated to favorable prognosis in both progression-free survival and overall survival. Limited to recurrent cases, metastasis to only lymph nodes was significantly related to high DDIT4 expression, whereas metastasis to other parenchymal organs was significantly dominant in patients with low DDIT4 expression. CONCLUSIONS The expression of DDIT4 enables to predict survival and recurrence in type II endometrial cancer.
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Affiliation(s)
- Nobuhisa Yoshikawa
- Department of Obstetrics and Gynecology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Kosuke Yoshida
- Department of Obstetrics and Gynecology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Wenting Liu
- Bell Research Center, Department of Obstetrics and Gynecology Collaborative Research, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Tetsuya Matsukawa
- Department of Obstetrics and Gynecology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Satomi Hattori
- Department of Obstetrics and Gynecology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Masato Yoshihara
- Department of Obstetrics and Gynecology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Satoshi Tamauchi
- Department of Obstetrics and Gynecology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yoshiki Ikeda
- Department of Obstetrics and Gynecology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Akira Yokoi
- Department of Obstetrics and Gynecology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yusuke Shimizu
- Department of Obstetrics and Gynecology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Kaoru Niimi
- Department of Obstetrics and Gynecology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Hiroaki Kajiyama
- Department of Obstetrics and Gynecology, Nagoya University Graduate School of Medicine, Nagoya, Japan
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Lim MCC, Jantaree P, Naumann M. The conundrum of Helicobacter pylori-associated apoptosis in gastric cancer. Trends Cancer 2023:S2405-8033(23)00080-8. [PMID: 37230895 DOI: 10.1016/j.trecan.2023.04.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 04/21/2023] [Accepted: 04/27/2023] [Indexed: 05/27/2023]
Abstract
Helicobacter pylori is a human microbial pathogen that colonizes the gastric epithelium and causes type B gastritis with varying degrees of active inflammatory infiltrates. The underlying chronic inflammation induced by H. pylori and other environmental factors may promote the development of neoplasms and adenocarcinoma of the stomach. Dysregulation of various cellular processes in the gastric epithelium and in different cells of the microenvironment is a hallmark of H. pylori infection. We address the conundrum of H. pylori-associated apoptosis and review distinct mechanisms induced in host cells that either promote or suppress apoptosis in gastric epithelial cells, often simultaneously. We highlight key processes in the microenvironment that contribute to apoptosis and gastric carcinogenesis.
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Affiliation(s)
- Michelle C C Lim
- Institute of Experimental Internal Medicine, Otto von Guericke University Magdeburg, 39120 Magdeburg, Germany
| | - Phatcharida Jantaree
- Institute of Experimental Internal Medicine, Otto von Guericke University Magdeburg, 39120 Magdeburg, Germany
| | - Michael Naumann
- Institute of Experimental Internal Medicine, Otto von Guericke University Magdeburg, 39120 Magdeburg, Germany.
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135
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Peralta S, Grenier JK, Webb SM, Miller AD, Miranda IC, Parker JSL. Transcriptomic signatures of feline chronic gingivostomatitis are influenced by upregulated IL6. RESEARCH SQUARE 2023:rs.3.rs-2852140. [PMID: 37205490 PMCID: PMC10187381 DOI: 10.21203/rs.3.rs-2852140/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Feline chronic gingivostomatitis (FCGS) is a relatively common and debilitating disease characterized by bilateral inflammation and ulceration of the caudal oral mucosa, alveolar and buccal mucosa, and varying degrees of periodontal disease. The etiopathogenesis of FCGS remains unresolved. In this study, we performed bulk RNA-seq molecular profiling of affected tissues derived from a cohort of client-owned cats with FCGS compared to tissues from unaffected animals, to identify candidate genes and pathways that can help guide future exploration of novel clinical solutions. We complemented transcriptomic findings with immunohistochemistry and in situ hybridization assays to better understand the biological significance of the results and performed RNA-seq validation of selected differentially expressed genes using qPCR assays to demonstrate technical reproducibility. Transcriptomic profiles of oral mucosal tissues in cats with FCGS are enriched with immune- and inflammation-related genes and pathways that appear to be largely influenced by IL6 , and include NFKB, JAK/STAT, IL-17 and IFN type I and II signaling, offering new opportunities to develop novel clinical applications based on a more rational understanding of the disease.
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Affiliation(s)
| | | | | | | | - Ileana C Miranda
- Memorial Sloan Kettering Cancer Center, Weill Cornell Medical College, The Rockefeller University
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Zaki MSA, Eldeen MA, Abdulsahib WK, Shati AA, Alqahtani YA, Al-Qahtani SM, Otifi HM, Asiri A, Hassan HM, Emam Mohammed Ahmed H, Dawood SA, Negm A, Eid RA. A Comprehensive Pan-Cancer Analysis Identifies CEP55 as a Potential Oncogene and Novel Therapeutic Target. Diagnostics (Basel) 2023; 13:1613. [PMID: 37175004 PMCID: PMC10178510 DOI: 10.3390/diagnostics13091613] [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: 02/25/2023] [Revised: 03/27/2023] [Accepted: 04/08/2023] [Indexed: 05/15/2023] Open
Abstract
Emerging research findings have shown that a centrosomal protein (CEP55) is a potential oncogene in numerous human malignancies. Nevertheless, no pan-cancer analysis has been conducted to investigate the various aspects and behavior of this oncogene in different human cancerous tissues. Numerous databases were investigated to conduct a detailed analysis of CEP55. Initially, we evaluated the expression of CEP55 in several types of cancers and attempted to find the correlation between that and the stage of the examined malignancies. Then, we conducted a survival analysis to determine the relationship between CEP55 overexpression in malignancies and the patient's survival. Furthermore, we examined the genetic alteration forms and the methylation status of this oncogene. Additionally, the interference of CEP55 expression with immune cell infiltration, the response to various chemotherapeutic agents, and the putative molecular mechanism of CEP55 in tumorigenesis were investigated. The current study found that CEP55 was upregulated in cancerous tissues versus normal controls where this upregulation was correlated with a poor prognosis in multiple forms of human cancers. Additionally, it influenced the level of different immune cell infiltration and several chemokines levels in the tumor microenvironment in addition to the response to several antitumor drugs. Herein, we provide an in-depth understanding of the oncogenic activities of CEP55, identifying it as a possible predictive marker as well as a specific target for developing anticancer therapies.
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Affiliation(s)
- Mohamed Samir A. Zaki
- Anatomy Department, College of Medicine, King Khalid University, Abha P.O. Box 62529, Saudi Arabia
| | - Muhammad Alaa Eldeen
- Cell Biology, Histology & Genetics Division, Biology Department, Faculty of Science, Zagazig University, Zagazig 44519, Egypt
| | - Waleed K. Abdulsahib
- Pharmacology and Toxicology Department, College of Pharmacy, Al Farahidi University, Baghdad 00965, Iraq
| | - Ayed A. Shati
- Department of Child Health, College of Medicine, King Khalid University, Abha P.O. Box 62529, Saudi Arabia
| | - Youssef A. Alqahtani
- Department of Child Health, College of Medicine, King Khalid University, Abha P.O. Box 62529, Saudi Arabia
| | - Saleh M. Al-Qahtani
- Department of Child Health, College of Medicine, King Khalid University, Abha P.O. Box 62529, Saudi Arabia
| | - Hassan M. Otifi
- Pathology Department, College of Medicine, King Khalid University, Abha P.O. Box 62529, Saudi Arabia
| | - Ashwag Asiri
- Department of Child Health, College of Medicine, King Khalid University, Abha P.O. Box 62529, Saudi Arabia
| | - Hesham M. Hassan
- Pathology Department, College of Medicine, King Khalid University, Abha P.O. Box 62529, Saudi Arabia
| | | | - Samy A. Dawood
- Department of Child Health, College of Medicine, King Khalid University, Abha P.O. Box 62529, Saudi Arabia
| | - Amr Negm
- Department of Chemistry, College of Science, King Faisal University, Al-Ahsa 31982, Saudi Arabia
- Chemistry Department, Faculty of Science, Mansoura University, Mansoura 35516, Egypt
| | - Refaat A. Eid
- Pathology Department, College of Medicine, King Khalid University, Abha P.O. Box 62529, Saudi Arabia
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Wagner M, Sobczyński M, Jasek M, Pawełczyk K, Porębska I, Kuśnierczyk P, Wiśniewski A. Down-regulation of ERAP1 mRNA expression in non-small cell lung cancer. BMC Cancer 2023; 23:383. [PMID: 37101107 PMCID: PMC10134604 DOI: 10.1186/s12885-023-10785-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 03/28/2023] [Indexed: 04/28/2023] Open
Abstract
BACKGROUND ERAP1 is a major aminopeptidase that serves as an editor of the peptide repertoire by trimming N-terminal residues of antigenic peptides, creating a pool of peptides with the optimal length for MHC-I binding. As an important component of the antigen processing and presenting machinery - APM, ERAP1 is frequently down-regulated in many cancers. Since ERAP1 expression has not yet been thoroughly investigated in non-small cell lung cancer (NSCLC), we decided to analyze ERAP1 mRNA levels in tissues collected from NSCLC patients. METHODS Using real-time qPCR, we evaluated ERAP1 mRNA expression in samples of tumor and adjacent non-tumor tissue (serving as control tissue) from 61 NSCLC patients. RESULTS We observed a significantly lower level of ERAP1 mRNA expression in tumor tissue (MedTumor = 0.75) in comparison to non-tumor tissue (MedNon-tumor = 1.1), p = 0.008. One of the five tested polymorphisms, namely rs26653, turned out to be significantly associated with ERAP1 expression in non-tumor tissue (difference [d] = 0.59 CI95% (0.14;1.05), p = 0.0086), but not in tumor tissue. The levels of ERAP1 mRNA expression did not affect the overall survival of NSCLC patients, either in the case of the tumor (p = 0.788) or in non-tumor (p = 0.298) tissue. We did not detect any association between mRNA ERAP1 expression level in normal tissue and: (i) age at diagnosis (p = 0.8386), (ii) patient's sex (p = 0.3616), (iii) histological type of cancer (p = 0.7580) and (iv) clinical stage of NSCLC (p = 0.7549). Furthermore, in the case of tumor tissue none of the abovementioned clinical parameters were associated with ERAP1 expression (p = 0.76). CONCLUSION Down-regulation of ERAP1 mRNA observed in NSCLC tissue may be related to tumor immune evasion strategy. The rs26653 polymorphism can be considered an expression quantitative trait locus (eQTL) associated with ERAP1 expression in normal lung tissue.
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Affiliation(s)
- Marta Wagner
- Laboratory of Genetics and Epigenetics of Human Diseases, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wrocław, Poland
| | - Maciej Sobczyński
- Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology of the Polish Academy of Sciences, Warsaw, Poland
| | - Monika Jasek
- Laboratory of Genetics and Epigenetics of Human Diseases, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wrocław, Poland
| | - Konrad Pawełczyk
- Department of Thoracic Surgery, Lower Silesian Centre of Oncology, Pulmonology and Haematology, Wrocław, Poland
| | - Irena Porębska
- Department of Pulmonology and Lung Oncology, Wrocław Medical University, Wrocław, Poland
| | - Piotr Kuśnierczyk
- Laboratory of Immunogenetics and Tissue Immunology, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wrocław, Poland
| | - Andrzej Wiśniewski
- Laboratory of Immunogenetics and Tissue Immunology, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wrocław, Poland.
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Li B, Liang Y, Bao H, Li D, Zhang Y, Dun X, Xu Z, Ji A, Zhang Z, Li Y, Zhang R, Chen W, Zheng Y, Cui L. Real-ambient particulate matter exposure-induced FGFR1 methylation contributes to cardiac dysfunction via lipid metabolism disruption. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 870:161903. [PMID: 36731555 DOI: 10.1016/j.scitotenv.2023.161903] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 01/18/2023] [Accepted: 01/26/2023] [Indexed: 06/18/2023]
Abstract
Particulate matter (PM)-induced cardiometabolic disorder contributes to the progression of cardiac diseases, but its epigenetic mechanisms are largely unknown. This study used bioinformatic analysis, in vivo and in vitro multiple models to investigate the role of PM-induced cardiac fibroblast growth factor 1 (FGFR1) methylation and its impact on cardiomyocyte lipid metabolic disruption. Bioinformatic analysis revealed that FGFR1 was associated with cardiac pathologies, mitochondrial function and metabolism, supporting the possibility that FGFR1 may play regulatory roles in PM-induced cardiac functional impairment and lipid metabolism disorders. Individually ventilated cage (IVC)-based real-ambient PM exposure system mouse models were used to expose C57/BL6 mice for six and fifteen weeks. The results showed that PM induced cardiac lipid metabolism disorder, DNA nucleotide methyltransferases (DNMTs) alterations and FGFR1 expression declines in mouse heart. Lipidomics analysis revealed that carnitines, phosphoglycerides and lysophosphoglycerides were most significantly affected by PM exposure. At the cellular level, AC16 cells treated with FGFR1 inhibitor (PD173074) led to impaired mitochondrial and metabolic functions in cardiomyocytes. Inhibition of DNA methylation in cells by 5-AZA partially restored the FGFR1 expression, ameliorated cardiomyocyte injury and mitochondrial functions. These changes involved alterations in AMP-activated protein kinase (AMPK)-peroxisome proliferator activated receptors gamma, coactivator 1 alpha (PGC1α) pathways. Bisulfite sequencing PCR (BSP) and DNA methylation specific PCR (MSP) confirmed that PM exposure induced FGFR1 gene promoter region methylation. These results suggested that, by inducing FGFR1 methylation, PM exposure would affect cardiac injury and deranged lipid metabolism. Overexpression of FGFR1 in mouse heart using adeno-associated virus 9 (AAV9) effectively alleviated PM-induced cardiac impairment and metabolic disorder. Our findings identified that FGFR1 methylation might be one of the potential indicators for PM-induced cardiac mitochondrial and metabolic dysfunction, providing novel insights into underlying PM-related cardiotoxic mechanisms.
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Affiliation(s)
- Benying Li
- Department of Toxicology, School of Public Health, Qingdao University, Qingdao, China
| | - Yanan Liang
- Department of Toxicology, School of Public Health, Qingdao University, Qingdao, China
| | - Hongxu Bao
- Department of Toxicology, School of Public Health, Qingdao University, Qingdao, China
| | - Daochuan Li
- Department of Toxicology, School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Ying Zhang
- Department of Toxicology, School of Public Health, Qingdao University, Qingdao, China
| | - Xinyu Dun
- Department of Toxicology, School of Public Health, Qingdao University, Qingdao, China
| | - Zijian Xu
- Department of Toxicology, School of Public Health, Qingdao University, Qingdao, China
| | - Andong Ji
- Department of Toxicology, School of Public Health, Qingdao University, Qingdao, China
| | - Zhen Zhang
- Department of Toxicology, School of Public Health, Qingdao University, Qingdao, China
| | - Yahui Li
- Department of Toxicology, School of Public Health, Qingdao University, Qingdao, China
| | - Rong Zhang
- Department of Toxicology, School of Public Health, Hebei Medical University, Shijiazhuang, China
| | - Wen Chen
- Department of Toxicology, School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Yuxin Zheng
- Department of Toxicology, School of Public Health, Qingdao University, Qingdao, China
| | - Lianhua Cui
- Department of Toxicology, School of Public Health, Qingdao University, Qingdao, China.
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Liu Y, Chen M. Histone Demethylation Profiles in Nonalcoholic Fatty Liver Disease and Prognostic Values in Hepatocellular Carcinoma: A Bioinformatic Analysis. Curr Issues Mol Biol 2023; 45:3640-3657. [PMID: 37185761 PMCID: PMC10136463 DOI: 10.3390/cimb45040237] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 03/30/2023] [Accepted: 04/10/2023] [Indexed: 05/17/2023] Open
Abstract
Nonalcoholic fatty liver disease (NAFLD) is the most common chronic liver disease with multifactorial pathogenesis; histone demethylases (HDMs) are emerging as attractive targets. We identified HDM genes (including KDM5C, KDM6B, KDM8, KDM4A, and JMJD7) that were differentially expressed in NAFLD and normal samples by exploring gene expression profiling datasets. There was no significant difference in the expression of genes related to histone demethylation between mild and advanced NAFLD. In vitro and in vivo studies indicated that KDM6B and JMJD7 were upregulated at the mRNA level in NAFLD. We explored the expression levels and prognostic values of the identified HDM genes in hepatocellular carcinoma (HCC). KDM5C and KDM4A were upregulated in HCC compared to normal tissue, while KDM8 showed downregulation. The abnormal expression levels of these HDMs could provide prognostic values. Furthermore, KDM5C and KDM4A were associated with immune cell infiltration in HCC. HDMs were associated with cellular and metabolic processes and may be involved in the regulation of gene expression. Differentially expressed HDM genes identified in NAFLD may provide value to understanding pathogenesis and in the development of epigenetic therapeutic targets. However, on the basis of the inconsistent results of in vitro studies, future in vivo experiments combined with transcriptomic analysis are needed for further validation.
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Affiliation(s)
- Yuanbin Liu
- Department of Gastroenterology, Renmin Hospital of Wuhan University, No. 99 Zhang Zhidong Road, Wuhan 430000, China
| | - Mingkai Chen
- Department of Gastroenterology, Renmin Hospital of Wuhan University, No. 99 Zhang Zhidong Road, Wuhan 430000, China
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Martínez-Zamudio RI, Stefa A, Nabuco Leva Ferreira Freitas JA, Vasilopoulos T, Simpson M, Doré G, Roux PF, Galan MA, Chokshi RJ, Bischof O, Herbig U. Escape from oncogene-induced senescence is controlled by POU2F2 and memorized by chromatin scars. CELL GENOMICS 2023; 3:100293. [PMID: 37082139 PMCID: PMC10112333 DOI: 10.1016/j.xgen.2023.100293] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 01/13/2023] [Accepted: 03/02/2023] [Indexed: 04/22/2023]
Abstract
Although oncogene-induced senescence (OIS) is a potent tumor-suppressor mechanism, recent studies revealed that cells could escape from OIS with features of transformed cells. However, the mechanisms that promote OIS escape remain unclear, and evidence of post-senescent cells in human cancers is missing. Here, we unravel the regulatory mechanisms underlying OIS escape using dynamic multidimensional profiling. We demonstrate a critical role for AP1 and POU2F2 transcription factors in escape from OIS and identify senescence-associated chromatin scars (SACSs) as an epigenetic memory of OIS detectable during colorectal cancer progression. POU2F2 levels are already elevated in precancerous lesions and as cells escape from OIS, and its expression and binding activity to cis-regulatory elements are associated with decreased patient survival. Our results support a model in which POU2F2 exploits a precoded enhancer landscape necessary for senescence escape and reveal POU2F2 and SACS gene signatures as valuable biomarkers with diagnostic and prognostic potential.
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Affiliation(s)
- Ricardo Iván Martínez-Zamudio
- Center for Cell Signaling, Department of Microbiology, Biochemistry, and Molecular Genetics, New Jersey Medical School, Rutgers University, Newark, NJ 07103, USA
- Department of Pharmacology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ 08854, USA
| | - Alketa Stefa
- Center for Cell Signaling, Department of Microbiology, Biochemistry, and Molecular Genetics, New Jersey Medical School, Rutgers University, Newark, NJ 07103, USA
- Graduate School of Biomedical and Health Sciences, Rutgers University, Newark, NJ 07103 USA
| | - José Américo Nabuco Leva Ferreira Freitas
- Sorbonne Université, UMR 8256, Biological Adaptation and Ageing – IBPS, 75005 Paris, France
- INSERM U1164, 75005 Paris, France
- IMRB, Mondor Institute for Biomedical Research, INSERM U955 – Université Paris Est Créteil, UPEC, Faculté de Médecine de Créteil 8, rue du Général Sarrail, 94010 Créteil, France
| | - Themistoklis Vasilopoulos
- Center for Cell Signaling, Department of Microbiology, Biochemistry, and Molecular Genetics, New Jersey Medical School, Rutgers University, Newark, NJ 07103, USA
- Graduate School of Biomedical and Health Sciences, Rutgers University, Newark, NJ 07103 USA
| | - Mark Simpson
- Center for Cell Signaling, Department of Microbiology, Biochemistry, and Molecular Genetics, New Jersey Medical School, Rutgers University, Newark, NJ 07103, USA
| | - Gregory Doré
- Institut Pasteur, Plasmodium RNA Biology Unit, 25 Rue du Docteur Roux, 75724 Cedex 15 Paris, France
| | - Pierre-François Roux
- IRCM, Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, Université de Montpellier, Institut Régional du Cancer de Montpellier, Montpellier, France
| | - Mark A. Galan
- Department of Pathology and Laboratory Medicine, New Jersey Medical School, Rutgers University, Newark, NJ 07103, USA
| | - Ravi J. Chokshi
- Department of Surgery, New Jersey Medical School, Rutgers University, Newark, NJ 07103, USA
| | - Oliver Bischof
- IMRB, Mondor Institute for Biomedical Research, INSERM U955 – Université Paris Est Créteil, UPEC, Faculté de Médecine de Créteil 8, rue du Général Sarrail, 94010 Créteil, France
| | - Utz Herbig
- Center for Cell Signaling, Department of Microbiology, Biochemistry, and Molecular Genetics, New Jersey Medical School, Rutgers University, Newark, NJ 07103, USA
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Men X, Marshe V, Elsheikh SS, Alexopoulos GS, Marino P, Meyers BS, Mulsant BH, Rothschild AJ, Voineskos AN, Whyte EM, Kennedy JL, Flint AJ, Müller DJ. Genomic Investigation of Remission and Relapse of Psychotic Depression Treated with Sertraline plus Olanzapine: The STOP-PD II Study. Neuropsychobiology 2023; 82:168-178. [PMID: 37015192 PMCID: PMC10871684 DOI: 10.1159/000529637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 01/30/2023] [Indexed: 04/06/2023]
Abstract
INTRODUCTION Little is known regarding genetic factors associated with treatment outcome of psychotic depression. We explored genomic associations of remission and relapse of psychotic depression treated with pharmacotherapy. METHODS Genomic analyses were performed in 171 men and women aged 18-85 years with an episode of psychotic depression who participated in the Study of the Pharmacotherapy of Psychotic Depression II (STOP-PD II). Participants were treated with open-label sertraline plus olanzapine for up to 12 weeks; those who achieved remission or near-remission and maintained it following 8 weeks of stabilization were eligible to participate in a 36-week randomized controlled trial that compared sertraline plus olanzapine with sertraline plus placebo in preventing relapse. RESULTS There were no genome-wide significant associations with either remission or relapse. However, at a suggestive threshold, SNP rs1026501 (31 kb from SYNPO2) in the whole sample and rs6844137 (within the intronic region of SYNPO2) in the European ancestry subsample were associated with a decreased likelihood of remission. In polygenic risk analyses, participants who had greater improvement after antidepressant treatments showed a higher likelihood of reaching remission. Those who achieved remission and had a higher polygenic risk for Alzheimer's disease had a significantly decreased likelihood of relapse. CONCLUSION Our analyses provide preliminary insights into the genetic architecture of remission and relapse in a well-characterized group of patients with psychotic depression.
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Affiliation(s)
- Xiaoyu Men
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario, Canada,
- Pharmacogenetics Research Clinic, Campbell Family Mental Health Research Institute, Center for Addiction and Mental Health, Toronto, Ontario, Canada,
| | - Victoria Marshe
- Pharmacogenetics Research Clinic, Campbell Family Mental Health Research Institute, Center for Addiction and Mental Health, Toronto, Ontario, Canada
- Institute of Medical Science, University of Toronto, Toronto, Ontario, Canada
| | - Samar S Elsheikh
- Pharmacogenetics Research Clinic, Campbell Family Mental Health Research Institute, Center for Addiction and Mental Health, Toronto, Ontario, Canada
| | - George S Alexopoulos
- Department of Psychiatry, Weill Cornell Medicine of Cornell University and New York Presbyterian Hospital, Westchester Division, New York, New York, USA
| | - Patricia Marino
- Department of Psychiatry, Weill Cornell Medicine of Cornell University and New York Presbyterian Hospital, Westchester Division, New York, New York, USA
| | - Barnett S Meyers
- Department of Psychiatry, Weill Cornell Medicine of Cornell University and New York Presbyterian Hospital, Westchester Division, New York, New York, USA
| | - Benoit H Mulsant
- Institute of Medical Science, University of Toronto, Toronto, Ontario, Canada
- Department of Psychiatry, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Anthony J Rothschild
- University of Massachusetts Chan Medical School and UMass Memorial Health Care, Worcester, Massachusetts, USA
| | - Aristotle N Voineskos
- Pharmacogenetics Research Clinic, Campbell Family Mental Health Research Institute, Center for Addiction and Mental Health, Toronto, Ontario, Canada
- Department of Psychiatry, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Ellen M Whyte
- UPMC Western Psychiatric Hospital, Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - James Lowery Kennedy
- Pharmacogenetics Research Clinic, Campbell Family Mental Health Research Institute, Center for Addiction and Mental Health, Toronto, Ontario, Canada
- Department of Psychiatry, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Alastair J Flint
- Department of Psychiatry, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
- University Health Network, Toronto, Ontario, Canada
| | - Daniel J Müller
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario, Canada
- Pharmacogenetics Research Clinic, Campbell Family Mental Health Research Institute, Center for Addiction and Mental Health, Toronto, Ontario, Canada
- Department of Psychiatry, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
- Department of Psychiatry, Psychosomatics and Psychotherapy, Center of Mental Health, University Hospital of Würzburg, Würzburg, Germany
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Yaguchi T, Kimura A, Takekoshi A, Matsuo M, Tomita H, Shimohata T. Autoimmune glial fibrillary acidic protein astrocytopathy associated with breast cancer: a case report. BMC Neurol 2023; 23:145. [PMID: 37016352 PMCID: PMC10071775 DOI: 10.1186/s12883-023-03194-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Accepted: 03/30/2023] [Indexed: 04/06/2023] Open
Abstract
BACKGROUND Autoimmune glial fibrillary acidic protein (GFAP) astrocytopathy (GFAP-A) is an autoimmune inflammatory central nervous system disorder characterized by the detection of autoantibodies that recognize GFAP in CSF. The pathogenesis of GFAP-A is poorly understood. Some patients had a neoplasm detected and GFAP expressed by neoplasms is plausible as immunogen triggering paraneoplastic neurological autoimmunity. CASE PRESENTATION We report a case of 76-year-old female patient with GFAP-A complicated with breast cancer. She presented with altered consciousness, nuchal rigidity, speech disturbances, and weakness. Her clinical symptoms were improved by immunotherapy and cancer treatments. Immunohistochemical analysis showed that the restricted tumor expressed GFAP. The infiltration of CD3 + T cells were observed in the peritumoral and intratumoral areas. The most common infiltrating lymphocytes were CD8 + T cells. CD4 + T cells and CD20 + B cells were also observed in the predominant peritumoral area. CONCLUSIONS These results suggest that GFAP-A may occur in a paraneoplastic neurological syndrome associated with breast cancer.
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Affiliation(s)
- Tomonori Yaguchi
- Department of Neurology, Gifu Prefectural General Medical Center, Gifu, Japan
| | - Akio Kimura
- Department of Neurology, Gifu University Graduate School of Medicine, 1-1 Yanagido, Gifu, 501-1194, Japan
| | - Akira Takekoshi
- Department of Neurology, Gifu University Graduate School of Medicine, 1-1 Yanagido, Gifu, 501-1194, Japan
| | - Mikiko Matsuo
- Department of Tumor Pathology, Gifu University Graduate School of Medicine, Gifu, Japan
| | - Hiroyuki Tomita
- Department of Tumor Pathology, Gifu University Graduate School of Medicine, Gifu, Japan
| | - Takayoshi Shimohata
- Department of Neurology, Gifu University Graduate School of Medicine, 1-1 Yanagido, Gifu, 501-1194, Japan.
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Eddfair MM, Abdulrahman O, Alqawi O, Assidi M, Buhmeida A, Elturki A, Jebriel A, Elfagieh M, Ermiah E. Correlations of demographical and clinicopathological features with patient outcome of pancreatic ductal adenocarcinoma: A retrospective study (2010-2018) from a Libyan Cohort. J Cancer Res Ther 2023; 19:745-752. [PMID: 37470604 DOI: 10.4103/jcrt.jcrt_1778_21] [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: 11/04/2022]
Abstract
Objective The aim of the study was to study the correlations of demographical and clinicopathological variables of patients with pancreatic ductal adenocarcinoma (PDAC) and evaluate the association of these variables with patients' survival outcomes. Patients and Methods A retrospective analysis of 123 patients with PDAC were diagnosed and treated at the National Cancer Institute, Misurata, Libya during the 2010-2108 period. Data for demographics, clinicopathological, biological variables, risk factors, presentation, treatment, and survival-related data were collected from the patients' medical records. Results The mean age of patient was 61.2 years (range: 19-90 years) and most of patients (80.5%) were aged >50 years. For gender distribution, PDAC was more frequent in males (59.3%). Abdominal pain was the most frequent presenting symptom (84.6%) and 78% (96 patients) among them had head tumors. Most patients (80.5%) presented with unresectable tumor at diagnosis. Disease-free survival was better in patients with early stage (P < 0.0001), low-grade tumor (P = 0.001), resectable tumor (P < 0.0001), and with carcinoembryonic antigen levels <5 ng/ml (P = 0.004). Multivariate Cox's regression analysis showed that tumor stage is an independent poor survival factor (P = 0.002). Age at diagnosis, gender, family history, and position of tumor did not show any significant associations with patient outcome. Conclusion Libyan patients with PDAC had different demographics, clinicopathological, and biological variables. Typically, they presented with unresectable tumor, advanced stages, and had very short survival times. These results urge us to conduct in-depth biomolecular research studies to identify effective early diagnostics and therapeutics biomarkers in order to fight this disease before it escalates.
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Affiliation(s)
| | - Othman Abdulrahman
- Department of Medical Oncology, National Cancer Institute, Misurata, Libya
| | - Omar Alqawi
- Biotechnology Research Centre, National Cancer Institute-Misurata, Misurata 218-51, Libya
| | - Mourad Assidi
- Center of Excellence in Genomic Medicine Research, King Abdulaziz University; Medical Laboratory Department, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Abdelbaset Buhmeida
- Center of Excellence in Genomic Medicine Research, King Abdulaziz University; Medical Laboratory Department, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Abdulfattah Elturki
- Department of Medical Oncology and Haematology, National Cancer Institute, Misurata, Libya
| | - Abdalla Jebriel
- Department of Medical Oncology, National Cancer Institute, Misurata, Libya
| | - Mohamed Elfagieh
- Department of Surgery, National Cancer Institute, Misurata, Libya
| | - Eramah Ermiah
- Medical Research Unit, National Cancer Institute, Misurata, Libya
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Estep JA, Sun LO, Riccomagno MM. A luciferase fragment complementation assay to detect focal adhesion kinase (FAK) signaling events. Heliyon 2023; 9:e15282. [PMID: 37089315 PMCID: PMC10119766 DOI: 10.1016/j.heliyon.2023.e15282] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 03/29/2023] [Accepted: 03/31/2023] [Indexed: 04/08/2023] Open
Abstract
Integrin Adhesion Complexes (IACs) serve as links between the cytoskeleton and extracellular environment, acting as mechanosensing and signaling hubs. As such, IACs participate in many aspects of cellular motility, tissue morphogenesis, anchorage-dependent growth and cell survival. Focal Adhesion Kinase (FAK) has emerged as a critical organizer of IAC signaling events due to its early recruitment and diverse substrates, and thus has become a genetic and therapeutic target. Here we present the design and characterization of simple, reversible, and scalable Bimolecular Complementation sensors to monitor FAK phosphorylation in living cells. These probes provide novel means to quantify IAC signaling, expanding on the currently available toolkit for interrogating FAK phosphorylation during diverse cellular processes.
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Affiliation(s)
- Jason A. Estep
- Cell, Molecular and Developmental Biology Program, Department of Molecular, Cell and Systems Biology, University of California, Riverside, CA 92521, USA
| | - Lu O. Sun
- Department of Molecular Biology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Martin M. Riccomagno
- Cell, Molecular and Developmental Biology Program, Department of Molecular, Cell and Systems Biology, University of California, Riverside, CA 92521, USA
- Neuroscience Program, Department of Molecular, Cell and Systems Biology, University of California, Riverside, CA 92521, USA
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145
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Yang G, Zuo C, Lin Y, Zhou X, Wen P, Zhang C, Xiao H, Jiang M, Fujita M, Gao XD, Fu F. Comprehensive proteome, phosphoproteome and kinome characterization of luminal A breast cancer. Front Oncol 2023; 13:1127446. [PMID: 37064116 PMCID: PMC10102592 DOI: 10.3389/fonc.2023.1127446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 03/08/2023] [Indexed: 04/03/2023] Open
Abstract
BackgroundBreast cancer is one of the most frequently occurring malignant cancers worldwide. Invasive ductal carcinoma (IDC) and invasive lobular carcinoma (ILC) are the two most common histological subtypes of breast cancer. In this study, we aimed to deeply explore molecular characteristics and the relationship between IDC and ILC subtypes in luminal A subgroup of breast cancer using comprehensive proteomics and phosphoproteomics analysis.MethodsCancer tissues and noncancerous adjacent tissues (NATs) with the luminal A subtype (ER- and PR-positive, HER2-negative) were obtained from paired IDC and ILC patients respectively. Label-free quantitative proteomics and phosphoproteomics methods were used to detect differential proteins and the phosphorylation status between 10 paired breast cancer and NATs. Then, the difference in protein expression and its phosphorylation between IDC and ILC subtypes were explored. Meanwhile, the activation of kinases and their substrates was also revealed by Kinase-Substrate Enrichment Analysis (KSEA).ResultsIn the luminal A breast cancer, a total of 5,044 high-confidence proteins and 3,808 phosphoproteins were identified from 10 paired tissues. The protein phosphorylation level in ILC tissues was higher than that in IDC tissues. Histone H1.10 was significantly increased in IDC but decreased in ILC, Conversely, complement C4-B and Crk-like protein were significantly decreased in IDC but increased in ILC. Moreover, the increased protein expression of Septin-2, Septin-9, Heterogeneous nuclear ribonucleoprotein A1 and Kinectin but reduce of their phosphorylation could clearly distinguish IDC from ILC. In addition, IDC was primarily related to energy metabolism and MAPK pathway, while ILC was more closely involved in the AMPK and p53/p21 pathways. Furthermore, the kinomes in IDC were primarily significantly activated in the CMGC groups.ConclusionsOur research provides insights into the molecular characterization of IDC and ILC and contributes to discovering novel targets for further drug development and targeted treatment.
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Affiliation(s)
- Ganglong Yang
- The Key Laboratory of Carbohydrate Chemistry & Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, China
| | - Chenyang Zuo
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, China
| | - Yuxiang Lin
- Department of Breast Surgery, Fujian Medical University Union Hospital, Fuzhou, Fujian, China
- Department of General Surgery, Fujian Medical University Union Hospital, Fuzhou, Fujian, China
- Breast Cancer Institute, Fujian Medical University, Fuzhou, Fujian, China
| | - Xiaoman Zhou
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, China
| | - Piaopiao Wen
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, China
| | - Chairui Zhang
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, China
| | - Han Xiao
- Department of Pathology, Fujian Medical University Union Hospital, Fuzhou, Fujian, China
| | - Meichen Jiang
- Department of Pathology, Fujian Medical University Union Hospital, Fuzhou, Fujian, China
| | - Morihisa Fujita
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, China
| | - Xiao-Dong Gao
- The Key Laboratory of Carbohydrate Chemistry & Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
- *Correspondence: Xiao-Dong Gao, ; Fangmeng Fu,
| | - Fangmeng Fu
- Department of Breast Surgery, Fujian Medical University Union Hospital, Fuzhou, Fujian, China
- Department of General Surgery, Fujian Medical University Union Hospital, Fuzhou, Fujian, China
- Breast Cancer Institute, Fujian Medical University, Fuzhou, Fujian, China
- *Correspondence: Xiao-Dong Gao, ; Fangmeng Fu,
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Regal JA, Guerra García ME, Jain V, Chandramohan V, Ashley DM, Gregory SG, Thompson EM, López GY, Reitman ZJ. Ganglioglioma deep transcriptomics reveals primitive neuroectoderm neural precursor-like population. Acta Neuropathol Commun 2023; 11:50. [PMID: 36966348 PMCID: PMC10039537 DOI: 10.1186/s40478-023-01548-3] [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: 12/18/2022] [Accepted: 03/06/2023] [Indexed: 03/27/2023] Open
Abstract
Gangliogliomas are brain tumors composed of neuron-like and macroglia-like components that occur in children and young adults. Gangliogliomas are often characterized by a rare population of immature astrocyte-appearing cells expressing CD34, a marker expressed in the neuroectoderm (neural precursor cells) during embryogenesis. New insights are needed to refine tumor classification and to identify therapeutic approaches. We evaluated five gangliogliomas with single nucleus RNA-seq, cellular indexing of transcriptomes and epitopes by sequencing, and/or spatially-resolved RNA-seq. We uncovered a population of CD34+ neoplastic cells with mixed neuroectodermal, immature astrocyte, and neuronal markers. Gene regulatory network interrogation in these neuroectoderm-like cells revealed control of transcriptional programming by TCF7L2/MEIS1-PAX6 and SOX2, similar to that found during neuroectodermal/neural development. Developmental trajectory analyses place neuroectoderm-like tumor cells as precursor cells that give rise to neuron-like and macroglia-like neoplastic cells. Spatially-resolved transcriptomics revealed a neuroectoderm-like tumor cell niche with relative lack of vascular and immune cells. We used these high resolution results to deconvolute clinically-annotated transcriptomic data, confirming that CD34+ cell-associated gene programs associate with gangliogliomas compared to other glial brain tumors. Together, these deep transcriptomic approaches characterized a ganglioglioma cellular hierarchy-confirming CD34+ neuroectoderm-like tumor precursor cells, controlling transcription programs, cell signaling, and associated immune cell states. These findings may guide tumor classification, diagnosis, prognostication, and therapeutic investigations.
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Affiliation(s)
- Joshua A Regal
- Department of Radiation Oncology, Duke University, Durham, NC, 27710, USA
| | | | - Vaibhav Jain
- Duke Molecular Physiology Institute, Duke University, Durham, NC, 27710, USA
| | | | - David M Ashley
- Department of Neurosurgery, Duke University, Durham, NC, 27710, USA
| | - Simon G Gregory
- Duke Molecular Physiology Institute, Duke University, Durham, NC, 27710, USA
| | - Eric M Thompson
- Department of Neurosurgery, Duke University, Durham, NC, 27710, USA
| | - Giselle Y López
- Department of Neurosurgery, Duke University, Durham, NC, 27710, USA
- Department of Pathology, Duke University, Durham, NC, 27710, USA
| | - Zachary J Reitman
- Department of Radiation Oncology, Duke University, Durham, NC, 27710, USA.
- Department of Neurosurgery, Duke University, Durham, NC, 27710, USA.
- Department of Pathology, Duke University, Durham, NC, 27710, USA.
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147
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Li X, Kang K, Shen L, Shen L, Zhou Y. Integrative Analysis of the Predictive Value of Perilipin Family on Clinical Significance, Prognosis and Immunotherapy of Glioma. Biomedicines 2023; 11:biomedicines11041009. [PMID: 37189627 DOI: 10.3390/biomedicines11041009] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 03/06/2023] [Accepted: 03/07/2023] [Indexed: 03/29/2023] Open
Abstract
Gliomas are common tumors of the central nervous system. The PLINs family is widely involved in the regulation of lipid metabolism and has been associated with the development and invasive metastasis of various malignancies. However, the biological role of the PLINs family in gliomas is still unclear. TIMER and UALCAN were used to assess PLINs mRNA expression in gliomas. “Survminer” and “Survival” were used to evaluate the connection between PLINs expression and glioma patients’ survival. cBioPortal was applied to assess PLINs’ genetic alterations in glioblastoma multiforme (GBM) and low-grade glioma (LGG). The correlation of PLINs expression with tumor immune cells was analyzed by TIMER. The expressions of PLIN1, PLIN4, and PLIN5 were decreased in GBM compared to normal tissues. However, PLIN2 and PLIN3 were significantly increased in GBM. Prognostic analysis showed that LGG patients with high PLIN1 expression had better overall survival (OS), and high expression of PLIN2/3/4/5 was associated with unfavorable OS. We further determined that the expression of PLINs members in gliomas was strongly related to tumor immune cells and immune checkpoint-associated genes. PLINS may be potential biomarkers for regulating the tumor microenvironment and predicting the efficacy of immunotherapy. In addition, we determined that PLIN1 may affect glioma patients’ therapeutic sensitivity to temozolomide. Our results demonstrated the biological significance and clinical values of PLINs in gliomas and provide a basis for future in-depth exploration of the specific mechanisms of each member of PLINs in gliomas.
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148
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Li J, Huang HY, Lin YCD, Zuo H, Tang Y, Huang HD. Cinnamomi ramulus inhibits cancer cells growth by inducing G2/M arrest. Front Pharmacol 2023; 14:1121799. [PMID: 37007025 PMCID: PMC10063822 DOI: 10.3389/fphar.2023.1121799] [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: 12/12/2022] [Accepted: 02/13/2023] [Indexed: 03/19/2023] Open
Abstract
Introduction: Cinnamomi ramulus (CR) is one of the most widely used traditional Chinese medicine (TCM) with anti-cancer effects. Analyzing transcriptomic responses of different human cell lines to TCM treatment is a promising approach to understand the unbiased mechanism of TCM. Methods: This study treated ten cancer cell lines with different CR concentrations, followed by mRNA sequencing. Differential expression (DE) analysis and gene set enrichment analysis (GSEA) were utilized to analyze transcriptomic data. Finally, the in silico screening results were verified by in vitro experiments. Results: Both DE and GSEA analysis suggested the Cell cycle pathway was the most perturbated pathway by CR across these cell lines. By analyzing the clinical significance and prognosis of G2/M related genes (PLK1, CDK1, CCNB1, and CCNB2) in various cancer tissues, we found that they were up-regulated in most cancer types, and their down-regulation showed better overall survival rates in cancer patients. Finally, in vitro experiments validation on A549, Hep G2, and HeLa cells suggested that CR can inhibit cell growth by suppressing the PLK1/CDK1/ Cyclin B axis. Discussion: This is the first study to apply transcriptomic analysis to investigate the cancer cell growth inhibition of CR on various human cancer cell lines. The core effect of CR on ten cancer cell lines is to induce G2/M arrest by inhibiting the PLK1/CDK1/Cyclin B axis.
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Affiliation(s)
- Jing Li
- School of Medicine, The Chinese University of Hong Kong, Shenzhen, Guangdong, China
- Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Shenzhen, Guangdong, China
| | - Hsi-Yuan Huang
- School of Medicine, The Chinese University of Hong Kong, Shenzhen, Guangdong, China
- Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Shenzhen, Guangdong, China
| | - Yang-Chi-Dung Lin
- School of Medicine, The Chinese University of Hong Kong, Shenzhen, Guangdong, China
- Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Shenzhen, Guangdong, China
| | - Huali Zuo
- School of Medicine, The Chinese University of Hong Kong, Shenzhen, Guangdong, China
- Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Shenzhen, Guangdong, China
| | - Yun Tang
- School of Medicine, The Chinese University of Hong Kong, Shenzhen, Guangdong, China
- Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Shenzhen, Guangdong, China
| | - Hsien-Da Huang
- School of Medicine, The Chinese University of Hong Kong, Shenzhen, Guangdong, China
- Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Shenzhen, Guangdong, China
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149
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Ruan GY, Ye LX, Lin JS, Lin HY, Yu LR, Wang CY, Mao XD, Zhang SH, Sun PM. An integrated approach of network pharmacology, molecular docking, and experimental verification uncovers kaempferol as the effective modulator of HSD17B1 for treatment of endometrial cancer. J Transl Med 2023; 21:204. [PMID: 36932403 PMCID: PMC10022092 DOI: 10.1186/s12967-023-04048-z] [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: 12/19/2022] [Accepted: 03/08/2023] [Indexed: 03/19/2023] Open
Abstract
BACKGROUND Endometrial cancer (EC) is one of the most common gynecological malignancies globally, and the development of innovative, effective drugs against EC remains a key issue. Phytoestrogen kaempferol exhibits anti-cancer effects, but the action mechanisms are still unclear. METHOD MTT assays, colony-forming assays, flow cytometry, scratch healing, and transwell assays were used to evaluate the proliferation, apoptosis, cell cycle, migration, and invasion of both ER-subtype EC cells. Xenograft experiments were used to assess the effects of kaempferol inhibition on tumor growth. Next-generation RNA sequencing was used to compare the gene expression levels in vehicle-treated versus kaempferol-treated Ishikawa and HEC-1-A cells. A network pharmacology and molecular docking technique were applied to identify the anti-cancer mechanism of kaempferol, including the building of target-pathway network. GO analysis and KEGG pathway enrichment analysis were used to identify cancer-related targets. Finally, the study validated the mRNA and protein expression using real-time quantitative PCR, western blotting, and immunohistochemical analysis. RESULTS Kaempferol was found to suppress the proliferation, promote apoptosis, and limit the tumor-forming, scratch healing, invasion, and migration capacities of EC cells. Kaempferol inhibited tumor growth and promotes apoptosis in a human endometrial cancer xenograft mouse model. No significant toxicity of kaempferol was found in human monocytes and normal cell lines at non-cytotoxic concentrations. No adverse effects or significant changes in body weight or organ coefficients were observed in 3-7 weeks' kaempferol-treated animals. The RNA sequencing, network pharmacology, and molecular docking approaches identified the overall survival-related differentially expressed gene HSD17B1. Interestingly, kaempferol upregulated HSD17B1 expression and sensitivity in ER-negative EC cells. Kaempferol differentially regulated PPARG expression in EC cells of different ER subtypes, independent of its effect on ESR1. HSD17B1 and HSD17B1-associated genes, such as ESR1, ESRRA, PPARG, AKT1, and AKR1C1\2\3, were involved in several estrogen metabolism pathways, such as steroid binding, 17-beta-hydroxysteroid dehydrogenase (NADP+) activity, steroid hormone biosynthesis, and regulation of hormone levels. The molecular basis of the effects of kaempferol treatment was evaluated. CONCLUSIONS Kaempferol is a novel therapeutic candidate for EC via HSD17B1-related estrogen metabolism pathways. These results provide new insights into the efficiency of the medical translation of phytoestrogens.
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Affiliation(s)
- Guan-Yu Ruan
- Laboratory of Gynecologic Oncology, College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Maternity and Child Health Hospital, Fujian Medical University, No. 18 Dao Shan Road, Fuzhou, 350001, Fujian, People's Republic of China
- Fujian Key Laboratory of Women and Children's Critical Diseases Research, Fujian Maternity and Child Health Hospital, Fuzhou, 350001, Fujian, People's Republic of China
- Fujian Clinical Research Center for Gynecologic Oncology, Fujian Maternity and Child Health Hospital (Fujian Obstetrics and Gynecology Hospital), Fuzhou, 350001, Fujian, People's Republic of China
| | - Li-Xiang Ye
- Fujian Center for Safety Evaluation of New Drugs, Fujian Medical University, No.1 Xue Fu Bei Road, University Town, Fuzhou, 350001, Fujian, People's Republic of China
| | - Jian-Song Lin
- Department of Pathology, College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Maternity and Child Health Hospital, Fujian Medical University, Fuzhou, 350001, Fujian, People's Republic of China
| | - Hong-Yu Lin
- Collage of Pharmacy, Fujian Medical University, Fuzhou, 351004, Fujian, People's Republic of China
| | - Li-Rui Yu
- Laboratory of Gynecologic Oncology, College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Maternity and Child Health Hospital, Fujian Medical University, No. 18 Dao Shan Road, Fuzhou, 350001, Fujian, People's Republic of China
| | - Cheng-Yan Wang
- Animal Research Institute, Fujian Medical University, Fuzhou, 351004, Fujian, People's Republic of China
| | - Xiao-Dan Mao
- Laboratory of Gynecologic Oncology, College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Maternity and Child Health Hospital, Fujian Medical University, No. 18 Dao Shan Road, Fuzhou, 350001, Fujian, People's Republic of China
- Fujian Key Laboratory of Women and Children's Critical Diseases Research, Fujian Maternity and Child Health Hospital, Fuzhou, 350001, Fujian, People's Republic of China
- Fujian Clinical Research Center for Gynecologic Oncology, Fujian Maternity and Child Health Hospital (Fujian Obstetrics and Gynecology Hospital), Fuzhou, 350001, Fujian, People's Republic of China
| | - Shui-Hua Zhang
- Fujian Center for Safety Evaluation of New Drugs, Fujian Medical University, No.1 Xue Fu Bei Road, University Town, Fuzhou, 350001, Fujian, People's Republic of China.
| | - Peng-Ming Sun
- Laboratory of Gynecologic Oncology, College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Maternity and Child Health Hospital, Fujian Medical University, No. 18 Dao Shan Road, Fuzhou, 350001, Fujian, People's Republic of China.
- Fujian Key Laboratory of Women and Children's Critical Diseases Research, Fujian Maternity and Child Health Hospital, Fuzhou, 350001, Fujian, People's Republic of China.
- Fujian Clinical Research Center for Gynecologic Oncology, Fujian Maternity and Child Health Hospital (Fujian Obstetrics and Gynecology Hospital), Fuzhou, 350001, Fujian, People's Republic of China.
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Lv J, Jiang Z, Yuan J, Zhuang M, Guan X, Liu H, Yin Y, Ma Y, Liu Z, Wang H, Wang X. Pan-cancer analysis identifies PD-L2 as a tumor promotor in the tumor microenvironment. Front Immunol 2023; 14:1093716. [PMID: 37006239 PMCID: PMC10060638 DOI: 10.3389/fimmu.2023.1093716] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 01/19/2023] [Indexed: 03/18/2023] Open
Abstract
BACKGROUND Programmed cell death protein 1 (PD-1) receptor has two ligands,programmed death-ligand 1 (PD-L1) and PD-L2. When compared with PD-L1, PD-L2 has not received much attention, and its role remains unclear. METHODS The expression profiles of pdcd1lg2 (PD-L2-encoding gene) mRNA and PD-L2 protein were analyzed using TCGA, ICGC, and HPA databases. Kaplan-Meier and Cox regression analyses were used to assess the prognostic significance of PD-L2. We used GSEA, Spearman's correlation analysis and PPI network to explore the biological functions of PD-L2. PD-L2-associated immune cell infiltration was evaluated using the ESTIMATE algorithm and TIMER 2.0. The expressions of PD-L2 in tumor-associated macrophages (TAMs) in human colon cancer samples, and in mice in an immunocompetent syngeneic setting were verified using scRNA-seq datasets, multiplex immunofluorescence staining, and flow cytometry. After fluorescence-activated cell sorting, flow cytometry and qRT-PCR and transwell and colony formation assays were used to evaluate the phenotype and functions of PD-L2+TAMs. Immune checkpoint inhibitors (ICIs) therapy prediction analysis was performed using TIDE and TISMO. Last, a series of targeted small-molecule drugs with promising therapeutic effects were predicted using the GSCA platform. RESULTS PD-L2 was expressed in all the common human cancer types and deteriorated outcomes in multiple cancers. PPI network and Spearman's correlation analysis revealed that PD-L2 was closely associated with many immune molecules. Moreover, both GSEA results of KEGG pathways and GSEA results for Reactome analysis indicated that PD-L2 expression played an important role in cancer immune response. Further analysis showed that PD-L2 expression was strongly associated with the infiltration of immune cells in tumor tissue in almost all cancer types, among which macrophages were the most positively associated with PD-L2 in colon cancer. According to the results mentioned above, we verified the expression of PD-L2 in TAMs in colon cancer and found that PD-L2+TAMs population was not static. Additionally, PD-L2+TAMs exhibited protumor M2 phenotype and increased the migration, invasion, and proliferative capacity of colon cancer cells. Furthermore, PD-L2 had a substantial predictive value for ICIs therapy cohorts. CONCLUSION PD-L2 in the TME, especially expressed on TAMs, could be applied as a potential therapeutic target.
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Affiliation(s)
- Jingfang Lv
- Department of Colorectal Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Zheng Jiang
- Department of Colorectal Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Junhu Yuan
- State Key Laboratory of Molecular Oncology, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Meng Zhuang
- Department of Colorectal Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xu Guan
- Department of Colorectal Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Hengchang Liu
- Department of Colorectal Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yefeng Yin
- Department of Colorectal Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yiming Ma
- State Key Laboratory of Molecular Oncology, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Zheng Liu
- Department of Colorectal Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Hongying Wang
- State Key Laboratory of Molecular Oncology, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xishan Wang
- Department of Colorectal Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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