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Shi Q, He J, Chen G, Xu J, Zeng Z, Zhao X, Zhao B, Gao X, Ye Z, Xiao M, Li H. The chemical composition of Diwu YangGan capsule and its potential inhibitory roles on hepatocellular carcinoma by microarray-based transcriptomics. J Tradit Complement Med 2024; 14:381-390. [PMID: 39035694 PMCID: PMC11259662 DOI: 10.1016/j.jtcme.2023.12.002] [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: 07/18/2023] [Revised: 09/28/2023] [Accepted: 12/24/2023] [Indexed: 07/23/2024] Open
Abstract
The Traditional Chinese Medicine compound preparation known as Diwu Yanggan capsule (DWYG) can effectively hinder the onset and progression of hepatocellular carcinoma (HCC), which is recognized worldwide as a significant contributor to fatalities associated with cancer. Nevertheless, the precise mechanisms implicated have remained ambiguous. In present study, the model of HCC was set up by the 2-acetylaminofluorene (2-AAF)/partial hepatectomy (PH) in rats. To confirm the differentially expressed genes (DEGs) identified in the microarray analysis, real-time quantitative reverse transcription PCR (qRT-PCR) was conducted. In the meantime, the liquid chromatography-quadrupole time of flight mass spectrometry (LC-QTOF-MS/MS) was employed to characterize the component profile of DWYG. Consequently, the DWYG treatment exhibited the ability to reverse 51 variation genes induced by 2-AAF/PH. Additionally, there was an overlap of 54 variation genes between the normal and model groups. Upon conducting RT-qPCR analysis, it was observed that the expression levels of all genes were increased by 2-AAF/PH and subsequently reversed after DWYG treatment. Notably, the fold change of expression levels for all genes was below 0.5, with 3 genes falling below 0.25. Moreover, an investigation was conducted to determine the signaling pathway that was activated/inhibited in the HCC group and subsequently reversed in the DWYG group. Moreover, the component profile of DWYG encompassed a comprehensive compilation of 206 compounds that were identified or characterized. The findings of this study elucidated the potential alleviative mechanisms of DWYG in the context of HCC, thereby holding significant implications for its future clinical utilization and widespread adoption.
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Affiliation(s)
- Qingxin Shi
- School of Pharmacy, Hubei University of Chinese Medicine, Wuhan, 430065, China
| | - Jiangcheng He
- Wuhan Integrated Traditional Chinese and Western Medicine Orthopedic Hospital, Affiliated Hospital of Wuhan Sports University, Wuhan, 430079, China
| | - Guangya Chen
- School of Pharmacy, Hubei University of Chinese Medicine, Wuhan, 430065, China
| | - Jinlin Xu
- School of Pharmacy, Hubei University of Chinese Medicine, Wuhan, 430065, China
| | - Zhaoxiang Zeng
- School of Pharmacy, Hubei University of Chinese Medicine, Wuhan, 430065, China
| | - Xueyan Zhao
- School of Pharmacy, Hubei University of Chinese Medicine, Wuhan, 430065, China
| | - Binbin Zhao
- School of Basic Medicine, Hubei University of Chinese Medicine, Wuhan, 430065, China
| | - Xiang Gao
- Institute of Liver Diseases, Hubei Key Laboratory of the Theory and Application Research of Liver and Kidney in Traditional Chinese Medicine, Hubei Provincial Hospital of Traditional Chinese Medicine, Wuhan, 430061, China
- Affiliated Hospital of Hubei University of Chinese Medicine, Wuhan, 430074, China
- Hubei Province Academy of Traditional Chinese Medicine, Wuhan, 430074, China
| | - Zhihua Ye
- Institute of Liver Diseases, Hubei Key Laboratory of the Theory and Application Research of Liver and Kidney in Traditional Chinese Medicine, Hubei Provincial Hospital of Traditional Chinese Medicine, Wuhan, 430061, China
- Affiliated Hospital of Hubei University of Chinese Medicine, Wuhan, 430074, China
- Hubei Province Academy of Traditional Chinese Medicine, Wuhan, 430074, China
| | - Mingzhong Xiao
- Institute of Liver Diseases, Hubei Key Laboratory of the Theory and Application Research of Liver and Kidney in Traditional Chinese Medicine, Hubei Provincial Hospital of Traditional Chinese Medicine, Wuhan, 430061, China
- Affiliated Hospital of Hubei University of Chinese Medicine, Wuhan, 430074, China
- Hubei Province Academy of Traditional Chinese Medicine, Wuhan, 430074, China
| | - Hanmin Li
- Institute of Liver Diseases, Hubei Key Laboratory of the Theory and Application Research of Liver and Kidney in Traditional Chinese Medicine, Hubei Provincial Hospital of Traditional Chinese Medicine, Wuhan, 430061, China
- Affiliated Hospital of Hubei University of Chinese Medicine, Wuhan, 430074, China
- Hubei Province Academy of Traditional Chinese Medicine, Wuhan, 430074, China
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Peng YC, Xu JX, You XM, Huang YY, Ma L, Li LQ, Qi LN. Specific gut microbiome signature predicts hepatitis B virus-related hepatocellular carcinoma patients with microvascular invasion. Ann Med 2023; 55:2283160. [PMID: 38112540 PMCID: PMC10986448 DOI: 10.1080/07853890.2023.2283160] [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: 07/30/2023] [Accepted: 11/08/2023] [Indexed: 12/21/2023] Open
Abstract
BACKGROUND We aimed to assess differences in intestinal microflora between patients with operable hepatitis B virus-related hepatocellular carcinoma (HBV-HCC) with microvascular invasion (MVI) and those without MVI. Additionally, we investigated the potential of the microbiome as a non-invasive biomarker for patients with MVI. METHODS We analyzed the preoperative gut microbiomes (GMs) of two groups, the MVI (n = 46) and non-MVI (n = 56) groups, using 16S ribosomal RNA gene sequencing data. At the operational taxonomic unit level, we employed random forest models to predict MVI risk and validated the results in independent validation cohorts [MVI group (n = 17) and non-MVI group (n = 15)]. RESULTS β diversity analysis, utilizing weighted UniFrac distances, revealed a significant difference between the MVI and non-MVI groups, as indicated by non-metric multidimensional scaling and principal coordinate analysis. We also observed a significant correlation between the characteristic intestinal microbial communities at the genus level and their main functions. Nine optimal microbial markers were identified, with an area under the curve of 79.76% between 46 MVI and 56 non-MVI samples and 79.80% in the independent verification group. CONCLUSION This pioneering analysis of the GM in patients with operable HBV-HCC with and without MVI opens new avenues for treating HBV-HCC with MVI. We successfully established a diagnostic model and independently verified microbial markers for patients with MVI. As preoperative targeted biomarkers, GM holds potential as a non-invasive tool for patients with HBV-HCC with MVI.
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Affiliation(s)
- Yu-Chong Peng
- Department of General Surgery, Chongqing Hospital of Traditional Chinese Medicine, Chongqing, China
| | - Jing-Xuan Xu
- Department of Hepatobiliary Surgery, Guangxi Medical University Cancer Hospital, Nanning, China
- Ministry of Education, Key Laboratory of Early Prevention and Treatment for Regional High Frequency Tumor, Nanning, China
| | - Xue-Mei You
- Department of Hepatobiliary Surgery, Guangxi Medical University Cancer Hospital, Nanning, China
- Ministry of Education, Key Laboratory of Early Prevention and Treatment for Regional High Frequency Tumor, Nanning, China
| | - Yi-Yue Huang
- Department of Hepatobiliary Surgery, Guangxi Medical University Cancer Hospital, Nanning, China
- Ministry of Education, Key Laboratory of Early Prevention and Treatment for Regional High Frequency Tumor, Nanning, China
| | - Liang Ma
- Department of Hepatobiliary Surgery, Guangxi Medical University Cancer Hospital, Nanning, China
- Ministry of Education, Key Laboratory of Early Prevention and Treatment for Regional High Frequency Tumor, Nanning, China
| | - Le-Qun Li
- Department of Hepatobiliary Surgery, Guangxi Medical University Cancer Hospital, Nanning, China
- Ministry of Education, Key Laboratory of Early Prevention and Treatment for Regional High Frequency Tumor, Nanning, China
- Guangxi Liver Cancer Diagnosis and Treatment Engineering and Technology Research Center, Nanning, China
| | - Lu-Nan Qi
- Department of Hepatobiliary Surgery, Guangxi Medical University Cancer Hospital, Nanning, China
- Ministry of Education, Key Laboratory of Early Prevention and Treatment for Regional High Frequency Tumor, Nanning, China
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Moon SJ, Jung SM, Baek IW, Park KS, Kim KJ. Molecular signature of neutrophil extracellular trap mediating disease module in idiopathic inflammatory myopathy. J Autoimmun 2023; 138:103063. [PMID: 37220716 DOI: 10.1016/j.jaut.2023.103063] [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: 03/20/2023] [Revised: 05/07/2023] [Accepted: 05/09/2023] [Indexed: 05/25/2023]
Abstract
The rarity and heterogeneity of idiopathic inflammatory myopathy (IIM) pose challenges for researching IIM in affected individuals. We analyzed integrated transcriptomic datasets obtained using muscle tissues from patients with five distinct IIM subtypes to investigate the shared and distinctive cellular and molecular characteristics. A transcriptomic dataset of muscle tissues from normal controls (n = 105) and patients with dermatomyositis (n = 89), polymyositis (n = 33), inclusion body myositis (n = 121), immune-mediated necrotizing myositis (n = 75), and anti-synthetase syndrome (n = 18) was used for differential gene-expression analysis, functional-enrichment analysis, gene set-enrichment analysis, disease-module identification, and kernel-based diffusion scoring. Damage-associated molecular pattern-associated pathways and neutrophil-mediated immunity were significantly enriched across different IIM subtypes, although their activities varied. Interferons-signaling pathways were differentially activated across all five IIM subtypes. In particular, neutrophil extracellular trap (NET) formation was significantly activated and correlated with Fcγ R-mediated signaling pathways. NET formation-associated genes were key for establishing disease modules, and FCGRs, C1QA, and SERPINE1 markedly perturbed the disease modules. Integrated transcriptomic analysis of muscle tissues identified NETs as key components of neutrophil-mediated immunity involved in the pathogenesis of IIM subtypes and, thus, has therapeutically targetable value.
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Affiliation(s)
- Su-Jin Moon
- Division of Rheumatology, Department of Internal Medicine, Yeouido St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Seung Min Jung
- Division of Rheumatology, Department of Internal Medicine, St. Vincent's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - In-Woon Baek
- Division of Rheumatology, Department of Internal Medicine, Ewha Womans University College of Medicine, Seoul, Republic of Korea
| | - Kyung-Su Park
- Division of Rheumatology, Department of Internal Medicine, St. Vincent's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Ki-Jo Kim
- Division of Rheumatology, Department of Internal Medicine, St. Vincent's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea.
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Graves OK, Kim W, Özcan M, Ashraf S, Turkez H, Yuan M, Zhang C, Mardinoglu A, Li X. Discovery of drug targets and therapeutic agents based on drug repositioning to treat lung adenocarcinoma. Biomed Pharmacother 2023; 161:114486. [PMID: 36906970 DOI: 10.1016/j.biopha.2023.114486] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 02/20/2023] [Accepted: 03/07/2023] [Indexed: 03/12/2023] Open
Abstract
BACKGROUND Lung adenocarcinoma (LUAD) is the one of the most common subtypes in lung cancer. Although various targeted therapies have been used in the clinical practice, the 5-year overall survival rate of patients is still low. Thus, it is urgent to identify new therapeutic targets and develop new drugs for the treatment of the LUAD patients. METHODS Survival analysis was used to identify the prognostic genes. Gene co-expression network analysis was used to identify the hub genes driving the tumor development. A profile-based drug repositioning approach was used to repurpose the potentially useful drugs for targeting the hub genes. MTT and LDH assay were used to measure the cell viability and drug cytotoxicity, respectively. Western blot was used to detect the expression of the proteins. FINDINGS We identified 341 consistent prognostic genes from two independent LUAD cohorts, whose high expression was associated with poor survival outcomes of patients. Among them, eight genes were identified as hub genes due to their high centrality in the key functional modules in the gene-co-expression network analysis and these genes were associated with the various hallmarks of cancer (e.g., DNA replication and cell cycle). We performed drug repositioning analysis for three of the eight genes (CDCA8, MCM6, and TTK) based on our drug repositioning approach. Finally, we repurposed five drugs for inhibiting the protein expression level of each target gene and validated the drug efficacy by performing in vitro experiments. INTERPRETATION We found the consensus targetable genes for the treatment of LUAD patients with different races and geographic characteristics. We also proved the feasibility of our drug repositioning approach for the development of new drugs for disease treatment.
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Affiliation(s)
| | - Woonghee Kim
- Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm SE-17165, Sweden.
| | - Mehmet Özcan
- Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm SE-17165, Sweden.
| | - Sajda Ashraf
- Trustlife Labs, Drug Research & Development Center, 34774 Istanbul, Turkey.
| | - Hasan Turkez
- Trustlife Labs, Drug Research & Development Center, 34774 Istanbul, Turkey.
| | - Meng Yuan
- Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm SE-17165, Sweden.
| | - Cheng Zhang
- Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm SE-17165, Sweden.
| | - Adil Mardinoglu
- Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm SE-17165, Sweden; Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King's College London, London SE1 9RT, UK.
| | - Xiangyu Li
- Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm SE-17165, Sweden; Bash Biotech Inc, 600 West Broadway, Suite 700, San Diego, CA 92101, USA; Guangzhou Laboratory, Guangzhou 510005, China.
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Chapola H, de Bastiani MA, Duarte MM, Freitas MB, Schuster JS, de Vargas DM, Klamt F. A comparative study of COVID-19 transcriptional signatures between clinical samples and preclinical cell models in the search for disease master regulators and drug repositioning candidates. Virus Res 2023; 326:199053. [PMID: 36709793 PMCID: PMC9877318 DOI: 10.1016/j.virusres.2023.199053] [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: 10/12/2022] [Revised: 12/29/2022] [Accepted: 01/24/2023] [Indexed: 01/27/2023]
Abstract
Coronavirus disease 2019 (COVID-19) is an acute viral disease with millions of cases worldwide. Although the number of daily new cases and deaths has been dropping, there is still a need for therapeutic alternatives to deal with severe cases. A promising strategy to prospect new therapeutic candidates is to investigate the regulatory mechanisms involved in COVID-19 progression using integrated transcriptomics approaches. In this work, we aimed to identify COVID-19 Master Regulators (MRs) using a series of publicly available gene expression datasets of lung tissue from patients which developed the severe form of the disease. We were able to identify a set of six potential COVID-19 MRs related to its severe form, namely TAL1, TEAD4, EPAS1, ATOH8, ERG, and ARNTL2. In addition, using the Connectivity Map drug repositioning approach, we identified 52 different drugs which could be used to revert the disease signature, thus being candidates for the design of novel clinical treatments. Furthermore, we compared the identified signature and drugs with the ones obtained from the analysis of nasopharyngeal swab samples from infected patients and preclinical cell models. This comparison showed significant similarities between them, although also revealing some limitations on the overlap between clinical and preclinical data in COVID-19, highlighting the need for careful selection of the best model for each disease stage.
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Affiliation(s)
- Henrique Chapola
- Laboratory of Cellular Biochemistry, Biochemistry Department, Institute of Health Sciences (ICBS), Federal University of Rio Grande do Sul (UFRGS), Porto Alegre, RS 90035-003, Brazil
| | - Marco Antônio de Bastiani
- Laboratory of Cellular Biochemistry, Biochemistry Department, Institute of Health Sciences (ICBS), Federal University of Rio Grande do Sul (UFRGS), Porto Alegre, RS 90035-003, Brazil; Zimmer Lab, Biochemistry Department, Institute of Health Sciences (ICBS), Federal University of Rio Grande do Sul (UFRGS), Porto Alegre, RS 90035-003, Brazil
| | - Marcelo Mendes Duarte
- Laboratory of Cellular Biochemistry, Biochemistry Department, Institute of Health Sciences (ICBS), Federal University of Rio Grande do Sul (UFRGS), Porto Alegre, RS 90035-003, Brazil
| | - Matheus Becker Freitas
- Estacio College of Rio Grande do Sul (ESTACIO FARGS), Porto Alegre, RS 90020-060, Brazil
| | | | - Daiani Machado de Vargas
- Laboratory of Cellular Biochemistry, Biochemistry Department, Institute of Health Sciences (ICBS), Federal University of Rio Grande do Sul (UFRGS), Porto Alegre, RS 90035-003, Brazil.
| | - Fábio Klamt
- Laboratory of Cellular Biochemistry, Biochemistry Department, Institute of Health Sciences (ICBS), Federal University of Rio Grande do Sul (UFRGS), Porto Alegre, RS 90035-003, Brazil; Zimmer Lab, Biochemistry Department, Institute of Health Sciences (ICBS), Federal University of Rio Grande do Sul (UFRGS), Porto Alegre, RS 90035-003, Brazil; National Institutes of Science & Technology, Translational Medicine (INCT-TM), Porto Alegre, RS 90035-903, Brazil; IMMUNESHARE - MCTI Trial (CNPq/MCTI #137541939766794), Brazil
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Jung SM, Baek IW, Park KS, Kim KJ. De novo molecular subtyping of salivary gland tissue in the context of Sjögren's syndrome heterogeneity. Clin Immunol 2022; 245:109171. [DOI: 10.1016/j.clim.2022.109171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 10/26/2022] [Accepted: 10/27/2022] [Indexed: 11/08/2022]
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Zhao C, Xiong K, Adam A, Ji Z, Li X. Necroptosis Identifies Novel Molecular Phenotypes and Influences Tumor Immune Microenvironment of Lung Adenocarcinoma. Front Immunol 2022; 13:934494. [PMID: 35911707 PMCID: PMC9331758 DOI: 10.3389/fimmu.2022.934494] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 06/22/2022] [Indexed: 12/24/2022] Open
Abstract
This study aims to investigate the immune and epigenetic mutational landscape of necroptosis in lung adenocarcinoma (LUAD), identify novel molecular phenotypes, and develop a prognostic scoring system based on necroptosis regulatory molecules for a better understanding of the tumor immune microenvironment (TIME) in LUAD. Based on the Cancer Genome Atlas and Gene Expression Omnibus database, a total of 29 overlapped necroptosis-related genes were enrolled to classify patients into different necroptosis phenotypes using unsupervised consensus clustering. We systematically correlated the phenotypes with clinical features, immunocyte infiltrating levels, and epigenetic mutation characteristics. A novel scoring system was then constructed, termed NecroScore, to quantify necroptosis of LUAD by principal component analysis. Three distinct necroptosis phenotypes were confirmed. Two clusters with high expression of necroptosis-related regulators were “hot tumors”, while another phenotype with low expression was a “cold tumor”. Molecular characteristics, including mutational frequency and types, copy number variation, and regulon activity differed significantly among the subtypes. The NecroScore, as an independent prognostic factor (HR=1.086, 95%CI=1.040-1.133, p<0.001), was able to predict the survival outcomes and show that patients with higher scores experienced a poorer prognosis. It could also evaluate the responses to immunotherapy and chemotherapeutic efficiency. In conclusion, necroptosis-related molecules are correlated with genome diversity in pan-cancer, playing a significant role in forming the TIME of LUAD. Necroptosis phenotypes can distinguish different TIME and molecular features, and the NecroScore is a promising biomarker for predicting prognosis, as well as immuno- and chemotherapeutic benefits in LUAD.
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Affiliation(s)
- Chen Zhao
- Department of Oncology, Renmin Hospital of Wuhan University, Wuhan, China
- *Correspondence: Chen Zhao, ; Xiangpan Li,
| | - Kewei Xiong
- Department of Oncology, Renmin Hospital of Wuhan University, Wuhan, China
- School of Mathematics and Statistics, Central China Normal University, Wuhan, China
| | - Abdalla Adam
- School of Medicine, Wuhan University, Wuhan, China
| | - Zhiqiang Ji
- School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Xiangpan Li
- Department of Oncology, Renmin Hospital of Wuhan University, Wuhan, China
- *Correspondence: Chen Zhao, ; Xiangpan Li,
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Nie J, Gong L, Li Z, Ou D, Zhang L, Liu Y, Zhang J, Liu D. Bioinformatics Analysis of mRNAs and miRNAs for Identifying Potential Biomarkers in Lung Adenosquamous Carcinoma. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2022; 2022:5851269. [PMID: 35281953 PMCID: PMC8906974 DOI: 10.1155/2022/5851269] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 01/19/2022] [Accepted: 01/22/2022] [Indexed: 12/25/2022]
Abstract
Background Lung adenosquamous carcinoma (LASC) is a special type of lung cancer. LASC is a malignant tumor with strong aggressiveness and a poor prognosis. Previous studies have revealed that microRNAs (miRNAs) are widely involved in the development of tumors by targeting mRNA. This study is aimed at identifying the key mRNAs and miRNAs of LASC and constructing miRNA-mRNA networks for deeply comprehending the latent molecular mechanisms. Methods mRNA dataset (GSE51852) and miRNA dataset (GSE51853) were extracted and downloaded from the Gene Expression Omnibus (GEO) database. Differentially expressed genes (DEGs) and differentially expressed miRNAs (DEMs) were picked out by the GEO2R web tool. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) functional enrichment analyses were conducted in the DAVID database. The protein-protein interaction (PPI) network was performed and analyzed by using the STRING database and Cytoscape software, respectively. TransmiR v2.0 was applied to predict potential transcription factors of miRNAs. The target genes of DEMs were predicted in the miRWalk database. Results In comparison to normal tissues, a total of 1458 DEGs (511 upregulated and 947 downregulated) and 13 DEMs (5 upregulated and 8 downregulated) were screened out in LASC tissues. The PPI network of the DEGs displayed five key modules and seventeen hub genes. Six target genes of the DEMs were predicted, and five essential miRNA-mRNA regulatory pairs were established. Ensuingly, CENPF, one of the target genes, was also the hub genes of GSE51852, which was obtained from MCODE and cytoHubba and regulated by hsa-miR-205. Conclusions We constructed the miRNA-mRNA regulatory pairs, which are helpful to study the potential regulatory mechanisms and find out promising diagnosis biomarkers and therapeutic targets for LASC.
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Affiliation(s)
- Jin Nie
- The Second Department of Respiratory and Critical Care Medicine, Affiliated Hospital of Zunyi Medical University, Zunyi, 563000, China
| | - Ling Gong
- Department of Respiratory Medicine, The Third Affiliated Hospital of Zunyi Medical University (The First People Hospital of Zunyi), Zunyi, 563000, China
| | - Zhu Li
- Department of Respiratory Medicine, The Third Affiliated Hospital of Zunyi Medical University (The First People Hospital of Zunyi), Zunyi, 563000, China
| | - Dong Ou
- Department of Respiratory Medicine, The Third Affiliated Hospital of Zunyi Medical University (The First People Hospital of Zunyi), Zunyi, 563000, China
| | - Ling Zhang
- Department of Respiratory Medicine, The Third Affiliated Hospital of Zunyi Medical University (The First People Hospital of Zunyi), Zunyi, 563000, China
| | - Yi Liu
- Zunyi Medical University, Zunyi, 563000, China
| | - Jianyong Zhang
- The Second Department of Respiratory and Critical Care Medicine, Affiliated Hospital of Zunyi Medical University, Zunyi, 563000, China
| | - Daishun Liu
- Zunyi Medical University, Zunyi, 563000, China
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Patrizi S, Pederiva F, d'Adamo AP. Whole-Genome Methylation Study of Congenital Lung Malformations in Children. Front Oncol 2021; 11:689833. [PMID: 34262872 PMCID: PMC8273538 DOI: 10.3389/fonc.2021.689833] [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: 04/01/2021] [Accepted: 06/07/2021] [Indexed: 11/30/2022] Open
Abstract
Background and Objectives The treatment of asymptomatic patients with congenital pulmonary malformations (CPMs) remains controversial, partially because the relationship between congenital lung malformations and malignancy is still undefined. Change in methylation pattern is a crucial event in human cancer, including lung cancer. We therefore studied all differentially methylated regions (DMRs) in a series of CPMs in an attempt to find methylation anomalies in genes already described in association with malignancy. Methods The DNA extracted from resected congenital lung malformations and control lung tissue was screened using Illumina MethylationEPIC arrays. Comparisons between the group of malformed samples or the malformed samples of same histology or each malformed sample and the controls and between a pleuropulmonary blastoma (PPB) and controls were performed. Moreover, each malformed sample was pairwise compared with its respective control. All differentially methylated regions (DMRs) with an adjusted p-value <0,05 were studied. Results Every comparison highlighted a number of DMRs closed to genes involved either in cell proliferation or in embryonic development or included in the Cancer Gene Census. Their abnormal methylation had been already described in lung tumors. Conclusions Methylation anomalies already described in lung tumors and also shared by the PPB were found in congenital lung malformations, regardless the histology. The presence of methylation abnormalities is suggestive of a correlation between congenital lung malformations and some step of malignant transformation.
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Affiliation(s)
- Sara Patrizi
- Medical, Surgical and Health Sciences Department, University of Trieste, Trieste, Italy
| | - Federica Pederiva
- Pediatric Surgery, Institute for Maternal and Child Health-IRCCS "Burlo Garofolo", Trieste, Italy
| | - Adamo Pio d'Adamo
- Medical, Surgical and Health Sciences Department, University of Trieste, Trieste, Italy.,Laboratory of Medical Genetics, Institute for Maternal and Child Health-IRCCS "Burlo Garofolo", Trieste, Italy
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Venkatraman S, Meller J, Hongeng S, Tohtong R, Chutipongtanate S. Transcriptional Regulation of Cancer Immune Checkpoints: Emerging Strategies for Immunotherapy. Vaccines (Basel) 2020; 8:E735. [PMID: 33291616 PMCID: PMC7761936 DOI: 10.3390/vaccines8040735] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 12/01/2020] [Accepted: 12/02/2020] [Indexed: 12/19/2022] Open
Abstract
The study of immune evasion has gained a well-deserved eminence in cancer research by successfully developing a new class of therapeutics, immune checkpoint inhibitors, such as pembrolizumab and nivolumab, anti-PD-1 antibodies. By aiming at the immune checkpoint blockade (ICB), these new therapeutics have advanced cancer treatment with notable increases in overall survival and tumor remission. However, recent reports reveal that 40-60% of patients fail to benefit from ICB therapy due to acquired resistance or tumor relapse. This resistance may stem from increased expression of co-inhibitory immune checkpoints or alterations in the tumor microenvironment that promotes immune suppression. Because these mechanisms are poorly elucidated, the transcription factors that regulate immune checkpoints, known as "master regulators", have garnered interest. These include AP-1, IRF-1, MYC, and STAT3, which are known to regulate PD/PD-L1 and CTLA-4. Identifying these and other potential master regulators as putative therapeutic targets or biomarkers can be facilitated by mining cancer literature, public datasets, and cancer genomics resources. In this review, we describe recent advances in master regulator identification and characterization of the mechanisms underlying immune checkpoints regulation, and discuss how these master regulators of immune checkpoint molecular expression can be targeted as a form of auxiliary therapeutic strategy to complement traditional immunotherapy.
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Affiliation(s)
- Simran Venkatraman
- Graduate Program in Molecular Medicine, Faculty of Science Joint Program Faculty of Medicine Ramathibodi Hospital, Faculty of Medicine Siriraj Hospital, Faculty of Dentistry, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand;
| | - Jarek Meller
- Departments of Environmental and Public Health Sciences, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA;
- Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45267, USA
| | - Suradej Hongeng
- Division of Hematology and Oncology, Department of Pediatrics, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand;
| | - Rutaiwan Tohtong
- Graduate Program in Molecular Medicine, Faculty of Science Joint Program Faculty of Medicine Ramathibodi Hospital, Faculty of Medicine Siriraj Hospital, Faculty of Dentistry, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand;
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
| | - Somchai Chutipongtanate
- Pediatric Translational Research Unit, Department of Pediatrics, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand
- Department of Clinical Epidemiology and Biostatistics, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand
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Parkinson's Disease Master Regulators on Substantia Nigra and Frontal Cortex and Their Use for Drug Repositioning. Mol Neurobiol 2020; 58:1517-1534. [PMID: 33211252 DOI: 10.1007/s12035-020-02203-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 11/03/2020] [Indexed: 12/14/2022]
Abstract
Parkinson's disease (PD) is among the most prevalent neurodegenerative diseases. Available evidences support the view of PD as a complex disease, being the outcome of interactions between genetic and environmental factors. In face of diagnosis and therapy challenges, and the elusive PD etiology, the use of alternative methodological approaches for the elucidation of the disease pathophysiological mechanisms and proposal of novel potential therapeutic interventions has become increasingly necessary. In the present study, we first reconstructed the transcriptional regulatory networks (TN), centered on transcription factors (TF), of two brain regions affected in PD, the substantia nigra pars compacta (SNc) and the frontal cortex (FCtx). Then, we used case-control studies data from these regions to identify TFs working as master regulators (MR) of the disease, based on region-specific TNs. Twenty-nine regulatory units enriched with differentially expressed genes were identified for the SNc, and twenty for the FCtx, all of which were considered MR candidates for PD. Three consensus MR candidates were found for SNc and FCtx, namely ATF2, SLC30A9, and ZFP69B. In order to search for novel potential therapeutic interventions, we used these consensus MR candidate signatures as input to the Connectivity Map (CMap), a computational drug repositioning webtool. This analysis resulted in the identification of four drugs that reverse the expression pattern of all three MR consensus simultaneously, benperidol, harmaline, tubocurarine chloride, and vorinostat, thus suggested as novel potential PD therapeutic interventions.
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Duan M, Song H, Wang C, Zheng J, Xie H, He Y, Huang L, Zhou F. Detection and Independent Validation of Model-Based Quantitative Transcriptional Regulation Relationships Altered in Lung Cancers. Front Bioeng Biotechnol 2020; 8:582. [PMID: 32656193 PMCID: PMC7325891 DOI: 10.3389/fbioe.2020.00582] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 05/13/2020] [Indexed: 12/27/2022] Open
Abstract
Differential expressions of genes are widely evaluated for the diagnosis and prognosis correlations with diseases. But limited studies investigate how transcriptional regulations are quantitatively altered in diseases. This study proposes a novel model-based quantitative measurement of transcriptional regulatory relationships between mRNA genes and Transcription Factor (TF) genes (mqTrans features). This study didn't consider the regulatory relationships between TF genes, so the mRNA genes were the protein-coding genes excluding the TF genes. The models are trained in the control samples in a lung cancer dataset and evaluated in two independent datasets and the hold-out testing samples from the third dataset. Twenty-nine mRNA genes are detected with transcriptional regulations quantitatively altered in lung cancers. The transcriptional modification technologies like RNA interference (RNAi) may be utilized to restore the altered transcriptional regulations in lung cancers.
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Affiliation(s)
- Meiyu Duan
- Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, College of Computer Science and Technology, Jilin University, Changchun, China
| | - Haoqiu Song
- Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, College of Computer Science and Technology, Jilin University, Changchun, China.,College of Computer Science, Hubei University of Technology, Wuhan, China
| | - Chaoyu Wang
- Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, College of Software, Jilin University, Changchun, China
| | - Jiaxin Zheng
- Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, College of Software, Jilin University, Changchun, China
| | - Hui Xie
- Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, College of Computer Science and Technology, Jilin University, Changchun, China
| | - Yupeng He
- Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, College of Software, Jilin University, Changchun, China
| | - Lan Huang
- Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, College of Computer Science and Technology, Jilin University, Changchun, China
| | - Fengfeng Zhou
- Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, College of Computer Science and Technology, Jilin University, Changchun, China
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De Bastiani MA, Klamt F. Integrated transcriptomics reveals master regulators of lung adenocarcinoma and novel repositioning of drug candidates. Cancer Med 2019; 8:6717-6729. [PMID: 31503425 PMCID: PMC6825976 DOI: 10.1002/cam4.2493] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 07/18/2019] [Accepted: 07/31/2019] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Lung adenocarcinoma is the major cause of cancer-related deaths in the world. Given this, the importance of research on its pathophysiology and therapy remains a key health issue. To assist in this endeavor, recent oncology studies are adopting Systems Biology approaches and bioinformatics to analyze and understand omics data, bringing new insights about this disease and its treatment. METHODS We used reverse engineering of transcriptomic data to reconstruct nontumorous lung reference networks, focusing on transcription factors (TFs) and their inferred target genes, referred as regulatory units or regulons. Afterwards, we used 13 case-control studies to identify TFs acting as master regulators of the disease and their regulatory units. Furthermore, the inferred activation patterns of regulons were used to evaluate patient survival and search drug candidates for repositioning. RESULTS The regulatory units under the influence of ATOH8, DACH1, EPAS1, ETV5, FOXA2, FOXM1, HOXA4, SMAD6, and UHRF1 transcription factors were consistently associated with the pathological phenotype, suggesting that they may be master regulators of lung adenocarcinoma. We also observed that the inferred activity of FOXA2, FOXM1, and UHRF1 was significantly associated with risk of death in patients. Finally, we obtained deptropine, promazine, valproic acid, azacyclonol, methotrexate, and ChemBridge ID compound 5109870 as potential candidates to revert the molecular profile leading to decreased survival. CONCLUSION Using an integrated transcriptomics approach, we identified master regulator candidates involved with the development and prognostic of lung adenocarcinoma, as well as potential drugs for repurposing.
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Affiliation(s)
- Marco Antônio De Bastiani
- Laboratory of Cellular Biochemistry, Department of Biochemistry, Federal University of Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil.,National Institute of Science and Technology for Translational Medicine (INCT-TM), Porto Alegre, RS, Brazil
| | - Fábio Klamt
- Laboratory of Cellular Biochemistry, Department of Biochemistry, Federal University of Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil.,National Institute of Science and Technology for Translational Medicine (INCT-TM), Porto Alegre, RS, Brazil
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