1
|
Baruah B, Dutta MP, Banerjee S, Bhattacharyya DK. EnsemBic: An effective ensemble of biclustering to identify potential biomarkers of esophageal squamous cell carcinoma. Comput Biol Chem 2024; 110:108090. [PMID: 38759483 DOI: 10.1016/j.compbiolchem.2024.108090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 03/28/2024] [Accepted: 04/29/2024] [Indexed: 05/19/2024]
Abstract
The development of functionally enriched and biologically competent biclustering algorithm is essential for extracting hidden information from massive biological datasets. This paper presents a novel biclustering ensemble called EnsemBic based on p-value, which calculates the functional similarity of genetic associations. To validate the effectiveness and robustness of EnsemBic, we apply three well-known biclustering techniques, viz. Laplace Prior, iBBiG, and xMotif to implement EnsemBic and have been compared using different leading parameters. It is observed that the EnsemBic outperforms its competing algorithms in several prominent functional and biological measures. Next, the biclusters obtained from EnsemBic are used to identify potential biomarkers of Esophageal Squamous Cell Carcinoma (ESCC) by exploring topological and biological relevance with reference to the elite genes, attained from genecards. Finally, we discover that the genes F2RL3, APPL1, CALM1, IFNGR1, LPAR1, ANGPT2, ARPC2, CGN, CLDN7, ATP6V1C2, CEACAM1, FTL, PLAU,PSMB4, and EPHB2 carry both the topological and biological significance of previously established ESCC elite genes. Therefore, we declare the aforementioned genes as potential biomarkers of ESCC.
Collapse
Affiliation(s)
- Bikash Baruah
- Dept. of Computer Science and Engineering, NIT Arunachal Pradesh, India
| | - Manash P Dutta
- Dept. of Computer Science & Information Technology, Cotton University, Guwahati, Assam, India.
| | | | - Dhruba K Bhattacharyya
- Dept. of Computer Science and Engineering, Tezpur University, School of Engineering, Tezpur, India
| |
Collapse
|
2
|
Solovev YV, Evpak AS, Kudriaeva AA, Gabibov AG, Belogurov AA. Evaluation of Clinically Significant miRNAs Level by Machine Learning Approaches Utilizing Total Transcriptome Data. DOKL BIOCHEM BIOPHYS 2024; 516:98-106. [PMID: 38539010 DOI: 10.1134/s1607672924700790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 01/25/2024] [Accepted: 02/03/2024] [Indexed: 05/26/2024]
Abstract
Analysis of the mechanisms underlying the occurrence and progression of cancer represents a key objective in contemporary clinical bioinformatics and molecular biology. Utilizing omics data, particularly transcriptomes, enables a detailed characterization of expression patterns and post-transcriptional regulation across various RNA types relative to the entire transcriptome. Here, we assembled a dataset comprising transcriptomic data from approximately 16 000 patients encompassing over 160 types of cancer. We employed state-of-the-art gradient boosting algorithms to discern intricate correlations in the expression levels of four clinically significant microRNAs, specifically, hsa-mir-21, hsa-let-7a-1, hsa-let-7b, and hsa-let-7i, with the expression levels of the remaining 60 660 unique RNAs. Our analysis revealed a dependence of the expression levels of the studied microRNAs on the concentrations of several small nucleolar RNAs and regulatory long noncoding RNAs. Notably, the roles of these RNAs in the development of specific cancer types had been previously established through experimental evidence. Subsequent evaluation of the created database will facilitate the identification of a broader spectrum of overarching dependencies related to changes in the expression levels of various RNA classes in diverse cancers. In future, it will make possible to discover unique alterations specific to certain types of malignant transformations.
Collapse
Affiliation(s)
- Ya V Solovev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia.
| | - A S Evpak
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia.
| | - A A Kudriaeva
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - A G Gabibov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
- Moscow State University, Moscow, Russia
| | - A A Belogurov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
- Moscow State University of Medicine and Dentistry, 127473, Moscow, Russia
| |
Collapse
|
3
|
Guo J, Wang H, Huang C, Lai C, Shang W, Luo S, Chen L. PLAU, transcriptionally negatively regulated by GATA6, promotes lung squamous carcinoma cell proliferation and migration. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2024; 1871:119744. [PMID: 38702016 DOI: 10.1016/j.bbamcr.2024.119744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 03/31/2024] [Accepted: 04/24/2024] [Indexed: 05/06/2024]
Abstract
BACKGROUND Lung squamous cell carcinoma (LUSC) is associated with high mortality and has limited therapeutic treatment options. Plasminogen activator urokinase (PLAU) plays important roles in tumor cell malignancy. However, the oncogenic role of PLAU in the progression of LUSC remains unknown. GATA-binding factor 6 (GATA6), a key regulator of lung development, inhibits LUSC cell proliferation and migration, but the underlying regulatory mechanism remains to be further explored. Moreover, the regulatory effect of GATA6 on PLAU expression has not been reported. The aim of this study was to identify the role of PLAU and the transcriptional inhibition mechanism of GATA6 on PLAU expression in LUSC. METHODS To identify the potential target genes regulated by GATA6, differentially expressed genes (DEGs) obtained from GEO datasets analysis and RNA-seq experiment were subjected to Venn analysis and correlation heatmap analysis. The transcriptional regulatory effects of GATA6 on PLAU expression were detected by real-time PCR, immunoblotting, and dual-luciferase reporter assays. The oncogenic effects of PLAU on LUSC cell proliferation and migration were evaluated by EdU incorporation, Matrigel 3D culture and Transwell assays. PLAU expression was detected in tissue microarray of LUSC via immunohistochemistry (IHC) assay. To determine prognostic factors for prognosis of LUSC patients, the clinicopathological characteristics and PLAU expression were subjected to univariate Cox regression analysis. RESULTS PLAU overexpression promoted LUSC cell proliferation and migration. PLAU is overexpressed in LUSC tissues compared with normal tissues. Consistently, high PLAU expression, which acts as an independent risk factor, is associated with poor prognosis of LUSC patients. Furthermore, the expression of PLAU is transcriptionally regulated by GATA6. CONCLUSION In this work, it was revealed that PLAU is a novel oncogene for LUSC and a new molecular regulatory mechanism of GATA6 in LUSC was unveiled. Targeting the GATA6/PLAU pathway might help in the development of novel therapeutic treatment strategies for LUSC.
Collapse
Affiliation(s)
- Jiankun Guo
- Center for Experimental Medicine, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi 330006, China; Medical Innovation Center, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi 330006, China
| | - Hailong Wang
- Medical Innovation Center, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi 330006, China
| | - Changhua Huang
- Center for Experimental Medicine, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi 330006, China; Medical Innovation Center, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi 330006, China
| | - Caihong Lai
- Huankui Academy, Nanchang University, Nanchang, Jiangxi 330031, China
| | - Wenli Shang
- Huankui Academy, Nanchang University, Nanchang, Jiangxi 330031, China
| | - Shiwen Luo
- Center for Experimental Medicine, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi 330006, China
| | - Limin Chen
- Medical Innovation Center, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi 330006, China.
| |
Collapse
|
4
|
Mares-Quiñones MD, Galán-Vásquez E, Pérez-Rueda E, Pérez-Ishiwara DG, Medel-Flores MO, Gómez-García MDC. Identification of modules and key genes associated with breast cancer subtypes through network analysis. Sci Rep 2024; 14:12350. [PMID: 38811600 PMCID: PMC11137066 DOI: 10.1038/s41598-024-61908-4] [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: 07/13/2023] [Accepted: 05/10/2024] [Indexed: 05/31/2024] Open
Abstract
Breast cancer is the most common malignancy in women around the world. Intratumor and intertumoral heterogeneity persist in mammary tumors. Therefore, the identification of biomarkers is essential for the treatment of this malignancy. This study analyzed 28,143 genes expressed in 49 breast cancer cell lines using a Weighted Gene Co-expression Network Analysis to determine specific target proteins for Basal A, Basal B, Luminal A, Luminal B, and HER2 ampl breast cancer subtypes. Sixty-five modules were identified, of which five were characterized as having a high correlation with breast cancer subtypes. Genes overexpressed in the tumor were found to participate in the following mechanisms: regulation of the apoptotic process, transcriptional regulation, angiogenesis, signaling, and cellular survival. In particular, we identified the following genes, considered as hubs: IFIT3, an inhibitor of viral and cellular processes; ETS1, a transcription factor involved in cell death and tumorigenesis; ENSG00000259723 lncRNA, expressed in cancers; AL033519.3, a hypothetical gene; and TMEM86A, important for regulating keratinocyte membrane properties, considered as a key in Basal A, Basal B, Luminal A, Luminal B, and HER2 ampl breast cancer subtypes, respectively. The modules and genes identified in this work can be used to identify possible biomarkers or therapeutic targets in different breast cancer subtypes.
Collapse
Affiliation(s)
- María Daniela Mares-Quiñones
- Laboratorio de Biomedicina Molecular, Programa de Doctorado en Biotecnología, Escuela Nacional de Medicina y Homeopatía, Instituto Politécnico Nacional, Ciudad de México, Mexico
| | - Edgardo Galán-Vásquez
- Departamento de Ingeniería de Sistemas Computacionales y Automatización, Instituto de Investigaciones en Matemáticas Aplicadas y en Sistemas, Universidad Nacional Autónoma de México, Ciudad Universitaria, Ciudad de México, Mexico
| | - Ernesto Pérez-Rueda
- Instituto de Investigaciones en Matemáticas Aplicadas y en Sistemas, Universidad Nacional Autónoma de México, Unidad Académica del Estado de Yucatán, Mérida, Mexico
| | - D Guillermo Pérez-Ishiwara
- Laboratorio de Biomedicina Molecular, Programa de Doctorado en Biotecnología, Escuela Nacional de Medicina y Homeopatía, Instituto Politécnico Nacional, Ciudad de México, Mexico
| | - María Olivia Medel-Flores
- Laboratorio de Biomedicina Molecular, Programa de Doctorado en Biotecnología, Escuela Nacional de Medicina y Homeopatía, Instituto Politécnico Nacional, Ciudad de México, Mexico
| | - María Del Consuelo Gómez-García
- Laboratorio de Biomedicina Molecular, Programa de Doctorado en Biotecnología, Escuela Nacional de Medicina y Homeopatía, Instituto Politécnico Nacional, Ciudad de México, Mexico.
| |
Collapse
|
5
|
Zhang WQ, Sun JX, Lan ST, Sun XM, Guo YJ, Wen BC, Chen J, Liu G. Regulation of Fuzheng Huayu capsule on inhibiting the fibrosis-associated hepatocellular carcinogenesis. JOURNAL OF ASIAN NATURAL PRODUCTS RESEARCH 2024:1-20. [PMID: 38780602 DOI: 10.1080/10286020.2024.2355132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Accepted: 05/09/2024] [Indexed: 05/25/2024]
Abstract
In the current study, bioinformatics analysis of the hepatocellular carcinoma (HCC) dataset was conducted with the hepatoprotective effect of the Fuzheng Huayu (FZHY) capsule against the diethylnitrosamine-induced HCC progression analyzed. Eight cell clusters were defined and tanshinone IIA, arachidonic acid, and quercetin, compounds of the FZHY capsule, inhibit HCC progression-related fibrosis by regulating the expression of PLAU and IGFBP3. Combined with the ameliorative effect of the FZHY capsule against liver dysfunctions and expression of PLAU and IGFBP3, our study confirmed the effect of the FZHY capsule on inhibiting the fibrosis-associated HCC progression via regulating the expression of PLAU and IGFBP3.
Collapse
Affiliation(s)
- Wen-Qi Zhang
- Key Laboratory of Medical Cell Biology, Department of Achievement Transformation, Affiliated Hospital of Inner Mongolia Medical University, Hohhot 010050, China
| | - Jia-Xin Sun
- Key Laboratory of Medical Cell Biology, Department of Achievement Transformation, Affiliated Hospital of Inner Mongolia Medical University, Hohhot 010050, China
| | - Shu-Ting Lan
- Key Laboratory of Medical Cell Biology, Department of Achievement Transformation, Affiliated Hospital of Inner Mongolia Medical University, Hohhot 010050, China
| | - Xiao-Mei Sun
- Key Laboratory of Medical Cell Biology, Department of Achievement Transformation, Affiliated Hospital of Inner Mongolia Medical University, Hohhot 010050, China
| | - Yi-Jing Guo
- Key Laboratory of Medical Cell Biology, Department of Achievement Transformation, Affiliated Hospital of Inner Mongolia Medical University, Hohhot 010050, China
| | - Bi-Chao Wen
- Key Laboratory of Medical Cell Biology, Department of Achievement Transformation, Affiliated Hospital of Inner Mongolia Medical University, Hohhot 010050, China
| | - Jie Chen
- Key Laboratory of Medical Cell Biology, Department of Achievement Transformation, Affiliated Hospital of Inner Mongolia Medical University, Hohhot 010050, China
| | - Gang Liu
- Key Laboratory of Medical Cell Biology, Department of Achievement Transformation, Affiliated Hospital of Inner Mongolia Medical University, Hohhot 010050, China
| |
Collapse
|
6
|
Guo B, Sun Y, Wang Y, Zhang Y, Zheng Y, Xu S, Yang G, Ren W. Evolutionary genetics of pulmonary anatomical adaptations in deep-diving cetaceans. BMC Genomics 2024; 25:339. [PMID: 38575860 PMCID: PMC10993460 DOI: 10.1186/s12864-024-10263-9] [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: 11/21/2023] [Accepted: 03/27/2024] [Indexed: 04/06/2024] Open
Abstract
BACKGROUND Cetaceans, having experienced prolonged adaptation to aquatic environments, have undergone evolutionary changes in their respiratory systems. This process of evolution has resulted in the emergence of distinctive phenotypic traits, notably the abundance of elastic fibers and thickened alveolar walls in their lungs, which may facilitate alveolar collapse during diving. This structure helps selective exchange of oxygen and carbon dioxide, while minimizing nitrogen exchange, thereby reducing the risk of DCS. Nevertheless, the scientific inquiry into the mechanisms through which these unique phenotypic characteristics govern the diving behavior of marine mammals, including cetaceans, remains unresolved. RESULTS This study entails an evolutionary analysis of 42 genes associated with pulmonary fibrosis across 45 mammalian species. Twenty-one genes in cetaceans exhibited accelerated evolution, featuring specific amino acid substitutions in 14 of them. Primarily linked to the development of the respiratory system and lung morphological construction, these genes play a crucial role. Moreover, among marine mammals, we identified eight genes undergoing positive selection, and the evolutionary rates of three genes significantly correlated with diving depth. Specifically, the SFTPC gene exhibited convergent amino acid substitutions. Through in vitro cellular experiments, we illustrated that convergent amino acid site mutations in SFTPC contribute positively to pulmonary fibrosis in marine mammals, and the presence of this phenotype can induce deep alveolar collapse during diving, thereby reducing the risk of DCS during diving. CONCLUSIONS The study unveils pivotal genetic signals in cetaceans and other marine mammals, arising through evolution. These genetic signals may influence lung characteristics in marine mammals and have been linked to a reduced risk of developing DCS. Moreover, the research serves as a valuable reference for delving deeper into human diving physiology.
Collapse
Affiliation(s)
- Boxiong Guo
- Jiangsu Key Laboratory for Bioaffiliationersity and Biotechnology, College of Life Sciences, Nanjing Normal University, 210023, Nanjing, China
| | - Yixuan Sun
- Jiangsu Key Laboratory for Bioaffiliationersity and Biotechnology, College of Life Sciences, Nanjing Normal University, 210023, Nanjing, China
| | - Yuehua Wang
- Jiangsu Key Laboratory for Bioaffiliationersity and Biotechnology, College of Life Sciences, Nanjing Normal University, 210023, Nanjing, China
| | - Ya Zhang
- Jiangsu Key Laboratory for Bioaffiliationersity and Biotechnology, College of Life Sciences, Nanjing Normal University, 210023, Nanjing, China
| | - Yu Zheng
- Jiangsu Key Laboratory for Bioaffiliationersity and Biotechnology, College of Life Sciences, Nanjing Normal University, 210023, Nanjing, China
| | - Shixia Xu
- Jiangsu Key Laboratory for Bioaffiliationersity and Biotechnology, College of Life Sciences, Nanjing Normal University, 210023, Nanjing, China
| | - Guang Yang
- Jiangsu Key Laboratory for Bioaffiliationersity and Biotechnology, College of Life Sciences, Nanjing Normal University, 210023, Nanjing, China
| | - Wenhua Ren
- Jiangsu Key Laboratory for Bioaffiliationersity and Biotechnology, College of Life Sciences, Nanjing Normal University, 210023, Nanjing, China.
| |
Collapse
|
7
|
Wang W, Chen G, Zhang W, Zhang X, Huang M, Li C, Wang L, Lu Z, Xia J. The crucial prognostic signaling pathways of pancreatic ductal adenocarcinoma were identified by single-cell and bulk RNA sequencing data. Hum Genet 2024:10.1007/s00439-024-02663-4. [PMID: 38526745 DOI: 10.1007/s00439-024-02663-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Accepted: 02/24/2024] [Indexed: 03/27/2024]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is a malignant tumor with poor prognosis and high mortality. Although a large number of studies have explored its potential prognostic markers using traditional RNA sequencing (RNA-Seq) data, they have not achieved good prediction effect. In order to explore the possible prognostic signaling pathways leading to the difference in prognosis, we identified differentially expressed genes from one scRNA-seq cohort and four GEO cohorts, respectively. Then Cox and Lasso regression analysis showed that 12 genes were independent prognostic factors for PDAC. AUC and calibration curve analysis showed that the prognostic model had good discrimination and calibration. Compared with the low-risk group, the high-risk group had a higher proportion of gene mutations than the low-risk group. Immune infiltration analysis revealed differences in macrophages and monocytes between the two groups. Prognosis related genes were mainly distributed in fibroblasts, macrophages and type 2 ducts. The results of cell communication analysis showed that there was a strong communication between cancer-associated fibroblasts (CAF) and type 2 ductal cells, and collagen formation was the main interaction pathway.
Collapse
Affiliation(s)
- Wenwen Wang
- Department of Health Statistics, School of Military Preventive Medicine, Ministry of Education Key Lab of Hazard Assessment and Control in Special Operational Environment, Fourth Military Medical University, Xi'an, 710032, Shaanxi Province, China.
| | - Guo Chen
- Shaanxi Provincial Key Laboratory of Infection and Immune Diseases, Shaanxi Provincial People's Hospital, Xi'an, 710068, Shaanxi Province, China
| | - Wenli Zhang
- Shaanxi Provincial Key Laboratory of Infection and Immune Diseases, Shaanxi Provincial People's Hospital, Xi'an, 710068, Shaanxi Province, China
| | - Xihua Zhang
- Department of Health Statistics, School of Military Preventive Medicine, Ministry of Education Key Lab of Hazard Assessment and Control in Special Operational Environment, Fourth Military Medical University, Xi'an, 710032, Shaanxi Province, China
| | - Manli Huang
- Department of Health Statistics, School of Military Preventive Medicine, Ministry of Education Key Lab of Hazard Assessment and Control in Special Operational Environment, Fourth Military Medical University, Xi'an, 710032, Shaanxi Province, China
| | - Chen Li
- Department of Health Statistics, School of Military Preventive Medicine, Ministry of Education Key Lab of Hazard Assessment and Control in Special Operational Environment, Fourth Military Medical University, Xi'an, 710032, Shaanxi Province, China
| | - Ling Wang
- Department of Health Statistics, School of Military Preventive Medicine, Ministry of Education Key Lab of Hazard Assessment and Control in Special Operational Environment, Fourth Military Medical University, Xi'an, 710032, Shaanxi Province, China
| | - Zifan Lu
- Shaanxi Provincial Key Laboratory of Infection and Immune Diseases, Shaanxi Provincial People's Hospital, Xi'an, 710068, Shaanxi Province, China
| | - Jielai Xia
- Department of Health Statistics, School of Military Preventive Medicine, Ministry of Education Key Lab of Hazard Assessment and Control in Special Operational Environment, Fourth Military Medical University, Xi'an, 710032, Shaanxi Province, China
| |
Collapse
|
8
|
Chen J, Zhao D, Zhang L, Zhang J, Xiao Y, Wu Q, Wang Y, Zhan Q. Tumor-associated macrophage (TAM)-secreted CCL22 confers cisplatin resistance of esophageal squamous cell carcinoma (ESCC) cells via regulating the activity of diacylglycerol kinase α (DGKα)/NOX4 axis. Drug Resist Updat 2024; 73:101055. [PMID: 38387281 DOI: 10.1016/j.drup.2024.101055] [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: 05/05/2023] [Revised: 12/29/2023] [Accepted: 01/14/2024] [Indexed: 02/24/2024]
Abstract
Tumor-associated macrophages (TAMs) are often associated with chemoresistance and resultant poor clinical outcome in solid tumors. Here, we demonstrated that TAMs-released chemokine-C-C motif chemokine 22 (CCL22) in esophageal squamous cell carcinoma (ESCC) stroma was tightly correlated with the chemoresistance of ESCC patients. TAMs-secreted CCL22 was able to block the growth inhibitory and apoptosis-promoting effects of cisplatin on ESCC cells. Mechanistically, CCL22 stimulated intratumoral diacylglycerol kinase α (DGKα) to produce phosphatidic acid (PA), which suppressed the activity of NADPH oxidase 4 (NOX4) and then blocked the overproduction of intratumoral reactive species oxygen (ROS) induced by cisplatin. CCL22 activated DGKα/nuclear factor-κB (NF-κB) axis to upregulate the level of several members of ATP binding cassette (ABC) transporter superfamily, including ABC sub-family G member 4 (ABCG4), ABC sub-family A member 3 (ABCA3), and ABC sub-family A member 5 (ABCA5), to lower the intratumoral concentration of cisplatin. Consequently, these processes induced the cisplatin resistance in ESCC cells. In xenografted models, targeting DGKα with 5'-cholesterol-conjugated small-interfering (si) RNA enhanced the chemosensitivity of cisplatin in ESCC treatment, especially in the context of TAMs. Our data establish the correlation between the TAMs-induced intratumoral metabolic product/ROS axis and chemotherapy efficacy in ESCC treatment and reveal relevant molecular mechanisms.
Collapse
Affiliation(s)
- Jie Chen
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Molecular Oncology, Peking University Cancer Hospital & Institute, Beijing 100142, China; Peking University International Cancer Institute, Peking University, Beijing 100191, China; Research Unit of Molecular Cancer Research, Chinese Academy of Medical Sciences, Beijing, China; Soochow University Cancer Institute, Suzhou 215000, China.
| | - Di Zhao
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Molecular Oncology, Peking University Cancer Hospital & Institute, Beijing 100142, China; Peking University International Cancer Institute, Peking University, Beijing 100191, China; Research Unit of Molecular Cancer Research, Chinese Academy of Medical Sciences, Beijing, China
| | - Lingyuan Zhang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Molecular Oncology, Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Jing Zhang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Molecular Oncology, Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Yuanfan Xiao
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Molecular Oncology, Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Qingnan Wu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Molecular Oncology, Peking University Cancer Hospital & Institute, Beijing 100142, China; Peking University International Cancer Institute, Peking University, Beijing 100191, China; Research Unit of Molecular Cancer Research, Chinese Academy of Medical Sciences, Beijing, China
| | - Yan Wang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Molecular Oncology, Peking University Cancer Hospital & Institute, Beijing 100142, China; Peking University International Cancer Institute, Peking University, Beijing 100191, China; Research Unit of Molecular Cancer Research, Chinese Academy of Medical Sciences, Beijing, China
| | - Qimin Zhan
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Molecular Oncology, Peking University Cancer Hospital & Institute, Beijing 100142, China; Peking University International Cancer Institute, Peking University, Beijing 100191, China; Research Unit of Molecular Cancer Research, Chinese Academy of Medical Sciences, Beijing, China; Soochow University Cancer Institute, Suzhou 215000, China; Institute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen 518107, China.
| |
Collapse
|
9
|
Zhang X, Zhang M, Sun H, Wang X, Wang X, Sheng W, Xu M. The role of transcription factors in the crosstalk between cancer-associated fibroblasts and tumor cells. J Adv Res 2024:S2090-1232(24)00046-8. [PMID: 38309692 DOI: 10.1016/j.jare.2024.01.033] [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: 11/29/2023] [Revised: 01/27/2024] [Accepted: 01/29/2024] [Indexed: 02/05/2024] Open
Abstract
BACKGROUND Transcription factors (TFs) fulfill a critical role in the formation and maintenance of different cell types during the developmental process as well as disease. It is believed that cancer-associated fibroblasts (CAFs) are activation status of tissue-resident fibroblasts or derived from form other cell types via transdifferentiation or dedifferentiation. Despite a subgroup of CAFs exhibit anti-cancer effects, most of them are reported to exert effects on tumor progression, further indicating their heterogeneous origin. AIM OF REVIEW This review aimed to summarize and review the roles of TFs in the reciprocal crosstalk between CAFs and tumor cells, discuss the emerging mechanisms, and their roles in cell-fate decision, cellular reprogramming and advancing our understanding of the gene regulatory networks over the period of cancer initiation and progression. KEY SCIENTIFIC CONCEPTS OF REVIEW This manuscript delves into the key contributory factors of TFs that are involved in activating CAFs and maintaining their unique states. Additionally, it explores how TFs play a pivotal and multifaceted role in the reciprocal crosstalk between CAFs and tumor cells. This includes their involvement in processes such as epithelial-mesenchymal transition (EMT), proliferation, invasion, and metastasis, as well as metabolic reprogramming. TFs also have a role in constructing an immunosuppressive microenvironment, inducing resistance to radiation and chemotherapy, facilitating angiogenesis, and even 'educating' CAFs to support the malignancies of tumor cells. Furthermore, this manuscript delves into the current status of TF-targeted therapy and considers the future directions of TFs in conjunction with anti-CAFs therapies to address the challenges in clinical cancer treatment.
Collapse
Affiliation(s)
- Xiaoyan Zhang
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China; Institute of Pathology, Fudan University, Shanghai 200032, China
| | - Meng Zhang
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China; Institute of Pathology, Fudan University, Shanghai 200032, China
| | - Hui Sun
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China; Institute of Pathology, Fudan University, Shanghai 200032, China
| | - Xu Wang
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China; Institute of Pathology, Fudan University, Shanghai 200032, China
| | - Xin Wang
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China; Institute of Pathology, Fudan University, Shanghai 200032, China
| | - Weiqi Sheng
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China; Institute of Pathology, Fudan University, Shanghai 200032, China.
| | - Midie Xu
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China; Institute of Pathology, Fudan University, Shanghai 200032, China.
| |
Collapse
|
10
|
Fu D, Hu Z, Ma H, Xiong X, Chen X, Wang J, Zheng X, Yin Q. PLAU and GREM1 are prognostic biomarkers for predicting immune response in lung adenocarcinoma. Medicine (Baltimore) 2024; 103:e37041. [PMID: 38306567 PMCID: PMC10843304 DOI: 10.1097/md.0000000000037041] [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: 08/01/2023] [Accepted: 01/03/2024] [Indexed: 02/04/2024] Open
Abstract
Lung adenocarcinoma (LUAD) is a common malignant tumor. Identification of biomarkers and understanding their potential functions will facilitate the treatment and diagnosis in LUAD patients. The yellow module (cor = 0.31, P = 2e-6) was selected as the core module based on weighted gene co-expression network analysis (WGCNA) by integrating RNA-seq data and tumor stage. Two upregulated genes (PLAU and GREM1) in yellow module were identified to be biomarkers. Kaplan-Meier curve analysis displayed that high expression levels of them had a poor overall survival (OS). And, their high expression levels revealed higher tumor stage and relapse possibility in LUAD patients, and could be a prognostic parameter. Both biomarkers showed similar immune cell expression profiles in low- and high-expression groups. Strongly positive correlation between both biomarkers and biomarkers of tumor-infiltrating lymphocytes were also clarified in TCGA-LUAD cohort. Importantly, single gene GSEA showed that transcriptional mis-regulation in cancer and microRNAs in cancer were enriched in LUAD patients. Therefore, a miRNA-mRNA-transcription factors (TFs) co-expression regulatory networks was constructed for each biomarker, various miRNAs and TFs were related to PLAU and GREM1. Among which, 6 downstream TFs were overlapped genes for both biomarkers. Notably, 2 of these TFs (FOXF1 and TFAP2A) exhibited significantly abnormal expression levels. Among which, FOXF1 was downregulated and TFAP2A was upregulated in TCGA-LUAD cohort. Both TFs showed a significantly positive correlation with the expression level of PLAU. In conclusion, we identified 2 biomarkers related to immune response and achieved a good accuracy in predicting OS in patients with LUAD.
Collapse
Affiliation(s)
- Dongliao Fu
- School of Medical Technology and Engineering, Henan University of Science and Technology, Luoyang, China
| | - Zhigang Hu
- School of Medical Technology and Engineering, Henan University of Science and Technology, Luoyang, China
| | - Haodi Ma
- School of Medical Technology and Engineering, Henan University of Science and Technology, Luoyang, China
| | - Xin Xiong
- Department of Pathology, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Xingang Chen
- School of Medical Technology and Engineering, Henan University of Science and Technology, Luoyang, China
| | - Jingjing Wang
- School of Medical Technology and Engineering, Henan University of Science and Technology, Luoyang, China
| | - Xuewei Zheng
- School of Medical Technology and Engineering, Henan University of Science and Technology, Luoyang, China
| | - Qinan Yin
- School of Medical Technology and Engineering, Henan University of Science and Technology, Luoyang, China
| |
Collapse
|
11
|
Wei R, Song J, Liu X, Huo S, Liu C, Liu X. Immunosuppressive MFAP2 + cancer associated fibroblasts conferred unfavorable prognosis and therapeutic resistance in gastric cancer. Cell Oncol (Dordr) 2024; 47:55-68. [PMID: 37540308 DOI: 10.1007/s13402-023-00849-y] [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] [Accepted: 07/24/2023] [Indexed: 08/05/2023] Open
Abstract
PURPOSE To explore the predictive merit of MFAP2+ cancer associated fibroblasts (CAFs) infiltration for clinical outcomes and adjuvant chemotherapy or immunotherapy responsiveness in gastric cancer (GC). METHODS In this study, several independent cohorts were included respectively to dissect the relationship of clinical outcomes, therapeutic responses and tumor microenvironment with different MFAP2+ CAFs infiltration. Drug sensitivity analysis was conducted to predict the relationship between MFAP2+ CAFs infiltration and targeted drug response. Kaplan-Meier curves and the log-rank test were used to compare clinical outcomes of patients with different MFAP2+ CAFs infiltration. RESULTS High MFAP2+ CAFs infiltration yielded inferior prognosis in terms of overall survival, progress free survival and recurrence free survival in GC. Patients with low MFAP2+ CAFs infiltration were more likely to gain benefit from adjuvant therapy. Moreover, low MFAP2+ CAFs infiltration could predict a promising response to immunotherapy in GC patients. MFAP2+ CAFs with immunosuppressive features were highly relevant to immune evasive contexture characterized by the dysfunction of CD8+ T cells. We found that MFAP2+ CAFs communicated with T cells, B cells and Macrophages through releasing macrophage migration inhibitor factor (MIF), which further suggested that MFAP2+ CAFs might promote therapeutic resistance through regulating T cells dysfunction and M2 macrophages polarization. CONCLUSION Immunosuppressive MFAP2+ CAFs constructed an immune evasive tumor microenvironment characterized by incapacitated immune effector cells, consequently predicting inferior clinical outcomes and response on adjuvant therapy and immunotherapy in patients with GC. The potential of immunosuppressive MFAP2+ CAFs as a therapeutic target for GC deserved thoroughly exploration.
Collapse
Affiliation(s)
- Rongyuan Wei
- Department of Gastric Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College of Fudan University, Shanghai, China
| | - Junquan Song
- Department of Gastric Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College of Fudan University, Shanghai, China
| | - Xuanjun Liu
- Department of Gastric Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College of Fudan University, Shanghai, China
| | - Shiying Huo
- Department of Gastric Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College of Fudan University, Shanghai, China
| | - Chenchen Liu
- Department of Gastric Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.
- Department of Oncology, Shanghai Medical College of Fudan University, Shanghai, China.
| | - Xiaowen Liu
- Department of Gastric Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.
- Department of Oncology, Shanghai Medical College of Fudan University, Shanghai, China.
| |
Collapse
|
12
|
Meng T, Liu X, Zhang J, Li S, He W, Li W. MicroRNA-181b attenuates lipopolysaccharide-induced inflammatory responses in pulpitis via the PLAU/AKT/NF-κB axis. Int Immunopharmacol 2024; 127:111451. [PMID: 38154211 DOI: 10.1016/j.intimp.2023.111451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Revised: 12/17/2023] [Accepted: 12/23/2023] [Indexed: 12/30/2023]
Abstract
OBJECTIVE This study aimed to investigate the role and underlying mechanisms of microRNA (miRNA)-181b in the inflammatory response in pulpitis. METHODS Quantitative reverse-transcription polymerase chain reaction (qRT-PCR), fluorescence in situ hybridization (FISH), and immunofluorescence techniques were used to determine the miRNA-181b and urokinase-type plasminogen activator (PLAU) expression levels in inflamed human dental pulp tissues (HDPTs) and lipopolysaccharide (LPS)-stimulated human dental pulp cells (hDPCs). The targets of miRNA-181b were identified and confirmed using a bioinformatics analysis, RNA sequencing, and dual-luciferase gene reporter assays. The effect of miRNA-181b or PLAU on proinflammatory cytokine expression in hDPCs was examined using qRT-PCR and western blotting. RNA sequencing was conducted to examine the signaling pathways implicated in miRNA-181b-mediated pulpitis. Western blotting and qRT-PCR were used to determine the miRNA-181b /PLAU/AKT/NF-κB signaling axis in pulpitis. A rat pulpitis model was created to observe the histopathological changes in the dental pulp tissue after the topical application of miRNA-181b agomir. RESULTS A significant decrease in miRNA-181b and an increase in PLAU were observed in HDPTs compared to the healthy controls, and these two factors showed a negative correlation. MiRNA-181b directly targeted PLAU. The miRNA-181b inhibitor resulted in a significant upregulation of IL-1β, IL-6 and TNF-α, whereas the knockdown of PLAU reversed this proinflammatory effect. Conversely, PLAU overexpression prevented the anti-inflammatory effects of the miRNA-181b mimics. Mechanistically, miRNA-181b inhibited the AKT/NF-κB pathway by targeting PLAU. In vivo application of the miRNA-181b agomir to inflamed pulp tissue alleviated inflammation. CONCLUSION MiRNA-181b targets PLAU, negatively regulating pro-inflammatory cytokine expression via the AKT/NF-κB signaling pathway.
Collapse
Affiliation(s)
- Tiantian Meng
- College & Hospital of Stomatology, Anhui Medical University, Key Lab. of Oral Diseases Research of Anhui Province, 69# Mei Shan Road, Hefei 230032, Anhui, China.
| | - Xinpai Liu
- College & Hospital of Stomatology, Anhui Medical University, Key Lab. of Oral Diseases Research of Anhui Province, 69# Mei Shan Road, Hefei 230032, Anhui, China.
| | - Jing Zhang
- College & Hospital of Stomatology, Anhui Medical University, Key Lab. of Oral Diseases Research of Anhui Province, 69# Mei Shan Road, Hefei 230032, Anhui, China.
| | - Song Li
- College & Hospital of Stomatology, Anhui Medical University, Key Lab. of Oral Diseases Research of Anhui Province, 69# Mei Shan Road, Hefei 230032, Anhui, China.
| | - Wei He
- College & Hospital of Stomatology, Anhui Medical University, Key Lab. of Oral Diseases Research of Anhui Province, 69# Mei Shan Road, Hefei 230032, Anhui, China; School of Basic Medical Sciences, Anhui Medical University, 81#Mei Shan Road, Hefei 230032, Anhui, China.
| | - Wuli Li
- College & Hospital of Stomatology, Anhui Medical University, Key Lab. of Oral Diseases Research of Anhui Province, 69# Mei Shan Road, Hefei 230032, Anhui, China.
| |
Collapse
|
13
|
Li W, Xu T, Jin H, Li M, Jia Q. Emerging role of cancer-associated fibroblasts in esophageal squamous cell carcinoma. Pathol Res Pract 2024; 253:155002. [PMID: 38056131 DOI: 10.1016/j.prp.2023.155002] [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: 11/07/2023] [Revised: 11/26/2023] [Accepted: 11/27/2023] [Indexed: 12/08/2023]
Abstract
Esophageal carcinoma is the sixth leading cause of cancer death globally and the majority of global cases are esophageal squamous cell carcinoma (ESCC). Difficulty in diagnosis exists as more than 70% of ESCC patients are diagnosed at the intermediate or advanced stage. Cancer-associated fibroblasts (CAFs) have been considered one of the crucial components in the process of tumor growth, promoting communications between cancer cells and the tumor microenvironment (TME). CAFs grow alongside malignancies dynamically and interact with ESCC cells to promote their progression, proliferation, invasion, tumor escape, chemo- and radio-resistance, etc. It is believed that CAFs qualify as a promising direction for treatment. Analyzing CAFs' subtypes and functions will elucidate the involvement of CAFs in ESCC and aid in therapeutics. This review summarizes current information on CAFs in ESCC and focuses on the latest interaction between CAFs and ESCC cancer cell discoveries. The origin of CAFs and their communication with ESCC cells and TME are also demonstrated. On the foundation of a thorough analysis, we highlight the clinical prospects and CAFs-related therapies in ESCC in the future.
Collapse
Affiliation(s)
- Wenqing Li
- State Key Laboratory of Cancer Biology, Department of Pathology, Xijing Hospital and School of Basic Medicine, Fourth Military Medical University, Xi'an, China
| | - Tianqi Xu
- State Key Laboratory of Cancer Biology, Department of Pathology, Xijing Hospital and School of Basic Medicine, Fourth Military Medical University, Xi'an, China
| | - Hai Jin
- Department of Neurosurgery, General Hospital of Northern Theater Command, Shenyang, China.
| | - Mingyang Li
- State Key Laboratory of Cancer Biology, Department of Pathology, Xijing Hospital and School of Basic Medicine, Fourth Military Medical University, Xi'an, China.
| | - Qingge Jia
- Department of Reproductive Medicine, Xi'an International Medical Center Hospital, Northwest University, Xi'an, China.
| |
Collapse
|
14
|
Zou J, Qin Z, Li R, Yan X, Huang H, Yang B, Zhou F, Zhang L. iProPhos: A Web-Based Interactive Platform for Integrated Proteome and Phosphoproteome Analysis. Mol Cell Proteomics 2024; 23:100693. [PMID: 38097182 PMCID: PMC10828474 DOI: 10.1016/j.mcpro.2023.100693] [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: 06/15/2023] [Revised: 11/06/2023] [Accepted: 12/11/2023] [Indexed: 01/29/2024] Open
Abstract
Large-scale omics studies have generated a wealth of mass spectrometry-based proteomics data, which provide additional insights into disease biology spanning genomic boundaries. However, there is a notable lack of web-based analysis and visualization tools that facilitate the reutilization of these data. Given this challenge, we present iProPhos, a user-friendly web server to deliver interactive and customizable functionalities. iProPhos incorporates a large number of samples, including 1444 tumor samples and 746 normal samples across 12 cancer types, sourced from the Clinical Proteomic Tumor Analysis Consortium. Additionally, users can also upload their own proteomics/phosphoproteomics data for analysis and visualization. In iProPhos, users can perform profiling plotting and differential expression, patient survival, clinical feature-related, and correlation analyses, including protein-protein, mRNA-protein, and kinase-substrate correlations. Furthermore, functional enrichment, protein-protein interaction network, and kinase-substrate enrichment analyses are accessible. iProPhos displays the analytical results in interactive figures and tables with various selectable parameters. It is freely accessible at http://longlab-zju.cn/iProPhos without login requirement. We present two case studies to demonstrate that iProPhos can identify potential drug targets and upstream kinases contributing to site-specific phosphorylation. Ultimately, iProPhos allows end-users to leverage the value of big data in cancer proteomics more effectively and accelerates the discovery of novel therapeutic targets.
Collapse
Affiliation(s)
- Jing Zou
- The Second Affiliated Hospital and Life Sciences Institute and School of Medicine, The MOE Key Laboratory of Biosystems Homeostasis and Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Zhejiang University, Hangzhou, China
| | - Ziran Qin
- The Second Affiliated Hospital and Life Sciences Institute and School of Medicine, The MOE Key Laboratory of Biosystems Homeostasis and Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Zhejiang University, Hangzhou, China
| | - Ran Li
- School of Medicine, Hangzhou City University, Hangzhou, China.
| | - Xiaohua Yan
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Nanchang University, Nanchang, China
| | - Huizhe Huang
- The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Bing Yang
- The Second Affiliated Hospital and Life Sciences Institute and School of Medicine, The MOE Key Laboratory of Biosystems Homeostasis and Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Zhejiang University, Hangzhou, China; Department of Pharmaceutical Chemistry and the Cardiovascular Research Institute, University of California, San Francisco, California, USA
| | - Fangfang Zhou
- Institutes of Biology and Medical Sciences, Soochow University, Suzhou, China.
| | - Long Zhang
- The Second Affiliated Hospital and Life Sciences Institute and School of Medicine, The MOE Key Laboratory of Biosystems Homeostasis and Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Zhejiang University, Hangzhou, China; Cancer Center, Zhejiang University, Hangzhou, China.
| |
Collapse
|
15
|
Jiang Y, Wang Y, Wang Z, Zhang Y, Hou Y, Wang X. Anoikis-related genes signature development for clear cell renal cell carcinoma prognosis and tumor microenvironment. Sci Rep 2023; 13:18909. [PMID: 37919386 PMCID: PMC10622575 DOI: 10.1038/s41598-023-46398-0] [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: 05/05/2023] [Accepted: 10/31/2023] [Indexed: 11/04/2023] Open
Abstract
Clear cell renal cell carcinoma (ccRCC) is one of the most common primary malignancies of the urinary tract, highly heterogeneous, and increasing in incidence worldwide. Anoikis is a specific type of programmed cell death in which solid tumor cells or normal epithelial cells that do not have metastatic properties lose adhesion to the extracellular matrix or undergo inappropriate cell adhesion-induced apoptosis. Anoikis is thought to play a critical role in tumorigenesis, maintenance, and treatment, according to an increasing amount of research. However, there is still some uncertainty regarding the general impact of anoikis-related genes (ARGs) on the prognostic importance, tumor microenvironment characteristics, and treatment reaction of ccRCC patients. For this study, we used The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus datasets to access the RNA sequencing results and clinical information from ccRCC patients. 29 ARGs related to survival were found using differential analysis and univariate Cox regression analysis. The samples were then divided into two clusters that had different immune traits via unsupervised cluster analysis using 29 prognosis-associated differently expressed ARGs. Then, to build an ARGs signature, 7 genes (PLAU, EDA2R, AFP, PLG, TUBB3, APOBEC3G, and MALAT1) were found using Least Absolute Shrinkage and Selection Operator regression analysis. The new ARGs signature demonstrated outstanding prognostic capability for ccRCC patients' overall survival. In conclusion, for ccRCC patients, we created an ARGs signature that strongly connects to immunological traits and therapy response. Clinicians may find this ARGs signature helpful in developing more individualized and detailed treatment strategies for ccRCC patients.
Collapse
Affiliation(s)
- Yinglei Jiang
- Dialysis Room, The Affiliated Hospital of Changchun University of Chinese Medicine, Changchun, 120000, China
| | - Ying Wang
- Dialysis Room, The Affiliated Hospital of Changchun University of Chinese Medicine, Changchun, 120000, China
| | - Zhengyan Wang
- Changchun University of Chinese Medicine, Changchun, 120000, China
| | - Yinzhen Zhang
- Changchun University of Chinese Medicine, Changchun, 120000, China
| | - Yulong Hou
- Changchun University of Chinese Medicine, Changchun, 120000, China
| | - Xukai Wang
- Dialysis Room, The Affiliated Hospital of Changchun University of Chinese Medicine, Changchun, 120000, China.
| |
Collapse
|
16
|
Xue M, Tong Y, Xiong Y, Yu C. Role of cancer-associated fibroblasts in the progression, therapeutic resistance and targeted therapy of oesophageal squamous cell carcinoma. Front Oncol 2023; 13:1257266. [PMID: 37927475 PMCID: PMC10623436 DOI: 10.3389/fonc.2023.1257266] [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: 07/12/2023] [Accepted: 09/11/2023] [Indexed: 11/07/2023] Open
Abstract
Oesophageal squamous cell carcinoma (ESCC) is one of the most aggressive malignant tumours with high morbidity and mortality. Although surgery, radiotherapy and chemotherapy are common treatment options available for oesophageal cancer, the 5-year survival rate remains low after treatment. On the one hand, many oesophageal cancers are are discovered at an advanced stage and, on the other hand, treatment resistance is a major obstacle to treating locally advanced ESCC. Cancer-associated fibroblasts (CAFs), the main type of stromal cell in the tumour microenvironment, enhance tumour progression and treatment resistance and have emerged as a major focus of study on targeted therapy of oesophageal cancer.With the aim of providing potential, prospective targets for improving therapeutic efficacy, this review summarises the origin and activation of CAFs and their specific role in regulating tumour progression and treatment resistance in ESCC. We also emphasize the clinical potential and emerging trends of ESCC CAFs-targeted treatments.
Collapse
Affiliation(s)
| | | | | | - Changhua Yu
- Department of Radiotherapy, The Affiliated Huaian No.1 People’s Hospital of Nanjing Medical University, Huaian, China
| |
Collapse
|
17
|
Han J, Li X, Liang B, Ma S, Pu Y, Yu F, Lu J, Ma Y, MacHugh DE, Jiang L. Transcriptome profiling of differentiating adipose-derived stem cells across species reveals new genes regulating adipogenesis. Biochim Biophys Acta Mol Cell Biol Lipids 2023; 1868:159378. [PMID: 37572997 DOI: 10.1016/j.bbalip.2023.159378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 07/31/2023] [Accepted: 08/02/2023] [Indexed: 08/14/2023]
Abstract
Adipose-derived stem cells (ADSCs) that are enriched in adipose tissue with multilineage differentiation potential have become an important tool in therapeutic research and tissue engineering. Certain breeds of sheep exhibit a unique fat tail trait such that tail tissue accounts for approximately 10 % of body weight and can provide an excellent source of ADSCs. Here, we describe isolation of primary ADSCs from ovine embryonic fat tail tissues that displayed high self-renewal capacity, multilineage differentiation and excellent adipogenic ability. Through transcriptome analysis covering ADSCs differentiating into adipocytes, 37 transcription factors were involved in early transcriptional events that initiate a regulatory cascade of adipogenesis; the entire adipogenic activity consists of a reduction in proliferation ability and upregulation of genes related to lipid generation and energy metabolism, as well as several genes associated with myogenesis. Furthermore, Comparative transcriptome analysis across species (sheep, human, and mouse) revealed enhanced basal metabolic ability in differentiating ovine ADSCs, which may relate to the excellent adipogenic capability of these cells. We also identified a small evolutionarily conserved gene set, consisting of 21 and 22 genes exhibiting increased and decreased expression, respectively. Almost half (20) of these genes have not previously been reported to regulate adipogenesis in mammals. In this study, we identified important regulators that trigger ovine adipocyte differentiation, main biological pathways involved in adipogenesis as well as the evolutionarily conserved genes governing adipogenic process across species. Our study provides a novel excellent biomaterial and novel genes regulating adipogenesis for cellular transplantation therapy and investigations of fat metabolism.
Collapse
Affiliation(s)
- Jiangang Han
- Laboratory of Animal Genetics Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China; Animal Genomics Laboratory, UCD School of Agriculture and Food Science, UCD College of Health and Agricultural Sciences, University College Dublin, Belfield, Dublin D04 V1W8, Ireland
| | - Xiaojie Li
- Laboratory of Animal Genetics Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China; National Germplasm Center of Domestic Animal Resources, Ministry of Technology, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Benmeng Liang
- Laboratory of Animal Genetics Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China; National Germplasm Center of Domestic Animal Resources, Ministry of Technology, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Sijia Ma
- Laboratory of Animal Genetics Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China; Agricultural College, Ningxia University, Yinchuan, Ningxia, China
| | - Yabin Pu
- Laboratory of Animal Genetics Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China; National Germplasm Center of Domestic Animal Resources, Ministry of Technology, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Fuqing Yu
- National Animal Husbandry Service, Beijing 100193, China
| | - Jian Lu
- National Animal Husbandry Service, Beijing 100193, China
| | - Yuehui Ma
- Laboratory of Animal Genetics Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China; National Germplasm Center of Domestic Animal Resources, Ministry of Technology, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - David E MacHugh
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, UCD College of Health and Agricultural Sciences, University College Dublin, Belfield, Dublin D04 V1W8, Ireland; UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin D04 V1W8, Ireland.
| | - Lin Jiang
- Laboratory of Animal Genetics Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China; National Germplasm Center of Domestic Animal Resources, Ministry of Technology, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China.
| |
Collapse
|
18
|
Chen Y, Deng Q, Chen H, Yang J, Chen Z, Li J, Fu Z. Cancer-associated fibroblast-related prognostic signature predicts prognosis and immunotherapy response in pancreatic adenocarcinoma based on single-cell and bulk RNA-sequencing. Sci Rep 2023; 13:16408. [PMID: 37775715 PMCID: PMC10541448 DOI: 10.1038/s41598-023-43495-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 09/25/2023] [Indexed: 10/01/2023] Open
Abstract
Cancer-associated fibroblasts (CAFs) influence many aspects of pancreatic adenocarcinoma (PAAD) carcinogenesis, including tumor cell proliferation, angiogenesis, invasion, and metastasis. A six-gene prognostic signature was constructed for PAAD based on the 189 CAF marker genes identified in single-cell RNA-sequencing data. Multivariate analyses showed that the risk score was independently prognostic for survival in the TCGA (P < 0.001) and ICGC (P = 0.004) cohorts. Tumor infiltration of CD8 T (P = 0.005) cells and naïve B cells (P = 0.001) was greater in the low-risk than in the high-risk group, with infiltration of these cells negatively correlated with risk score. Moreover, the TMB score was lower in the low-risk than in the high-risk group (P = 0.0051). Importantly, patients in low-risk group had better immunotherapy responses than in the high-risk group in an independent immunotherapy cohort (IMvigor210) (P = 0.039). The CAV1 and SOD3 were highly expressed in CAFs of PAAD tissues, which revealed by immunohistochemical staining. In summary, this comprehensive analysis resulted in the development of a novel prognostic signature, which was associated with immune cell infiltration, drug sensitivity, and TMB, and could predict the prognosis and immunotherapy response of patients with PAAD.
Collapse
Affiliation(s)
- Yajun Chen
- Department of General Surgery, The Third Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Qican Deng
- Department of General Surgery, The Third Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Hui Chen
- Institute of Hepatopancreatobiliary Surgery, Chongqing General Hospital, Chongqing, China
| | - Jianguo Yang
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Zhenzhou Chen
- Department of General Surgery, The Third Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Juncai Li
- Department of Surgery, The People's Hospital of Yubei District of Chongqing, Chongqing, China.
| | - Zhongxue Fu
- Department of General Surgery, The Third Affiliated Hospital of Chongqing Medical University, Chongqing, China.
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China.
| |
Collapse
|
19
|
Wu D, Gaskins JT, Sekula M, Datta S. Inferring Cell-Cell Communications from Spatially Resolved Transcriptomics Data Using a Bayesian Tweedie Model. Genes (Basel) 2023; 14:1368. [PMID: 37510272 PMCID: PMC10379215 DOI: 10.3390/genes14071368] [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: 04/30/2023] [Revised: 06/16/2023] [Accepted: 06/26/2023] [Indexed: 07/30/2023] Open
Abstract
Cellular communication through biochemical signaling is fundamental to every biological activity. Investigating cell signaling diffusions across cell types can further help understand biological mechanisms. In recent years, this has become an important research topic as single-cell sequencing technologies have matured. However, cell signaling activities are spatially constrained, and single-cell data cannot provide spatial information for each cell. This issue may cause a high false discovery rate, and using spatially resolved transcriptomics data is necessary. On the other hand, as far as we know, most existing methods focus on providing an ad hoc measurement to estimate intercellular communication instead of relying on a statistical model. It is undeniable that descriptive statistics are straightforward and accessible, but a suitable statistical model can provide more accurate and reliable inference. In this way, we propose a generalized linear regression model to infer cellular communications from spatially resolved transcriptomics data, especially spot-based data. Our BAyesian Tweedie modeling of COMmunications (BATCOM) method estimates the communication scores between cell types with the consideration of their corresponding distances. Due to the properties of the regression model, BATCOM naturally provides the direction of the communication between cell types and the interaction of ligands and receptors that other approaches cannot offer. We conduct simulation studies to assess the performance under different scenarios. We also employ BATCOM in a real-data application and compare it with other existing algorithms. In summary, our innovative model can fill gaps in the inference of cell-cell communication and provide a robust and straightforward result.
Collapse
Affiliation(s)
- Dongyuan Wu
- Department of Biostatistics, University of Florida, Gainesville, FL 32603, USA
| | - Jeremy T Gaskins
- Department of Bioinformatics and Biostatistics, University of Louisville, Louisville, KY 40202, USA
| | - Michael Sekula
- Department of Bioinformatics and Biostatistics, University of Louisville, Louisville, KY 40202, USA
| | - Susmita Datta
- Department of Biostatistics, University of Florida, Gainesville, FL 32603, USA
| |
Collapse
|
20
|
Sasaki T, Yoshikawa Y, Kageyama T, Sugino Y, Kato M, Masui S, Nishikawa K, Inoue T. Prostate fibroblasts enhance androgen receptor splice variant 7 expression in prostate cancer cells. Prostate 2023; 83:364-375. [PMID: 36479717 DOI: 10.1002/pros.24468] [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: 04/18/2022] [Revised: 10/22/2022] [Accepted: 11/20/2022] [Indexed: 12/12/2022]
Abstract
BACKGROUND Androgen receptor splice variant (AR-V) expression has been associated with prostate cancer (PCa) progression to castration-resistant PCa during androgen deprivation therapy, which reduces androgen production and inhibits androgen action in PCa cells. However, the mechanisms whereby aberrant AR-V expression is increased in PCa are still largely unknown. Fibroblasts in tumor stroma influence PCa initiation and aggressiveness, and which may play a crucial role in eliciting genetic changes during malignant transformation in human prostate epithelium. Here, our aim was to determine whether prostate fibroblasts in tumor stroma induce aberrant AR-V7 expression in PCa cells under low androgen concentration. METHODS We performed in vitro experiments using androgen-sensitive, AR-positive PCa cell lines (LNCaP and 22Rv1 cells), commercially available prostate stromal cells (PrSC), and primary cultured prostate fibroblasts (pcPrF) from PCa specimens collected from biopsies of patients with advanced PCa. PCa cells were cocultured with each of the three fibroblast lines (PrSC, pcPrF-M37, and pcPrF-M48). RESULTS The proliferation under low androgen concentration of LNCaP and 22Rv1 cells cocultured with PrSC, pcPrF-M37, or pcPrF-M48 was significantly increased compared to that of PCa cells cultured alone. Androgen receptor-full length (AR-FL) protein expression was increased in LNCaP and 22Rv1 cells cocultured with PrSC, pcPrF-M37, or pcPrF-M48. AR-V7 protein expression was increased in 22Rv1 cells cocultured with PrSC, pcPrF-M37, or pcPrF-M48. Under low androgen concentration, AR-V7 protein expression was slightly detected in LNCaP cells cocultured with PrSC or pcPrF-M37. Cytokine array analysis revealed that monocyte chemotactic protein-1 (MCP-1) and interleukin-8 (IL-8) levels in the conditioned medium of 22Rv1 cells cocultured with PrSC, pcPrF-M37, or pcPrF-M48 were increased under low androgen concentration. High IL-8 concentration (30 ng/ml) resulted in significantly increased protein expression of AR-FL, AR-V7, and phospho-NF-κB p65 in 22Rv1 cells. In contrast, IL-8 antibody (1 µg/ml) decreased AR-V7 protein expression in 22Rv1 cells cocultured with PrSC, pcPrF-M37, or pcPrF-M48. CONCLUSIONS pcPrF from PCa specimens increase the expression of aberrant AR-V7 in PCa cells. IL-8 may be a target for preventing the expression of aberrant AR-Vs in PCa.
Collapse
Affiliation(s)
- Takeshi Sasaki
- Department of Nephro-Urologic Surgery and Andrology, Mie University Graduate School of Medicine, Mie, Japan
| | - Yumi Yoshikawa
- Department of Nephro-Urologic Surgery and Andrology, Mie University Graduate School of Medicine, Mie, Japan
| | - Takumi Kageyama
- Department of Nephro-Urologic Surgery and Andrology, Mie University Graduate School of Medicine, Mie, Japan
| | - Yusuke Sugino
- Department of Nephro-Urologic Surgery and Andrology, Mie University Graduate School of Medicine, Mie, Japan
| | - Manabu Kato
- Department of Nephro-Urologic Surgery and Andrology, Mie University Graduate School of Medicine, Mie, Japan
| | - Satoru Masui
- Department of Nephro-Urologic Surgery and Andrology, Mie University Graduate School of Medicine, Mie, Japan
| | - Kouhei Nishikawa
- Department of Nephro-Urologic Surgery and Andrology, Mie University Graduate School of Medicine, Mie, Japan
| | - Takahiro Inoue
- Department of Nephro-Urologic Surgery and Andrology, Mie University Graduate School of Medicine, Mie, Japan
| |
Collapse
|
21
|
Xu X, Yu Y, Yang L, Wang B, Fan Y, Ruan B, Zhang X, Dai H, Mei W, Jie W, Zheng S. Integrated analysis of Dendrobium nobile extract Dendrobin A against pancreatic ductal adenocarcinoma based on network pharmacology, bioinformatics, and validation experiments. Front Pharmacol 2023; 14:1079539. [PMID: 36937875 PMCID: PMC10014786 DOI: 10.3389/fphar.2023.1079539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 02/20/2023] [Indexed: 03/05/2023] Open
Abstract
Background: Dendrobium nobile (D. nobile), a traditional Chinese medicine, has received attention as an anti-tumor drug, but its mechanism is still unclear. In this study, we applied network pharmacology, bioinformatics, and in vitro experiments to explore the effect and mechanism of Dendrobin A, the active ingredient of D. nobile, against pancreatic ductal adenocarcinoma (PDAC). Methods: The databases of SwissTargetPrediction and PharmMapper were used to obtain the potential targets of Dendrobin A, and the differentially expressed genes (DEGs) between PDAC and normal pancreatic tissues were obtained from The Cancer Genome Atlas and Genotype-Tissue Expression databases. The protein-protein interaction (PPI) network for Dendrobin A anti-PDAC targets was constructed based on the STRING database. Molecular docking was used to assess Dendrobin A anti-PDAC targets. PLAU, one of the key targets of Dendrobin A anti-PDAC, was immunohistochemically stained in clinical tissue arrays. Finally, in vitro experiments were used to validate the effects of Dendrobin A on PLAU expression and the proliferation, apoptosis, cell cycle, migration, and invasion of PDAC cells. Results: A total of 90 genes for Dendrobin A anti-PDAC were screened, and a PPI network for Dendrobin A anti-PDAC targets was constructed. Notably, a scale-free module with 19 genes in the PPI indicated that the PPI is highly credible. Among these 19 genes, PLAU was positively correlated with the cachexia status while negatively correlated with the overall survival of PDAC patients. Through molecular docking, Dendrobin A was found to bind to PLAU, and the Dendrobin A treatment led to an attenuated PLAU expression in PDAC cells. Based on clinical tissue arrays, PLAU protein was highly expressed in PDAC cells compared to normal controls, and PLAU protein levels were associated with the differentiation and lymph node metastatic status of PDAC. In vitro experiments further showed that Dendrobin A treatment significantly inhibited the proliferation, migration, and invasion, inducing apoptosis and arresting the cell cycle of PDAC cells at the G2/M phase. Conclusion: Dendrobin A, a representative active ingredient of D. nobile, can effectively fight against PDAC by targeting PLAU. Our results provide the foundation for future PDAC treatment based on D. nobile.
Collapse
Affiliation(s)
- Xiaoqing Xu
- Department of Oncology of the First Affiliated Hospital & Cancer Institute, Hainan Medical University, Haikou, China
| | - Yaping Yu
- Department of Oncology of the First Affiliated Hospital & Cancer Institute, Hainan Medical University, Haikou, China
| | - Li Yang
- Key Laboratory of Natural Products Research and Development from Li Folk Medicine of Hainan Province, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Bingshu Wang
- Department of Oncology of the First Affiliated Hospital & Cancer Institute, Hainan Medical University, Haikou, China
| | - Yonghao Fan
- Department of Oncology of the First Affiliated Hospital & Cancer Institute, Hainan Medical University, Haikou, China
| | - Banzhan Ruan
- Department of Oncology of the First Affiliated Hospital & Cancer Institute, Hainan Medical University, Haikou, China
| | - Xiaodian Zhang
- Department of Oncology of the First Affiliated Hospital & Cancer Institute, Hainan Medical University, Haikou, China
| | - Haofu Dai
- Key Laboratory of Natural Products Research and Development from Li Folk Medicine of Hainan Province, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Wenli Mei
- Key Laboratory of Natural Products Research and Development from Li Folk Medicine of Hainan Province, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- *Correspondence: Wenli Mei, ; Wei Jie, ; Shaojiang Zheng,
| | - Wei Jie
- Department of Oncology of the First Affiliated Hospital & Cancer Institute, Hainan Medical University, Haikou, China
- *Correspondence: Wenli Mei, ; Wei Jie, ; Shaojiang Zheng,
| | - Shaojiang Zheng
- Department of Oncology of the First Affiliated Hospital & Cancer Institute, Hainan Medical University, Haikou, China
- Key Laboratory of Emergency and Trauma of Ministry of Education & Key Laboratory of Tropical Cardiovascular Diseases Research of Hainan Province & Hainan Women and Children’s Medical Center, Hainan Medical University, Haikou, China
- *Correspondence: Wenli Mei, ; Wei Jie, ; Shaojiang Zheng,
| |
Collapse
|
22
|
Identification of an Immune-Related Gene Signature Associated with Prognosis and Tumor Microenvironment in Esophageal Cancer. BIOMED RESEARCH INTERNATIONAL 2022; 2022:7413535. [PMID: 36588538 PMCID: PMC9803573 DOI: 10.1155/2022/7413535] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 11/30/2022] [Accepted: 12/05/2022] [Indexed: 12/24/2022]
Abstract
Background Esophageal cancer (EC) is a common malignant tumor of the digestive system with high mortality and morbidity. Current evidence suggests that immune cells and molecules regulate the initiation and progression of EC. Accordingly, it is necessary to identify immune-related genes (IRGs) affecting the biological behaviors and microenvironmental characteristics of EC. Methods Bioinformatics methods, including differential expression analysis, Cox regression, and immune infiltration prediction, were conducted using R software to analyze the Gene Expression Omnibus (GEO) dataset. The Cancer Genome Atlas (TCGA) cohort was used to validate the prognostic signature. Patients were stratified into high- and low-risk groups for further analyses, including functional enrichment, immune infiltration, checkpoint relevance, clinicopathological characteristics, and therapeutic sensitivity analyses. Results A prognostic signature was established based on 21 IRGs (S100A7, S100A7A, LCN1, CR2, STAT4, GAST, ANGPTL5, TRAV39, F2RL2, PGLYRP3, KLRD1, TRIM36, PDGFA, SLPI, PCSK2, APLN, TICAM1, ITPR3, MAPK9, GATA4, and PLAU). Compared with high-risk patients, better overall survival rates and clinicopathological characteristics were found in low-risk patients. The areas under the curve of the two cohorts were 0.885 and 0.718, respectively. Higher proportions of resting CD4+ memory T lymphocytes, M2 macrophages, and resting dendritic cells and lower proportions of follicular helper T lymphocytes, plasma cells, and neutrophils were found in the high-risk tumors. Moreover, the high-risk group showed higher expression of CD44 and TNFSF4, lower expression of PDCD1 and CD40, and higher TIDE scores, suggesting they may respond poorly to immunotherapy. High-risk patients responded better to chemotherapeutic agents such as docetaxel, doxorubicin, and gemcitabine. Furthermore, IRGs associated with tumor progression, including PDGFA, ITPR3, SLPI, TICAM1, and GATA4, were identified. Conclusion Our immune-related signature yielded reliable value in evaluating the prognosis, microenvironmental characteristics, and therapeutic sensitivity of EC and may help with the precise treatment of this patient population.
Collapse
|
23
|
Hosen SMZ, Uddin MN, Xu Z, Buckley BJ, Perera C, Pang TCY, Mekapogu AR, Moni MA, Notta F, Gallinger S, Pirola R, Wilson J, Ranson M, Goldstein D, Apte M. Metastatic phenotype and immunosuppressive tumour microenvironment in pancreatic ductal adenocarcinoma: Key role of the urokinase plasminogen activator (PLAU). Front Immunol 2022; 13:1060957. [PMID: 36591282 PMCID: PMC9794594 DOI: 10.3389/fimmu.2022.1060957] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 11/22/2022] [Indexed: 12/15/2022] Open
Abstract
Background Previous studies have revealed the role of dysregulated urokinase plasminogen activator (encoded by PLAU) expression and activity in several pathways associated with cancer progression. However, systematic investigation into the association of PLAU expression with factors that modulate PDAC (pancreatic ductal adenocarcinoma) progression is lacking, such as those affecting stromal (pancreatic stellate cell, PSC)-cancer cell interactions, tumour immunity, PDAC subtypes and clinical outcomes from potential PLAU inhibition. Methods This study used an integrated bioinformatics approach to identify prognostic markers correlated with PLAU expression using different transcriptomics, proteomics, and clinical data sets. We then determined the association of dysregulated PLAU and correlated signatures with oncogenic pathways, metastatic phenotypes, stroma, immunosuppressive tumour microenvironment (TME) and clinical outcome. Finally, using an in vivo orthotopic model of pancreatic cancer, we confirmed the predicted effect of inhibiting PLAU on tumour growth and metastasis. Results Our analyses revealed that PLAU upregulation is not only associated with numerous other prognostic markers but also associated with the activation of various oncogenic signalling pathways, aggressive phenotypes relevant to PDAC growth and metastasis, such as proliferation, epithelial-mesenchymal transition (EMT), stemness, hypoxia, extracellular cell matrix (ECM) degradation, upregulation of stromal signatures, and immune suppression in the tumour microenvironment (TME). Moreover, the upregulation of PLAU was directly connected with signalling pathways known to mediate PSC-cancer cell interactions. Furthermore, PLAU upregulation was associated with the aggressive basal/squamous phenotype of PDAC and significantly reduced overall survival, indicating that this subset of patients may benefit from therapeutic interventions to inhibit PLAU activity. Our studies with a clinically relevant orthotopic pancreatic model showed that even short-term PLAU inhibition is sufficient to significantly halt tumour growth and, importantly, eliminate visible metastasis. Conclusion Elevated PLAU correlates with increased aggressive phenotypes, stromal score, and immune suppression in PDAC. PLAU upregulation is also closely associated with the basal subtype type of PDAC; patients with this subtype are at high risk of mortality from the disease and may benefit from therapeutic targeting of PLAU.
Collapse
Affiliation(s)
- S. M. Zahid Hosen
- Pancreatic Research Group, SWS Clinical Campus, School of Clinical Medicine, Faculty of Medicine and Health, UNSW Sydney, Sydney, NSW, Australia,Ingham Institute for Applied Medical Research, Liverpool, NSW, Australia
| | - Md. Nazim Uddin
- Institute of Food Science and Technology, Bangladesh Council of Scientific and Industrial Research (BCSIR), Dhaka, Bangladesh
| | - Zhihong Xu
- Pancreatic Research Group, SWS Clinical Campus, School of Clinical Medicine, Faculty of Medicine and Health, UNSW Sydney, Sydney, NSW, Australia,Ingham Institute for Applied Medical Research, Liverpool, NSW, Australia
| | - Benjamin J. Buckley
- Molecular Horizons and School of Chemistry & Molecular Bioscience, Faculty of Science, Medicine and Health, University of Wollongong, Wollongong, NSW, Australia,Illawarra Health and Medical Research Institute, Wollongong, NSW, Australia
| | - Chamini Perera
- Pancreatic Research Group, SWS Clinical Campus, School of Clinical Medicine, Faculty of Medicine and Health, UNSW Sydney, Sydney, NSW, Australia,Ingham Institute for Applied Medical Research, Liverpool, NSW, Australia
| | - Tony C. Y. Pang
- Pancreatic Research Group, SWS Clinical Campus, School of Clinical Medicine, Faculty of Medicine and Health, UNSW Sydney, Sydney, NSW, Australia,Westmead Clinical School, Faculty of Medicine and Health, University of Sydney, The University of Sydney, Sydney, NSW, Australia
| | - Alpha Raj Mekapogu
- Pancreatic Research Group, SWS Clinical Campus, School of Clinical Medicine, Faculty of Medicine and Health, UNSW Sydney, Sydney, NSW, Australia,Ingham Institute for Applied Medical Research, Liverpool, NSW, Australia
| | - Mohammad Ali Moni
- School of Health and Rehabilitation Sciences, Faculty of Health and Behavioural Sciences, The University of Queensland, St Lucia, QLD, Australia
| | - Faiyaz Notta
- PanCuRx Translational Research Initiative, Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Steven Gallinger
- PanCuRx Translational Research Initiative, Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Ron Pirola
- Pancreatic Research Group, SWS Clinical Campus, School of Clinical Medicine, Faculty of Medicine and Health, UNSW Sydney, Sydney, NSW, Australia
| | - Jeremy Wilson
- Pancreatic Research Group, SWS Clinical Campus, School of Clinical Medicine, Faculty of Medicine and Health, UNSW Sydney, Sydney, NSW, Australia
| | - Marie Ranson
- Molecular Horizons and School of Chemistry & Molecular Bioscience, Faculty of Science, Medicine and Health, University of Wollongong, Wollongong, NSW, Australia,Illawarra Health and Medical Research Institute, Wollongong, NSW, Australia
| | - David Goldstein
- Prince of Wales Clinical School, University of New South Wales, Sydney, NSW, Australia,Department of Medical Oncology, Prince of Wales Hospital, Randwick, NSW, Australia
| | - Minoti Apte
- Pancreatic Research Group, SWS Clinical Campus, School of Clinical Medicine, Faculty of Medicine and Health, UNSW Sydney, Sydney, NSW, Australia,Ingham Institute for Applied Medical Research, Liverpool, NSW, Australia,*Correspondence: Minoti Apte,
| |
Collapse
|
24
|
Kumari P, Kumar S, Sethy M, Bhue S, Mohanta BK, Dixit A. Identification of therapeutically potential targets and their ligands for the treatment of OSCC. Front Oncol 2022; 12:910494. [PMID: 36203433 PMCID: PMC9530560 DOI: 10.3389/fonc.2022.910494] [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: 04/05/2022] [Accepted: 08/15/2022] [Indexed: 11/30/2022] Open
Abstract
Recent advancements in cancer biology have revealed molecular changes associated with carcinogenesis and chemotherapeutic exposure. The available information is being gainfully utilized to develop therapies targeting specific molecules involved in cancer cell growth, survival, and chemoresistance. Targeted therapies have dramatically increased overall survival (OS) in many cancers. Therefore, developing such targeted therapies against oral squamous cell carcinoma (OSCC) is anticipated to have significant clinical implications. In the current work, we have identified drug-specific sensitivity-related prognostic biomarkers (BOP1, CCNA2, CKS2, PLAU, and SERPINE1) using gene expression, Cox proportional hazards regression, and machine learning in OSCC. Dysregulation of these markers is significantly associated with OS in many cancers. Their elevated expression is related to cellular proliferation and aggressive malignancy in various cancers. Mechanistically, inhibition of these biomarkers should significantly reduce cellular proliferation and metastasis in OSCC and should result in better OS. It is pertinent to note that no effective small-molecule candidate has been identified against these biomarkers to date. Therefore, a comprehensive in silico drug design strategy assimilating homology modeling, extensive molecular dynamics (MD) simulation, and ensemble molecular docking has been applied to identify potential compounds against identified targets, and potential molecules have been identified. We hope that this study will help in deciphering potential genes having roles in chemoresistance and a significant impact on OS. It will also result in the identification of new targeted therapeutics against OSCC.
Collapse
Affiliation(s)
- Pratima Kumari
- Computational Biology and Bioinformatics Laboratory, Institute of Life Sciences, Bhubaneswar, India
- Regional Centre for Biotechnology (RCB), Faridabad, India
| | - Sugandh Kumar
- Computational Biology and Bioinformatics Laboratory, Institute of Life Sciences, Bhubaneswar, India
| | - Madhusmita Sethy
- Computational Biology and Bioinformatics Laboratory, Institute of Life Sciences, Bhubaneswar, India
| | - Shyamlal Bhue
- Computational Biology and Bioinformatics Laboratory, Institute of Life Sciences, Bhubaneswar, India
- Regional Centre for Biotechnology (RCB), Faridabad, India
| | - Bineet Kumar Mohanta
- Computational Biology and Bioinformatics Laboratory, Institute of Life Sciences, Bhubaneswar, India
- Regional Centre for Biotechnology (RCB), Faridabad, India
| | - Anshuman Dixit
- Computational Biology and Bioinformatics Laboratory, Institute of Life Sciences, Bhubaneswar, India
- *Correspondence: Anshuman Dixit,
| |
Collapse
|
25
|
Qiu L, Yue J, Ding L, Yin Z, Zhang K, Zhang H. Cancer-associated fibroblasts: An emerging target against esophageal squamous cell carcinoma. Cancer Lett 2022; 546:215860. [DOI: 10.1016/j.canlet.2022.215860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 07/18/2022] [Accepted: 08/01/2022] [Indexed: 11/02/2022]
|
26
|
Li J, Chen S, Liao Y, Wang H, Zhou D, Zhang B. Arecoline Is Associated With Inhibition of Cuproptosis and Proliferation of Cancer-Associated Fibroblasts in Oral Squamous Cell Carcinoma: A Potential Mechanism for Tumor Metastasis. Front Oncol 2022; 12:925743. [PMID: 35875097 PMCID: PMC9303015 DOI: 10.3389/fonc.2022.925743] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 06/06/2022] [Indexed: 11/13/2022] Open
Abstract
BackgroundMetastatic disease remains the primary cause of death in patients with oral squamous cell carcinoma (OSCC), especially those who use betel nut. The different steps of the metastatic cascade rely on reciprocal interactions between cancer cells and the tumor microenvironment (TME). Cancer-associated fibroblasts (CAFs) are regarded as a significant component in the TME of OSCC. However, the precise mechanisms regulating CAFs in OSCC are poorly understood.MethodsThirteen genes related to the arecoline were analyzed to explore the significant ones involved in arecoline-related OSCC metastasis. The GSE139869 (n = 10) and The Cancer Genome Atlas (TCGA)-OSCC data (n = 361) were mined for the identification of the differentially expressed genes. The least absolute shrinkage and selection operator (LASSO) regression was performed to identify the independent prognostic signatures. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were conducted to explore the functional enrichment of selected genes, and gene set enrichment analysis of cuproptosis-related genes was completed. Spearman’s analysis and Tumor Immune Estimation Resource (TIMER) were used to visualize the correlation between the infiltration of CAFs and the gene expression. The correlation analysis of the cells and different genes, including CAF infiltration and transcripts per million expression, was assessed. The relationship between arecoline and CAFs was confirmed by cell counting kit-8 assay (CCK-8). CancerSEA was searched to identify the single-cell phenotype.ResultArecoline-associated fibrosis-related OSCC differentially expressed genes (AFOC-DEGs), namely, PLAU, IL1A, SPP1, CCL11, TERT, and COL1A2, were screened out and selected from the Gene Expression Omnibus (GEO) database and TCGA database. AFOC-DEGs were highly expressed in OSCC, which led to poor survival of patients. Functional enrichment analysis, protein–protein interaction network construction, and Spearman’s correlation analysis all suggested that AFOC-DEGs were closely associated with cuproptosis. Cellular experiments demonstrated that arecoline stimulation could significantly increase the cell viability of CAFs. Single-sample Gene Set Enrichment Analysis (ssGSEA) results showed that GLS and MTF1 were highly expressed when fibroblasts proliferated at high enrichment levels. In addition, analysis of single-cell sequencing results suggested that OSCC cells with high expression of AFOC-DEGs were associated with OSCC metastasis.ConclusionWe found a close association between arecoline, cuproptosis, and CAFs, which might play an important role in the metastasis of OSCC.
Collapse
Affiliation(s)
- Jinfei Li
- Department of Stomatology, Third Xiangya Hospital of Central South University, Changsha, China
- Xiangya School of Medicine, Central South University, Changsha, China
| | - Shuangyi Chen
- Department of Stomatology, Third Xiangya Hospital of Central South University, Changsha, China
- Xiangya School of Medicine, Central South University, Changsha, China
| | - Yuxuan Liao
- Department of Stomatology, Third Xiangya Hospital of Central South University, Changsha, China
- Xiangya School of Medicine, Central South University, Changsha, China
| | - Hongyi Wang
- Department of Stomatology, Third Xiangya Hospital of Central South University, Changsha, China
- Xiangya School of Medicine, Central South University, Changsha, China
| | - Dawei Zhou
- Department of Stomatology, Third Xiangya Hospital of Central South University, Changsha, China
- Xiangya School of Medicine, Central South University, Changsha, China
| | - Bo Zhang
- Department of Stomatology, Third Xiangya Hospital of Central South University, Changsha, China
- *Correspondence: Bo Zhang,
| |
Collapse
|
27
|
Wang H, Lu L, Liang X, Chen Y. Identification of prognostic genes in the pancreatic adenocarcinoma immune microenvironment by integrated bioinformatics analysis. Cancer Immunol Immunother 2022; 71:1757-1769. [PMID: 34854950 DOI: 10.1007/s00262-021-03110-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 11/11/2021] [Indexed: 01/07/2023]
Abstract
PURPOSE Pancreatic adenocarcinoma (PAAD) is one of the most common causes of death among solid tumors, and its pathogenesis remains to be clarified. This study aims to elucidate the value of immune/stromal-related genes in the prognosis of PAAD through comprehensive bioinformatics analysis based on the immune microenvironment and validated in Chinese pancreatic cancer patients. METHODS Gene expression profiles of pancreatic cancer patients were obtained from TCGA database. Differentially expressed genes (DEGs) were identified based on the ESTIMATE algorithm. Gene co-expression networks were constructed using WGCNA. In the key module, survival analysis was used to reveal the prognostic value. Subsequently, we performed functional enrichment analysis to construct a protein-protein interaction (PPI) network. The relationship between tumor immune infiltration and hub genes was analyzed by TIMER and CIBERSORT. Finally, it was validated in the GEO database and in tissues of Chinese pancreatic cancer patients. RESULTS In the TCGA pancreatic cancer cohort, a low immune/stromal score was associated with a good prognosis. After bioinformatic analysis, 57 genes were identified to be significantly associated with pancreatic cancer prognosis. Among them, up-regulation of four genes (COL6A3, PLAU, MMP11 and MMP14) indicated poor prognosis and was associated with multiple immune cell infiltration. IHC results showed that PLAU protein levels from Chinese pancreatic cancer tissues were significantly higher than those from adjacent non-tumor tissues and were also associated with tumor TNM stage and lymph node metastasis. CONCLUSION In conclusion, this study demonstrates that PLAU may serve as a new diagnostic and therapeutic target, which is highly expressed in Chinese pancreatic cancer tissues and associated with lymph node metastasis.
Collapse
Affiliation(s)
- Haolan Wang
- NHC Key Laboratory of Cancer Proteomics, Laboratory of Structural Biology, Department of Oncology, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Liqing Lu
- NHC Key Laboratory of Cancer Proteomics, Laboratory of Structural Biology, Department of Oncology, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Xujun Liang
- NHC Key Laboratory of Cancer Proteomics, Laboratory of Structural Biology, Department of Oncology, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Yongheng Chen
- NHC Key Laboratory of Cancer Proteomics, Laboratory of Structural Biology, Department of Oncology, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China.
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China.
| |
Collapse
|
28
|
Zheng S, Liu B, Guan X. The Role of Tumor Microenvironment in Invasion and Metastasis of Esophageal Squamous Cell Carcinoma. Front Oncol 2022; 12:911285. [PMID: 35814365 PMCID: PMC9257257 DOI: 10.3389/fonc.2022.911285] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Accepted: 05/18/2022] [Indexed: 12/24/2022] Open
Abstract
Esophageal squamous cell carcinoma (ESCC) is one of the most common cancers in the world, with a high rate of morbidity. The invasion and metastasis of ESCC is the main reason for high mortality. More and more evidence suggests that metastasized cancer cells require cellular elements that contribute to ESCC tumor microenvironment (TME) formation. TME contains many immune cells and stromal components, which are critical to epithelial–mesenchymal transition, immune escape, angiogenesis/lymphangiogenesis, metastasis niche formation, and invasion/metastasis. In this review, we will focus on the mechanism of different microenvironment cellular elements in ESCC invasion and metastasis and discuss recent therapeutic attempts to restore the tumor-suppressing function of cells within the TME. It will represent the whole picture of TME in the metastasis and invasion process of ESCC.
Collapse
Affiliation(s)
- Shuyue Zheng
- Department of Clinical Oncology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, Hong Kong SAR, China
- Department of Clinical Oncology, The University of Hong Kong-Shenzhen Hospital, Shenzhen, China
| | - Beilei Liu
- Department of Clinical Oncology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, Hong Kong SAR, China
- Department of Clinical Oncology, The University of Hong Kong-Shenzhen Hospital, Shenzhen, China
| | - Xinyuan Guan
- Department of Clinical Oncology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, Hong Kong SAR, China
- Department of Clinical Oncology, The University of Hong Kong-Shenzhen Hospital, Shenzhen, China
- State Key Laboratory of Oncology in Southern China, Sun Yat-sen University Cancer Center, Guangzhou, China
- *Correspondence: Xinyuan Guan,
| |
Collapse
|
29
|
Lu SY, Hua J, Liu J, Wei MY, Liang C, Meng QC, Zhang B, Yu XJ, Wang W, Xu J. Construction of a paclitaxel-related competitive endogenous RNA network and identification of a potential regulatory axis in pancreatic cancer. Transl Oncol 2022; 20:101419. [PMID: 35413498 PMCID: PMC9018166 DOI: 10.1016/j.tranon.2022.101419] [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: 02/14/2022] [Revised: 03/17/2022] [Accepted: 03/30/2022] [Indexed: 11/28/2022] Open
Abstract
It is the first study to focus on paclitaxel sensitivity and construct ceRNA network in pancreatic cancer. We confirmed a potential PART1/hsa-mir-21/SCRN1 axis and verified it by qPCR. The exploration of the prognostic signature of paclitaxel is significant to its clinical chemotherapy and immune related therapy.
Background Increasing numbers of studies have elucidated the role of competitive endogenous RNA (ceRNA) networks in carcinogenesis. However, the potential role of the paclitaxel-related ceRNA network in the innate mechanism and prognosis of pancreatic cancer has not been identified. Methods Comprehensive bioinformatics analyses were performed to identify drug-related miRNAs (DRmiRNAs), drug-related mRNAs (DRmRNAs) and drug-related lncRNAs (DRlncRNAs) and construct a ceRNA network. The ssGSEA and CIBERSORT algorithms were utilized for immune cell infiltration analysis. Additionally, we validated our paclitaxel-related ceRNA regulatory axis at the gene expression level; functional experiments were conducted to explore the biological functions of the key genes. Results A total of 182 mRNAs, 13 miRNAs, and 53 lncRNAs were confirmed in the paclitaxel-related ceRNA network. In total, 6 mRNAs, 4 miRNAs, and 6 lncRNAs were identified to establish a risk signature and exhibited optimal prognostic effects. The mRNA signature can predict the abundance of immune cell infiltration and the sensitivity of different chemotherapeutic drugs and may also have a guiding effect in immune checkpoint therapy. A potential PART1/hsa-mir-21/SCRN1 axis was confirmed according to the ceRNA theory and was verified by qPCR. The results indicated that PART1 knockdown markedly increased hsa-mir-21 expression but inhibited SCRN1 expression, weakening the proliferation and migration abilities. Conclusions We hypothesized that the paclitaxel-related ceRNA network strongly influences the innate mechanism, prognosis, and immune infiltration of pancreatic cancer. Our risk signatures can accurately predict survival outcomes and provide a clinical basis.
Collapse
|
30
|
Gupta YH, Khanom A, Acton SE. Control of Dendritic Cell Function Within the Tumour Microenvironment. Front Immunol 2022; 13:733800. [PMID: 35355992 PMCID: PMC8960065 DOI: 10.3389/fimmu.2022.733800] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 02/09/2022] [Indexed: 12/12/2022] Open
Abstract
The tumour microenvironment (TME) presents a major block to anti-tumour immune responses and to effective cancer immunotherapy. The inflammatory mediators such as cytokines, chemokines, growth factors and prostaglandins generated in the TME alter the phenotype and function of dendritic cells (DCs) that are critical for a successful adaptive immune response against the growing tumour. In this mini review we discuss how tumour cells and the surrounding stroma modulate DC maturation and trafficking to impact T cell function. Fibroblastic stroma and the associated extracellular matrix around tumours can also provide physical restrictions to infiltrating DCs and other leukocytes. We discuss interactions between the inflammatory TME and infiltrating immune cell function, exploring how the inflammatory TME affects generation of T cell-driven anti-tumour immunity. We discuss the open question of the relative importance of antigen-presentation site; locally within the TME versus tumour-draining lymph nodes. Addressing these questions will potentially increase immune surveillance and enhance anti-tumour immunity.
Collapse
Affiliation(s)
- Yukti Hari Gupta
- Stromal Immunology Laboratory, MRC Laboratory for Molecular Cell Biology, University College London, London, United Kingdom
| | | | - Sophie E. Acton
- Stromal Immunology Laboratory, MRC Laboratory for Molecular Cell Biology, University College London, London, United Kingdom
| |
Collapse
|
31
|
Haque E, Teeli AS, Winiarczyk D, Taguchi M, Sakuraba S, Kono H, Leszczyński P, Pierzchała M, Taniguchi H. HNF1A POU Domain Mutations Found in Japanese Liver Cancer Patients Cause Downregulation of HNF4A Promoter Activity with Possible Disruption in Transcription Networks. Genes (Basel) 2022; 13:genes13030413. [PMID: 35327967 PMCID: PMC8949677 DOI: 10.3390/genes13030413] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 02/18/2022] [Accepted: 02/19/2022] [Indexed: 11/25/2022] Open
Abstract
Hepatocyte nuclear factor 1A (HNF1A) is the master regulator of liver homeostasis and organogenesis and regulates many aspects of hepatocyte functions. It acts as a tumor suppressor in the liver, evidenced by the increased proliferation in HNF1A knockout (KO) hepatocytes. Hence, we postulated that any loss-of-function variation in the gene structure or composition (mutation) could trigger dysfunction, including disrupted transcriptional networks in liver cells. From the International Cancer Genome Consortium (ICGC) database of cancer genomes, we identified several HNF1A mutations located in the functional Pit-Oct-Unc (POU) domain. In our biochemical analysis, we found that the HNF1A POU-domain mutations Y122C, R229Q and V259F suppressed HNF4A promoter activity and disrupted the binding of HNF1A to its target HNF4A promoter without any effect on the nuclear localization. Our results suggest that the decreased transcriptional activity of HNF1A mutants is due to impaired DNA binding. Through structural simulation analysis, we found that a V259F mutation was likely to affect DNA interaction by inducing large conformational changes in the N-terminal region of HNF1A. The results suggest that POU-domain mutations of HNF1A downregulate HNF4A gene expression. Therefore, to mimic the HNF1A mutation phenotype in transcription networks, we performed siRNA-mediated knockdown (KD) of HNF4A. Through RNA-Seq data analysis for the HNF4A KD, we found 748 differentially expressed genes (DEGs), of which 311 genes were downregulated (e.g., HNF1A, ApoB and SOAT2) and 437 genes were upregulated. Kyoto Encyclopedia of Genes and Genomes (KEGG) mapping revealed that the DEGs were involved in several signaling pathways (e.g., lipid and cholesterol metabolic pathways). Protein–protein network analysis suggested that the downregulated genes were related to lipid and cholesterol metabolism pathways, which are implicated in hepatocellular carcinoma (HCC) development. Our study demonstrates that mutations of HNF1A in the POU domain result in the downregulation of HNF1A target genes, including HNF4A, and this may trigger HCC development through the disruption of HNF4A–HNF1A transcriptional networks.
Collapse
Affiliation(s)
- Effi Haque
- Institute of Genetics and Animal Biotechnology of the Polish Academy of Sciences, 05-552 Jastrzebiec, Poland; (E.H.); (A.S.T.); (D.W.); (P.L.); (M.P.)
| | - Aamir Salam Teeli
- Institute of Genetics and Animal Biotechnology of the Polish Academy of Sciences, 05-552 Jastrzebiec, Poland; (E.H.); (A.S.T.); (D.W.); (P.L.); (M.P.)
| | - Dawid Winiarczyk
- Institute of Genetics and Animal Biotechnology of the Polish Academy of Sciences, 05-552 Jastrzebiec, Poland; (E.H.); (A.S.T.); (D.W.); (P.L.); (M.P.)
| | - Masahiko Taguchi
- Molecular Modeling and Simulation Group, National Institutes for Quantum Science and Technology, Kizugawa 619-0215, Japan; (M.T.); (S.S.); (H.K.)
| | - Shun Sakuraba
- Molecular Modeling and Simulation Group, National Institutes for Quantum Science and Technology, Kizugawa 619-0215, Japan; (M.T.); (S.S.); (H.K.)
| | - Hidetoshi Kono
- Molecular Modeling and Simulation Group, National Institutes for Quantum Science and Technology, Kizugawa 619-0215, Japan; (M.T.); (S.S.); (H.K.)
| | - Paweł Leszczyński
- Institute of Genetics and Animal Biotechnology of the Polish Academy of Sciences, 05-552 Jastrzebiec, Poland; (E.H.); (A.S.T.); (D.W.); (P.L.); (M.P.)
| | - Mariusz Pierzchała
- Institute of Genetics and Animal Biotechnology of the Polish Academy of Sciences, 05-552 Jastrzebiec, Poland; (E.H.); (A.S.T.); (D.W.); (P.L.); (M.P.)
| | - Hiroaki Taniguchi
- Institute of Genetics and Animal Biotechnology of the Polish Academy of Sciences, 05-552 Jastrzebiec, Poland; (E.H.); (A.S.T.); (D.W.); (P.L.); (M.P.)
- Correspondence: ; Tel.: +48-22-736-70-95
| |
Collapse
|
32
|
Baruah B, Dutta MP, Bhattacharyya DK. Identification of ESCC potential biomarkers using biclustering algorithms. GENE REPORTS 2022. [DOI: 10.1016/j.genrep.2022.101563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
|
33
|
Bioinformatics Characterization of Candidate Genes Associated with Gene Network and miRNA Regulation in Esophageal Squamous Cell Carcinoma Patients. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12031083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The present study aimed to identify potential therapeutic targets for esophageal squamous cell carcinoma (ESCC). The gene expression profile GSE161533 contained 84 samples, in that 28 tumor tissues and 28 normal tissues encoded as ESCC patients were retrieved from the Gene Expression Omnibus database. The obtained data were validated and screened for differentially expressed genes (DEGs) between normal and tumor tissues with the GEO2R tool. Next, the protein–protein network (PPI) was constructed using the (STRING 2.0) and reconstructed with Cytoscape 3.8.2, and the top ten hub genes (HGsT10) were predicted using the Maximal Clique Centrality (MCC) algorithm of the CytoHubba plugin. The identified hub genes were mapped in GSE161533, and their expression was determined and compared with The Cancer Genome Atlas (TCGA.) ESCC patient’s samples. The overall survival rate for HGsT10 wild and mutated types was analyzed with the Gene Expression Profiling Interactive Analysis2 (GEPIA2) server and UCSC Xena database. The functional and pathway enrichment analysis was performed using the WebGestalt database with the reference gene from lumina human ref 8.v3.0 version. The promoter methylation for the HGsT10 was identified using the UALCAN server. Additionally, the miRNA-HGsT10 regulatory network was constructed to identify the top ten hub miRNAs (miRT10). Finally, we identified the top ten novel driving genes from the DEGs of GSE161533 ESCC patient’s sample using a multi-omics approach. It may provide new insights into the diagnosis and treatment for the ESCC affected patients early in the future.
Collapse
|
34
|
Hassan MS, Cwidak N, Awasthi N, von Holzen U. Cytokine Interaction With Cancer-Associated Fibroblasts in Esophageal Cancer. Cancer Control 2022; 29:10732748221078470. [PMID: 35442094 PMCID: PMC9024076 DOI: 10.1177/10732748221078470] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Esophageal cancer (EC) is a highly aggressive cancer with poor outcomes under current treatment regimens. More recent findings suggest stroma elements, specifically cancer-associated fibroblasts (CAFs), play a role in disease occurrence and progression. Cancer-associated fibroblasts are largely the product of converted fibroblasts, but a variety of other local cell types including epithelial cells, endothelial cells, and mesenchymal cells have also been shown to transform to CAFs under the correct conditions. Cancer-associated fibroblasts primarily function in the communication between the tumor microenvironment and cancer cells via cytokine and chemokine secretions that accentuate immunosuppression and cancer growth. Cancer-associated fibroblasts also pose issues for EC treatment by contributing to resistance of current chemotherapeutics like cisplatin. Targeting this cell type directly proves difficult given the heterogeneity between CAFs subpopulations, but emerging research provides hope that treatment is on the horizon. This review aims to unravel some of the complexities surrounding CAFs’ impact on EC growth and therapy.
Collapse
Affiliation(s)
- Md Sazzad Hassan
- Department of Surgery, 158720Indiana University School of Medicine, South Bend, IN 46617, USA.,Harper Cancer Research Institute, South Bend, IN 46617, USA
| | - Nicholas Cwidak
- Department of Surgery, 158720Indiana University School of Medicine, South Bend, IN 46617, USA
| | - Niranjan Awasthi
- Department of Surgery, 158720Indiana University School of Medicine, South Bend, IN 46617, USA.,Harper Cancer Research Institute, South Bend, IN 46617, USA
| | - Urs von Holzen
- Department of Surgery, 158720Indiana University School of Medicine, South Bend, IN 46617, USA.,Harper Cancer Research Institute, South Bend, IN 46617, USA.,Goshen Center for Cancer Care, Goshen, Goshen, IN 46526, USA.,University of Basel, Basel, Switzerland
| |
Collapse
|
35
|
Cui Y, Kang Y, Zhang P, Wang Y, Yang Z, Lu C, Zhang P. Mig-6 could inhibit cell proliferation and induce apoptosis in esophageal squamous cell carcinoma. Thorac Cancer 2021; 13:54-60. [PMID: 34845855 PMCID: PMC8720621 DOI: 10.1111/1759-7714.14223] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 10/21/2021] [Accepted: 10/22/2021] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND To investigate the expression and biological functions of mitogen-induced gene 6 (Mig-6) in esophageal squamous cell carcinoma (ESCC). METHODS The expression of Mig-6 in ESCC tissues and normal esophageal epithelial tissues were measured by immunohistochemistry (IHC) assay. MTT test was applied to detect the proliferative ability of ESCC cells after Mig-6 was upregulated by transfection. A fluid cytology assay was used to detect apoptosis of ESCC cells. Agilent whole human genome oligo microarray was used to screen different expressed genes and the possible signaling pathways which might be involved. RESULTS The expression of Mig-6 protein was lower in ESCC tissues compared to normal esophageal epithelial tissues. Mig-6 could restrain the ESCC cell growth and induce cell apoptosis. PPAR, CAMs and MAPK signaling pathways might be involved. CONCLUSIONS Mig-6 might be a new tumor suppressor gene and a possible target for the specific therapy of ESCC.
Collapse
Affiliation(s)
- Yuantao Cui
- Department of Cardiothoracic Surgery, Tianjin Medical University General Hospital, Tianjin Medical University, Tianjin, China
| | - Ying Kang
- Department of Cardiothoracic Surgery, Tianjin Medical University General Hospital, Tianjin Medical University, Tianjin, China
| | - Peng Zhang
- Department of Cardiothoracic Surgery, Tianjin Medical University General Hospital, Tianjin Medical University, Tianjin, China
| | - Yuanguo Wang
- Department of Cardiothoracic Surgery, Tianjin Medical University General Hospital, Tianjin Medical University, Tianjin, China
| | - Zhaoyu Yang
- Department of Cardiothoracic Surgery, Tianjin Medical University General Hospital, Tianjin Medical University, Tianjin, China
| | - Chao Lu
- Department of Cardiothoracic Surgery, Tianjin Medical University General Hospital, Tianjin Medical University, Tianjin, China
| | - Peng Zhang
- Department of Cardiothoracic Surgery, Tianjin Medical University General Hospital, Tianjin Medical University, Tianjin, China
| |
Collapse
|
36
|
Zhang Y, Chen P, Zhou Q, Wang H, Hua Q, Wang J, Zhong H. A Novel Immune-Related Prognostic Signature in Head and Neck Squamous Cell Carcinoma. Front Genet 2021; 12:570336. [PMID: 34220923 PMCID: PMC8249947 DOI: 10.3389/fgene.2021.570336] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 04/20/2021] [Indexed: 02/05/2023] Open
Abstract
The immune response within the tumor microenvironment plays a key role in tumorigenesis and determines the clinical outcomes of head and neck squamous cell carcinoma (HNSCC). However, to date, very limited robust and reliable immunological biomarkers have been developed that are capable of estimating prognosis in HNSCC patients. In this study, we aimed to identify the effects of novel immune-related gene signatures (IRGs) that can predict HNSCC prognosis. Based on gene expression profiles and clinical data of HNSCC patient cohorts from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) database, a total of 439 highly variable expressed immune-related genes (including 239 upregulated and 200 downregulated genes) were identified by using differential gene expression analysis. Pathway enrichment analysis indicated that these immune-related differentially expressed genes were enriched in inflammatory functions. After process screening in the training TCGA cohort, six immune-related genes (PLAU, STC2, TNFRSF4, PDGFA, DKK1, and CHGB) were significantly associated with overall survival (OS) based on the LASSO Cox regression model. Integrating these genes with clinicopathological features, a multivariable model was built and suggested better performance in determining patients’ OS in the testing cohort, and the independent validation cohort. In conclusion, a well-established model encompassing both immune-related gene signatures and clinicopathological factors would serve as a promising tool for the prognostic prediction of HNSCC.
Collapse
Affiliation(s)
- Yi Zhang
- Department of Otolaryngology-Head and Neck Surgery, Beijing Chaoyang Hospital, Capital Medical University, Beijing, China
| | - Ping Chen
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Qiang Zhou
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Hongyan Wang
- Department of Otolaryngology-Head and Neck Surgery, Beijing Chaoyang Hospital, Capital Medical University, Beijing, China
| | - Qingquan Hua
- Department of Otolaryngology-Head and Neck Surgery, Renmin Hospital of Wuhan University, Wuhan, China
| | - Jie Wang
- Department of Otolaryngology-Head and Neck Surgery, Renmin Hospital of Wuhan University, Wuhan, China
| | - Hongliang Zhong
- Department of Neurosurgery, Beijing Chaoyang Hospital, Capital Medical University, Beijing, China
| |
Collapse
|