1
|
Pham DT, Tran TD. Drivergene.net: A Cytoscape app for the identification of driver nodes of large-scale complex networks and case studies in discovery of drug target genes. Comput Biol Med 2024; 179:108888. [PMID: 39047507 DOI: 10.1016/j.compbiomed.2024.108888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 06/15/2024] [Accepted: 07/11/2024] [Indexed: 07/27/2024]
Abstract
There are no tools to identify driver nodes of large-scale networks in approach of competition-based controllability. This study proposed a novel method for this computation of large-scale networks. It implemented the method in a new Cytoscape plug-in app called Drivergene.net. Experiments of the software on large-scale biomolecular networks have shown outstanding speed and computing power. Interestingly, 86.67% of the top 10 driver nodes found on these networks are anticancer drug target genes that reside mostly at the innermost K-cores of the networks. Finally, compared method with those of five other researchers and confirmed that the proposed method outperforms the other methods on identification of anticancer drug target genes. Taken together, Drivergene.net is a reliable tool that efficiently detects not only drug target genes from biomolecular networks but also driver nodes of large-scale complex networks. Drivergene.net with a user manual and example datasets are available https://github.com/tinhpd/Drivergene.git.
Collapse
Affiliation(s)
- Duc-Tinh Pham
- Complex Systems and Bioinformatics Lab, Hanoi University of Industry, 298 Cau Dien Street, Bac Tu Liem District, Hanoi, Viet Nam; Graduate University of Science and Technology, Academy of Science and Technology Viet Nam, 18 Hoang Quoc Viet Street, Cau Giay District, Hanoi, Viet Nam
| | - Tien-Dzung Tran
- Complex Systems and Bioinformatics Lab, Hanoi University of Industry, 298 Cau Dien Street, Bac Tu Liem District, Hanoi, Viet Nam; Faculty of Information and Communication Technology, Hanoi University of Industry, 298 Cau Dien Street, Bac Tu Liem District, Hanoi, Viet Nam.
| |
Collapse
|
2
|
Zhao C, Zhao R, Wu X, Tang K, Xu P, Chen X, Zhu P, He Y. Function of unconventional T cells in oral lichen planus revealed by single-cell RNA sequencing. Inflamm Res 2024; 73:1477-1492. [PMID: 39073597 DOI: 10.1007/s00011-024-01912-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 06/26/2024] [Accepted: 06/27/2024] [Indexed: 07/30/2024] Open
Abstract
OBJECTIVE We intended to map the single-cell profile of OLP, explore the molecular characteristics of unconventional T cells in OLP tissues. METHODS Buccal mucosa samples from OLP patients and healthy individuals were used to prepare single-cell suspension. Single-cell RNA sequencing was used to analyze the proportion of all the cells, and the molecular characteristics of unconventional T cells. Immunohistochemical staining was used to detect the expression of unconventional T cells marker genes. RESULTS The cell clusters from buccal mucosa were categorized into immune cells, fibroblasts, endothelial cells, and epithelial cells. Unconventional T cells with phenotype of CD247+TRDC+NCAM1+ were identified. Immunohistochemical staining revealed higher expression of unconventional T cell marker genes in OLP tissue, predominantly in the lamina propria. In OLP, unconventional T cells are in a unique stress response state, exhibited enhanced NF-κB signaling and apoptosis inhibition, enhanced heat shock protein genes expression, weakened cytotoxic function. A large number of ligand-receptor pairs were found between unconventional T cells and other cells, particularly with fibroblasts and endothelial cells. CONCLUSIONS This study mapped the single-cell profile of OLP, delineated the molecular characteristics of unconventional T cells in OLP, and uncovered that these unconventional T cells are in a stress response state.
Collapse
Affiliation(s)
- Chen Zhao
- Shanghai Engineering Research Center of Tooth Restoration and Regeneration & Tongji Research Institute of Stomatology & Department of Oral Medicine, School of Stomatology, Stomatological Hospital and Dental School, Tongji University, Shanghai, 200072, China
| | - Ruowen Zhao
- Shanghai Engineering Research Center of Tooth Restoration and Regeneration & Tongji Research Institute of Stomatology & Department of Oral Medicine, School of Stomatology, Stomatological Hospital and Dental School, Tongji University, Shanghai, 200072, China
| | - Xinwen Wu
- School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Kailin Tang
- School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Pan Xu
- Shanghai Engineering Research Center of Tooth Restoration and Regeneration & Tongji Research Institute of Stomatology & Department of Oral Medicine, School of Stomatology, Stomatological Hospital and Dental School, Tongji University, Shanghai, 200072, China
| | - Xin Chen
- Shanghai Engineering Research Center of Tooth Restoration and Regeneration & Tongji Research Institute of Stomatology & Department of Oral Medicine, School of Stomatology, Stomatological Hospital and Dental School, Tongji University, Shanghai, 200072, China
| | - Pingyi Zhu
- Shanghai Engineering Research Center of Tooth Restoration and Regeneration & Tongji Research Institute of Stomatology & Department of Oral Medicine, School of Stomatology, Stomatological Hospital and Dental School, Tongji University, Shanghai, 200072, China
| | - Yuan He
- Shanghai Engineering Research Center of Tooth Restoration and Regeneration & Tongji Research Institute of Stomatology & Department of Oral Medicine, School of Stomatology, Stomatological Hospital and Dental School, Tongji University, Shanghai, 200072, China.
| |
Collapse
|
3
|
Jiang YY, Dong HH, Zhou WT, Luo JZ, Wei X, Huang YQ. Preparation of kakkatin derivatives and their anti-tumor activity. World J Clin Oncol 2024; 15:1078-1091. [PMID: 39193163 PMCID: PMC11346066 DOI: 10.5306/wjco.v15.i8.1078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 07/20/2024] [Accepted: 07/29/2024] [Indexed: 08/16/2024] Open
Abstract
BACKGROUND Modern pharmacological studies have confirmed that plant-derived compounds from Puerariae flos (PF) has significant biological activities against liver damage, tumors and inflammation. Kakkatin is an isoflavone polyphenolic compound isolated from PF flower. However, the effect of kakkatin and its derivatives on anti-tumor has not been well explored. AIM To design and synthesize a kakkatin derivative [6-(hept-6-yn-1-yloxy)-3-(4-hydroxyphenyl)-7-methoxy-4H-chromen-4-one (HK)] to explore its anti-tumor biological activity. METHODS Hept-6-yn-1-yl ethanesulfonate was introduced to replace hydrogen at the hydroxyl position of kakkatin phenol, and the derivative of kakkatin was prepared; the 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide was used to detect cell viability, a clone formation assay was adopted to detect cell proliferation, apoptosis, necrosis, and cell cycles were analyzed by Annexin V/propidium iodide staining and flow cytometry. Cell migration and invasion ability were evaluated by cell scratch assay and transwell assay. The potential mechanism of HK on hepatocellular carcinoma (HCC) SMMC-7721 cells was explored through network pharmacology and molecular docking, and finally real-time PCR assays was used to verify the potential targets and evaluate the biological activity of HK. RESULTS Compared with kakkatin, the modified HK did not significantly increase the inhibitory activity of gastric cancer MGC803 cells, but the inhibitory activity of HCC SMMC-7721 cells was increased by about 30 times, with an IC50 value of 2.5 μM, and the tumor inhibition effect was better than cisplatin, which could significantly inhibit the cloning, invasion and metastasis of HCC SMMC-7721 cells, and induce apoptosis and G2/M cycle arrest. Its mechanism of action is mainly related to the upregulation of PDE3B and NFKB1 target proteins in the cAMP pathway. CONCLUSION HK have a significant inhibitory effect on HCC SMMC-7721 cells, and the targets of their action may be PDE3B and NFKB1 proteins in the cAMP pathway, making it a good lead drug for the treatment of HCC.
Collapse
Affiliation(s)
- Yu-Ying Jiang
- Guangxi Technology Innovation Cooperation Base of Prevention and Control Pathogenic Microbes with Drug Resistance, Youjiang Medical University for Nationalities, Baise 533000, Guangxi Zhuang Autonomous Region, China
- Key Laboratory of the Prevention and Treatment of Drug Resistant Microbial Infecting, Youjiang Medical University for Nationalities, Baise 533000, Guangxi Zhuang Autonomous Region, China
| | - Hui-Hua Dong
- Guangxi Technology Innovation Cooperation Base of Prevention and Control Pathogenic Microbes with Drug Resistance, Youjiang Medical University for Nationalities, Baise 533000, Guangxi Zhuang Autonomous Region, China
- Key Laboratory of the Prevention and Treatment of Drug Resistant Microbial Infecting, Youjiang Medical University for Nationalities, Baise 533000, Guangxi Zhuang Autonomous Region, China
| | - Wen-Ting Zhou
- Guangxi Technology Innovation Cooperation Base of Prevention and Control Pathogenic Microbes with Drug Resistance, Youjiang Medical University for Nationalities, Baise 533000, Guangxi Zhuang Autonomous Region, China
- Key Laboratory of the Prevention and Treatment of Drug Resistant Microbial Infecting, Youjiang Medical University for Nationalities, Baise 533000, Guangxi Zhuang Autonomous Region, China
| | - Jia-Zi Luo
- Key Laboratory of the Prevention and Treatment of Drug Resistant Microbial Infecting, Youjiang Medical University for Nationalities, Baise 533000, Guangxi Zhuang Autonomous Region, China
- Collaborative Innovation Center for Guangxi Ethnic Medicine, The School of Chemistry and Pharmaceutical Sciences, Youjiang Medical University for Nationalities, Baise 533000, Guangxi Zhuang Autonomous Region, China
| | - Xian Wei
- Key Laboratory of the Prevention and Treatment of Drug Resistant Microbial Infecting, Youjiang Medical University for Nationalities, Baise 533000, Guangxi Zhuang Autonomous Region, China
- Research Center for the Prevention and Treatment of Drug Resistant Microbial Infecting, Youjiang Medical University for Nationalities, Baise 533000, Guangxi Zhuang Autonomous Region, China
| | - Yan-Qiang Huang
- Guangxi Technology Innovation Cooperation Base of Prevention and Control Pathogenic Microbes with Drug Resistance, Youjiang Medical University for Nationalities, Baise 533000, Guangxi Zhuang Autonomous Region, China
| |
Collapse
|
4
|
Tang C, Chen P, Xu LL, Lv JC, Shi SF, Zhou XJ, Liu LJ, Zhang H. Circulating Proteins and IgA Nephropathy: A Multiancestry Proteome-Wide Mendelian Randomization Study. J Am Soc Nephrol 2024; 35:1045-1057. [PMID: 38687828 DOI: 10.1681/asn.0000000000000379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 04/23/2024] [Indexed: 05/02/2024] Open
Abstract
Key Points
A multiancestry proteome-wide Mendelian randomization analysis was conducted for IgA nephropathy.The findings from the study would help prioritize new drug targets and drug-repurposing opportunities.
Background
The therapeutic options for IgA nephropathy are rapidly evolving, but early diagnosis and targeted treatment remain challenging. We aimed to identify circulating plasma proteins associated with IgA nephropathy by proteome-wide Mendelian randomization studies across multiple ancestry populations.
Methods
In this study, we applied Mendelian randomization and colocalization analyses to estimate the putative causal effects of 2615 proteins on IgA nephropathy in Europeans and 235 proteins in East Asians. Following two-stage network Mendelian randomization, multitrait colocalization analysis and protein-altering variant annotation were performed to strengthen the reliability of the results. A protein–protein interaction network was constructed to investigate the interactions between the identified proteins and the targets of existing medications.
Results
Putative causal effects of 184 and 13 protein–disease pairs in European and East Asian ancestries were identified, respectively. Two protein–disease pairs showed shared causal effects across them (CFHR1 and FCRL2). Supported by the evidence from colocalization analysis, potential therapeutic targets were prioritized and four drug-repurposing opportunities were suggested. The protein–protein interaction network further provided strong evidence for existing medications and pathways that are known to be therapeutically important.
Conclusions
Our study identified a number of circulating proteins associated with IgA nephropathy and prioritized several potential drug targets that require further investigation.
Collapse
Affiliation(s)
- Chen Tang
- Renal Division, Peking University First Hospital, Peking University Institute of Nephrology, Beijing, China; Key Laboratory of Renal Disease, Ministry of Health of China, Key Laboratory of Chronic Kidney Disease Prevention and Treatment (Peking University), Ministry of Education, Beijing, China; and Research Units of Diagnosis and Treatment of Immune-Mediated Kidney Diseases, Chinese Academy of Medical Sciences, Beijing, China
| | | | | | | | | | | | | | | |
Collapse
|
5
|
Jung S, Wang S, Lee D. CancerGATE: Prediction of cancer-driver genes using graph attention autoencoders. Comput Biol Med 2024; 176:108568. [PMID: 38744009 DOI: 10.1016/j.compbiomed.2024.108568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 04/13/2024] [Accepted: 05/05/2024] [Indexed: 05/16/2024]
Abstract
Discovery of the cancer type specific-driver genes is important for understanding the molecular mechanisms of each cancer type and for providing proper treatment. Recently, graph deep learning methods became widely used in finding cancer-driver genes. However, previous methods had limited performance in individual cancer types due to a small number of cancer-driver genes used in training and biases toward the cancer-driver genes used in training the models. Here, we introduce a novel pipeline, CancerGATE that predicts the cancer-driver genes using graph attention autoencoder (GATE) to learn in a self-supervised manner and can be applied to each of the cancer types. CancerGATE utilizes biological network topology and multi-omics data from 15 types of cancer of 20,079 samples from the cancer genome atlas (TCGA). Attention coefficients calculated in the model are used to prioritize cancer-driver genes by comparing coefficients of cancer and normal contexts. CancerGATE shows a higher AUPRC with a difference ranging from 1.5 % to 36.5 % compared to the previous graph deep learning models in each cancer type. We also show that CancerGATE is free from the bias toward cancer-driver genes used in training, revealing mechanisms of the cancer-driver genes in specific cancer types. Finally, we propose novel cancer-driver gene candidates that could be therapeutic targets for specific cancer types.
Collapse
Affiliation(s)
- Seunghwan Jung
- Department of Bio and Brain Engineering, KAIST, Daejeon 34141, Republic of Korea.
| | - Seunghyun Wang
- Department of Bio and Brain Engineering, KAIST, Daejeon 34141, Republic of Korea.
| | - Doheon Lee
- Department of Bio and Brain Engineering, KAIST, Daejeon 34141, Republic of Korea.
| |
Collapse
|
6
|
Wu P, Wang X, Yin M, Zhu W, Chen Z, Zhang Y, Jiang Z, Shi L, Zhu Q. ULK1 Mediated Autophagy-Promoting Effects of Rutin-Loaded Chitosan Nanoparticles Contribute to the Activation of NF-κB Signaling Besides Inhibiting EMT in Hep3B Hepatoma Cells. Int J Nanomedicine 2024; 19:4465-4493. [PMID: 38779103 PMCID: PMC11110815 DOI: 10.2147/ijn.s443117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 05/08/2024] [Indexed: 05/25/2024] Open
Abstract
Background Liver cancer remains to be one of the leading causes of cancer worldwide. The treatment options face several challenges and nanomaterials have proven to improve the bioavailability of several drug candidates and their applications in nanomedicine. Specifically, chitosan nanoparticles (CNPs) are extremely biodegradable, pose enhanced biocompatibility and are considered safe for use in medicine. Methods CNPs were synthesized by ionic gelation, loaded with rutin (rCNPs) and characterized by ultraviolet-visible spectroscopy (UV-Vis), Fourier-transform infrared spectroscopy (FTIR), dynamic light scattering (DLS) and transmission electron microscopy (TEM). The rCNPs were tested for their cytotoxic effects on human hepatoma Hep3B cells, and experiments were conducted to determine the mechanism of such effects. Further, the biocompatibility of the rCNPs was tested on L929 fibroblasts, and their hemocompatibility was determined. Results Initially, UV-vis and FTIR analyses indicated the possible loading of rutin on rCNPs. Further, the rutin load was quantitatively measured using Ultra-Performance Liquid Chromatography (UPLC) and the concentration was 88 µg/mL for 0.22 micron filtered rCNPs. The drug loading capacity (LC%) of the rCNPs was observed to be 13.29 ± 0.68%, and encapsulation efficiency (EE%) was 19.55 ± 1.01%. The drug release was pH-responsive as 88.58% of the drug was released after 24 hrs at the lysosomal pH 5.5, whereas 91.44% of the drug was released at physiological pH 7.4 after 102 hrs. The cytotoxic effects were prominent in 0.22 micron filtered samples of 5 mg/mL rutin precursor. The particle size for the rCNPs at this concentration was 144.1 nm and the polydispersity index (PDI) was 0.244, which is deemed to be ideal for tumor targeting. A zeta potential (ζ-potential) value of 16.4 mV indicated rCNPs with good stability. The IC50 value for the cytotoxic effects of rCNPs on human hepatoma Hep3B cells was 9.7 ± 0.19 μg/mL of rutin load. In addition, the increased production of reactive oxygen species (ROS) and changes in mitochondrial membrane potential (MMP) were observed. Gene expression studies indicated that the mechanism for cytotoxic effects of rCNPs on Hep3B cells was due to the activation of Unc-51-like autophagy-activating kinase (ULK1) mediated autophagy and nuclear factor kappa B (NF-κB) signaling besides inhibiting the epithelial-mesenchymal Transition (EMT). In addition, the rCNPs were less toxic on NCTC clone 929 (L929) fibroblasts in comparison to the Hep3B cells and possessed excellent hemocompatibility (less than 2% of hemolysis). Conclusion The synthesized rCNPs were pH-responsive and possessed the physicochemical properties suitable for tumor targeting. The particles were effectively cytotoxic on Hep3B cells in comparison to normal cells and possessed excellent hemocompatibility. The very low hemolytic profile of rCNPs indicates that the drug could be administered intravenously for cancer therapy.
Collapse
Affiliation(s)
- Peng Wu
- Children’s Hospital of Nanjing Medical University, Nanjing, People’s Republic of China
| | - Xiaoyong Wang
- The People’s Hospital of Rugao, Nantong, People’s Republic of China
| | - Min Yin
- Children’s Hospital of Nanjing Medical University, Nanjing, People’s Republic of China
| | - Wenjie Zhu
- Kangda College of Nanjing Medical University, Nanjing, People’s Republic of China
| | - Zheng Chen
- Children’s Hospital of Nanjing Medical University, Nanjing, People’s Republic of China
| | - Yang Zhang
- Children’s Hospital of Nanjing Medical University, Nanjing, People’s Republic of China
| | - Ziyu Jiang
- Department of Oncology, Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, 210028, People’s Republic of China
| | - Longqing Shi
- Department of Hepatobiliary and Pancreatic Surgery, Third Affiliated Hospital of Soochow University, Jiangsu, People’s Republic of China
| | - Qiang Zhu
- Children’s Hospital of Nanjing Medical University, Nanjing, People’s Republic of China
| |
Collapse
|
7
|
Barnes P, Mensah A, Derkyi-Kwarteng L, Adankwa E, Agbo E, Yahaya ES, Amoani B, Adjei G, Apewe Ka-Chungu SM, Akakpo PK, Halm-Lai F, Dankwa K, Amoako-Sakyi D, Nuvor SV, Obiri-Yeboah D, Saahene RO. Prognostic Significance of Nuclear Factor Kappa B (p65) among Breast Cancer Patients in Cape Coast Teaching Hospital. Med Princ Pract 2024; 33:1-11. [PMID: 38723618 PMCID: PMC11324227 DOI: 10.1159/000539241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 05/06/2024] [Indexed: 06/13/2024] Open
Abstract
Breast cancer is the most prevalent cancer among African women, with high mortality rates in Ghana. Nuclear factor kappa B (NF-kB) has been associated with tumor progression in breast cancer. However, its clinical validation is controversial and understudied with no known published data on NF-kB (p65) among breast cancer patients in Ghana and other African countries. This study assessed the prognostic significance of NF-kB (p65) expression and its association with various clinicopathological features in breast cancer patients. Ninety formalin-fixed breast cancer tissues and 15 normal breast tissues were used to determine the expression of NF-kB (p65) using immunohistochemistry. We explored the correlation between expression of NF-kB (p65) and clinicopathological features. NF-kB (p65) was expressed in 86.7% of breast cancer tissues. There was a significant relationship between NF-kB (p65) expression and tumor grade, proliferation index (Ki67), and molecular subtype. High NF-kB (p65) expression in tumor grade 3 was about 10 times that of grade 1 (54.2% vs. 5.1%), and Ki67 > 20 was 79.7% compared to 20.3% for Ki67 ≤ 20. Patients with triple-negative breast cancer (TNBC) had 49.1% overexpression of NF-kB (p65) compared to 17%, 25.4%, and 8.5% for luminal A, luminal B, and HER2 cases, respectively. This study demonstrates that NF-kB (p65) was highly expressed among breast cancer patients at Cape Coast Teaching Hospital, Ghana, especially in TNBC. NF-kB (p65) could serve as a biomarker for cancer stage, progression, prognosis and as a therapeutic target.
Collapse
Affiliation(s)
- Precious Barnes
- Department of Physician Assistant Studies, School of Allied Health Sciences, College of Health and Allied Sciences, University of Cape Coast, Cape Coast, Ghana
| | - Abraham Mensah
- Department of Microbiology and Immunology, School of Medical Sciences, College of Health and Allied Sciences, University of Cape Coast, Cape Coast, Ghana
| | - Leonard Derkyi-Kwarteng
- Department of Pathology, School of Medical Sciences, College of Health and Allied Sciences, University of Cape Coast, Cape Coast, Ghana
| | - Ernest Adankwa
- Department of Medical Diagnostics, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Elvis Agbo
- Department of Human Anatomy, Histology and Embryology, College of Medicine, Jinggangshan University, Ji’an, China
| | - Ewura Seidu Yahaya
- Department of Pharmacology, School of Medical Sciences, College of Health and Allied Sciences, University of Cape Coast, Cape Coast, Ghana
| | - Benjamin Amoani
- Department of Biomedical Sciences, School of Allied Health Sciences, College of Health and Allied Sciences, University of Cape Coast, Cape Coast, Ghana
| | - George Adjei
- Department of Community Medicine, School of Medical Sciences, College of Health and Allied Sciences, University of Cape Coast, Cape Coast, Ghana
| | | | - Patrick Kafui Akakpo
- Department of Pathology, School of Medical Sciences, College of Health and Allied Sciences, University of Cape Coast, Cape Coast, Ghana
| | - Faustina Halm-Lai
- Department of Microbiology and Immunology, School of Medical Sciences, College of Health and Allied Sciences, University of Cape Coast, Cape Coast, Ghana
| | - Kwabena Dankwa
- Department of Microbiology and Immunology, School of Medical Sciences, College of Health and Allied Sciences, University of Cape Coast, Cape Coast, Ghana
| | - Daniel Amoako-Sakyi
- Department of Microbiology and Immunology, School of Medical Sciences, College of Health and Allied Sciences, University of Cape Coast, Cape Coast, Ghana
| | - Samuel Victor Nuvor
- Department of Microbiology and Immunology, School of Medical Sciences, College of Health and Allied Sciences, University of Cape Coast, Cape Coast, Ghana
| | - Dorcas Obiri-Yeboah
- Department of Microbiology and Immunology, School of Medical Sciences, College of Health and Allied Sciences, University of Cape Coast, Cape Coast, Ghana
| | - Roland Osei Saahene
- Department of Microbiology and Immunology, School of Medical Sciences, College of Health and Allied Sciences, University of Cape Coast, Cape Coast, Ghana
| |
Collapse
|
8
|
Wang Q, Zhang J, Wen Y, Qi S, Duan Y, Liu Q, Li C. The pleiotropic enhancer enh9 promotes cell proliferation and migration in non-small cell lung cancer via ERMP1 and PD-L1. Biochim Biophys Acta Mol Basis Dis 2024; 1870:167015. [PMID: 38182069 DOI: 10.1016/j.bbadis.2023.167015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Revised: 12/27/2023] [Accepted: 12/28/2023] [Indexed: 01/07/2024]
Abstract
Enhancers, cis-acting DNA elements for transcriptional regulation, are important regulators of cell identity and disease. However, of the hundreds of thousands of enhancers annotated in the human genome, only a few have been studied for their regulatory mechanisms and functions in cancer progression and therapeutic resistance. Here, we report the pleiotropy of one enhancer (named enh9) in both cell proliferation and migration in non-small cell lung cancer (NSCLC) cells. By integrating multi-genomic data, ERMP1 and PD-L1 were screened out as potential targets of enh9. CUT&Tag sequencing demonstrated that enh9 was involved in the genomic interactions between the transcription factor RELA and the promoters of ERMP1 and PD-L1. In addition, ERMP1 and PD-L1 were validated to be involved in cell proliferation and migration, respectively. Our study fully elucidated the function and transcriptional regulation mechanisms of enh9 in NSCLC. The exploration on enhancers is promising to provide new insights for cancer diagnosis and therapy.
Collapse
Affiliation(s)
- Qilin Wang
- School of Engineering Medicine, Beihang University, Beijing 100191, China; Key Laboratory of Big Data-Based Precision Medicine (Ministry of Industry and Information Technology), Beihang University, Beijing 100191, China; School of Biological Science and Medical Engineering, Beihang University, Beijing 100191, China
| | - Junyou Zhang
- School of Engineering Medicine, Beihang University, Beijing 100191, China; Key Laboratory of Big Data-Based Precision Medicine (Ministry of Industry and Information Technology), Beihang University, Beijing 100191, China; School of Biological Science and Medical Engineering, Beihang University, Beijing 100191, China
| | - Yanling Wen
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Shenzhen, Guangdong 518112, China; The Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong 518112, China
| | - Sihan Qi
- School of Engineering Medicine, Beihang University, Beijing 100191, China; Key Laboratory of Big Data-Based Precision Medicine (Ministry of Industry and Information Technology), Beihang University, Beijing 100191, China; School of Biological Science and Medical Engineering, Beihang University, Beijing 100191, China
| | - Yingying Duan
- School of Engineering Medicine, Beihang University, Beijing 100191, China; Key Laboratory of Big Data-Based Precision Medicine (Ministry of Industry and Information Technology), Beihang University, Beijing 100191, China; School of Biological Science and Medical Engineering, Beihang University, Beijing 100191, China
| | - Qian Liu
- School of Engineering Medicine, Beihang University, Beijing 100191, China; Key Laboratory of Big Data-Based Precision Medicine (Ministry of Industry and Information Technology), Beihang University, Beijing 100191, China; School of Biological Science and Medical Engineering, Beihang University, Beijing 100191, China
| | - Chunyan Li
- School of Engineering Medicine, Beihang University, Beijing 100191, China; Key Laboratory of Big Data-Based Precision Medicine (Ministry of Industry and Information Technology), Beihang University, Beijing 100191, China; School of Biological Science and Medical Engineering, Beihang University, Beijing 100191, China; Beijing Advanced Innovation Center for Big Data-Based Precision Medicine, Beihang University, Beijing 100191, China.
| |
Collapse
|
9
|
Yap RS, Kumar J, Teoh SL. Potential Neuroprotective Role of Neurotrophin in Traumatic Brain Injury. CNS & NEUROLOGICAL DISORDERS DRUG TARGETS 2024; 23:1189-1202. [PMID: 38279761 DOI: 10.2174/0118715273289222231219094225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 12/04/2023] [Accepted: 12/12/2023] [Indexed: 01/28/2024]
Abstract
Traumatic brain injury (TBI) is a major global health issue that affects millions of people every year. It is caused by any form of external force, resulting in temporary or permanent impairments in the brain. The pathophysiological process following TBI usually involves excitotoxicity, mitochondrial dysfunction, oxidative stress, inflammation, ischemia, and apoptotic cell death. It is challenging to find treatment for TBI due to its heterogeneous nature, and no therapeutic interventions have been approved thus far. Neurotrophins may represent an alternative approach for TBI treatment because they influence various functional activities in the brain. The present review highlights recent studies on neurotrophins shown to possess neuroprotective roles in TBI. Neurotrophins, specifically brain-derived neurotrophic factor (BDNF) and nerve growth factor (NGF) have demonstrated reduced neuronal death, alleviated neuroinflammatory responses and improved neurological functions following TBI via their immunomodulatory, anti-inflammatory and antioxidant properties. Further studies are required to ensure the efficacy and safety of neurotrophins to be used as TBI treatment in clinical settings.
Collapse
Affiliation(s)
- Rei Shian Yap
- Department of Anatomy, Faculty of Medicine, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Jaya Kumar
- Department of Physiology, Faculty of Medicine, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Seong Lin Teoh
- Department of Anatomy, Faculty of Medicine, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| |
Collapse
|
10
|
Sun Z, Chung D, Neelon B, Millar-Wilson A, Ethier SP, Xiao F, Zheng Y, Wallace K, Hardiman G. A Bayesian framework for pathway-guided identification of cancer subgroups by integrating multiple types of genomic data. Stat Med 2023; 42:5266-5284. [PMID: 37715500 DOI: 10.1002/sim.9911] [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: 03/19/2021] [Revised: 07/15/2023] [Accepted: 09/05/2023] [Indexed: 09/17/2023]
Abstract
In recent years, comprehensive cancer genomics platforms, such as The Cancer Genome Atlas (TCGA), provide access to an enormous amount of high throughput genomic datasets for each patient, including gene expression, DNA copy number alterations, DNA methylation, and somatic mutation. While the integration of these multi-omics datasets has the potential to provide novel insights that can lead to personalized medicine, most existing approaches only focus on gene-level analysis and lack the ability to facilitate biological findings at the pathway-level. In this article, we propose Bayes-InGRiD (Bayesian Integrative Genomics Robust iDentification of cancer subgroups), a novel pathway-guided Bayesian sparse latent factor model for the simultaneous identification of cancer patient subgroups (clustering) and key molecular features (variable selection) within a unified framework, based on the joint analysis of continuous, binary, and count data. By utilizing pathway (gene set) information, Bayes-InGRiD does not only enhance the accuracy and robustness of cancer patient subgroup and key molecular feature identification, but also promotes biological understanding and interpretation. Finally, to facilitate an efficient posterior sampling, an alternative Gibbs sampler for logistic and negative binomial models is proposed using Pólya-Gamma mixtures of normal to represent latent variables for binary and count data, which yields a conditionally Gaussian representation of the posterior. The R package "INGRID" implementing the proposed approach is currently available in our research group GitHub webpage (https://dongjunchung.github.io/INGRID/).
Collapse
Affiliation(s)
- Zequn Sun
- Department of Preventive Medicine, Northwestern University, Chicago, Illinois
| | - Dongjun Chung
- Department of Biomedical Informatics, The Ohio State University, Columbus, Ohio
- The Pelotonia Institute for Immuno-Oncology, The Ohio State University Comprehensive Cancer Center, Columbus, Ohio
| | - Brian Neelon
- Department of Public Health Sciences, Medical University of South Carolina, Charleston, South Carolina
| | | | - Stephen P Ethier
- Department of Pathology and Laboratory Medicine, Medical University of South Carolina, Charleston, South Carolina
| | - Feifei Xiao
- Department of Biostatistics, University of Florida, Gainesville, Florida
| | - Yinan Zheng
- Department of Preventive Medicine, Northwestern University, Chicago, Illinois
| | - Kristin Wallace
- Department of Public Health Sciences, Medical University of South Carolina, Charleston, South Carolina
| | - Gary Hardiman
- Department of Public Health Sciences, Medical University of South Carolina, Charleston, South Carolina
- Faculty of Medicine, Health and Life Sciences, School of Biological Sciences and Institute for Global Food Security, Queen's University Belfast, Belfast, UK
| |
Collapse
|
11
|
Salah A, Sleem R, Abd-Elaziz A, Khalil H. Regulation of NF-κB Expression by Thymoquinone; A Role in Regulating Pro-Inflammatory Cytokines and Programmed Cell Death in Hepatic Cancer Cells. Asian Pac J Cancer Prev 2023; 24:3739-3748. [PMID: 38019231 PMCID: PMC10772774 DOI: 10.31557/apjcp.2023.24.11.3739] [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: 05/03/2023] [Accepted: 11/10/2023] [Indexed: 11/30/2023] Open
Abstract
BACKGROUND The miracle herb Nigella sativa (N. sativa) is a member of the Ranunculaceae family that possesses many properties, such as antioxidant, anticancer, analgesic, antibacterial, and anti-inflammatory. Thymoquinone (TQ) is the primary ingredient that makes up N. sativa, which is responsible for its many properties. So, our research focused on the biological role of TQ and its anticancer activities. METHODS A wide range of TQ concentrations (50µg/µl, 25µg/ µl, and 12.5µg µl) was prepared and evaluated for their potential regulatory role in cell lines of hepatocellular carcinoma (HepG2 cell line) compared with normal hepatocytes cells, untreated and DMSO-treated cells. RESULTS The more significant level of LDH obtained after TQ treatment compared to untreated cells provides evidence of the cytotoxic effects of TQ on HepG2 cells. Notably, the normal hepatocyte cells subjected to the same concentrations of TQ showed neglected influence in cell viability rate, indicating the selective regulatory role of TQ in cancer cell proliferation. Interestingly, as a critical mediator of malignancy transformation, the nuclear factor-kappa B expression level (NF-κB) significantly decreased in a time and dose-dependent manner of TQ treatment. Furthermore, we investigated whether TQ regulates the expression of deleted liver cancer 1 (DLC1) and Caspase 3 (Casp3). Notably, the treatment with TQ showed increased expression levels of DLC1 and Casp3 upon treatment. TQ extract sufficiently mediated the secretion of the released pro-inflammatory cytokines from treated cells. This regulation of released cytokines by TQ may affect the activation of NF-κB in treated cells. CONCLUSION These results indicate that TQ mediates the activation of Casp3, DLC1, and NF-κB, providing a new function of TQ in treating hepatocellular carcinoma (HCC).
Collapse
|
12
|
Kim MJ, Kulkarni V, Goode MA, Sivesind TE. Exploring the interactions of antihistamine with retinoic acid receptor beta (RARB) by molecular dynamics simulations and genome-wide meta-analysis. J Mol Graph Model 2023; 124:108539. [PMID: 37331258 PMCID: PMC10529808 DOI: 10.1016/j.jmgm.2023.108539] [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: 02/23/2023] [Revised: 06/03/2023] [Accepted: 06/05/2023] [Indexed: 06/20/2023]
Abstract
Kaposi sarcoma (KS) is one of the most common AIDS-related malignant neoplasms, which can leave lesions on the skin among HIV patients. These lesions can be treated with 9-cis-retinoic acid (9-cis-RA), an endogenous ligand of retinoic acid receptors that has been FDA-approved for treatment of KS. However, topical application of 9-cis-RA can induce several unpleasant side effects, like headache, hyperlipidemia, and nausea. Hence, alternative therapeutics with less side effects are desirable. There are case reports associating over-the-counter antihistamine usage with regression of KS. Antihistamines competitively bind to H1 receptor and block the action of histamine, best known for being released in response to allergens. Furthermore, there are already dozens of antihistamines that are FDA-approved with less side effects than 9-cis-RA. This led our team to conduct a series of in-silico assays to determine whether antihistamines can activate retinoic acid receptors. First, we utilized high-throughput virtual screening and molecular dynamics simulations to model high-affinity interactions between antihistamines and retinoic acid receptor beta (RARβ). We then performed systems genetics analysis to identify a genetic association between H1 receptor itself and molecular pathways involved in KS. Together, these findings advocate for exploration of antihistamines against KS, starting with our two promising hit compounds, bepotastine and hydroxyzine, for experimental validation study in the future.
Collapse
Affiliation(s)
- Minjae J Kim
- University of Tennessee Health Sciences Center School of Medicine, Memphis, TN, USA.
| | | | - Micah A Goode
- University of Tennessee Health Sciences Center School of Medicine, Memphis, TN, USA.
| | - Torunn E Sivesind
- Department of Dermatology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.
| |
Collapse
|
13
|
Tang Q, Liu M, Zhao H, Chen L. Glycogen-binding protein STBD1: Molecule and role in pathophysiology. J Cell Physiol 2023; 238:2010-2025. [PMID: 37435888 DOI: 10.1002/jcp.31078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 06/19/2023] [Accepted: 06/23/2023] [Indexed: 07/13/2023]
Abstract
Starch-binding domain-containing protein 1 (STBD1) is a glycogen-binding protein discovered in skeletal muscle gene differential expression that is pivotal to cellular energy metabolism. Recent studies have indicated that STBD1 is involved in many physiological processes, such as glycophagy, glycogen accumulation, and lipid droplet formation. Moreover, dysregulation of STBD1 causes multiple diseases, including cardiovascular disease, metabolic disease, and even cancer. Deletions and/or mutations in STBD1 promote tumorigenesis. Therefore, STBD1 has garnered considerable interest in the pathology community. In this review, we first summarized the current understanding of STBD1, including its structure, subcellular localization, tissue distribution, and biological functions. Next, we examined the roles and molecular mechanisms of STBD1 in related diseases. Based on available research, we discussed the novel function and future of STBD1, including its potential application as a therapeutic target in glycogen-related diseases. Given the significance of STBD1 in energy metabolism, an in-depth understanding of the protein is crucial for understanding physiological processes and developing therapeutic strategies for related diseases.
Collapse
Affiliation(s)
- Qiannan Tang
- Hunan Provincial Key Laboratory of Tumor Microenvironment Responsive Drug Research, Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, Institute of Pharmacy and Pharmacology, Hengyang Medical School, University of South China, Hengyang, China
| | - Meiqing Liu
- Key Laboratory of Cardiovascular Diseases of Yunnan Province, Key Laboratory of Tumor Immunological Prevention and Treatment of Yunnan Province, Central Laboratory of Yan'an Hospital Affiliated to Kunming Medical University, Kunming, China
| | - Hong Zhao
- Nursing College, Hengyang Medical School, University of South China, Hengyang, Hunan, China
| | - Linxi Chen
- Hunan Provincial Key Laboratory of Tumor Microenvironment Responsive Drug Research, Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, Institute of Pharmacy and Pharmacology, Hengyang Medical School, University of South China, Hengyang, China
| |
Collapse
|
14
|
Zmarzły N, Januszyk S, Mieszczański P, Czarniecka J, Bednarska-Czerwińska A, Boroń D, Oplawski M, Grabarek BO. The influence of selected microRNAs on the expression profile of genes and proteins related to the tumor necrosis factor-alpha signaling pathways in endometrioid endometrial cancer. J Cancer Res Clin Oncol 2023; 149:9679-9689. [PMID: 37233761 PMCID: PMC10423110 DOI: 10.1007/s00432-023-04863-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 05/16/2023] [Indexed: 05/27/2023]
Abstract
PURPOSE Tumor necrosis factor exerts many adverse biological effects, from cell proliferation to cell death. Accurate diagnosis and treatment are therefore difficult due to many factors influencing tumor necrosis factor-alpha (TNF-α) signaling, including microRNAs (miRNAs), especially in tumors. The aim of the study was to determine the influence of miRNAs on the expression profile of genes and proteins related to TNF-α signaling in endometrial cancer. METHODS The material consisted of 45 endometrioid endometrial cancer and 45 normal endometrium tissue samples. Gene expression was determined with microarrays and then validated for TNF-α, tumor necrosis factor receptor 1 (TNFR1) and 2 (TNFR2), caveolin 1 (CAV1), nuclear factor kappa B subunit 1 (NFKB1), and TGF-beta activated kinase 1 (MAP3K7)-binding protein 2 (TAB2) using real-time quantitative reverse transcription reaction (RT-qPCR). The protein concentration was assessed by enzyme-linked immunosorbent assay (ELISA). In addition, differentiating miRNAs were identified using miRNA microarrays and their relationships with TNF-α signaling genes were evaluated using the mirDIP tool. RESULTS TNF-α, TNFR1, TNFR2, CAV1, NFKB1, and TAB2 were upregulated both on the mRNA and protein levels. The decrease in the activity of miR-1207-5p, miR-1910-3p, and miR-940 may be related to CAV1 overexpression. Similarly for miR-572 and NFKB1 as well as miR-939-5p and TNF-α. In turn, miR-3178 may partially inhibit TNFR1 activity up to grade 2 cancer. CONCLUSION TNF-α signaling, especially the TNF-α/NF-κB axis, is disrupted in endometrial cancer and worsens with disease progression. The observed changes may be the result of miRNAs' activity in the initial stage of endometrial cancer and its gradual loss in later grades.
Collapse
Affiliation(s)
- Nikola Zmarzły
- Department of Histology, Cytophysiology and Embryology, Faculty of Medicine in Zabrze, Academy of Silesia in Katowice, 41-800, Zabrze, Poland.
- Department of Gynecology and Obstetrics, Faculty of Medicine in Zabrze, Academy of Silesia in Katowice, 41-800, Zabrze, Poland.
| | | | - Paweł Mieszczański
- Hospital of Ministry of Interior and Administration, 40-052, Katowice, Poland
| | - Justyna Czarniecka
- Department of Histology, Cytophysiology and Embryology, Faculty of Medicine in Zabrze, Academy of Silesia in Katowice, 41-800, Zabrze, Poland
| | - Anna Bednarska-Czerwińska
- Department of Histology, Cytophysiology and Embryology, Faculty of Medicine in Zabrze, Academy of Silesia in Katowice, 41-800, Zabrze, Poland
- Gyncentrum, Laboratory of Molecular Biology and Virology, 40-851, Katowice, Poland
- American Medical Clinic, 40-600, Katowice, Poland
| | - Dariusz Boroń
- Department of Histology, Cytophysiology and Embryology, Faculty of Medicine in Zabrze, Academy of Silesia in Katowice, 41-800, Zabrze, Poland
- Department of Gynecology and Obstetrics, Faculty of Medicine in Zabrze, Academy of Silesia in Katowice, 41-800, Zabrze, Poland
- Department of Gynecology and Obstetrics with Gynecologic Oncology, Ludwik Rydygier Memorial Specialized Hospital, 31-826, Kraków, Poland
- Department of Gynecology and Obstetrics, TOMMED Specjalisci od Zdrowia, 40-662, Katowice, Poland
| | - Marcin Oplawski
- Department of Gynecology and Obstetrics with Gynecologic Oncology, Ludwik Rydygier Memorial Specialized Hospital, 31-826, Kraków, Poland
- Department of Gynecology and Obstetrics, Faculty of Medicine and Health Sciences, Andrzej Frycz Modrzewski University in Cracow, 30-705, Cracow, Poland
| | - Beniamin Oskar Grabarek
- Department of Histology, Cytophysiology and Embryology, Faculty of Medicine in Zabrze, Academy of Silesia in Katowice, 41-800, Zabrze, Poland
- Department of Gynecology and Obstetrics, Faculty of Medicine in Zabrze, Academy of Silesia in Katowice, 41-800, Zabrze, Poland
- Gyncentrum, Laboratory of Molecular Biology and Virology, 40-851, Katowice, Poland
- Department of Gynecology and Obstetrics with Gynecologic Oncology, Ludwik Rydygier Memorial Specialized Hospital, 31-826, Kraków, Poland
- Department of Gynecology and Obstetrics, TOMMED Specjalisci od Zdrowia, 40-662, Katowice, Poland
| |
Collapse
|
15
|
Ren Y, Kaweesa EN, Tian L, Wu S, Sydara K, Xayvue M, Moore CE, Soejarto DD, Cheng X, Yu J, Burdette JE, Kinghorn AD. The Cytotoxic Cardiac Glycoside (-)-Cryptanoside A from the Stems of Cryptolepis dubia and Its Molecular Targets. JOURNAL OF NATURAL PRODUCTS 2023; 86:1411-1419. [PMID: 37216676 PMCID: PMC10331789 DOI: 10.1021/acs.jnatprod.3c00094] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
A cardiac glycoside epoxide, (-)-cryptanoside A (1), was isolated from the stems of Cryptolepis dubia collected in Laos, for which the complete structure was confirmed by analysis of its spectroscopic and single-crystal X-ray diffraction data, using copper radiation at a low temperature. This cardiac glycoside epoxide exhibited potent cytotoxicity against several human cancer cell lines tested, including HT-29 colon, MDA-MB-231 breast, OVCAR3 and OVCAR5 ovarian cancer, and MDA-MB-435 melanoma cells, with the IC50 values found to be in the range 0.1-0.5 μM, which is comparable with that observed for digoxin. However, it exhibited less potent activity (IC50 1.1 μM) against FT194 benign/nonmalignant human fallopian tube secretory epithelial cells when compared with digoxin (IC50 0.16 μM), indicating its more selective activity toward human cancer versus benign/nonmalignant cells. (-)-Cryptanoside A (1) also inhibited Na+/K+-ATPase activity and increased the expression of Akt and the p65 subunit of NF-κB but did not show any effects on the expression of PI3K. A molecular docking profile showed that (-)-cryptanoside A (1) binds to Na+/K+-ATPase, and thus 1 may directly target Na+/K+-ATPase to mediate its cancer cell cytotoxicity.
Collapse
Affiliation(s)
- Yulin Ren
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, OH 43210, United States
| | - Elizabeth N. Kaweesa
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60612, United States
| | - Lei Tian
- City of Hope National Medical Center, Duarte, CA 91010, United States
| | - Sijin Wu
- Shenzhen Jingtai Technology Co., Shenzhen 518000, Guangdong Province, People’s Republic of China
| | - Kongmany Sydara
- Institute of Traditional Medicine, Ministry of Health, Vientiane, Lao People’s Democratic Republic
| | - Mouachanh Xayvue
- Institute of Traditional Medicine, Ministry of Health, Vientiane, Lao People’s Democratic Republic
| | - Curtis E. Moore
- X-ray Crystallography Facility, Department of Chemistry and Biochemistry, College of Arts and Sciences, The Ohio State University, Columbus, OH 43210, United States
| | - Djaja D. Soejarto
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60612, United States
- Science and Education, Field Museum of Natural History, Chicago, IL 60605, United States
| | - Xiaolin Cheng
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, OH 43210, United States
| | - Jianhua Yu
- City of Hope National Medical Center, Duarte, CA 91010, United States
| | - Joanna E. Burdette
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60612, United States
| | - A. Douglas Kinghorn
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, OH 43210, United States
| |
Collapse
|
16
|
Fan AT, Boyle BT, Ferguson FM. A new avenue for molecular glues: Rapid discovery of a NFKB1 degrader. Cell Chem Biol 2023; 30:340-342. [PMID: 37084716 DOI: 10.1016/j.chembiol.2023.04.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/23/2023]
Abstract
Targeted protein degradation using molecular glues is a powerful method for targeting traditionally undruggable proteins. One challenge in molecular glue discovery is the absence of rational discovery methods. Here, King et al. leverage covalent library screening with chemoproteomics platforms to rapidly discover a molecular glue targeting NFKB1 via UBE2D recruitment.
Collapse
Affiliation(s)
- Angela T Fan
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, USA
| | - Bridget T Boyle
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, USA
| | - Fleur M Ferguson
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, USA; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| |
Collapse
|
17
|
Bogaert DJ, Kuehn HS, Bordon V, Haerynck F. Editorial: The role of transcription factors in inborn errors of immunity. Front Immunol 2023; 14:1189312. [PMID: 37051249 PMCID: PMC10083482 DOI: 10.3389/fimmu.2023.1189312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2023] [Accepted: 03/21/2023] [Indexed: 03/29/2023] Open
Affiliation(s)
- Delfien J. Bogaert
- Department of Pediatrics, Division of Pediatric Hemato-Oncology and Stem Cell Transplantation, Ghent University Hospital, Ghent, Belgium
- Department of Internal Medicine and Pediatrics, Primary Immunodeficiency (PID) Research Laboratory, Center for Primary Immunodeficiency Ghent, Jeffrey Modell Diagnosis and Research Center, Ghent University, Ghent, Belgium
| | - Hye Sun Kuehn
- Immunology Service, Department of Laboratory Medicine, National Institutes of Health, Clinical Center, Bethesda, MD, United States
| | - Victoria Bordon
- Department of Pediatrics, Division of Pediatric Hemato-Oncology and Stem Cell Transplantation, Ghent University Hospital, Ghent, Belgium
| | - Filomeen Haerynck
- Department of Internal Medicine and Pediatrics, Primary Immunodeficiency (PID) Research Laboratory, Center for Primary Immunodeficiency Ghent, Jeffrey Modell Diagnosis and Research Center, Ghent University, Ghent, Belgium
- Department of Pediatrics, Division of Pediatric Pulmonology, Immunology and Infectious Diseases, Ghent University Hospital, Ghent, Belgium
- *Correspondence: Filomeen Haerynck,
| |
Collapse
|
18
|
Wang L, Gong S, Zhang X, Azhar Z, Chen J. Investigation of the regulatory effects of synthesized antisense oligonucleotides on androgen receptor (AR) exon 3 splicing in prostate cancer cells. Gene 2023; 866:147330. [PMID: 36871670 DOI: 10.1016/j.gene.2023.147330] [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: 11/30/2022] [Revised: 02/10/2023] [Accepted: 02/28/2023] [Indexed: 03/07/2023]
Abstract
The Androgen Receptor (AR) gene plays a key role in castration-resistant prostate cancer (CRPC). Controlling the progression of CRPC by inhibiting AR gene expression is one of the core directions for prostate cancer (Pca) drug development. A 23-amino acids retention, named exon 3a, into the DNA binding domain of the splice variant AR23 has been shown to prevent AR from entering the nucleus and restore the sensitivity of cancer cells to related therapies. In this study, we conducted a preliminary investigation of the splicing modulation of the AR gene in order to develop a splice-switching therapy for Pca by promoting exon 3a inclusion. Using mutagenesis-coupled RT-PCR with AR minigene and over-expression of certain splicing factors, we found that serine/arginine-rich (SR) proteins are key factors facilitating the recognition of the 3' splice site of exon 3a (L-3' SS), while the deletion or blocking of the polypyrimidine tract (PPT) region of the original 3' splice site of exon 3 (S-3' SS) could strongly enhance exon 3a splicing without affecting the function of any SR protein. Furthermore, we designed a series of antisense oligonucleotides (ASOs) to screen drug candidates, and ASOs targeting S-3' SS and its PPT region or the exonic region of exon 3 turned out to be most effective in rescuing exon 3a splicing. A dose-response test indicated ASO12 as the lead candidate drug significantly promoting the inclusion of exon 3a to more than 85%. MTT assay confirmed that the cell proliferation was significantly inhibited after ASO treatment. Our results provide the first glance to AR splicing regulation. With several promising therapeutic ASO candidates obtained here, further development of ASO drugs to treat CRPC is strongly encouraged.
Collapse
Affiliation(s)
- Li Wang
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, China.
| | - Shuaishuai Gong
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, China
| | - Xi Zhang
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, China
| | - Zeb Azhar
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, China
| | - Jialin Chen
- Institute of Neuroscience, Soochow University, Suzhou, Jiangsu, China.
| |
Collapse
|
19
|
Pereira EEB, Modesto AAC, Fernandes BM, Burbano RMR, Assumpção PP, Fernandes MR, Guerreiro JF, dos Santos SEB, dos Santos NPC. Association between Polymorphism of Genes IL-1A, NFKB1, PAR1, TP53, and UCP2 and Susceptibility to Non-Small Cell Lung Cancer in the Brazilian Amazon. Genes (Basel) 2023; 14:461. [PMID: 36833388 PMCID: PMC9957054 DOI: 10.3390/genes14020461] [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: 09/12/2022] [Revised: 12/23/2022] [Accepted: 12/27/2022] [Indexed: 02/15/2023] Open
Abstract
Non-small cell lung cancer (NSCLC) accounts for the vast majority of cases of lung neoplasms. It is formed in multiple stages, with interactions between environmental risk factors and individual genetic susceptibility and with genes involved in the immune and inflammatory response paths, cell or genome stability, and metabolism, among others. Our objective was to evaluate the association between five genetic variants (IL-1A, NFKB1, PAR1, TP53, and UCP2) and the development of NSCLC in the Brazilian Amazon. The study included 263 individuals with and without lung cancer. The samples were analyzed for the genetic variants of NFKB1 (rs28362491), PAR1 (rs11267092), TP53 (rs17878362), IL-1A (rs3783553), and UCP2 (INDEL 45-bp), which were genotyped in PCR, followed by an analysis of the fragments, in which we applied a previously developed set of informative ancestral markers. We used a logistic regression model to identify differences in the allele and the genotypic frequencies among individuals and their association with NSCLC. The variables of gender, age, and smoking were controlled in the multivariate analysis to prevent confusion by association. The individuals that were homozygous for the Del/Del of polymorphism NFKB1 (rs28362491) (p = 0.018; OR = 0.332) demonstrate a significant association with NSCLC, which was similar to that observed in the variants of PAR1 (rs11267092) (p = 0.023; OR = 0.471) and TP53 (rs17878362) (p = 0.041; OR = 0.510). Moreover, the individuals with the Ins/Ins genotype of polymorphism IL-1A (rs3783553) demonstrated greater risk for NSCLC (p = 0.033; OR = 2.002), as did the volunteers with the Del/Del of UCP2 (INDEL 45-bp) (p = 0.031; OR = 2.031). The five polymorphisms investigated can contribute towards NSCLC susceptibility in the population of the Brazilian Amazon.
Collapse
Affiliation(s)
- Esdras E. B. Pereira
- Laboratory of Human and Medical Genetics, Institute of Biological Science, Federal University of Pará, Belem 66077-830, PA, Brazil
- Oncology Research Center, Federal University of Pará, Belem 66073-005, PA, Brazil
- Instituto Tocantinense Presidente Antônio Carlos (ITPAC), Abaetetuba 68440-000, PA, Brazil
| | - Antônio A. C. Modesto
- Laboratory of Human and Medical Genetics, Institute of Biological Science, Federal University of Pará, Belem 66077-830, PA, Brazil
- Oncology Research Center, Federal University of Pará, Belem 66073-005, PA, Brazil
| | - Bruno M. Fernandes
- Oncology Research Center, Federal University of Pará, Belem 66073-005, PA, Brazil
| | - Rommel M. R. Burbano
- Laboratory of Human and Medical Genetics, Institute of Biological Science, Federal University of Pará, Belem 66077-830, PA, Brazil
- Oncology Research Center, Federal University of Pará, Belem 66073-005, PA, Brazil
| | - Paulo P. Assumpção
- Oncology Research Center, Federal University of Pará, Belem 66073-005, PA, Brazil
| | | | - João F. Guerreiro
- Laboratory of Human and Medical Genetics, Institute of Biological Science, Federal University of Pará, Belem 66077-830, PA, Brazil
| | - Sidney E. B. dos Santos
- Laboratory of Human and Medical Genetics, Institute of Biological Science, Federal University of Pará, Belem 66077-830, PA, Brazil
- Oncology Research Center, Federal University of Pará, Belem 66073-005, PA, Brazil
| | - Ney P. C. dos Santos
- Laboratory of Human and Medical Genetics, Institute of Biological Science, Federal University of Pará, Belem 66077-830, PA, Brazil
- Oncology Research Center, Federal University of Pará, Belem 66073-005, PA, Brazil
| |
Collapse
|
20
|
Jain P, Sudandiradoss C. Andrographolide-based potential anti-inflammatory transcription inhibitors against nuclear factor NF-kappa-B p50 subunit (NF-κB p50): an integrated molecular and quantum mechanical approach. 3 Biotech 2023; 13:15. [PMID: 36540414 PMCID: PMC9759609 DOI: 10.1007/s13205-022-03431-9] [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: 07/22/2022] [Accepted: 12/07/2022] [Indexed: 12/23/2022] Open
Abstract
The unregulated activation of nuclear factor-κB (NF-κB) is a critical event in the progression of various inflammatory diseases such as ulcerative colitis, asthma, rheumatoid arthritis, bacterial induced gastritis, etc. Hence, blocking the transcriptional activity of NF-κB is a promising strategy towards the development of an anti-inflammatory agent. In this study, an integrated molecular and quantum mechanical approach was carried out to find a new potent andrographolide (AGP)-based analog that can inhibit DNA binding to NF-κB p50 and manifest anti-inflammatory activity. Our approach includes multiple sequence alignment, virtual screening, molecular docking (protein-ligand and protein-DNA), in silico site-directed mutagenesis, ADMET prediction, DFT (HOMO, LUMO, HLG, and EPM energy) analysis, MD simulation, and MM/GBSA rescoring. The virtual screening analysis of 237 AGP analogs yielded the five lead compounds based on the binding affinity. Further, molecular interactive docking and ADMET prediction of hit analogs revealed that Ana2 ((3Z,4S)-3-[2-[(4aR,6aS,7R,10aS,10bR)-3,3,6a,10b-tetramethyl-8-methylidene-1,4a,5,6,7,9,10,10a-octahydronaphtho[2,1-d][1,3]dioxin-7-yl]ethylidene]-4-hydroxyoxolan-2-one) is the most potent moiety as it displays the strongest binding affinity and better molecular/pharmacokinetic features. Moreover, DFT, MD simulation, and MM/GBSA studies corroborated the docking results and demonstrated better chemical and dynamic stability with the least binding free energy (- 29.99 kcal/mol) for the Ana2. Site-directed mutagenesis investigation (Cys62Ala) establishes the importance of the Cys62 amino acid residue towards the binding interaction and stability of Ana2 with NF-κB p50. Overall, the identified NF-κB p50 inhibitor opens up a new research horizon towards the development of plant-based anti-inflammatory drugs to combat progressive inflammatory diseases. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-022-03431-9.
Collapse
Affiliation(s)
- Priyanka Jain
- School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu 632014 India
| | - C Sudandiradoss
- School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu 632014 India
| |
Collapse
|
21
|
Mao Y, Zhou Q, Wang J, Zhao R, Yang X, Shi Y, Yin J, Jiang C, He Y. CircP50 functions through the phosphorylation- and acetylation-activated p53 pathway to mediate inorganic arsenic-induced apoptosis in A549 cells. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:91232-91240. [PMID: 35881289 DOI: 10.1007/s11356-022-22094-w] [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: 04/14/2022] [Accepted: 07/14/2022] [Indexed: 06/15/2023]
Abstract
As a class I carcinogen, arsenic has been reported to cause diseases accompanied by circRNAs regulating proliferation and apoptosis at the molecular level, but whether circP50 (circBase ID: hsa_circ_0008012) does the same has not been demonstrated. The aim of this study is to provide the basis for anti-lung cancer mechanism research, by studying the expression of circP50 under arsenic-induced conditions, and the effect and mechanism on the proliferation and apoptosis of A549 cells based on the circP50 knockdown models. To explore whether the circP50 is responsive to arsenic exposure, the qRT-PCR was applied to discover that the relative expression of circP50 in A549 cells increased only with increasing NaAsO2 dose and independent of its metabolites. We further determined the mechanism of circP50 by establishing circP50 knockdown models. The results of cell viability and EdU assays indicated the proliferation of A549 cells. According to the western blotting, phosphorylation of p53 at Ser15, Ser376, and Ser392 and acetylation of p53 at Lys370 and Lys382 were inhibited, resulting in the deficiency of p53 expression. Subsequently, the expression of genes downstream of p53 was reduced, including p21, PUMA, Caspase3, and Bcl-xS. Furthermore, the expressions of IKB-α, p65, and p50 decreased, but C-myc expression did not change significantly, referring to the NF-κB pathway was not dominant. The results suggest that circP50 mainly functions through the p53 pathway to mediate apoptosis in response to arsenic exposure.
Collapse
Affiliation(s)
- Yizhu Mao
- School of Public Health, Kunming Medical University, No.1168 Chunrongxi Road Chenggong District, Kunming, Yunnan Province, China
| | - Qian Zhou
- School of Public Health, Kunming Medical University, No.1168 Chunrongxi Road Chenggong District, Kunming, Yunnan Province, China
| | - Jinhua Wang
- Bijie Weining Autonomous County Maternal and Child Health Hospital, No.166 Mingzhu Avenue, Haibin Street, Weining Autonomous County, Bijie, Guizhou Province, China
| | - Ruihuan Zhao
- School of Public Health, Kunming Medical University, No.1168 Chunrongxi Road Chenggong District, Kunming, Yunnan Province, China
| | - Xuefei Yang
- School of Public Health, Kunming Medical University, No.1168 Chunrongxi Road Chenggong District, Kunming, Yunnan Province, China
| | - Ya Shi
- School of Public Health, Kunming Medical University, No.1168 Chunrongxi Road Chenggong District, Kunming, Yunnan Province, China
| | - Jinyao Yin
- School of Public Health, Kunming Medical University, No.1168 Chunrongxi Road Chenggong District, Kunming, Yunnan Province, China
| | - Chenglan Jiang
- School of Public Health, Kunming Medical University, No.1168 Chunrongxi Road Chenggong District, Kunming, Yunnan Province, China
| | - Yuefeng He
- School of Public Health, Kunming Medical University, No.1168 Chunrongxi Road Chenggong District, Kunming, Yunnan Province, China.
| |
Collapse
|
22
|
Nagao T, Yoshifuji K, Sadato D, Motomura Y, Saito M, Yamamoto K, Yamamoto K, Nogami A. Establishment and characterization of a new activated B-cell-like DLBCL cell line, TMD12. Exp Hematol 2022; 116:37-49. [PMID: 36191884 DOI: 10.1016/j.exphem.2022.09.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Revised: 09/25/2022] [Accepted: 09/26/2022] [Indexed: 12/29/2022]
Abstract
We report the establishment of a novel activated B-cell-like (ABC) diffuse large B-cell lymphoma (DLBCL) cell line, designated as TMD12, from a patient with highly refractory DLBCL. ABC-DLBCL is a subtype with a relatively unfavorable prognosis that was originally categorized using gene expression profiling according to its cell of origin. TMD12 cells were isolated from the pleural effusion of the patient at relapse and passaged continuously in vitro for >4 years. The cells displayed cluster of differentiation (CD)19, CD20, CD22, CD38, human leukocyte antigen-DR isotype, and κ positivity and CD5, CD10, CD23, and λ negativity, as detected using flow cytometric analysis. The chromosomal karyotypic analysis, including the spectral karyotyping method, confirmed t(1;19)(q21:q13.1), del(6q23), gain of chromosome 18, and other abnormalities. Mutation analyses, including whole-exome sequencing, revealed that TMD12 cells harbored mutations in MYD88 and CD79B, indicating an ABC subtype. TMD12 cells exhibited chronic active B-cell receptor signaling and constitutive activation of the nuclear factor κB pathway, which is typically associated with sensitivity to a specific Bruton tyrosine kinase inhibitor, ibrutinib. Intriguingly, TMD12 cells displayed moderate resistance to ibrutinib and lacked activation of Janus kinase/signal transducers and activators of transcription 3 signaling, another hallmark of this DLBCL subtype. Treatment with an inhibitor against tumor progression locus 2 (TPL2), a multifunctional intracellular kinase that is activated particularly downstream of Toll-like receptors or MYD88 and IκB kinase α/β (IKKα/β), suppressed the proliferation of TMD12 cells, implying the possible involvement of the TPL2-p105 pathway in the tumorigenesis of ABC-DLBCL. Because only a limited number of ABC-DLBCL cell lines are currently available, TMD12 cells might provide a useful tool in the search for novel druggable targets for this intractable lymphoma.
Collapse
Affiliation(s)
- Toshikage Nagao
- Department of Hematology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan.
| | - Kota Yoshifuji
- Department of Hematology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Daichi Sadato
- Clinical Research Support Center, Tokyo Metropolitan Center and Infection Disease Center, Komagome Hospital, Tokyo, Japan
| | - Yotaro Motomura
- Department of Hematology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Makiko Saito
- Department of Hematology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Kurara Yamamoto
- Department of Pathology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University Hospital, Tokyo, Japan
| | - Kouhei Yamamoto
- Department of Pathology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University Hospital, Tokyo, Japan
| | - Ayako Nogami
- Department of Hematology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan; Department of Laboratory Medicine, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| |
Collapse
|
23
|
Perry I, Hernadi SB, Cunha L, Short S, Marchbank A, Spurgeon DJ, Orozco-terWengel P, Kille P. Molecular insights into high-altitude adaption and acclimatisation of Aporrectodea caliginosa. Life Sci Alliance 2022; 5:5/11/e202201513. [PMID: 35977843 PMCID: PMC9386962 DOI: 10.26508/lsa.202201513] [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: 05/03/2022] [Revised: 07/28/2022] [Accepted: 07/29/2022] [Indexed: 12/02/2022] Open
Abstract
A megabase genome assembly for Aporrectodea caliginosa is presented with transcriptomic and SNP-based evidence for acclimatisation and adaption to extreme weather conditions found at high altitude. Here, we explore the high-altitude adaptions and acclimatisation of Aporrectodea caliginosa. Population diversity is assessed through mitochondrial barcoding, identifying closely related populations across the island of Pico (Azores). We present the first megabase N50 assembly size (1.2 Mbp) genome for A. caliginosa. High- and low-altitude populations were exposed experimentally to a range of oxygen and temperature conditions, simulating altitudinal conditions, and the transcriptomic responses explored. SNP densities are assessed to identify signatures of selective pressure and their link to differentially expressed genes. The high-altitude A. caliginosa population had lower differential expression and fewer co-expressed genes between conditions, indicating a more condition-refined epigenetic response. Genes identified as under adaptive pressure through Fst and nucleotide diversity in the high-altitude population clustered around the differentially expressed an upstream environmental response control gene, HMGB1. The high-altitude population of A. caliginosa indicated adaption and acclimatisation to high-altitude conditions and suggested resilience to extreme weather events. This mechanistic understanding could help offer a strategy in further identifying other species capable of maintaining soil fertility in extreme environments.
Collapse
Affiliation(s)
- Iain Perry
- Organisms and Environment, Cardiff University, Wales, UK .,Wales Gene Park, Cardiff University, Wales, UK
| | | | - Luis Cunha
- Department of Life Sciences, Centre for Functional Ecology, University of Coimbra, Coimbra, Portugal.,School of Applied Sciences, University of South Wales, Wales, UK
| | - Stephen Short
- Organisms and Environment, Cardiff University, Wales, UK.,UK Centre for Ecology and Hydrology, Maclean Building, Wallingford, UK
| | | | - David J Spurgeon
- UK Centre for Ecology and Hydrology, Maclean Building, Wallingford, UK
| | | | - Peter Kille
- Organisms and Environment, Cardiff University, Wales, UK
| |
Collapse
|
24
|
Li X, Liang W, Yu C, Meng Q, Zhang W, Wu X, Xue J, Deng S, Wang H. Potential therapeutic strategies for quercetin targeting critical pathological mechanisms associated with colon adenocarcinoma and COVID-19. Front Pharmacol 2022; 13:988153. [PMID: 36249762 PMCID: PMC9557079 DOI: 10.3389/fphar.2022.988153] [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: 07/07/2022] [Accepted: 08/30/2022] [Indexed: 11/13/2022] Open
Abstract
Patients with colon adenocarcinoma (COAD) are at a higher probability of infection with COVID-19 than healthy individuals. However, there is no globally accepted treatment protocol for patients with COAD/COVID-19. Quercetin has been found to have significant antitumor, antiviral and anti-inflammatory effects in several studies. Therefore, this study sought to evaluate the potential of quercetin as the agent for COAD/COVID-19 and to explore its mechanisms. We used bioinformatics algorithms to obtain COAD/COVID-19-related genes (CCRG) from COAD-related transcriptome data and COVID-related transcriptome sequencing data, and used these genes to construct a COAD prognostic model. We intersected the CCRG with the therapeutic target genes of quercetin and obtained a total of 105 genes (potential target genes of quercetin for the treatment of COAD/COVID-19). By constructing a protein-protein interaction (PPI) network, we ascertained FOS, NFKB1, NFKB1A, JUNB, and JUN as possible core target genes of quercetin for the treatment of COAD/COVID-19. Bioinformatic analysis of these 105 genes revealed that the mechanisms for quercetin the treatment of COAD/COVID-19 may be associated with oxidative stress, apoptosis, anti-inflammatory, immune, anti-viral and multiple pathways containing IL-17, TNF, HIF-1. In this study, we constructed a prognostic model of COAD/COVID19 patients by using CCRG and elucidated for the first time the potential target genes and molecular mechanisms of quercetin for the treatment of COAD/COVID-19, which may benefit the clinical treatment of COAD/COVID-19 patients. However, no clinical trials have yet been conducted to further validate the findings, but this will be the future direction of our research.
Collapse
Affiliation(s)
- Xiushen Li
- Department of Obstetrics and Gynecology, Shenzhen University General Hospital, Shenzhen, China
- Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, School of Biomedical Engineering, Shenzhen University Health Science Center, Shenzhen, China
- Shenzhen Key Laboratory, Shenzhen University General Hospital, Shenzhen, China
| | - Weizheng Liang
- Central Laboratory, The First Affiliated Hospital of Hebei North University, Zhangjiakou, China
| | - Chengwei Yu
- School of Future Technology, University of Chinese Academy of Sciences, Beijing, China
| | - Qingxue Meng
- Central Laboratory, The First Affiliated Hospital of Hebei North University, Zhangjiakou, China
| | - Weiwen Zhang
- Department of Obstetrics and Gynecology, Shenzhen University General Hospital, Shenzhen, China
| | - Xueliang Wu
- Department of General Surgery, The First Affiliated Hospital of Hebei North University, Zhangjiakou, China
| | - Jun Xue
- Central Laboratory, The First Affiliated Hospital of Hebei North University, Zhangjiakou, China
- Department of General Surgery, The First Affiliated Hospital of Hebei North University, Zhangjiakou, China
- *Correspondence: Jun Xue, ; Shoulong Deng, ; Hao Wang,
| | - Shoulong Deng
- National Health Commission of China (NHC) Key Laboratory of Human Disease Comparative Medicine, Institute of Laboratory Animal Sciences, Chinese Academy of Medical Sciences and Comparative Medicine Center, Peking Union Medical College, Beijing, China
- *Correspondence: Jun Xue, ; Shoulong Deng, ; Hao Wang,
| | - Hao Wang
- Department of Obstetrics and Gynecology, Shenzhen University General Hospital, Shenzhen, China
- Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, School of Biomedical Engineering, Shenzhen University Health Science Center, Shenzhen, China
- Shenzhen Key Laboratory, Shenzhen University General Hospital, Shenzhen, China
- *Correspondence: Jun Xue, ; Shoulong Deng, ; Hao Wang,
| |
Collapse
|
25
|
Nagel S, Pommerenke C, Quentmeier H, Meyer C, Kaufmann M, MacLeod RAF. Genomic Aberrations Generate Fusion Gene FOXK2::TP63 and Activate NFKB1 in Cutaneous T-Cell Lymphoma. Biomedicines 2022; 10:biomedicines10082038. [PMID: 36009586 PMCID: PMC9406051 DOI: 10.3390/biomedicines10082038] [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: 07/11/2022] [Revised: 08/16/2022] [Accepted: 08/19/2022] [Indexed: 11/21/2022] Open
Abstract
Cutaneous T-cell lymphoma (CTCL) is a severe lymphoid malignancy with a worse prognosis lacking curative treatment regimens. Several gene mutations and deregulated pathways, including NFkB signaling, have been implicated in its pathogenesis. Accordingly, CTCL cell line HUT-78 reportedly contains mutated NFKB2, which is constitutively activated via partial gene deletion, also demonstrating that genomic rearrangements cause driving mutations in this malignancy. Here, along with HUT-78, we analyzed CTCL cell line HH to identify additional aberrations underlying gene deregulation. Karyotyping and genomic profiling of HH showed several rearrangements worthy of detailed investigation. Corresponding to the established karyotype, RNA-seq data and PCR analysis confirmed the presence of t(3;17)(q28;q25), generating a novel fusion gene, FOXK2::TP63. Furthermore, chromosomal rearrangement t(1;4)(p32;q25) was connected to amplification at 4q24–26, affecting aberrant NFKB1 overexpression thereat. Transcription factor binding-site analysis and knockdown experiments demonstrated that IRF4 contributed to NFKB1 expression. Within the same amplicon, we identified amplification and overexpression of NFkB signaling activator CAMK2D (4q26) and p53-inhibitor UBE2D3 (4q24). Genomic profiling data for HUT-78 detailed a deletion at 10q25 underlying reported NFKB2 activation. Moreover, amplifications of ID1 (20q11) and IKZF2 (2q34) in this cell line drove overexpression of these NK cell differentiation factors and possibly thus formed corresponding lineage characteristics. Target gene analysis for NFKB1 via siRNA-mediated knockdown in HH revealed activation of TP63, MIR155, and NOTCH pathway component RBPJ. Finally, treatment of HH with NFkB inhibitor demonstrated a role for NFkB in supporting proliferation, while usage of inhibitor DAPT showed significant survival effects via the NOTCH pathway. Collectively, our data suggest that NFkB and/or NOTCH inhibitors may represent reasonable treatment options for subsets of CTCL patients.
Collapse
|
26
|
Yu Q, Xiu Z, Jian Y, Zhou J, Chen X, Chen X, Chen C, Chen H, Yang S, Yin L, Zeng W. microRNA-497 prevents pancreatic cancer stem cell gemcitabine resistance, migration, and invasion by directly targeting nuclear factor kappa B 1. Aging (Albany NY) 2022; 14:5908-5924. [PMID: 35896012 PMCID: PMC9365558 DOI: 10.18632/aging.204193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 05/23/2022] [Indexed: 11/25/2022]
Abstract
Objectives: Cancer stem cells (CSCs) comprise a small population of cells in cancerous tumors and play a critical role in tumor resistance to chemotherapy. miRNAs have been reported to enhance the sensitivity of pancreatic cancer to chemotherapy. However, the underlying molecular mechanism requires better understanding. Methods: Cell viability and proliferation were examined with CCK8 assays. Quantitative real-time polymerase chain reaction was executed to assess mRNA expression. StarBase database was used to select the target genes of miRNA, which were further affirmed by dual luciferase assay. Transwell assay was used to analyze cell invasion and migration. Results: We proved that miR-497 could be obviously downregulated in pancreatic cancer tissues and CSCs from Aspc-1 and Bxpc-3 cells. In addition, inhibition of miR-497 evidently accelerated pancreatic CSC gemcitabine resistance, migration and invasion. Moreover, we revealed that nuclear factor kappa B 1 (NFκB1) was prominently upregulated in pancreatic cancer tissues and pancreatic CSCs, and NFκB1 was also identified as a direct target of miR-497. Furthermore, we demonstrated that overexpression of NFκB1 could also notably promote the viability, migration, and invasion of gemcitabine-treated pancreatic CSCs, but this effect could be partially abolished by miR-497 overexpression. Conclusions: Those findings suggest that miR-497 overexpression could suppress gemcitabine resistance and the metastasis of pancreatic CSCs and non-CSCs by directly targeting NFκB1.
Collapse
Affiliation(s)
- Qiangfeng Yu
- The Second Department of General Surgery, Zhuhai People's Hospital, Zhuhai 51900, Guangdong, China
| | - Zhe Xiu
- Department of Hepatobiliary Surgery, The Second Hospital of Longyan, Longyan 364000, Fujian, China
| | - Yizeng Jian
- Department of Hepatobiliary Surgery, The Second Hospital of Longyan, Longyan 364000, Fujian, China
| | - Jianyin Zhou
- Department of Hepatobiliary and Pancreatic Surgery, Zhongshan Hospital, Xiamen University, Xiamen 361000, Fujian, China
| | - Xiaopeng Chen
- Department of Hepatobiliary Surgery, The Second Hospital of Longyan, Longyan 364000, Fujian, China
| | - Xiang Chen
- The Third Department of Surgery, The Second Hospital of Longyan, Longyan 364000, Fujian, China
| | - Chunxiang Chen
- Department of Science and Education, The Second Hospital of Longyan, Longyan 364000, Fujian, China
| | - Hongbao Chen
- Department of Pathology, The Second Hospital of Longyan, Longyan 364000, Fujian, China
| | - Sijia Yang
- The Second Department of General Surgery, Zhuhai People's Hospital, Zhuhai 51900, Guangdong, China
| | - Libo Yin
- The First People's Hospital of Wenling, The Affiliated Wenling Hospital of Wenzhou Medical University, Wenzhou 317500, Zhejiang, China
| | - Wenlong Zeng
- Department of Hepatobiliary Surgery, The Second Hospital of Longyan, Longyan 364000, Fujian, China
| |
Collapse
|
27
|
Ni Y, Low JT, Silke J, O’Reilly LA. Digesting the Role of JAK-STAT and Cytokine Signaling in Oral and Gastric Cancers. Front Immunol 2022; 13:835997. [PMID: 35844493 PMCID: PMC9277720 DOI: 10.3389/fimmu.2022.835997] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 05/16/2022] [Indexed: 12/12/2022] Open
Abstract
When small proteins such as cytokines bind to their associated receptors on the plasma membrane, they can activate multiple internal signaling cascades allowing information from one cell to affect another. Frequently the signaling cascade leads to a change in gene expression that can affect cell functions such as proliferation, differentiation and homeostasis. The Janus kinase-signal transducer and activator of transcription (JAK-STAT) and the tumor necrosis factor receptor (TNFR) are the pivotal mechanisms employed for such communication. When deregulated, the JAK-STAT and the TNF receptor signaling pathways can induce chronic inflammatory phenotypes by promoting more cytokine production. Furthermore, these signaling pathways can promote replication, survival and metastasis of cancer cells. This review will summarize the essentials of the JAK/STAT and TNF signaling pathways and their regulation and the molecular mechanisms that lead to the dysregulation of the JAK-STAT pathway. The consequences of dysregulation, as ascertained from founding work in haematopoietic malignancies to more recent research in solid oral-gastrointestinal cancers, will also be discussed. Finally, this review will highlight the development and future of therapeutic applications which modulate the JAK-STAT or the TNF signaling pathways in cancers.
Collapse
Affiliation(s)
- Yanhong Ni
- Central Laboratory, Nanjing Stomatological Hospital, Medical School of Nanjing University, Nanjing, China
| | - Jun T. Low
- Inflammation Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - John Silke
- Inflammation Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Lorraine A. O’Reilly
- Inflammation Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| |
Collapse
|
28
|
Lin S, Wen J, Xu X, Shi J, Zhang W, Zheng T, Hou Y, Zhang Y, Li Z, Wang K, Jin J, Yue L, Abay B, Li M, Yue Q, Fan L. Amygdalin Induced Mitochondria-Mediated Apoptosis of Lung Cancer Cells via Regulating NF[Formula: see text]B-1/NF[Formula: see text]B Signaling Cascade in Vitro and in Vivo. THE AMERICAN JOURNAL OF CHINESE MEDICINE 2022; 50:1361-1386. [PMID: 35681261 DOI: 10.1142/s0192415x22500586] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Lung cancer is the most commonly diagnosed cancer and the leading cause of cancer death worldwide. Amygdalin, a natural compound commonly distributed in plants of the Rosaceae species, owns anticancer activity, less side effects, wide source, and relatively low price. Although the apoptosis is a central process activated by amygdalin in cancer cells, the underlying molecular mechanisms through which amygdalin induces the apoptosis of lung cancer cells remain poorly understood. In this research work, amygdalin could suppress the proliferation of lung cancer A549 and PC9 cells by CCK8 assay. Amygdalin significantly promoted the apoptosis of lung cancer A549 and PC9 cells stained with Annexin V-FITC/PI by flow cytometry assay. Furthermore, amygdalin dose-dependently decreased the mitochondrial membrane potential (MMP) with JC-1 dye by flow cytometry. To investigate the underlying molecular mechanisms through which amygdalin induced mitochondria-mediated apoptosis of cancer cells, the differentially-expressed genes with a fold change >2.0 and [Formula: see text] < 0.05 were acquired from the cDNA microarray analysis. The results of qRT-PCR further confirmed that the differentially-expressed level of the NF[Formula: see text]B-1 gene was most obviously enhanced in lung cancer cells treated with amygdalin. The results of immunofluorescence staining, Western blotting and siRNA knockdown indicated that amygdalin induced mitochondria-mediated apoptosis of lung cancer cells via enhancing the expression of NF[Formula: see text]B-1 and inactivating NF[Formula: see text]B signaling cascade and further changing the expressions of proteins (Bax, Bcl-2, cytochrome C, caspase 9, caspase 3 and PARP) related to apoptosis, which were further checked by in vivo study of the lung cancer cell xenograft mice model accompanying with immunohistochemical staining and TUNEL staining. Our results indicated that amygdalin might be a potential activator of NF[Formula: see text]B-1, which sheds more light on the molecular mechanism of anticancer effects of amygdalin. These results highlighted amygdalin as a potential therapeutic anticancer agent, which warrants its development as a therapy for lung cancer.
Collapse
Affiliation(s)
- Shumeng Lin
- Institute of Energy Metabolism and Health, Shanghai 10th People's Hospital, Tongji University School of Medicine, Shanghai 200072, P. R. China.,Department of Respiratory Medicine, Shanghai 10th People's Hospital, Tongji University School of Medicine, Shanghai 200072, P. R. China
| | - Jing Wen
- Institute of Energy Metabolism and Health, Shanghai 10th People's Hospital, Tongji University School of Medicine, Shanghai 200072, P. R. China.,Department of Respiratory Medicine, Shanghai 10th People's Hospital, Tongji University School of Medicine, Shanghai 200072, P. R. China
| | - Xiao Xu
- Department of Respiratory Medicine, Shanghai 10th People's Hospital, Tongji University School of Medicine, Shanghai 200072, P. R. China
| | - Jiamin Shi
- Department of Respiratory Medicine, Shanghai 10th People's Hospital, Tongji University School of Medicine, Shanghai 200072, P. R. China
| | - Wen Zhang
- Department of Respiratory Medicine, Shanghai 10th People's Hospital, Tongji University School of Medicine, Shanghai 200072, P. R. China
| | - Tiansheng Zheng
- Department of Respiratory Medicine, Shanghai 10th People's Hospital, Tongji University School of Medicine, Shanghai 200072, P. R. China
| | - Yaqin Hou
- Department of Respiratory Medicine, Shanghai 10th People's Hospital, Tongji University School of Medicine, Shanghai 200072, P. R. China
| | - Yanfei Zhang
- Department of Respiratory Medicine, Shanghai 10th People's Hospital, Tongji University School of Medicine, Shanghai 200072, P. R. China
| | - Ziye Li
- Department of Respiratory Medicine, Shanghai 10th People's Hospital, Tongji University School of Medicine, Shanghai 200072, P. R. China
| | - Kai Wang
- Department of Respiratory Medicine, Shanghai 10th People's Hospital, Tongji University School of Medicine, Shanghai 200072, P. R. China
| | - Jing Jin
- Institute of Energy Metabolism and Health, Shanghai 10th People's Hospital, Tongji University School of Medicine, Shanghai 200072, P. R. China
| | - Liduo Yue
- Institute of Energy Metabolism and Health, Shanghai 10th People's Hospital, Tongji University School of Medicine, Shanghai 200072, P. R. China
| | - Baigenzhin Abay
- National Scientific Medical Research Center, Astana, Kazakhstan
| | - Ming Li
- Department of Respiratory Medicine, Shanghai 10th People's Hospital, Tongji University School of Medicine, Shanghai 200072, P. R. China
| | - Qingxi Yue
- Institute of Energy Metabolism and Health, Shanghai 10th People's Hospital, Tongji University School of Medicine, Shanghai 200072, P. R. China
| | - Lihong Fan
- Institute of Energy Metabolism and Health, Shanghai 10th People's Hospital, Tongji University School of Medicine, Shanghai 200072, P. R. China
| |
Collapse
|
29
|
Maity AK, Hu X, Zhu T, Teschendorff AE. Inference of age-associated transcription factor regulatory activity changes in single cells. NATURE AGING 2022; 2:548-561. [PMID: 37118452 DOI: 10.1038/s43587-022-00233-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 05/03/2022] [Indexed: 04/30/2023]
Abstract
Transcription factors (TFs) control cell identity and function. How their activity is altered during healthy aging is critical for an improved understanding of aging and disease risk, yet relatively little is known about such changes at cell-type resolution. Here we present and validate a TF activity estimation method for single cells from the hematopoietic system that is based on TF regulons, and apply it to a mouse single-cell RNA-sequencing atlas, to infer age-associated differentiation activity changes in the immune cells of different organs. This revealed an age-associated signature of macrophage dedifferentiation, which is shared across tissue types, and aggravated in tumor-associated macrophages. By extending the analysis to all major cell types, we reveal cell-type and tissue-type-independent age-associated alterations to regulatory factors controlling antigen processing, inflammation, collagen processing and circadian rhythm, that are implicated in age-related diseases. Finally, our study highlights the limitations of using TF expression to infer age-associated changes, underscoring the need to use regulatory activity inference methods.
Collapse
Affiliation(s)
- Alok K Maity
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Xue Hu
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Tianyu Zhu
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Andrew E Teschendorff
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China.
- UCL Cancer Institute, Paul O'Gorman Building, University College London, London, UK.
| |
Collapse
|
30
|
Long J, Tian L, Baranova A, Cao H, Yao Y, Rao S, Zhang F. Convergent lines of evidence supporting involvement of NFKB1 in schizophrenia. Psychiatry Res 2022; 312:114588. [PMID: 35524996 DOI: 10.1016/j.psychres.2022.114588] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 04/22/2022] [Accepted: 04/30/2022] [Indexed: 01/02/2023]
Abstract
OBJECTIVES NFKB1 was associated with treatment-refractory schizophrenia (SZ) and response to antipsychotics; however, the underlying mechanisms through which NFKB1 confers its risk for SZ are largely unknown. We aimed to investigate the potential role of NFKB1 in SZ. METHODS In the present study, we investigated the association of the risk SNP rs230529 of NFKB1 with gray matter density and with NFKB1 mRNA levels in various human brain regions. The spatiotemporal expression pattern of NFKB1 in human brains was explored. We constructed a miRNA-NFKB1-target gene regulatory network and analyzed its druggability through targeting NFKB1 for SZ treatment. RESULTS NFKB1 showed the highest expression levels in the cerebellum, in which these levels were stratified by genotypes of rs230529. Interestingly, the allelic state of rs230529 was significantly associated with regional gray matter density in multiple brain regions (including the cerebellum), which also differed between patients with schizophrenia and controls. Furthermore, regulatory targets of NFKB1 were enriched among SZ susceptibility genes. A substantial proportion of NFKB1 target genes were subject to combinatorial regulation by NFKB1 and miRNAs, constituting a hybrid NFKB1-miRNA-gene regulatory network. Some components of this network showed expression changes relevant to both the disease and the treatment. Finally, we detected the dynamic changes of NFKB1-miR-155-5p-GSK3B and NFKB1-miR-155-5p/let-7a-5p-IL6 networks in course of the treatment of SZ. CONCLUSION Taken together, our findings support the involvement of NFKB1-mediated dysregulation in the development of SZ.
Collapse
Affiliation(s)
- Jing Long
- Affiliated Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, 610075, China; Haihe Laboratory of Cell Ecosystem, State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
| | - Lin Tian
- Wuxi Mental Health Center of Nanjing Medical University, Wuxi, 214151, China
| | - Ancha Baranova
- School of Systems Biology, George Mason University, Fairfax, 22030, USA; Research Centre for Medical Genetics, Moscow, 115478, Russia
| | - Hongbao Cao
- School of Systems Biology, George Mason University, Fairfax, 22030, USA
| | - Yao Yao
- Haihe Laboratory of Cell Ecosystem, State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
| | - Shuquan Rao
- Haihe Laboratory of Cell Ecosystem, State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
| | - Fuquan Zhang
- Department of Psychiatry, The Affiliated Brain Hospital of Nanjing Medical University, Nanjing, 210029, China; Institute of Neuropsychiatry, The Affiliated Brain Hospital of Nanjing Medical University, Nanjing, 210029, China.
| |
Collapse
|
31
|
Laurella LC, Mirakian NT, Garcia MN, Grasso DH, Sülsen VP, Papademetrio DL. Sesquiterpene Lactones as Promising Candidates for Cancer Therapy: Focus on Pancreatic Cancer. Molecules 2022; 27:3492. [PMID: 35684434 PMCID: PMC9182036 DOI: 10.3390/molecules27113492] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 05/24/2022] [Accepted: 05/24/2022] [Indexed: 11/17/2022] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is a highly aggressive disease which confers to patients a poor prognosis at short term. PDAC is the fourth leading cause of death among cancers in the Western world. The rate of new cases of pancreatic cancer (incidence) is 10 per 100,000 but present a 5-year survival of less than 10%, highlighting the poor prognosis of this pathology. Furthermore, 90% of advanced PDAC tumor present KRAS mutations impacting in several oncogenic signaling pathways, many of them associated with cell proliferation and tumor progression. Different combinations of chemotherapeutic agents have been tested over the years without an improvement of significance in its treatment. PDAC remains as one the more challenging biomedical topics thus far. The lack of a proper early diagnosis, the notable mortality statistics and the poor outcome with the available therapies urge the entire scientific community to find novel approaches against PDAC with real improvements in patients' survival and life quality. Natural compounds have played an important role in the process of discovery and development of new drugs. Among them, terpenoids, such as sesquiterpene lactones, stand out due to their biological activities and pharmacological potential as antitumor agents. In this review, we will describe the sesquiterpene lactones with in vitro and in vivo activity against pancreatic tumor cells. We will also discuss the mechanism of action of the compounds as well as the signaling pathways associated with their activity.
Collapse
Affiliation(s)
- Laura Cecilia Laurella
- Instituto de Química y Metabolismo del Fármaco (IQUIMEFA), CONICET-Universidad de Buenos Aires, Junín 956, Piso 2, Buenos Aires CP 1113, Argentina;
- Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires CP 1113, Argentina;
| | - Nadia Talin Mirakian
- Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires CP 1113, Argentina;
| | - Maria Noé Garcia
- Cátedra de Inmunología, Departamento de Microbiología, Inmunología, Biotecnología y Genética, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires CP 1113, Argentina;
- Instituto de Estudios de la Inmunidad Humoral (IDEHU), CONICET-Universidad de Buenos Aires, Junín 956, Piso 4, Buenos Aires CP 1113, Argentina;
| | - Daniel Héctor Grasso
- Instituto de Estudios de la Inmunidad Humoral (IDEHU), CONICET-Universidad de Buenos Aires, Junín 956, Piso 4, Buenos Aires CP 1113, Argentina;
- Cátedra de Fisiopatología, Departamento de Ciencias Biológicas, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires CP 1113, Argentina
| | - Valeria Patricia Sülsen
- Instituto de Química y Metabolismo del Fármaco (IQUIMEFA), CONICET-Universidad de Buenos Aires, Junín 956, Piso 2, Buenos Aires CP 1113, Argentina;
- Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires CP 1113, Argentina;
| | - Daniela Laura Papademetrio
- Cátedra de Inmunología, Departamento de Microbiología, Inmunología, Biotecnología y Genética, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires CP 1113, Argentina;
- Instituto de Estudios de la Inmunidad Humoral (IDEHU), CONICET-Universidad de Buenos Aires, Junín 956, Piso 4, Buenos Aires CP 1113, Argentina;
| |
Collapse
|
32
|
Apoptosis-Associated Gene Expression Profiling Is One New Prognosis Risk Predictor of Human Rectal Cancer. DISEASE MARKERS 2022; 2022:4596810. [PMID: 35502302 PMCID: PMC9056267 DOI: 10.1155/2022/4596810] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 02/10/2022] [Accepted: 02/24/2022] [Indexed: 02/06/2023]
Abstract
Background. Prior research has revealed the predictive significance of a series of genetic markers in the prognosis of rectal cancer (RC), but the roles of apoptosis-associated genes in RC are rarely studied. Methods. The RNA-seq data as well as clinical data about patients with rectum adenocarcinoma (READ) were downloaded from The Cancer Genome Atlas (TCGA) and the Genotype-Tissue Expression (GTEx) project. Additionally, 87 apoptosis-associated genes were downloaded and acquired from Kyoto Encyclopedia of Genes and Genomes (KEGG) database. Comprehensive bioinformatics analysis was carried out for deep exploration of the expression and prognostic significance of these genes. Least absolute shrinkage and selection operator (LASSO) and multivariate Cox regression analysis was performed for the establishment of a risk scoring equation for the prognosis model and construction of a survival prognosis model. ROC curves were drawn for evaluating the accuracy of the model. A real-time quantitative PCR assay was conducted for quantification of apoptosis-associated proteins related to prognosis. Results. Eight genes were identified as hub genes associated with the prognosis of PFS. A risk model of prognosis prediction based on four gene signatures (CYCS, IKBKB, NFKB1, and TRADD) was constructed. According to further analysis of this model, the high-risk group experienced worse overall survival than the other. The prognosis model demonstrated a favorable predictive ability, with areas under the receiver operating characteristic curves (AUC) of 0.720, 0.641, and 0.677 in forecasting the 1-, 2-, and 3-year prognosis, respectively. In addition, CYCS and NFKB1 presented low expression, while IKBKB and TRADD presented high expression in TCGA and clinical tumor samples. Conclusions. A four-gene signature risk model for prognosis forecasting of RC has been constructed, which possesses favorable predictive ability, which offers ideas and breakthrough points to the apoptosis-associated development of RC.
Collapse
|
33
|
Jayathirtha M, Neagu AN, Whitham D, Alwine S, Darie CC. Investigation of the effects of overexpression of jumping translocation breakpoint (JTB) protein in MCF7 cells for potential use as a biomarker in breast cancer. Am J Cancer Res 2022; 12:1784-1823. [PMID: 35530281 PMCID: PMC9077082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 01/27/2022] [Indexed: 06/14/2023] Open
Abstract
Jumping translocation breakpoint (JTB) gene acts as a tumor suppressor or an oncogene in different malignancies, including breast cancer (BC), where it was reported as overexpressed. However, the molecular functions, biological processes and underlying mechanisms through which JTB protein causes increased cell growth, proliferation and invasion is still not fully deciphered. Our goal is to identify the functions of JTB protein by cellular proteomics approaches. MCF7 breast cancer cells were transfected with sense orientation of hJTB cDNA in HA, His and FLAG tagged CMV expression vector to overexpress hJTB and the expression levels were confirmed by Western blotting (WB). Proteins extracted from transfected cells were separated by SDS-PAGE and the in-gel digested peptides were analyzed by nano-liquid chromatography tandem mass spectrometry (nanoLC-MS/MS). By comparing the proteome of cells with upregulated conditions of JTB vs control and identifying the protein dysregulation patterns, we aim to understand the function of this protein and its contribution to tumorigenesis. Gene Set Enrichment Analysis (GSEA) algorithm was performed to investigate the biological processes and pathways that are associated with the JTB protein upregulation. The results demonstrated four significantly enriched gene sets from the following significantly upregulated pathways: mitotic spindle assembly, estrogen response late, epithelial-to-mesenchymal transition (EMT) and estrogen response early. JTB protein itself is involved in mitotic spindle pathway by its role in cell division/cytokinesis, and within estrogen response early and late pathways, contributing to discrimination between luminal and mesenchymal breast cancer. Thus, the overexpressed JTB condition was significantly associated with an increased expression of ACTNs, FLNA, FLNB, EZR, MYOF, COL3A1, COL11A1, HSPA1A, HSP90A, WDR, EPPK1, FASN and FOXA1 proteins related to deregulation of cytoskeletal organization and biogenesis, mitotic spindle organization, ECM remodeling, cellular response to estrogen, proliferation, migration, metastasis, increased lipid biogenesis, endocrine therapy resistance, antiapoptosis and discrimination between different breast cancer subtypes. Other upregulated proteins for overexpressed JTB condition are involved in multiple cellular functions and pathways that become dysregulated, such as tumor microenvironment (TME) acidification, the transmembrane transport pathways, glycolytic flux, iron metabolism and oxidative stress, metabolic reprogramming, nucleocytosolic mRNA transport, transcriptional activation, chromatin remodeling, modulation of cell death pathways, stress responsive pathways, and cancer drug resistance. The downregulated proteins for overexpressed JTB condition are involved in adaptive communication between external and internal environment of cells and maintenance between pro-apoptotic and anti-apoptotic signaling pathways, vesicle trafficking and secretion, DNA lesions repair and suppression of genes involved in tumor progression, proteostasis, redox state regulation, biosynthesis of macromolecules, lipolytic pathway, carbohydrate metabolism, dysregulation of ubiquitin-mediated degradation system, cancer cell immune escape, cell-to-cell and cell-to-ECM interactions, and cytoskeletal behaviour. There were no significantly enriched downregulated pathways.
Collapse
Affiliation(s)
- Madhuri Jayathirtha
- Biochemistry & Proteomics Group, Department of Chemistry and Biomolecular Science, Clarkson UniversityPotsdam, NY 13699-5810, USA
| | - Anca-Narcisa Neagu
- Laboratory of Animal Histology, Faculty of Biology, “Alexandru Ioan Cuza” University of IasiCarol I Bvd. No. 22, Iasi 700505, Romania
| | - Danielle Whitham
- Biochemistry & Proteomics Group, Department of Chemistry and Biomolecular Science, Clarkson UniversityPotsdam, NY 13699-5810, USA
| | - Shelby Alwine
- Biochemistry & Proteomics Group, Department of Chemistry and Biomolecular Science, Clarkson UniversityPotsdam, NY 13699-5810, USA
| | - Costel C Darie
- Biochemistry & Proteomics Group, Department of Chemistry and Biomolecular Science, Clarkson UniversityPotsdam, NY 13699-5810, USA
| |
Collapse
|
34
|
LncRNA MAFG-AS1 promotes the malignant phenotype of ovarian cancer by upregulating NFKB1-dependent IGF1. Cancer Gene Ther 2022; 29:277-291. [PMID: 34035482 DOI: 10.1038/s41417-021-00306-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 01/24/2021] [Accepted: 02/03/2021] [Indexed: 02/04/2023]
Abstract
Long non-coding RNAs (lncRNAs) were recently recognized to vitally function in a variety of cancer cellular events, including epithelial-mesenchymal transition (EMT), invasion, and migration, particularly in ovarian cancer (OC). Herein, we sought to investigate the potential role of MAFG-AS1 in the malignant behaviors of OC cells. The binding affinity between MAFG-AS1, miR-339-5p, NFKB1 or IGF1 was characterized so as to identify the underlying mechanism of corresponding their interactions. We conducted MAFG-AS1 overexpression or knockdown along with NFKB1 and IGF1 silencing to examine their effects on the EMT, migration, and invasion of OC cells. Tumors were xenografted in nude mice to validate the in vitro findings. Our data showed significantly high expression pattern of MAFG-AS1 in the OC tissues and cells. Further mechanistic investigations revealed that MAFG-AS1 upregulated the IGF1 expression pattern through recruitment of NFKB1, whereas MAFG-AS1 upregulated the NFKB1 expression pattern through binding to miR-339-5p. Thus, MAFG-AS1 overexpression accelerated the EMT, invasion, and migration of OC cells, which could be annulled by silencing of IGF1 or NFKB1. Besides, our in vitro findings were successfully recapitulated in the xenograft mice. These results determined that MAFG-AS1 stimulated the OC malignant progression by upregulating the NFKB1-mediated IGF1 via miR-339-5p, thus highlighting a novel potential therapeutic target against OC.
Collapse
|
35
|
Wang ZW, Gao YN, Huang SN, Wang JQ, Zheng N. Ex Vivo and In Vitro Studies Revealed Underlying Mechanisms of Immature Intestinal Inflammatory Responses Caused by Aflatoxin M1 Together with Ochratoxin A. Toxins (Basel) 2022; 14:toxins14030173. [PMID: 35324670 PMCID: PMC8953104 DOI: 10.3390/toxins14030173] [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: 01/05/2022] [Revised: 02/08/2022] [Accepted: 02/15/2022] [Indexed: 12/04/2022] Open
Abstract
Aflatoxin M1 (AFM1) and ochratoxin A (OTA), which are occasionally detected in milk and commercial baby foods, could easily enter and reach the gastrointestinal tract, posing impairment to the first line of defense and causing dysfunction of the tissue. The objective of this study was to investigate the immunostimulatory roles of individual and combined AFM1 and OTA on the immature intestine. Thus, we used ELISA assays to evaluate the generation of cytokines from ex vivo CD-1 fetal mouse jejunum induced by AFM1 and OTA and explored the related regulatory pathways and pivot genes using RNA-seq analysis. It was found that OTA exhibited much stronger ability in stimulating pro-inflammatory cytokine IL-6 from jejunum tissues than AFM1 (OTA of 4 μM versus AFM1 of 50 μM), whereas the combination of the two toxins seemed to exert antagonistic actions. In addition, transcriptomics also showed that most gene members in the enriched pathway ‘cytokine–cytokine receptor interaction’ were more highly expressed in OTA than the AFM1 group. By means of PPI network analysis, NFKB1 and RelB were regarded as hub genes in response to OTA but not AFM1. In the human FHs 74 Int cell line, both AFM1 and OTA enhanced the content of reactive oxygen species, and the oxidative response was more apparent in OTA-treated cells in comparison with AFM1. Furthermore, OTA and AFM1 + OTA raised the protein abundance of p50/RelB, and triggered the translocation of the dimer from cytosol to nucleus. Therefore, the experimental data ex vivo and in vitro showed that OTA-induced inflammation was thought to be bound up with the up-regulation and translocation of NF-κB, though AFM1 seemed to have no obvious impact. Since it was the first attempt to uncover the appearances and inner mechanisms regarding inflammation provoked by AFM1 and OTA on immature intestinal models, further efforts are needed to understand the detailed metabolic steps of the toxin in cells and to clarify their causal relationship with the signals proposed from current research.
Collapse
Affiliation(s)
- Zi-Wei Wang
- Key Laboratory of Quality & Safety Control for Milk and Dairy Products of Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (Z.-W.W.); (Y.-N.G.); (S.-N.H.); (J.-Q.W.)
- Laboratory of Quality and Safety Risk Assessment for Dairy Products of Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- Milk and Milk Products Inspection Center of Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Ya-Nan Gao
- Key Laboratory of Quality & Safety Control for Milk and Dairy Products of Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (Z.-W.W.); (Y.-N.G.); (S.-N.H.); (J.-Q.W.)
- Laboratory of Quality and Safety Risk Assessment for Dairy Products of Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- Milk and Milk Products Inspection Center of Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Sheng-Nan Huang
- Key Laboratory of Quality & Safety Control for Milk and Dairy Products of Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (Z.-W.W.); (Y.-N.G.); (S.-N.H.); (J.-Q.W.)
- Laboratory of Quality and Safety Risk Assessment for Dairy Products of Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- Milk and Milk Products Inspection Center of Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Jia-Qi Wang
- Key Laboratory of Quality & Safety Control for Milk and Dairy Products of Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (Z.-W.W.); (Y.-N.G.); (S.-N.H.); (J.-Q.W.)
- Laboratory of Quality and Safety Risk Assessment for Dairy Products of Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- Milk and Milk Products Inspection Center of Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Nan Zheng
- Key Laboratory of Quality & Safety Control for Milk and Dairy Products of Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (Z.-W.W.); (Y.-N.G.); (S.-N.H.); (J.-Q.W.)
- Laboratory of Quality and Safety Risk Assessment for Dairy Products of Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- Milk and Milk Products Inspection Center of Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- Correspondence:
| |
Collapse
|
36
|
Zou X, Guo B, Ling Q, Mo Z. Toll-Like Receptors Serve as Biomarkers for Early Diagnosis and Prognosis Assessment of Kidney Renal Clear Cell Carcinoma by Influencing the Immune Microenvironment: Comprehensive Bioinformatics Analysis Combined With Experimental Validation. Front Mol Biosci 2022; 9:832238. [PMID: 35127830 PMCID: PMC8814606 DOI: 10.3389/fmolb.2022.832238] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 01/06/2022] [Indexed: 12/17/2022] Open
Abstract
Background: Toll-like receptors (TLRs) are important initiators of innate and acquired immune responses. However, its role in kidney renal clear cell carcinoma (KIRC) remains unclear. Methods: TLRs and their relationships with KIRC were studied in detail by ONCOMINE, UALCAN, GEPIA, cBioPortal, GeneMANIA, FunRich, LinkedOmics, TIMER and TRRUST. Moreover, we used clinical samples to verify the expressions of TLR3 and TLR4 in early stage of KIRC by real-time fluorescence quantitative polymerase chain reaction (RT-qPCR), flow cytometry (FC) and immunohistochemistry (IHC). Results: The expression levels of TLRs in KIRC were generally different compared with adjacent normal tissues. Moreover, the expressions of TLR3 and TLR4 elevated significantly in the early stage of KIRC. Overexpressions of TLR1, TLR3, TLR4 and TLR8 in KIRC patients were associated with longer overall survival (OS), while inhibition of TLR9 expression was related to longer OS. Additionally, overexpressions of TLR1, TLR3 and TLR4 in KIRC patients were associated with longer disease free survival (DFS). There were general genetic alterations and obvious co-expression correlation of TLRs in KIRC. The PPI network between TLRs was rather complex, and the key gene connecting the TLRs interaction was MYD88. The GO analysis and KEGG pathway analysis indicated that TLRs were closely related to adaptive immunity, innate immunity and other immune-related processes. RELA, NFKB1, IRF8, IRF3 and HIF1A were key transcription factors regulating the expressions of TLRs. What’s more, the expression levels of all TLRs in KIRC were positively correlated with the infiltration levels of dendritic cells, macrophages, neutrophils, B cells, CD4+ T cells and CD8+ T cells. Finally, the results of RT-qPCR, FC and IHC confirmed that TLR3 and TLR4 were significantly elevated in the early stage of KIRC. Conclusion: The occurrence and development of KIRC are closely related to TLRs, and TLRs have the potential to be early diagnostic biomarkers of KIRC and biomarkers for judging the prognosis and immune status of KIRC. This study may provide new insights into the selection of KIRC immunotherapy targets.
Collapse
Affiliation(s)
- Xiong Zou
- Department of Urology, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
- Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, China
- Guangxi Collaborative Innovation Center for Genomic and Personalized Medicine, Nanning, China
- Guangxi Key Laboratory for Genomic and Personalized Medicine, Guangxi Key Laboratory of Colleges and Universities, Nanning, China
| | - Bingqian Guo
- Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, China
- Guangxi Collaborative Innovation Center for Genomic and Personalized Medicine, Nanning, China
- Guangxi Key Laboratory for Genomic and Personalized Medicine, Guangxi Key Laboratory of Colleges and Universities, Nanning, China
- Collaborative Innovation Center of Regenerative Medicine and Medical BioResource Development and Application, Guangxi Medical University, Nanning, China
| | - Qiang Ling
- Department of Urology, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
- Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, China
- Guangxi Collaborative Innovation Center for Genomic and Personalized Medicine, Nanning, China
- Guangxi Key Laboratory for Genomic and Personalized Medicine, Guangxi Key Laboratory of Colleges and Universities, Nanning, China
| | - Zengnan Mo
- Department of Urology, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
- Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, China
- Guangxi Collaborative Innovation Center for Genomic and Personalized Medicine, Nanning, China
- Guangxi Key Laboratory for Genomic and Personalized Medicine, Guangxi Key Laboratory of Colleges and Universities, Nanning, China
- Collaborative Innovation Center of Regenerative Medicine and Medical BioResource Development and Application, Guangxi Medical University, Nanning, China
- *Correspondence: Zengnan Mo,
| |
Collapse
|
37
|
Esparza-López J, Longoria O, De La Cruz-Escobar EN, Garibay-Díaz JC, León-Rodríguez E, De Jesús Ibarra-Sánchez M. Paclitaxel resistance is mediated by NF-κB on mesenchymal primary breast cancer cells. Oncol Lett 2022; 23:50. [PMID: 34992683 PMCID: PMC8721864 DOI: 10.3892/ol.2021.13168] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Accepted: 11/09/2021] [Indexed: 12/16/2022] Open
Abstract
Paclitaxel has been used widely to treat breast cancer and other types of cancer. However, resistance is a major cause of failure for treatment and results in cancer progression. The present study investigated the association between paclitaxel resistance and the mesenchymal phenotype, using a model of primary breast cancer cells and employing four different cultures, two with an epithelial phenotype (MBCDF and MBCD17) and two with a mesenchymal phenotype (MBCDF-D5 and MBCD3). Epithelial-mesenchymal markers were evaluated by western blotting; MBCDF and MBCD17 cells expressed E-cadherin, SNAIL, Slug, and Twist, low levels of N-cadherin, but not vimentin. MBCDF-D5 and MBCD3 cells expressed N-cadherin, vimentin, and higher levels of SNAIL, and low levels of E-cadherin, Slug, and Twist. Cell viability was evaluated using a crystal violet assay after paclitaxel treatment; primary breast cancer cells with mesenchymal phenotype were resistant to paclitaxel compared with the epithelial primary breast cancer cells. Furthermore, using western blotting, it was revealed that mesenchymal cells had elevated levels of nuclear factor-κΒ (NF-κB) p65 and IκB kinase (IKK). Additionally, it was demonstrated that paclitaxel-induced degradation of the inhibitor of NF-κB, activation of NF-κB in a dose-dependent manner, and Bcl-2 and Bcl-xL upregulation. Finally, employing western blotting and crystal violet assays, the effects of the proteasome inhibitor ALLN were assessed. ALLN inhibited paclitaxel-induced NF-κB activation and restored the sensitivity to paclitaxel. Together, these data suggest that targeting the NF-κB/IKK axis might be a promising strategy to overcome paclitaxel resistance.
Collapse
Affiliation(s)
- José Esparza-López
- Biochemistry Unit, Salvador Zubirán National Institute of Health Sciences and Nutrition, Mexico City 14080, Mexico.,Research Support Network, National Autonomous University of Mexico-Salvador Zubirán National Institute of Health Sciences and Nutrition, Mexico City 14080, Mexico
| | - Ossian Longoria
- Hematology and Oncology Department, Salvador Zubirán National Institute of Health Sciences and Nutrition, Mexico City 14080, Mexico
| | | | - Julio Cesar Garibay-Díaz
- Hematology and Oncology Department, Salvador Zubirán National Institute of Health Sciences and Nutrition, Mexico City 14080, Mexico
| | - Eucario León-Rodríguez
- Hematology and Oncology Department, Salvador Zubirán National Institute of Health Sciences and Nutrition, Mexico City 14080, Mexico
| | | |
Collapse
|
38
|
Zhang Y, Ma W, Fan W, Ren C, Xu J, Zeng F, Bao Z, Jiang T, Zhao Z. Comprehensive transcriptomic characterization reveals core genes and module associated with immunological changes via 1619 samples of brain glioma. Cell Death Dis 2021; 12:1140. [PMID: 34880206 PMCID: PMC8654825 DOI: 10.1038/s41419-021-04427-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 11/17/2021] [Accepted: 11/25/2021] [Indexed: 12/11/2022]
Abstract
Glioma is the most common primary malignant brain tumor with limited treatment options and poor prognosis. To investigate the potential relationships between transcriptional characteristics and clinical phenotypes, we applied weighted gene co-expression network analysis (WGCNA) to construct a free-scale gene co-expression network yielding four modules in gliomas. Turquoise and yellow modules were positively correlated with the most malignant glioma subtype (IDH-wildtype glioblastomas). Of them, genes in turquoise module were mainly involved in immune-related terms and were regulated by NFKB1, RELA, SP1, STAT1 and STAT3. Meanwhile, genes in yellow module mainly participated in cell-cycle and division processes and were regulated by E2F1, TP53, E2F4, YBX1 and E2F3. Furthermore, 14 genes in turquoise module were screened as hub genes. Among them, five prognostic hub genes (TNFRSF1B, LAIR1, TYROBP, VAMP8, and FCGR2A) were selected to construct a prognostic risk score model via LASSO method. The risk score of this immune-related gene signature is associated with clinical features, malignant phenotype, and somatic alterations. Moreover, this signature showed an accurate prediction of prognosis across different clinical and pathological subgroups in three independent datasets including 1619 samples. Our results showed that the high-risk group was characterized by active immune-related activities while the low-risk group enriched in neurophysiological-related pathway. Importantly, the high-risk score of our immune signature predicts an enrichment of glioma-associated microglia/macrophages and less response to immune checkpoint blockade (ICB) therapy in gliomas. This study not only provides new insights into the molecular pathogenesis of glioma, but may also help optimize the immunotherapies for glioma patients.
Collapse
Affiliation(s)
- Ying Zhang
- grid.24696.3f0000 0004 0369 153XBeijing Neurosurgical Institute, Capital Medical University, 100070 Beijing, China ,Chinese Glioma Genome Atlas Network (CGGA) and Asian Glioma Genome Atlas Network (AGGA), 100070 Beijing, China
| | - Wenping Ma
- grid.24696.3f0000 0004 0369 153XBeijing Neurosurgical Institute, Capital Medical University, 100070 Beijing, China ,Chinese Glioma Genome Atlas Network (CGGA) and Asian Glioma Genome Atlas Network (AGGA), 100070 Beijing, China ,grid.411617.40000 0004 0642 1244Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, 100070 Beijing, China
| | - Wenhua Fan
- grid.24696.3f0000 0004 0369 153XBeijing Neurosurgical Institute, Capital Medical University, 100070 Beijing, China ,Chinese Glioma Genome Atlas Network (CGGA) and Asian Glioma Genome Atlas Network (AGGA), 100070 Beijing, China ,grid.411617.40000 0004 0642 1244Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, 100070 Beijing, China
| | - Changyuan Ren
- grid.24696.3f0000 0004 0369 153XSanbo Brain Hospital, Capital Medical University, 100093 Beijing, China
| | - Jianbao Xu
- grid.412463.60000 0004 1762 6325The Second Affiliated Hospital of Harbin Medical University, 150001 Harbin, China
| | - Fan Zeng
- grid.24696.3f0000 0004 0369 153XBeijing Neurosurgical Institute, Capital Medical University, 100070 Beijing, China ,Chinese Glioma Genome Atlas Network (CGGA) and Asian Glioma Genome Atlas Network (AGGA), 100070 Beijing, China
| | - Zhaoshi Bao
- Chinese Glioma Genome Atlas Network (CGGA) and Asian Glioma Genome Atlas Network (AGGA), 100070 Beijing, China ,grid.411617.40000 0004 0642 1244Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, 100070 Beijing, China
| | - Tao Jiang
- Beijing Neurosurgical Institute, Capital Medical University, 100070, Beijing, China. .,Chinese Glioma Genome Atlas Network (CGGA) and Asian Glioma Genome Atlas Network (AGGA), 100070, Beijing, China. .,Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, 100070, Beijing, China. .,Center of Brain Tumor, Beijing Institute for Brain Disorders, 100069, Beijing, China. .,China National Clinical Research Center for Neurological Diseases, 100070, Beijing, China.
| | - Zheng Zhao
- Beijing Neurosurgical Institute, Capital Medical University, 100070, Beijing, China. .,Chinese Glioma Genome Atlas Network (CGGA) and Asian Glioma Genome Atlas Network (AGGA), 100070, Beijing, China.
| |
Collapse
|
39
|
Ren Y, Elkington BG, Henkin JM, Sydara K, Kinghorn AD, Soejarto DD. Bioactive small-molecule constituents of Lao plants. JOURNAL OF MEDICINAL PLANT RESEARCH 2021; 15:540-559. [PMID: 35178192 PMCID: PMC8849567 DOI: 10.5897/jmpr2021.7137] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Laos has a rich plant diversity, and medicinal plants are used extensively in Lao traditional medicine for the treatment of a variety of human diseases. However, only a relatively small number of these plants have been investigated for their major components with potential antitumor, anti-infective, and other types of bioactivities. These species include Asparagus cochinchinensis, Diospyros quaesita, Gongronema napalense, Marsypopetalum modestum, Nauclea orientalis, Rourea minor, Stemona pierrei, and Stemona tuberosa. Thus far, the bioactive compounds isolated from these Lao plants include alkaloids, glycerol esters, phenolic compounds such as lignans and stilbenoids, steroids, and triterpenoids. Of these, the norlignan, nyasol (1b), the triterpenes, pyracrenic acid [3β-O-trans-caffeoylbetulinic acid (3)] and betulinic acid (3b), and the dimeric thiopyridine, dipyrithione (5), were found to show both cancer cell cytotoxicity and anti-infective activity. The present review focuses on examples of promising lead compounds isolated from Lao plants, with their possible development as potential therapeutic agents being discussed. It is hoped that this contribution will provide useful information on higher plants growing in Laos to help stimulate future discoveries of potential agents for the treatment of cancer, infections, and other diseases.
Collapse
Affiliation(s)
- Yulin Ren
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, OH 43210, United States
| | - Bethany G. Elkington
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60612, United States
- Science and Education, Field Museum, Chicago, IL 60605, United States
| | - Joshua M. Henkin
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60612, United States
- Science and Education, Field Museum, Chicago, IL 60605, United States
| | - Kongmany Sydara
- Institute of Traditional Medicine, Ministry of Health, Vientiane, Lao PDR
| | - A. Douglas Kinghorn
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, OH 43210, United States
| | - Djaja D. Soejarto
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60612, United States
- Science and Education, Field Museum, Chicago, IL 60605, United States
| |
Collapse
|
40
|
Wu C, Ma C, Yuan J, Zhou P. Exploration of potential therapeutic and prognostic value of CXC chemokines in cervical squamous cell carcinoma and endocervical adenocarcinoma based on bioinformatics analysis. MATHEMATICAL BIOSCIENCES AND ENGINEERING : MBE 2021; 18:8201-8222. [PMID: 34814296 DOI: 10.3934/mbe.2021407] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Cervical cancer, as the second most common female malignancy, brings a great health burden to women worldwide. Cervical squamous cell carcinoma and endocervical adenocarcinoma (CESC) are the most common histological subtypes of cervical cancer. CXC chemokines (CXCLs) within the tumor microenvironment can modulate carcinogenesis and progression. The present study aimed to explore the therapeutic and prognostic value of different CXCLs in CESC. ONCOMINE, GEPIA, cBioPortal, TRRUST, GeneMANIA, STRING and TIMER were utilized to explore the expression, mutation and function of CXCLs in CESC, as well as their correlation with pathological and survival features of CESC patients. We found that the mRNA expression levels of CXCL1/8/9/10/11/13/16/17 in CESC were upregulated compared with normal cervical tissues, whereas CXCL12 was downregulated. No significant correlation was found between the expression levels and pathological stage of CESC patients. CESC patients with high expression of CXCL1/2/3/4/5/8 were significantly associated with poor overall survival, additionally, low mRNA level of CXCL3 was associated with better disease-free survival. Besides, a high mutation rate (43%) of CXCLs in CESC was observed. Depicted by co-expression analysis, the expression of CXCL1/2/3/6/8 showed a modest to strong correlation, while that of CXCL9/10/11/13 showed a very strong correlation. Differentially expressed CXCLs primarily functioned in chemokine signaling pathway and inflammation response, such as cell chemotaxis, chemokine activity and chemokine receptor binding. We also found the association of CXCLs with the tumor-infiltration of six types of immune cells (B cells, CD8+ T cells, CD4+ T cells, macrophages, neutrophils and dendritic cells) in CESC patients. The present study elucidated that CXCLs may have the potential to be novel therapeutic targets and prognosis predictors of CESC patients.
Collapse
Affiliation(s)
- Caiyun Wu
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, First Affiliated Hospital of Anhui Medical University, Hefei 230022, China
| | - Cong Ma
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, First Affiliated Hospital of Anhui Medical University, Hefei 230022, China
| | - Jing Yuan
- Prenatal Diagnosis Center, Department of Obstetrics and Gynecology, First Affiliated Hospital of Anhui Medical University, Hefei 230022, China
| | - Pei Zhou
- Prenatal Diagnosis Center, Department of Obstetrics and Gynecology, First Affiliated Hospital of Anhui Medical University, Hefei 230022, China
| |
Collapse
|
41
|
Silke J, O’Reilly LA. NF-κB and Pancreatic Cancer; Chapter and Verse. Cancers (Basel) 2021; 13:4510. [PMID: 34572737 PMCID: PMC8469693 DOI: 10.3390/cancers13184510] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 08/29/2021] [Accepted: 08/30/2021] [Indexed: 02/07/2023] Open
Abstract
Pancreatic Ductal Adenocarcinoma (PDAC) is one of the world's most lethal cancers. An increase in occurrence, coupled with, presently limited treatment options, necessitates the pursuit of new therapeutic approaches. Many human cancers, including PDAC are initiated by unresolved inflammation. The transcription factor NF-κB coordinates many signals that drive cellular activation and proliferation during immunity but also those involved in inflammation and autophagy which may instigate tumorigenesis. It is not surprising therefore, that activation of canonical and non-canonical NF-κB pathways is increasingly recognized as an important driver of pancreatic injury, progression to tumorigenesis and drug resistance. Paradoxically, NF-κB dysregulation has also been shown to inhibit pancreatic inflammation and pancreatic cancer, depending on the context. A pro-oncogenic or pro-suppressive role for individual components of the NF-κB pathway appears to be cell type, microenvironment and even stage dependent. This review provides an outline of NF-κB signaling, focusing on the role of the various NF-κB family members in the evolving inflammatory PDAC microenvironment. Finally, we discuss pharmacological control of NF-κB to curb inflammation, focussing on novel anti-cancer agents which reinstate the process of cancer cell death, the Smac mimetics and their pre-clinical and early clinical trials.
Collapse
Affiliation(s)
- John Silke
- Inflammation Division, Walter and Eliza Hall Institute of Medical Research (WEHI), Parkville, VIC 3052, Australia;
- Department of Medical Biology, University of Melbourne, Parkville, VIC 3010, Australia
| | - Lorraine Ann O’Reilly
- Inflammation Division, Walter and Eliza Hall Institute of Medical Research (WEHI), Parkville, VIC 3052, Australia;
- Department of Medical Biology, University of Melbourne, Parkville, VIC 3010, Australia
| |
Collapse
|
42
|
Gilmore TD. NF-κB and Human Cancer: What Have We Learned over the Past 35 Years? Biomedicines 2021; 9:biomedicines9080889. [PMID: 34440093 PMCID: PMC8389606 DOI: 10.3390/biomedicines9080889] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 07/18/2021] [Accepted: 07/22/2021] [Indexed: 02/06/2023] Open
Abstract
Transcription factor NF-κB has been extensively studied for its varied roles in cancer development since its initial characterization as a potent retroviral oncogene. It is now clear that NF-κB also plays a major role in a large variety of human cancers, including especially ones of immune cell origin. NF-κB is generally constitutively or aberrantly activated in human cancers where it is involved. These activations can occur due to mutations in the NF-κB transcription factors themselves, in upstream regulators of NF-κB, or in pathways that impact NF-κB. In addition, NF-κB can be activated by tumor-assisting processes such as inflammation, stromal effects, and genetic or epigenetic changes in chromatin. Aberrant NF-κB activity can affect many tumor-associated processes, including cell survival, cell cycle progression, inflammation, metastasis, angiogenesis, and regulatory T cell function. As such, inhibition of NF-κB has often been investigated as an anticancer strategy. Nevertheless, with a few exceptions, NF-κB inhibition has had limited success in human cancer treatment. This review covers general themes that have emerged regarding the biological roles and mechanisms by which NF-κB contributes to human cancers and new thoughts on how NF-κB may be targeted for cancer prognosis or therapy.
Collapse
|
43
|
Sun X, Chen Q, Zhang L, Chen J, Zhang X. Exploration of prognostic biomarkers and therapeutic targets in the microenvironment of bladder cancer based on CXC chemokines. MATHEMATICAL BIOSCIENCES AND ENGINEERING : MBE 2021; 18:6262-6287. [PMID: 34517533 DOI: 10.3934/mbe.2021313] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
BACKGROUND Bladder cancer (BLCA) has a high rate of morbidity and mortality, and is considered as one of the most malignant tumors of the urinary system. Tumor cells interact with surrounding interstitial cells, playing a key role in carcinogenesis and progression, which is partly mediated by chemokines. CXC chemokines exert anti-tumor biological roles in the tumor microenvironment and affect patient prognosis. Nevertheless, their expression and prognostic values patients with BLCA remain unclear. METHODS We used online tools, including Oncomine, UALCAN, GEPIA, GEO databases, cBioPortal, GeneMANIA, DAVID 6.8, Metascape, TRUST (version 2.0), LinkedOmics, TCGA, and TIMER2.0 to perform the relevant analysis. RESULTS The mRNA levels of C-X-C motif chemokine ligand (CXCL)1, CXCL5, CXCL6, CXCL7, CXCL9, CXCL10, CXCL11, CXCL13, CXCL16, and CXCL17 were increased significantly increased, and those of CXCL2, CXCL3, and CXCL12 were decreased significantly in BLCA tissues as assessed using the Oncomine, TCGA, and GEO databases. GEO showed that high levels of CXCL1, CXCL6, CXCL10, CXCL11, and CXCL13 mRNA expression are associated significantly with the poor overall survival (all p < 0.05), and similarly, those of CXCL2 and CXCL12 in the TCGA database (p < 0.05). The predominant signaling pathways involving the differentially expressed CXC chemokines are cell cycle, chemokine, and cytokine-cytokine receptor interaction. Moreover, transcription factors such as Sp1 transcription factor (SP1), nuclear factor kappa B subunit 1 (NFKB1), and RELA proto-oncogene, NF-KB subunit (RELA) were likely play critical roles in regulating CXC chemokine expression. LYN proto-oncogene, src family tyrosine kinase (LYN) and LCK proto-oncogene, src family tyrosine kinase (LCK) were identified as the key targets of these CXC chemokines. MicroRNAs miR200 and miR30 were identified as the main microRNAs that interact with several CXC chemokines through an miRNA-target network. The expression of these chemokines is closely associated with the infiltration of six categories of immune cells. CONCLUSION We explored the CXC chemokines superfamily-based biomarkers associated with BLCA prognosis using public databases, and provided possible chemokine targets for patients with BLCA.
Collapse
Affiliation(s)
- Xiaoqi Sun
- Department of Urology, Kaiping Central Hospital, Kaiping 529300, China
| | - Qunxi Chen
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
- Department of Pathology, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Lihong Zhang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
- Department of Pathology, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Jiewei Chen
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
- Department of Pathology, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Xinke Zhang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
- Department of Pathology, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| |
Collapse
|
44
|
Integrative Bioinformatics Study of Tangeretin Potential Targets for Preventing Metastatic Breast Cancer. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2021; 2021:2234554. [PMID: 34335799 PMCID: PMC8294962 DOI: 10.1155/2021/2234554] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 06/22/2021] [Indexed: 11/17/2022]
Abstract
Agents that target metastasis are important to improve treatment efficacy in patients with breast cancer. Tangeretin, a citrus flavonoid, exhibits antimetastatic effects on breast cancer cells, but its molecular mechanism remains unclear. Tangeretin targets were retrieved from PubChem, whereas metastatic breast cancer regulatory genes were downloaded from PubMed. In total, 58 genes were identified as potential therapeutic target genes of tangeretin (PTs). GO and KEGG pathway enrichment analyses of PTs were performed using WebGestalt (WEB-based Gene SeT AnaLysis Toolkit). The PPI network was analyzed using STRING-DB v11.0 and visualized by Cytoscape software. Hub genes were selected on the basis of the highest degree score as calculated by the CytoHubba plugin. Genetic alterations of the PTs were analyzed using cBioPortal. The prognostic values of the PTs were evaluated with the Kaplan-Meier plot. The expression of PTs across breast cancer samples was confirmed using GEPIA. The reliability of the PTs in metastatic breast cancer cells was validated using ONCOMINE. Molecular docking was performed to foresee the binding sites of tangeretin with PIK3Cα, MMP9, PTGS2, COX-2, and IKK. GO analysis showed that PTs participate in the biological process of stimulus response, are the cellular components of the nucleus and the membrane, and play molecular roles in enzyme regulation. KEGG pathway enrichment analysis revealed that PTs regulate the PI3K/Akt pathway. Genetic alterations for each target gene were MTOR (3%), NOTCH1 (4%), TP53 (42%), MMP9 (4%), NFKB1 (3%), PIK3CA (32%), PTGS2 (15%), and RELA (5%). The Kaplan-Meier plot showed that patients with low mRNA expression levels of MTOR, TP53, MMP9, NFKB1, PTGS2, and RELA and high expression of PIK3CA had a significantly better prognosis than their counterparts. Further validation of gene expression by using GEPIA revealed that the mRNA expression of MMP9 was significantly higher in breast cancer tissues than in normal tissues, whereas the mRNA expression of PTGS2 showed the opposite. Analysis with ONCOMINE demonstrated that the mRNA expression levels of MMP9 and NFKB1 were significantly higher in metastatic breast cancer cells than in normal tissues. The results of molecular docking analyses revealed the advantage of tangeretin as an inhibitor of PIK3CA, MMP9, PTGS2, and IKK. Tangeretin inhibits metastasis in breast cancer cells by targeting TP53, PTGS2, MMP9, and PIK3CA and regulating the PI3K/Akt signaling pathway. Further investigation is needed to validate the results of this study.
Collapse
|
45
|
Chen B, Xu X, Lin DD, Chen X, Xu YT, Liu X, Dong WG. KRT18 Modulates Alternative Splicing of Genes Involved in Proliferation and Apoptosis Processes in Both Gastric Cancer Cells and Clinical Samples. Front Genet 2021; 12:635429. [PMID: 34290732 PMCID: PMC8287183 DOI: 10.3389/fgene.2021.635429] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 02/26/2021] [Indexed: 12/13/2022] Open
Abstract
Keratin 18 (KRT18), one of the most abundant keratins in epithelial and endothelial cells, has been reported to be aberrantly expressed in many malignancies and extensively regarded as a biomarker and important regulator in multiple cancers, including gastric cancer (GC). But the molecular regulatory mechanisms of KRT18 in GC patients and cells are largely unknown. In the present study, we analyzed the expression level of KRT18 in 450 stomach adenocarcinoma tissue samples from TCGA database and found a significantly higher expression level in tumor tissues. We then explored the potential functions of KRT18 in AGS cells (human gastric adenocarcinoma cell line) by KRT18 knockdown using siRNA and whole transcriptome RNA-seq analysis. Notably, KRT18 selectively regulates expression of cell proliferation and apoptotic genes. Beyond this, KRT18 affects the alternative splicing of genes enriched in apoptosis, cell cycle, and other cancer-related pathways, which were then validated by reverse transcription-quantitative polymerase chain reaction approach. We validated KRT18-KD promoted apoptosis and inhibited proliferation in AGS cells. We then used RNA-seq data of GC samples to further demonstrate the modulation of KRT18 on alternative splicing regulation. These results together support the conclusion that KRT18 extensively modulates diverse alternative splicing events of genes enriched in proliferation and apoptosis processes. And the dysregulated splicing factors at transcriptional or posttranscriptional level by KRT18 may contribute to the alternative splicing change of many genes, which expands the functional importance of keratins in apoptotic and cell cycle pathways at the posttranscriptional level in GC.
Collapse
Affiliation(s)
- Biao Chen
- Cancer Center, Renmin Hospital of Wuhan University, Wuhan, China
| | - Ximing Xu
- Cancer Center, Renmin Hospital of Wuhan University, Wuhan, China
| | - Dan-dan Lin
- Cancer Center, Renmin Hospital of Wuhan University, Wuhan, China
| | - Xin Chen
- Cancer Center, Renmin Hospital of Wuhan University, Wuhan, China
| | - Yang-tao Xu
- Cancer Center, Renmin Hospital of Wuhan University, Wuhan, China
| | - Xin Liu
- Cancer Center, Renmin Hospital of Wuhan University, Wuhan, China
| | - Wei-guo Dong
- Department of Gastroenterology, Renmin Hospital of Wuhan University, Wuhan, China
| |
Collapse
|
46
|
Zhang FL, Kong L, Zhao AH, Ge W, Yan ZH, Li L, De Felici M, Shen W. Inflammatory cytokines as key players of apoptosis induced by environmental estrogens in the ovary. ENVIRONMENTAL RESEARCH 2021; 198:111225. [PMID: 33971129 DOI: 10.1016/j.envres.2021.111225] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 01/02/2021] [Accepted: 04/22/2021] [Indexed: 06/12/2023]
Abstract
Natural and synthetic environmental estrogens (EEs), interfering with the physiological functions of the body's estrogens, are widespread and are rising much concern for their possible deleterious effects on human and animal health, in particular on reproduction. In fact, increasing evidence indicate that EEs can be responsible for a variety of disfunctions of the reproductive system especially in females such as premature ovarian insufficiency (POI). Because of their great structural diversity, the modes of action of EEs are controversial. One important way through which EEs exert their effects on reproduction is the induction of apoptosis in the ovary. In general, EEs can exert pro-and anti-apoptotic effects by agonizing or antagonizing numerous estrogen-dependent signaling pathways. In the present work, results concerning apoptotic pathways and diseases induced by representative EEs (such as zearalenone, bisphenol A and di-2-ethylhexyl phthalate), in ovaries throughout development are presented into an integrated network. By reviewing and elaborating these studies, we propose inflammatory factors, centered on the production of tumor necrosis factor (TNF), as a major cause of the induction of apoptosis by EEs in the mammalian ovary. As a consequence, potential strategies to prevent such EE effect are suggested.
Collapse
Affiliation(s)
- Fa-Li Zhang
- College of Life Sciences, Key Laboratory of Animal Reproduction and Germplasm Enhancement in Universities of Shandong, Qingdao Agricultural University, Qingdao, 266109, China
| | - Li Kong
- College of Life Sciences, Key Laboratory of Animal Reproduction and Germplasm Enhancement in Universities of Shandong, Qingdao Agricultural University, Qingdao, 266109, China
| | - Ai-Hong Zhao
- Qingdao Academy of Agricultural Sciences, Qingdao, 266100, China
| | - Wei Ge
- College of Life Sciences, Key Laboratory of Animal Reproduction and Germplasm Enhancement in Universities of Shandong, Qingdao Agricultural University, Qingdao, 266109, China
| | - Zi-Hui Yan
- College of Life Sciences, Key Laboratory of Animal Reproduction and Germplasm Enhancement in Universities of Shandong, Qingdao Agricultural University, Qingdao, 266109, China
| | - Lan Li
- College of Life Sciences, Key Laboratory of Animal Reproduction and Germplasm Enhancement in Universities of Shandong, Qingdao Agricultural University, Qingdao, 266109, China
| | - Massimo De Felici
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, 00133, Italy.
| | - Wei Shen
- College of Life Sciences, Key Laboratory of Animal Reproduction and Germplasm Enhancement in Universities of Shandong, Qingdao Agricultural University, Qingdao, 266109, China.
| |
Collapse
|
47
|
Manes NP, Nita-Lazar A. Molecular Mechanisms of the Toll-Like Receptor, STING, MAVS, Inflammasome, and Interferon Pathways. mSystems 2021; 6:e0033621. [PMID: 34184910 PMCID: PMC8269223 DOI: 10.1128/msystems.00336-21] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Pattern recognition receptors (PRRs) form the front line of defense against pathogens. Many of the molecular mechanisms that facilitate PRR signaling have been characterized in detail, which is critical for the development of accurate PRR pathway models at the molecular interaction level. These models could support the development of therapeutics for numerous diseases, including sepsis and COVID-19. This review describes the molecular mechanisms of the principal signaling interactions of the Toll-like receptor, STING, MAVS, and inflammasome pathways. A detailed molecular mechanism network is included as Data Set S1 in the supplemental material.
Collapse
Affiliation(s)
- Nathan P. Manes
- Functional Cellular Networks Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Aleksandra Nita-Lazar
- Functional Cellular Networks Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| |
Collapse
|
48
|
Padda J, Khalid K, Cooper AC, Jean-Charles G. Association Between Helicobacter pylori and Gastric Carcinoma. Cureus 2021; 13:e15165. [PMID: 34168929 PMCID: PMC8216031 DOI: 10.7759/cureus.15165] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/21/2021] [Indexed: 12/24/2022] Open
Abstract
Gastric carcinoma is the third leading cause of cancer mortality worldwide. In 2018, the incidence of gastric carcinoma worldwide was over 1,000,000 new cases, with approximately 783,000 deaths. The rate of new cases is noticeably increased in Eastern Asia. Helicobacter pylori is responsible for the increased incidence of gastric cancer. In the year 2015, H. pylori had an approximate prevalence of 4.4 billion positive cases worldwide, with the most positive cases found within the region of Africa, Latin America and the Caribbean, and of Asia. H. pylori is known to have multiple strains which allow it to survive in the host cell epithelium chronically. Research has shown many factors which play a significant role in developing infection and thereafter its progression to gastric carcinoma. After H. pylori colonizes the gastric mucosa, its effects can be potentiated by virulence factors, host factors, and environmental factors. H. pylori contains virulence factors that aid in the adhesion, translocation, inflammation, and infectivity of the host gastric epithelium. It alters the functions of the host immune response and cytokines, utilizing these factors to invade and persist in the gastric epithelium for a long period of time. The human body will identify H. pylori to be foreign and will exacerbate an inflammatory response in an effort to eradicate the bacterium. Consequently, this will cause H. pylori to induce a serious infection which may progress to cancer. In this review, we will discuss the various factors involved in the infectious process of H. pylori and how they help the infection progress to gastric carcinoma. This will allow us to better understand and modulate treatments to effectively eradicate this bacterium before it triggers the body into developing cancer.
Collapse
Affiliation(s)
| | | | | | - Gutteridge Jean-Charles
- Internal Medicine, Advent Health and Orlando Health Hospital/JC Medical Center, Orlando, USA
| |
Collapse
|
49
|
Crosstalk between miRNAs and signaling pathways involved in pancreatic cancer and pancreatic ductal adenocarcinoma. Eur J Pharmacol 2021; 901:174006. [PMID: 33711308 DOI: 10.1016/j.ejphar.2021.174006] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 01/19/2021] [Accepted: 03/02/2021] [Indexed: 02/08/2023]
Abstract
Pancreatic cancer (PC) is the seventh leading cause of cancer-related deaths worldwide with 5-year survival rates below 8%. Most patients with PC and pancreatic ductal adenocarcinoma (PDAC) die after relapse and cancer progression as well as resistance to treatment. Pancreatic tumors contain a high desmoplastic stroma that forms a rigid mass and has a potential role in tumor growth and metastasis. PC initiates from intraepithelial neoplasia lesions leading to invasive cancer through various pathways. These lesions harbor particular changes in signaling pathways involved in the tumorigenesis process. These events affect both the epithelial cells, including the tumor and the surrounding stroma, and eventually lead to the formation of complex signaling networks. Genetic studies of PC have revealed common molecular features such as the presence of mutations in KRAS gene in more than 90% of patients, as well as the inactivation or deletion mutations of some tumor suppressor genes including TP53, CDKN2A, and SMAD4. In recent years, studies have also identified different roles of microRNAs in PC pathogenesis as well as their importance in PC diagnosis and treatment, and their involvement in various signaling pathways. In this study, we discussed the most common pathways involved in PC and PDAC as well as their role in tumorigenesis and progression. Furthermore, the miRNAs participating in the regulation of these signaling pathways in PC progression are summarized in this study. Therefore, understanding more about pathways involved in PC can help with the development of new and effective therapies in the future.
Collapse
|
50
|
PARP Traps Rescue the Pro-Inflammatory Response of Human Macrophages in the In Vitro Model of LPS-Induced Tolerance. Pharmaceuticals (Basel) 2021; 14:ph14020170. [PMID: 33671709 PMCID: PMC7926882 DOI: 10.3390/ph14020170] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 02/19/2021] [Accepted: 02/20/2021] [Indexed: 12/29/2022] Open
Abstract
Secondary infections cause sepsis that lead to patient disability or death. Contact of macrophages with bacterial components (such as lipopolysaccharide—LPS) activates the intracellular signaling pathway downstream of Toll-like receptors (TLR), which initiate an immune proinflammatory response. However, the expression of nuclear factor-kappa B (NF-κB)-dependent proinflammatory cytokines significantly decreases after single high or multiple LPS stimulations. Knowing that poly(ADP-ribose) polymerase-1 (PARP1) serves as a cofactor of NF-κB, we aimed to verify a hypothesis of the possible contribution of PARP1 to the development of LPS-induced tolerance in human macrophages. Using TNF-α mRNA expression as a readout, we demonstrate that PARP1 interaction with the TNF-α promoter, controls macrophage immunoparalysis. We confirm that PARP1 is extruded from the gene promoter, whereas cell pretreatment with Olaparib maintains macrophage responsiveness to another LPS treatment. Furthermore, cell pretreatment with proteasome inhibitor MG132 completely abrogates the effect of Olaparib, suggesting that PARP1 acts with NF-κB in the same regulatory pathway, which controls pro-inflammatory cytokine transcription. Mechanistically, PARP1 trapping allows for the re-rebinding of p65 to the TNF-α promoter in LPS-stimulated cells. In conclusion, PARP traps prevent PARP1 extrusion from the TNF-α promoter upon macrophage stimulation, thereby maintaining chromatin responsiveness of TLR activation, allowing for the re-binding of p65 and TNF-α transcription.
Collapse
|