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Lo HC, Lin TE, Lin CY, Wang WH, Chen YC, Tsai PH, Su JC, Lu MK, Hsu WH, Lin TY. Targeting TGFβ receptor-mediated snail and twist: WSG, a polysaccharide from Ganoderma lucidum, and it-based dissolvable microneedle patch suppress melanoma cells. Carbohydr Polym 2024; 341:122298. [PMID: 38876710 DOI: 10.1016/j.carbpol.2024.122298] [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: 03/12/2024] [Revised: 04/18/2024] [Accepted: 05/19/2024] [Indexed: 06/16/2024]
Abstract
Cutaneous melanoma is a lethal skin cancer variant with pronounced aggressiveness and metastatic potential. However, few targeted medications inhibit the progression of melanoma. Ganoderma lucidum, which is a type of mushroom, is widely used as a non-toxic alternative adjunct therapy for cancer patients. This study determines the effect of WSG, which is a water-soluble glucan that is derived from G. lucidum, on melanoma cells. The results show that WSG inhibits cell viability and the mobility of melanoma cells. WSG induces changes in the expression of epithelial-to-mesenchymal transition (EMT)-related markers. WSG also downregulates EMT-related transcription factors, Snail and Twist. Signal transduction assays show that WSG reduces the protein levels in transforming growth factor β receptors (TGFβRs) and consequently inhibits the phosphorylation of intracellular signaling molecules, such as FAK, ERK1/2 and Smad2. An In vivo study shows that WSG suppresses melanoma growth in B16F10-bearing mice. To enhance transdermal drug delivery and prevent oxidation, two highly biocompatible compounds, polyvinyl alcohol (PVA) and polyvinylpyrrolidone (PVP), are used to synthesize a dissolvable microneedle patch that is loaded with WSG (MN-WSG). A functional assay shows that MN-WSG has an effect that is comparable to that of WSG alone. These results show that WSG has significant potential as a therapeutic agent for melanoma treatment. MN-WSG may allow groundbreaking therapeutic approaches and offers a novel method for delivering this potent compound effectively.
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Affiliation(s)
- Hung-Chih Lo
- Program in Molecular Medicine, National Yang Ming Chiao Tung University and Academia Sinica, Taipei, Taiwan; Institute of Traditional Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Tzu-En Lin
- Institute of Biomedical Engineering, National Yang Ming Chiao Tung University, Hsinchu, Taiwan; Institute of Applied Mechanics, National Taiwan University, Taipei, Taiwan
| | - Che-Yu Lin
- Institute of Applied Mechanics, National Taiwan University, Taipei, Taiwan
| | - Wei-Hao Wang
- Institute of Traditional Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Yu-Chen Chen
- Institute of Biomedical Engineering, National Yang Ming Chiao Tung University, Hsinchu, Taiwan
| | - Pei-Hsien Tsai
- Institute of Biomedical Engineering, National Yang Ming Chiao Tung University, Hsinchu, Taiwan
| | - Jung-Chen Su
- Department of Pharmacy, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Mei-Kuang Lu
- Institute of Traditional Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan; National Research Institute of Chinese Medicine, Ministry of Health and Welfare, Taipei, Taiwan; Department of Chinese Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan; Traditional Chinese Medicine Glycomics Research Center, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Wei-Hung Hsu
- Institute of Traditional Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan; LO-Sheng Hospital Ministry of Health and Welfare, Taipei, Taiwan; School of Oral Hygiene, College of Oral Medicine, Taipei Medical University, Taipei, Taiwan; Department of Chinese Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Tung-Yi Lin
- Program in Molecular Medicine, National Yang Ming Chiao Tung University and Academia Sinica, Taipei, Taiwan; Institute of Traditional Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan; Department of Chinese Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan; Traditional Chinese Medicine Glycomics Research Center, National Yang Ming Chiao Tung University, Taipei, Taiwan.
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Yu M, Huo D, Yu K, Zhou K, Xu F, Meng Q, Cai Y, Chen X. Crosstalk of different cell-death patterns predicts prognosis and drug sensitivity in glioma. Comput Biol Med 2024; 175:108532. [PMID: 38703547 DOI: 10.1016/j.compbiomed.2024.108532] [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: 02/27/2024] [Revised: 04/17/2024] [Accepted: 04/28/2024] [Indexed: 05/06/2024]
Abstract
BACKGROUND Glioma is a malignant brain tumor originating from glial cells, and there still a challenge to accurately predict the prognosis. Programmed cell death (PCD) plays a key role in tumorigenesis and immune response. However, the crosstalk and potential role of various PCDs in prognosis and tumor microenvironment remains unknown. Therefore, we comprehensively discussed the relationship between different models of PCD and the prognosis of glioma and provided new ideas for the optimal targeted therapy of glioma. MATERIALS AND METHODS We compared and analyzed the role of 14 PCD patterns on the prognosis from different levels. We constructed the cell death risk score (CDRS) index and conducted a comprehensive analysis of CDRS and TME characteristics, clinical characteristics, and drug response. RESULTS Effects of different PCDs at the genomic, functional, and immune microenvironment levels were discussed. CDRS index containing 6 gene signatures and a nomogram were established. High CDRS is associated with a worse prognosis. Through transcriptome and single-cell data, we found that patients with high CDRS showed stronger immunosuppressive characteristics. Moreover, the high-CDRS group was resistant to the traditional glioma chemotherapy drug Vincristine, but more sensitive to the Temozolomide and the clinical experimental drug Bortezomib. In addition, we identified 19 key potential therapeutic targets during malignant differentiation of tumor cells. CONCLUSION Overall, we provide the first systematic description of the role of 14 PCDs in glioma. A new CDRS model was built to predict the prognosis and to provide a new idea for the targeted therapy of glioma.
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Affiliation(s)
- Meini Yu
- Department of pharmacogenomics, College of Bioinformatics Science and Technology, Harbin Medical University, 150081, Harbin, Heilongjiang, China
| | - Diwei Huo
- Fourth Affiliated Hospital of Harbin Medical University, China
| | - Kexin Yu
- Department of pharmacogenomics, College of Bioinformatics Science and Technology, Harbin Medical University, 150081, Harbin, Heilongjiang, China
| | - Kun Zhou
- Department of pharmacogenomics, College of Bioinformatics Science and Technology, Harbin Medical University, 150081, Harbin, Heilongjiang, China
| | - Fei Xu
- Department of pharmacogenomics, College of Bioinformatics Science and Technology, Harbin Medical University, 150081, Harbin, Heilongjiang, China
| | - Qingkang Meng
- Department of pharmacogenomics, College of Bioinformatics Science and Technology, Harbin Medical University, 150081, Harbin, Heilongjiang, China
| | - Yiyang Cai
- Department of pharmacogenomics, College of Bioinformatics Science and Technology, Harbin Medical University, 150081, Harbin, Heilongjiang, China
| | - Xiujie Chen
- Department of pharmacogenomics, College of Bioinformatics Science and Technology, Harbin Medical University, 150081, Harbin, Heilongjiang, China.
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Diaw SH, Delcambre S, Much C, Ott F, Kostic VS, Gajos A, Münchau A, Zittel S, Busch H, Grünewald A, Klein C, Lohmann K. DYT-THAP1: exploring gene expression in fibroblasts for potential biomarker discovery. Neurogenetics 2024; 25:141-147. [PMID: 38498291 DOI: 10.1007/s10048-024-00752-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 03/04/2024] [Indexed: 03/20/2024]
Abstract
Dystonia due to pathogenic variants in the THAP1 gene (DYT-THAP1) shows variable expressivity and reduced penetrance of ~ 50%. Since THAP1 encodes a transcription factor, modifiers influencing this variability likely operate at the gene expression level. This study aimed to assess the transferability of differentially expressed genes (DEGs) in neuronal cells related to pathogenic variants in the THAP1 gene, which were previously identified by transcriptome analyses. For this, we performed quantitative (qPCR) and Digital PCR (dPCR) in cultured fibroblasts. RNA was extracted from THAP1 manifesting (MMCs) and non-manifesting mutation carriers (NMCs) as well as from healthy controls. The expression profiles of ten of 14 known neuronal DEGs demonstrated differences in fibroblasts between these three groups. This included transcription factors and targets (ATF4, CLN3, EIF2A, RRM1, YY1), genes involved in G protein-coupled receptor signaling (BDKRB2, LPAR1), and a gene linked to apoptosis and DNA replication/repair (CRADD), which all showed higher expression levels in MMCs and NMCs than in controls. Moreover, the analysis of genes linked to neurological disorders (STXBP1, TOR1A) unveiled differences in expression patterns between MMCs and controls. Notably, the genes CUEDC2, DRD4, ECH1, and SIX2 were not statistically significantly differentially expressed in fibroblast cultures. With > 70% of the tested genes being DEGs also in fibroblasts, fibroblasts seem to be a suitable model for DYT-THAP1 research despite some restrictions. Furthermore, at least some of these DEGs may potentially also serve as biomarkers of DYT-THAP1 and influence its penetrance and expressivity.
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Affiliation(s)
| | - Sylvie Delcambre
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, L-4362, Luxembourg
| | - Christoph Much
- Institute of Neurogenetics, University of Lübeck, 23562, Lübeck, Germany
| | - Fabian Ott
- Institute of Experimental Dermatology and Institute of Cardiogenetics, University of Lübeck, 23562, Lübeck, Germany
| | - Vladimir S Kostic
- Institute of Neurology, School of Medicine, University of Belgrade, Belgrade, 11000, Serbia
| | - Agata Gajos
- Department of Extrapyramidal Diseases, Medical University of Lodz, Lodz, 90-647, Poland
| | - Alexander Münchau
- Institute of Systems Motor Science, University of Lübeck, 23562, Lübeck, Germany
| | - Simone Zittel
- Department of Neurology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Hauke Busch
- Institute of Experimental Dermatology and Institute of Cardiogenetics, University of Lübeck, 23562, Lübeck, Germany
| | - Anne Grünewald
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, L-4362, Luxembourg
| | - Christine Klein
- Institute of Neurogenetics, University of Lübeck, 23562, Lübeck, Germany
| | - Katja Lohmann
- Institute of Neurogenetics, University of Lübeck, 23562, Lübeck, Germany.
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Wu M, Shi Y, Liu Y, Li Z, Wu H, Yu Z, Wang Z, Xu C. A Human Adenovirus C Infection-Related Gene Panel for Predicting Survival and Treatment Responsiveness in Glioma Patients. World Neurosurg 2024; 183:e173-e186. [PMID: 38097166 DOI: 10.1016/j.wneu.2023.12.051] [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: 11/30/2023] [Accepted: 12/10/2023] [Indexed: 01/14/2024]
Abstract
BACKGROUND Viruses are critical for the regulation of cancer development and for therapy. Human adenovirus C (HadVC) has been detected in central nervous system and glioma tissue. The objective of the present study was the development of a robust prognostic model based on HadVC infection (HadVCi)-relevant genes. METHODS The genome, transcriptome, and virome were systemically analyzed using The Cancer Genome Atlas dataset for training and 2 cohorts from the Chinese Glioma Genome Atlas and an immunotherapy trial cohort with 17 patients receiving anti-PD-1 treatment for validation. HadVCi-relevant gene selection from differentially expressed genes between HadVC-infected and non-HadVC-infected glioma patients using least absolute shrinkage and selection operator regression was followed by Cox regression modeling to establish a prognostic HadVCi score. Kaplan-Meier and receiver operating characteristic curve analyses were performed to estimate the predictive capacity of the HadVCi score. The χ2, Spearman, and Mann-Whitney U tests were used to identify the correlation with the clinicopathological parameters, treatment responsiveness, and immune landscape. Temozolomide-resistant glioma cells were established and analyzed at the transcriptional level using RNA sequencing data. RESULTS The HadVCi score was (-0.2526673∗TRPC6) + (-0.2244276∗RNF207) + (-0.0894468∗SEC31B) + (-0.0190214∗ZCRB1) + (-0.017122∗DNPH1) + (0.0495818∗CCDC34) + (0.1196349∗PURG) + (0.1778997∗LILRA5). The score possesses a strong ability to predict overall survival. Further analysis revealed a higher HadVCi score correlated with a malignant phenotype and poorer treatment responsiveness to temozolomide-based chemotherapy and combined therapies. Additionally, transcriptomic analysis showed malignancy-, stemness-, and radioresistant-related gene activation in the HadVCi group, which characterized the poor outcomes and limited sensitivity to standard therapy. CONCLUSIONS The HadVCi score could be an effective tool for survival prediction and treatment guidance for patients with glioma.
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Affiliation(s)
- Mengwan Wu
- Department of Oncology, Sichuan Academy of Medical Sciences, Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Ying Shi
- Department of Oncology, Sichuan Academy of Medical Sciences, Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Yuyang Liu
- Department of Neurosurgery, 920th Hospital of Joint Logistics Support Force, Kunming, China
| | - Zhaoshen Li
- Guangxi Medical University Cancer Hospital, Guangxi Medical University, Nanning, China
| | - Hong Wu
- Integrative Cancer Center & Cancer Clinical Research Center, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Zhuoyang Yu
- Department of Oncology, Sichuan Academy of Medical Sciences, Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Zhao Wang
- School of Electronic Science and Engineering, University of Electronic Science and Technology of China, Chengdu, China
| | - Chuan Xu
- Department of Oncology, Sichuan Academy of Medical Sciences, Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China.
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Hong J, Wang X, Jin H, Chen Y, Jiang Y, Du K, Chen D, Zheng S, Cao L. Environment relevant exposure of perfluorooctanoic acid accelerates the growth of hepatocellular carcinoma cells through mammalian target of rapamycin (mTOR) signal pathway. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 341:122910. [PMID: 37967710 DOI: 10.1016/j.envpol.2023.122910] [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: 08/26/2023] [Revised: 10/25/2023] [Accepted: 11/08/2023] [Indexed: 11/17/2023]
Abstract
Perfluorooctanoic acid (PFOA), a synthetic alkyl chain fluorinated compound, has emerged as a persistent organic pollutant of grave concern, casting a shadow over both ecological integrity and humans. Its insidious presence raises alarms due to its capacity to bioaccumulate within the human liver, potentially paving the treacherous path toward liver cancer. Yet, the intricate mechanisms underpinning PFOA's role in promoting the growth of hepatocellular carcinoma (HCC) remain shrouded in ambiguity. Here, we determined the proliferation and transcription changes of HCC after PFOA exposure through integrated experiments including cell culture, nude mice tests, and colony-forming assays. Based on our findings, PFOA effectively promotes the proliferation of HCC cells within the experimental range of concentrations, both in vivo and in vitro. The proliferation efficiency of HCC cells was observed to increase by approximately 10% due to overexposure to PFOA. Additionally, the cancer weight of tumor-bearing nude mice increased by 87.0% (p < 0.05). We systematically evaluated the effects of PFOA on HCC cells and found that PFOA's exposure can selectively activate the PI3K/AKT/mTOR/4E-BP1 signaling pathway, thereby playing a pro-cancer effect on HCC cells Confirmation echoed through western blot assays and inhibitor combination analyses. These insights summon a response to PFOA's dual nature as both an environmental threat and a promoter of liver cancer. Our work illuminates the obscured domain of PFOA-induced hepatoxicity, shedding light on its ties to hepatocellular carcinoma progression.
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Affiliation(s)
- Jiawei Hong
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, PR China; Zhejiang University School of Medicine, Zhejiang University, Hangzhou, 310003, PR China; NHC Key Laboratory of Combined Multi-organ Transplantation, Hangzhou, 310003, PR China
| | - Xiaoyan Wang
- Zhejiang University School of Medicine, Zhejiang University, Hangzhou, 310003, PR China
| | - Hangbiao Jin
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou, Zhejiang, 310032, PR China
| | - Yuanchen Chen
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou, Zhejiang, 310032, PR China
| | - Yifan Jiang
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, PR China; Zhejiang University School of Medicine, Zhejiang University, Hangzhou, 310003, PR China; NHC Key Laboratory of Combined Multi-organ Transplantation, Hangzhou, 310003, PR China
| | - Keyi Du
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, PR China; Zhejiang University School of Medicine, Zhejiang University, Hangzhou, 310003, PR China; NHC Key Laboratory of Combined Multi-organ Transplantation, Hangzhou, 310003, PR China
| | - Diyu Chen
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, PR China; Zhejiang University School of Medicine, Zhejiang University, Hangzhou, 310003, PR China; NHC Key Laboratory of Combined Multi-organ Transplantation, Hangzhou, 310003, PR China
| | - Shusen Zheng
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, PR China; Zhejiang University School of Medicine, Zhejiang University, Hangzhou, 310003, PR China; NHC Key Laboratory of Combined Multi-organ Transplantation, Hangzhou, 310003, PR China
| | - Linping Cao
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, PR China; Zhejiang University School of Medicine, Zhejiang University, Hangzhou, 310003, PR China; NHC Key Laboratory of Combined Multi-organ Transplantation, Hangzhou, 310003, PR China.
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Li C, Li Z, Zhang M, Dai J, Wang Y, Zhang Z. An overview of Twist1 in glioma progression and recurrence. INTERNATIONAL REVIEW OF NEUROBIOLOGY 2023; 172:285-301. [PMID: 37833014 DOI: 10.1016/bs.irn.2023.07.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/15/2023]
Abstract
Glioma cells are characterized by high migration ability, resulting in the aggressive growth of the tumors and poor prognosis of patients. Epithelial-to-mesenchymal transition (EMT) is one of the most important steps for tumor migration and metastasis and be elevated during glioma progression and recurrence. Twist1 is a basic helix-loop-helix transcription factor and a key transcription factor involved in the process of EMT. Twist1 is related to glioma mesenchymal change, invasion, heterogeneity, self-renewal of tumor stem cells, angiogenesis, etc., and may be used as a prognostic indicator and therapeutic target for glioma patients. This paper mainly reviews the structural characteristics, regulatory mechanisms, and apparent regulation of Twist1, as well as the roles of Twist1 during glioma progression and recurrence, providing new revelations for its use as a potential drug target and glioma treatment research.
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Affiliation(s)
- Cong Li
- The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangdong Province Hospital of Chinese Medicine, Guangzhou, Guangdong Province, P.R. China; The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong Province, P.R. China
| | - Zixuan Li
- The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong Province, P.R. China
| | - Mengyi Zhang
- The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong Province, P.R. China
| | - Jiaxuan Dai
- The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong Province, P.R. China
| | - Yunmin Wang
- The Jining City Center Blood Station, Jining, Shandong Province, P.R. China.
| | - Zhiqiang Zhang
- The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangdong Province Hospital of Chinese Medicine, Guangzhou, Guangdong Province, P.R. China; The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong Province, P.R. China.
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Li S, Chen X, Chen J, Wu B, Liu J, Guo Y, Li M, Pu X. Multi-omics integration analysis of GPCRs in pan-cancer to uncover inter-omics relationships and potential driver genes. Comput Biol Med 2023; 161:106988. [PMID: 37201441 DOI: 10.1016/j.compbiomed.2023.106988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 03/30/2023] [Accepted: 04/27/2023] [Indexed: 05/20/2023]
Abstract
G protein-coupled receptors (GPCRs) are the largest drug target family. Unfortunately, applications of GPCRs in cancer therapy are scarce due to very limited knowledge regarding their correlations with cancers. Multi-omics data enables systematic investigations of GPCRs, yet their effective integration remains a challenge due to the complexity of the data. Here, we adopt two types of integration strategies, multi-staged and meta-dimensional approaches, to fully characterize somatic mutations, somatic copy number alterations (SCNAs), DNA methylations, and mRNA expressions of GPCRs in 33 cancers. Results from the multi-staged integration reveal that GPCR mutations cannot well predict expression dysregulation. The correlations between expressions and SCNAs are primarily positive, while correlations of the methylations with expressions and SCNAs are bimodal with negative correlations predominating. Based on these correlations, 32 and 144 potential cancer-related GPCRs driven by aberrant SCNA and methylation are identified, respectively. In addition, the meta-dimensional integration analysis is carried out by using deep learning models, which predict more than one hundred GPCRs as potential oncogenes. When comparing results between the two integration strategies, 165 cancer-related GPCRs are common in both, suggesting that they should be prioritized in future studies. However, 172 GPCRs emerge in only one, indicating that the two integration strategies should be considered concurrently to complement the information missed by the other such that obtain a more comprehensive understanding. Finally, correlation analysis further reveals that GPCRs, in particular for the class A and adhesion receptors, are generally immune-related. In a whole, the work is for the first time to reveal the associations between different omics layers and highlight the necessity of combing the two strategies in identifying cancer-related GPCRs.
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Affiliation(s)
- Shiqi Li
- College of Chemistry, Sichuan University, Chengdu, 610064, China.
| | - Xin Chen
- College of Chemistry, Sichuan University, Chengdu, 610064, China.
| | - Jianfang Chen
- College of Chemistry, Sichuan University, Chengdu, 610064, China.
| | - Binjian Wu
- College of Chemistry, Sichuan University, Chengdu, 610064, China.
| | - Jing Liu
- College of Chemistry, Sichuan University, Chengdu, 610064, China.
| | - Yanzhi Guo
- College of Chemistry, Sichuan University, Chengdu, 610064, China.
| | - Menglong Li
- College of Chemistry, Sichuan University, Chengdu, 610064, China.
| | - Xuemei Pu
- College of Chemistry, Sichuan University, Chengdu, 610064, China.
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8
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Wong HH, Seet SH, Bascom CC, Isfort RJ, Bard F. Tonic repression of Collagen I by the Bradykinin receptor 2 in skin fibroblasts. Matrix Biol 2023; 118:110-128. [PMID: 36924903 DOI: 10.1016/j.matbio.2023.03.004] [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: 09/02/2022] [Revised: 03/06/2023] [Accepted: 03/06/2023] [Indexed: 03/18/2023]
Abstract
Imbalance of collagen I expression results in severe pathologies. Apart from activation by the TGFβ-receptor/Smad pathway, control of collagen I expression remains poorly understood. Here, we used human dermal fibroblasts expressing a mCherry fluorescent protein driven by endogenous COL1A1 promoter to functionally screen the kinome and phosphatome. We identify 8 negative regulators, revealing that collagen is under tonic repression. The cell surface receptor BDKRB2 represses collagen I and other pro-fibrotic genes. Interestingly, it also promotes other basal membrane ECM genes. This function is independent of the natural ligand, bradykinin, and of SMAD2/3 factors, instead requiring constant ERK1/2 repression. TGFβ stimulation induces rapid BDKRB2 transcriptional downregulation. Human fibrotic fibroblasts have reduced BDKRB2 levels and enhancing its expression in keloid fibroblasts represses COL1A1. We propose that tonic signalling by BDKRB2 prevents collagen overproduction in skin fibroblasts.
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Affiliation(s)
- Hui Hui Wong
- Institute of Molecular and Cell Biology, 61 Biopolis Drive, Singapore 138673
| | - Sze Hwee Seet
- Institute of Molecular and Cell Biology, 61 Biopolis Drive, Singapore 138673
| | - Charles C Bascom
- The Procter & Gamble Company, 8700 Mason-Montgomery Road, Cincinnati, OH 45040, USA
| | - Robert J Isfort
- The Procter & Gamble Company, 8700 Mason-Montgomery Road, Cincinnati, OH 45040, USA
| | - Frederic Bard
- Institute of Molecular and Cell Biology, 61 Biopolis Drive, Singapore 138673; Centre de Recherche en Cancérologie de Marseille, CRCM, Aix Marseille Université, Inserm, CNRS, Institut Paoli-Calmettes, Equipe Leader Fondation ARC 2021, 13009, Marseille, France..
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9
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Shikhevich S, Chadaeva I, Khandaev B, Kozhemyakina R, Zolotareva K, Kazachek A, Oshchepkov D, Bogomolov A, Klimova NV, Ivanisenko VA, Demenkov P, Mustafin Z, Markel A, Savinkova L, Kolchanov NA, Kozlov V, Ponomarenko M. Differentially Expressed Genes and Molecular Susceptibility to Human Age-Related Diseases. Int J Mol Sci 2023; 24:ijms24043996. [PMID: 36835409 PMCID: PMC9966505 DOI: 10.3390/ijms24043996] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 02/02/2023] [Accepted: 02/13/2023] [Indexed: 02/18/2023] Open
Abstract
Mainstream transcriptome profiling of susceptibility versus resistance to age-related diseases (ARDs) is focused on differentially expressed genes (DEGs) specific to gender, age, and pathogeneses. This approach fits in well with predictive, preventive, personalized, participatory medicine and helps understand how, why, when, and what ARDs one can develop depending on their genetic background. Within this mainstream paradigm, we wanted to find out whether the known ARD-linked DEGs available in PubMed can reveal a molecular marker that will serve the purpose in anyone's any tissue at any time. We sequenced the periaqueductal gray (PAG) transcriptome of tame versus aggressive rats, identified rat-behavior-related DEGs, and compared them with their known homologous animal ARD-linked DEGs. This analysis yielded statistically significant correlations between behavior-related and ARD-susceptibility-related fold changes (log2 values) in the expression of these DEG homologs. We found principal components, PC1 and PC2, corresponding to the half-sum and the half-difference of these log2 values, respectively. With the DEGs linked to ARD susceptibility and ARD resistance in humans used as controls, we verified these principal components. This yielded only one statistically significant common molecular marker for ARDs: an excess of Fcγ receptor IIb suppressing immune cell hyperactivation.
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Affiliation(s)
- Svetlana Shikhevich
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences (SB RAS), Novosibirsk 630090, Russia
| | - Irina Chadaeva
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences (SB RAS), Novosibirsk 630090, Russia
| | - Bato Khandaev
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences (SB RAS), Novosibirsk 630090, Russia
- The Natural Sciences Department, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Rimma Kozhemyakina
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences (SB RAS), Novosibirsk 630090, Russia
| | - Karina Zolotareva
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences (SB RAS), Novosibirsk 630090, Russia
- The Natural Sciences Department, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Anna Kazachek
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences (SB RAS), Novosibirsk 630090, Russia
- The Natural Sciences Department, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Dmitry Oshchepkov
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences (SB RAS), Novosibirsk 630090, Russia
- The Natural Sciences Department, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Anton Bogomolov
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences (SB RAS), Novosibirsk 630090, Russia
- The Natural Sciences Department, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Natalya V. Klimova
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences (SB RAS), Novosibirsk 630090, Russia
| | - Vladimir A. Ivanisenko
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences (SB RAS), Novosibirsk 630090, Russia
- The Natural Sciences Department, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Pavel Demenkov
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences (SB RAS), Novosibirsk 630090, Russia
| | - Zakhar Mustafin
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences (SB RAS), Novosibirsk 630090, Russia
- The Natural Sciences Department, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Arcady Markel
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences (SB RAS), Novosibirsk 630090, Russia
- The Natural Sciences Department, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Ludmila Savinkova
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences (SB RAS), Novosibirsk 630090, Russia
| | - Nikolay A. Kolchanov
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences (SB RAS), Novosibirsk 630090, Russia
- The Natural Sciences Department, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Vladimir Kozlov
- Research Institute of Fundamental and Clinical Immunology (RIFCI) SB RAS, Novosibirsk 630099, Russia
| | - Mikhail Ponomarenko
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences (SB RAS), Novosibirsk 630090, Russia
- Correspondence: ; Tel.: +7-(383)-363-4963 (ext. 1311)
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MicroRNA and mRNA Expression Changes in Glioblastoma Cells Cultivated under Conditions of Neurosphere Formation. Curr Issues Mol Biol 2022; 44:5294-5311. [PMID: 36354672 PMCID: PMC9688839 DOI: 10.3390/cimb44110360] [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: 10/05/2022] [Revised: 10/21/2022] [Accepted: 10/27/2022] [Indexed: 11/29/2022] Open
Abstract
Glioblastoma multiforme (GBM) is one of the most highly metastatic cancers. The study of the pathogenesis of GBM, as well as the development of targeted oncolytic drugs, require the use of actual cell models, in particular, the use of 3D cultures or neurospheres (NS). During the formation of NS, the adaptive molecular landscape of the transcriptome, which includes various regulatory RNAs, changes. The aim of this study was to reveal changes in the expression of microRNAs (miRNAs) and their target mRNAs in GBM cells under conditions of NS formation. Neurospheres were obtained from both immortalized U87 MG and patient-derived BR3 GBM cell cultures. Next generation sequencing analysis of small and long RNAs of adherent and NS cultures of GBM cells was carried out. It was found that the formation of NS proceeds with an increase in the level of seven and a decrease in the level of 11 miRNAs common to U87 MG and BR3, as well as an increase in the level of 38 and a decrease in the level of 12 mRNA/lncRNA. Upregulation of miRNAs hsa-miR: -139-5p; -148a-3p; -192-5p; -218-5p; -34a-5p; and -381-3p are accompanied by decreased levels of their target mRNAs: RTN4, FLNA, SH3BP4, DNPEP, ETS2, MICALL1, and GREM1. Downregulation of hsa-miR: -130b-5p, -25-5p, -335-3p and -339-5p occurs with increased levels of mRNA-targets BDKRB2, SPRY4, ERRFI1 and TGM2. The involvement of SPRY4, ERRFI1, and MICALL1 mRNAs in the regulation of EGFR/FGFR signaling highlights the role of hsa-miR: -130b-5p, -25-5p, -335-3p, and -34a-5p not only in the formation of NS, but also in the regulation of malignant growth and invasion of GBM. Our data provide the basis for the development of new approaches to the diagnosis and treatment of GBM.
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Chen J, Zhuang YD, Zhang Q, Liu S, Zhuang BB, Wang CH, Liang RS. Exploring the mechanism of cordycepin combined with doxorubicin in treating glioblastoma based on network pharmacology and biological verification. PeerJ 2022; 10:e12942. [PMID: 35186504 PMCID: PMC8855715 DOI: 10.7717/peerj.12942] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 01/24/2022] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND Glioblastoma is the most common and fatal primary malignant tumor in the central nervous system, and the prognosis is poor. Currently, there are no effective treatments for glioblastoma. Cordycepin is a natural active substance with significant anticancer activity and doxorubicin is a broad-spectrum anticancer drug. Cordycepin administered with doxorubicin is a potential drug combination for the treatment of glioblastoma. However, the mechanism of action for this drug combination has not yet been elucidated. AIM OF THE STUDY To explore the complex mechanism of cordycepin combined with doxorubicin against glioblastoma using network pharmacology and biological verification. MATERIALS AND METHODS We used an MTT assay, colony formation assay, and scratch healing to detect the growth, proliferation, and migration of LN-229, U251 and T98G cells. Putative targets and the potential mechanism of action for the drug combination in glioblastoma were obtained through online databases, network construction, and enrichment analyses. We verified the expression of EMT-related genes and identified important therapeutic targets by western blot. RESULTS In this study, the combination of doxorubicin and cordycepin was found to significantly inhibit cell proliferation and migration and can induce apoptosis. These effects are better together than with either drug alone. The drug combination inhibited EMT by upregulating the expression of E-cadherin protein and downregulating the expression of N-cadherin, ZEB1, and Twist1 proteins. There were 71 potential targets for the drug combination in glioblastoma, and Kyoto Encyclopedia of Genes and Genome analysis suggested that the anticancer process may be mediated by proteoglycans in cancer, the tumor necrosis factor signaling pathway, microRNA in cancer, pathways in cancer, and other pathways. To study the molecular mechanism of anticancer activity, we detected the expression of target proteins with downregulated expression of NFKB1, MAPK8, MYC, and MMP-9 proteins and upregulated expression of cleaved caspase 3 that promoted the apoptosis of LN-229 cells. CONCLUSIONS This study shows that the drug combination of doxorubicin and cordycepin effectively inhibits the growth and proliferation of LN-229 cells through multiple targets and multiple pathways, and the combination inhibits cell invasion and migration by regulating the EMT switch of tumor cells. Our findings provide new ideas about, and a theoretical basis for, the treatment of glioblastoma.
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Affiliation(s)
- Jing Chen
- Fujian Medical University Union Hospital, Fuzhou, Fujian, China
| | | | - Qiang Zhang
- Fujian Medical University Union Hospital, Fuzhou, China
| | - Shuang Liu
- Fujian Medical University Union Hospital, Fuzhou, China
| | | | - Chun-Hua Wang
- Fujian Medical University Union Hospital, Fuzhou, China
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Transcriptomics-Based Phenotypic Screening Supports Drug Discovery in Human Glioblastoma Cells. Cancers (Basel) 2021; 13:cancers13153780. [PMID: 34359681 PMCID: PMC8345128 DOI: 10.3390/cancers13153780] [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: 06/09/2021] [Revised: 07/16/2021] [Accepted: 07/20/2021] [Indexed: 12/11/2022] Open
Abstract
Simple Summary Glioblastoma (GBM) remains a particularly challenging cancer, with an aggressive phenotype and few promising treatment options. Future therapy will rely heavily on diagnosing and targeting aggressive GBM cellular phenotypes, both before and after drug treatment, as part of personalized therapy programs. Here, we use a genome-wide drug-induced gene expression (DIGEX) approach to define the cellular drug response phenotypes associated with two clinical drug candidates, the phosphodiesterase 10A inhibitor Mardepodect and the multi-kinase inhibitor Regorafenib. We identify genes encoding specific drug targets, some of which we validate as effective antiproliferative agents and combination therapies in human GBM cell models, including HMGCoA reductase (HMGCR), salt-inducible kinase 1 (SIK1), bradykinin receptor subtype B2 (BDKRB2), and Janus kinase isoform 2 (JAK2). Individual, personalized treatments will be essential if we are to address and overcome the pharmacological plasticity that GBM exhibits, and DIGEX will play a central role in validating future drugs, diagnostics, and possibly vaccine candidates for this challenging cancer. Abstract We have used three established human glioblastoma (GBM) cell lines—U87MG, A172, and T98G—as cellular systems to examine the plasticity of the drug-induced GBM cell phenotype, focusing on two clinical drugs, the phosphodiesterase PDE10A inhibitor Mardepodect and the multi-kinase inhibitor Regorafenib, using genome-wide drug-induced gene expression (DIGEX) to examine the drug response. Both drugs upregulate genes encoding specific growth factors, transcription factors, cellular signaling molecules, and cell surface proteins, while downregulating a broad range of targetable cell cycle and apoptosis-associated genes. A few upregulated genes encode therapeutic targets already addressed by FDA approved drugs, but the majority encode targets for which there are no approved drugs. Amongst the latter, we identify many novel druggable targets that could qualify for chemistry-led drug discovery campaigns. We also observe several highly upregulated transmembrane proteins suitable for combined drug, immunotherapy, and RNA vaccine approaches. DIGEX is a powerful way of visualizing the complex drug response networks emerging during GBM drug treatment, defining a phenotypic landscape which offers many new diagnostic and therapeutic opportunities. Nevertheless, the extreme heterogeneity we observe within drug-treated cells using this technique suggests that effective pan-GBM drug treatment will remain a significant challenge for many years to come.
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