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Wang Y, Chen X, Tang N, Guo M, Ai D. Boosting Clear Cell Renal Carcinoma-Specific Drug Discovery Using a Deep Learning Algorithm and Single-Cell Analysis. Int J Mol Sci 2024; 25:4134. [PMID: 38612943 PMCID: PMC11012314 DOI: 10.3390/ijms25074134] [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: 02/17/2024] [Revised: 03/26/2024] [Accepted: 04/03/2024] [Indexed: 04/14/2024] Open
Abstract
Clear cell renal carcinoma (ccRCC), the most common subtype of renal cell carcinoma, has the high heterogeneity of a highly complex tumor microenvironment. Existing clinical intervention strategies, such as target therapy and immunotherapy, have failed to achieve good therapeutic effects. In this article, single-cell transcriptome sequencing (scRNA-seq) data from six patients downloaded from the GEO database were adopted to describe the tumor microenvironment (TME) of ccRCC, including its T cells, tumor-associated macrophages (TAMs), endothelial cells (ECs), and cancer-associated fibroblasts (CAFs). Based on the differential typing of the TME, we identified tumor cell-specific regulatory programs that are mediated by three key transcription factors (TFs), whilst the TF EPAS1/HIF-2α was identified via drug virtual screening through our analysis of ccRCC's protein structure. Then, a combined deep graph neural network and machine learning algorithm were used to select anti-ccRCC compounds from bioactive compound libraries, including the FDA-approved drug library, natural product library, and human endogenous metabolite compound library. Finally, five compounds were obtained, including two FDA-approved drugs (flufenamic acid and fludarabine), one endogenous metabolite, one immunology/inflammation-related compound, and one inhibitor of DNA methyltransferase (N4-methylcytidine, a cytosine nucleoside analogue that, like zebularine, has the mechanism of inhibiting DNA methyltransferase). Based on the tumor microenvironment characteristics of ccRCC, five ccRCC-specific compounds were identified, which would give direction of the clinical treatment for ccRCC patients.
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Affiliation(s)
| | | | | | | | - Dongmei Ai
- School of Mathematics and Physics, University of Science and Technology Beijing, Beijing 100083, China; (Y.W.); (X.C.); (N.T.); (M.G.)
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White G, Nonaka D, Chung TT, Oakey RJ, Izatt L. Somatic EPAS1 Variants in Pheochromocytoma and Paraganglioma in Patients With Sickle Cell Disease. J Clin Endocrinol Metab 2023; 108:3302-3310. [PMID: 37285480 PMCID: PMC10655516 DOI: 10.1210/clinem/dgad311] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 05/09/2023] [Accepted: 05/26/2023] [Indexed: 06/09/2023]
Abstract
CONTEXT Somatic EPAS1 variants account for 5% to 8% of all pheochromocytoma and paragangliomas (PPGL) but are detected in over 90% of PPGL in patients with congenital cyanotic heart disease, where hypoxemia may select for EPAS1 gain-of-function variants. Sickle cell disease (SCD) is an inherited hemoglobinopathy associated with chronic hypoxia and there are isolated reports of PPGL in patients with SCD, but a genetic link between the conditions has yet to be established. OBJECTIVE To determine the phenotype and EPAS1 variant status of patients with PPGL and SCD. METHODS Records of 128 patients with PPGL under follow-up at our center from January 2017 to December 2022 were screened for SCD diagnosis. For identified patients, clinical data and biological specimens were obtained, including tumor, adjacent non-tumor tissue and peripheral blood. Sanger sequencing of exons 9 and 12 of EPAS1, followed by amplicon next-generation sequencing of identified variants was performed on all samples. RESULTS Four patients with both PPGL and SCD were identified. Median age at PPGL diagnosis was 28 years. Three tumors were abdominal paragangliomas and 1 was a pheochromocytoma. No germline pathogenic variants in PPGL-susceptibility genes were identified in the cohort. Genetic testing of tumor tissue detected unique EPAS1 variants in all 4 patients. Variants were not detected in the germline, and 1 variant was detected in lymph node tissue of a patient with metastatic disease. CONCLUSION We propose that somatic EPAS1 variants may be acquired through exposure to chronic hypoxia in SCD and drive PPGL development. Future work is needed to further characterize this association.
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Affiliation(s)
- Gemma White
- Department of Medical and Molecular Genetics, King's College London, London, SE1 9RT, UK
- Department of Clinical Genetics, Guy's and St Thomas’ NHS Foundation Trust, London, SE1 9RT, UK
| | - Daisuke Nonaka
- Department of Pathology, Guy's and St Thomas’ NHS Foundation Trust, London, SE1 7EH, UK
- Department of Cellular Pathology, King's College London, London, SE1 1UL, UK
| | - Teng-Teng Chung
- Department of Endocrinology, University College London Hospital NHS Foundation Trust, London, NW1 2BU, UK
| | - Rebecca J Oakey
- Department of Medical and Molecular Genetics, King's College London, London, SE1 9RT, UK
| | - Louise Izatt
- Department of Medical and Molecular Genetics, King's College London, London, SE1 9RT, UK
- Department of Clinical Genetics, Guy's and St Thomas’ NHS Foundation Trust, London, SE1 9RT, UK
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Qin D, Yu F, Wu D, Han C, Yao X, Yang L, Yang X, Wang Q, He D, Zhao B. The underlying molecular mechanisms and biomarkers between periodontitis and COVID-19. BMC Oral Health 2023; 23:524. [PMID: 37495990 PMCID: PMC10369766 DOI: 10.1186/s12903-023-03150-4] [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: 02/20/2023] [Accepted: 06/20/2023] [Indexed: 07/28/2023] Open
Abstract
OBJECTIVE Emerging evidence shows the clinical consequences of patient with COVID-19 and periodontitis are not promising, and periodontitis is a risk factor. Periodontitis and COVID-19 probably have a relationship. Hence, this study aimed to identify the common molecular mechanism that may help to devise potential therapeutic strategies in the future. MATERIAL AND METHODS We analyzed two RNA-seq datasets for differential expressed genes, enrichment of biological processes, transcription factors (TFs) and deconvolution-based immune cell types in periodontitis, COVID-19 and healthy controls. Relationships between TFs and mRNA were established by Pearson correlation analysis, and the common TFs-mRNA regulatory network and nine co-upregulated TFs of the two diseases was obtained. The RT-PCR detected the TFs. RESULTS A total of 1616 and 10201 differentially expressed gene (DEGs) from periodontitis and COVID-19 are found. Moreover, nine shared TFs and common biological processes associated with lymphocyte activation involved in immune response were identified across periodontitis and COVID-19. The cell type enrichment revealed elevated plasma cells among two diseases. The RT-PCR further confirmed the nine TFs up-regulation in periodontitis. CONCLUSION The pathogenesis of periodontitis and COVID-19 is closely related to the expression of TFs and lymphocyte activation, which can provide potential targets for treatment.
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Affiliation(s)
- Danlei Qin
- Shanxi Province Key Laboratory of Oral Diseases Prevention and New Materials, Shanxi Medical University School and Hospital of Stomatology, No 63, New South Road, Yingze District, Taiyuan, 030001, Shanxi, China
- Department of Medical Imaging, Shanxi Medical University, Taiyuan, 030001, Shanxi, China
| | - Feiyan Yu
- Shanxi Province Key Laboratory of Oral Diseases Prevention and New Materials, Shanxi Medical University School and Hospital of Stomatology, No 63, New South Road, Yingze District, Taiyuan, 030001, Shanxi, China
| | - Dongchao Wu
- Shanxi Province Key Laboratory of Oral Diseases Prevention and New Materials, Shanxi Medical University School and Hospital of Stomatology, No 63, New South Road, Yingze District, Taiyuan, 030001, Shanxi, China
| | - Chong Han
- Shanxi Province Key Laboratory of Oral Diseases Prevention and New Materials, Shanxi Medical University School and Hospital of Stomatology, No 63, New South Road, Yingze District, Taiyuan, 030001, Shanxi, China
| | - Xuemin Yao
- Shanxi Province Key Laboratory of Oral Diseases Prevention and New Materials, Shanxi Medical University School and Hospital of Stomatology, No 63, New South Road, Yingze District, Taiyuan, 030001, Shanxi, China
| | - Lulu Yang
- Shanxi Province Key Laboratory of Oral Diseases Prevention and New Materials, Shanxi Medical University School and Hospital of Stomatology, No 63, New South Road, Yingze District, Taiyuan, 030001, Shanxi, China
| | - Xi Yang
- Shanxi Province Key Laboratory of Oral Diseases Prevention and New Materials, Shanxi Medical University School and Hospital of Stomatology, No 63, New South Road, Yingze District, Taiyuan, 030001, Shanxi, China
| | - Qianqian Wang
- Shanxi Province Key Laboratory of Oral Diseases Prevention and New Materials, Shanxi Medical University School and Hospital of Stomatology, No 63, New South Road, Yingze District, Taiyuan, 030001, Shanxi, China
| | - Dongning He
- Shanxi Province Key Laboratory of Oral Diseases Prevention and New Materials, Shanxi Medical University School and Hospital of Stomatology, No 63, New South Road, Yingze District, Taiyuan, 030001, Shanxi, China.
| | - Bin Zhao
- Shanxi Province Key Laboratory of Oral Diseases Prevention and New Materials, Shanxi Medical University School and Hospital of Stomatology, No 63, New South Road, Yingze District, Taiyuan, 030001, Shanxi, China.
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Zohar Y, Mabjeesh NJ. Targeting HIF-1 for prostate cancer: a synthesis of preclinical evidence. Expert Opin Ther Targets 2023; 27:715-731. [PMID: 37596912 DOI: 10.1080/14728222.2023.2248381] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Revised: 07/20/2023] [Accepted: 08/10/2023] [Indexed: 08/21/2023]
Abstract
INTRODUCTION Hypoxia-inducible factor (HIF) mediates multiple intracellular processes that drive cellular metabolism and induce proliferation. Dysregulated HIF expression is associated with oncogenic cellular transformation. Moreover, high HIF levels correlate with tumor aggressiveness and chemoresistance, indicating the vital effect of HIF-1α on tumorigenicity. Currently, widespread in-vitro and in-vivo research is focusing on targeting HIF with drugs that have already been approved for use by the FDA, such as belzutifan, in renal cell carcinoma. HIF inhibition is mostly associated with tumor size reduction; however, drug toxicity remains a challenge. AREA COVERED In this review, we focus on the potential of targeting HIF in prostate cancer (PC) and summarize the scientific background of HIF activity in PC. This finding emphasizes the rationale for using HIF as a therapeutic target in this malignancy. We have listed known HIF inhibitors that are being investigated in preclinical studies and their potential as anticancer drugs for PC. EXPERT OPINION Although HIF-targeting agents have been investigated for over a decade, their use in therapy-resistant cancers remains relevant and should be explored further. In addition, the use of naturally occurring HIF inhibitors should be considered as an add-on therapy for the currently used regimens.
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Affiliation(s)
- Yarden Zohar
- Department of Urology, Health Sciences, Soroka University Medical Center, Ben-Gurion University of the Negev, Be'er-Sheva, Israel
| | - Nicola J Mabjeesh
- Department of Urology, Health Sciences, Soroka University Medical Center, Ben-Gurion University of the Negev, Be'er-Sheva, Israel
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Gao Z, Li Z, Li X, Xiao J, Li C. Regulation of erythroid differentiation in K562 cells by the EPAS1-IRS2 axis under hypoxic conditions. Front Cell Dev Biol 2023; 11:1161541. [PMID: 37325570 PMCID: PMC10267359 DOI: 10.3389/fcell.2023.1161541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 05/24/2023] [Indexed: 06/17/2023] Open
Abstract
Red blood cells (RBCs) produced in vitro have the potential to alleviate the worldwide demand for blood transfusion. Hematopoietic cell differentiation and proliferation are triggered by numerous cellular physiological processes, including low oxygen concentration (<5%). In addition, hypoxia inducible factor 2α (HIF-2α) and insulin receptor substrate 2 (IRS2) were found to be involved in the progression of erythroid differentiation. However, the function of the HIF-2α-IRS2 axis in the progression of erythropoiesis is not yet fully understood. Therefore, we used an in vitro model of erythropoiesis generated from K562 cells transduced with shEPAS1 at 5% O2 in the presence or absence of the IRS2 inhibitor NT157. We observed that erythroid differentiation was accelerated in K562 cells by hypoxia. Conversely, knockdown of EPAS1 expression reduced IRS2 expression and erythroid differentiation. Intriguingly, inhibition of IRS2 could impair the progression of hypoxia-induced erythropoiesis without affecting EPAS1 expression. These findings indicated that the EPAS1-IRS2 axis may be a crucial pathway that regulates erythropoiesis and that drugs targeting this pathway may become promising agents for promoting erythroid differentiation.
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Affiliation(s)
- Zhan Gao
- Department of Blood Transfusion, Air Force Medical Center, Beijing, China
| | - Zhicai Li
- The Fifth School of Clinical Medicine, Anhui Medical University, Hefei, Anhui, China
| | - Xiaowei Li
- Department of Blood Transfusion, Air Force Medical Center, Beijing, China
| | - Jun Xiao
- Department of Blood Transfusion, Air Force Medical Center, Beijing, China
| | - Cuiying Li
- Department of Blood Transfusion, Air Force Medical Center, Beijing, China
- The Fifth School of Clinical Medicine, Anhui Medical University, Hefei, Anhui, China
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Zhang M, Li J, Lin W, Qi L, Yao C, Zheng Z, Chen C, Duan S, Qi Y. EPAS1 Promoter Hypermethylation is a Diagnostic and Prognostic Biomarker for Non-Small Cell Lung Cancer. Genet Test Mol Biomarkers 2022; 26:360-374. [PMID: 35920832 DOI: 10.1089/gtmb.2021.0305] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Background: The importance of promoter methylation in non-small cell lung cancers (NSCLCs) remains to be understood. Thus, we aimed to determine the diagnostic and prognostic value of methylation of the endothelial Per-Arnt-Sim (PAS) domain-containing protein 1 (EPAS1) promoter in NSCLC. Materials and Methods: EPAS1 promoter methylation levels were quantitated by a methylation-specific polymerase chain reaction. Furthermore, we evaluated the expression, promoter methylation, prognostic value, and impact on immune cell infiltration of EPAS1 by analyzing TCGA database or by web-based bioinformatics tools such as GEPIA, UALCAN, and MethSurv. Results: Our results demonstrated that promoter methylation of EPAS1 downregulated its expression in NSCLC tissues. Additionally, an area under the curve value of 0.772 indicated that methylation of the EPAS1 promoter is a potential diagnostic marker for NSCLC. Kaplan-Meier analysis demonstrated that high methylation levels of CpG sites in the EPAS1 promoter were indicative of worse overall survival (OS). Furthermore, EPAS1 expression levels were strongly correlated with infiltration of several types of immune cells, for instance, γδ T cells, T follicular helper cells, CD8+ T cells, and CD4+ T cells. Conclusions: Collectively, our findings demonstrated that methylation of the EPAS1 promoter is a promising prognostic biomarker for NSCLC and EPAS1 potentially plays an important role in immune cell infiltration in NSCLC.
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Affiliation(s)
- Mingfang Zhang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Jing Li
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China.,Department of Pathology, Fujian Provincial Maternity Hospital, Fuzhou, China
| | - Weibin Lin
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Lin Qi
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Caiyun Yao
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Zhonghua Zheng
- Department of Clinical Medicine, School of Medicine, Zhejiang University City College, Hangzhou, China
| | - Chujia Chen
- Department of Clinical Medicine, School of Medicine, Zhejiang University City College, Hangzhou, China
| | - Shiwei Duan
- Department of Clinical Medicine, School of Medicine, Zhejiang University City College, Hangzhou, China
| | - Yuanlin Qi
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
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Mikec Š, Šimon M, Morton NM, Atanur SS, Konc J, Dovč P, Horvat S, Kunej T. Genetic variants of the hypoxia-inducible factor 3 alpha subunit (Hif3a) gene in the Fat and Lean mouse selection lines. Mol Biol Rep 2022; 49:4619-4631. [PMID: 35347545 DOI: 10.1007/s11033-022-07309-0] [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: 01/10/2022] [Accepted: 02/25/2022] [Indexed: 10/18/2022]
Abstract
BACKGROUND Adipose tissue hypoxia and members of the hypoxia-inducible factor alpha (HIFA) are involved in development of obesity. However, the mechanism and functions of HIF3A, one of three HIFA paralogs, in fat deposition have not been sufficiently studied. METHODS AND RESULTS In the present study, we investigated whether Hif3a sequence variants are associated with divergent fat deposition in mouse selection lines for fatness and leanness. Sequencing and RFLP were used to analyse sequence variants within Hif3a. To identify candidate regulatory variants, we performed literature screening and used databases and bioinformatics tools like Ensembl, MethPrimer, TargetScanMouse, miRDB, PolyAsite, RISE, LncRRIsearch, RNAfold, PredictProtein, CAIcal, and switches.ELM Resource. There are 90 sequence variants in Hif3a between the two mouse lines. While most Fat line variants locate within intronic regions, Lean line variants are mainly in 3' UTR. We constructed a map of Hif3a potential regulatory regions and identified 39 regulatory variants by integrating data on constrained and regulatory elements, CpGs, and miRNAs and lncRNAs binding sites. Moreover, 3' UTR and two exonic variants may influence mRNA stability, translation rate and protein functionality. We propose as priority candidates for further functional studies a missense (rs37398126) and synonymous (rs37739792) variants, and intronic (rs47471302) variant that overlap conserved element in promoter region and predicted lncRNAs binding site. CONCLUSION The results indicate a potential involvement of Hif3a in fat deposition. Additionally, approach used in the present study may serve as a general guideline for constructing an integrative gene map for prioritizing candidate gene variants with phenotypic effects.
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Affiliation(s)
- Špela Mikec
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Domžale, Slovenia
| | - Martin Šimon
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Domžale, Slovenia
| | - Nicholas M Morton
- The Queen's Medical Research Institute, Centre for Cardiovascular Science, University of Edinburgh, Edinburgh, UK
| | - Santosh S Atanur
- Centre for Genomic and Experimental Medicine, University of Edinburgh, Edinburgh, UK.,Department of Metabolism, Digestion, and Reproduction, Faculty of Medicine, Imperial College London, London, UK
| | - Janez Konc
- Laboratory for Molecular Modeling, National Institute of Chemistry, Ljubljana, Slovenia
| | - Peter Dovč
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Domžale, Slovenia
| | - Simon Horvat
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Domžale, Slovenia.
| | - Tanja Kunej
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Domžale, Slovenia.
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