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Alles M, Gunasena M, Isckarus C, De Silva I, Board S, Mulhern W, Collins PL, Demberg T, Liyanage NPM. Novel Oral Adjuvant to Enhance Cytotoxic Memory-Like NK Cell Responses in an HIV Vaccine Platform. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.11.593683. [PMID: 38798447 PMCID: PMC11118904 DOI: 10.1101/2024.05.11.593683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Antibody-dependent cell-mediated cytotoxicity, mediated by natural killer (NK) cells and antibodies, emerged as a secondary correlate of protection in the RV144 HIV vaccine clinical trial, the only vaccine thus far demonstrating some efficacy in human. Therefore, leveraging NK cells with enhanced cytotoxic effector responses may bolster vaccine induced protection against HIV. Here, we investigated the effect of orally administering indole-3-carbinol (I3C), an aryl hydrocarbon receptor (AHR) agonist, as an adjuvant to an RV144-like vaccine platform in a mouse model. We demonstrate the expansion of KLRG1-expressing NK cells induced by the vaccine together with I3C. This NK cell subset exhibited enhanced vaccine antigen-specific cytotoxic memory-like features. Our study underscores the potential of incorporating I3C as an oral adjuvant to HIV vaccine platforms to enhance antigen-specific (memory-like) cytotoxicity of NK cells against HIV-infected cells. This approach may contribute to enhancing the protective efficacy of HIV preventive vaccines against HIV acquisition.
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Shi Y, Ju M, Zhang Y, Liang L, Sun X, Di X. Comprehensive pan-cancer analysis of 33 human cancers reveals immunotherapeutic value of focal adhesion tyrosine kinase. Medicine (Baltimore) 2024; 103:e37362. [PMID: 38518034 PMCID: PMC10956984 DOI: 10.1097/md.0000000000037362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 02/02/2024] [Indexed: 03/24/2024] Open
Abstract
The immune environment in tumors is the key factor affecting the survival and immunotherapeutic response of patients. This research aimed to explore the underlying association between focal adhesion tyrosine kinase (FAK/PTK2) and cancer immunotherapy in 33 human cancers. Gene expression data and clinical features of 33 cancers were retrieved from the Cancer Genome Atlas Database. The immunotherapy cohorts included GSE67501, GSE78220, and IMVIGOR210, which were derived from the comprehensive gene expression database or from previous studies. Clinical parameters including patient age, gender, survival rate, and tumor stage were analyzed to evaluate the prognostic value of FAK/PTK2. FAK/PTK2 activity was detected by single-sample gene set enrichment analysis and used to compare the difference between FAK/PTK2 transcriptome and protein expression levels. To better understand the role of FAK/PTK2 in cancer immunotherapy, we analyzed its correlations with tumor microenvironment and with immune processes/elements (e.g., immune cell infiltration, immunosuppressants, and stimulants) and major histocompatible complexes. Potential pathways associated with FAK/PTK2 signaling in cancers were also explored. Correlations between FAK/PTK2 and 2 immunotherapeutic biomarkers (tumor mutation load and microsatellite instability) were studied. Finally, the 3 independent immunotherapy cohorts were used to study the relationship between FAK/PTK2 and immunotherapeutic response. Although FAK/PTK2 is not closely associated with age (13/33), gender (5/33), or tumor stage (5/33) in any of the studied human cancers, it has potential prognostic value for predicting patient survival. Consistency between FAK/PTK2 activity and expression exists in some cancers (3/33). Generally, FAK/PTK2 is robustly correlated with immune cell infiltration, immune modulators, and immunotherapeutic markers. Moreover, high FAK/PTK2 expression is significantly related to immune-relevant pathways. However, FAK/PTK2 is not significantly correlated with the immunotherapeutic response. Research on the immunotherapeutic value of FAK/PTK2 in 33 human cancers provides evidence regarding the function of FAK/PTK2 and its role in clinical treatment. However, given the use of a bioinformatics approach, our results are preliminary and require further validation.
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Affiliation(s)
- Yujing Shi
- Department of Oncology, The People’s Hospital of Jurong City, Jurong Hospital Affiliated to Jiangsu University, Zhenjiang, China
| | - Mengyang Ju
- Department of Radiation Oncology, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Yumeng Zhang
- Department of Radiation Center, Shanghai First Maternity and Infant Hospital. School of Medicine, Tongji University, Shanghai, China
| | - Liang Liang
- Department of Oncology, The People’s Hospital of Jurong City, Jurong Hospital Affiliated to Jiangsu University, Zhenjiang, China
| | - Xinchen Sun
- Department of Radiotherapy, Jiangsu Provincial People’s Hospital, Nanjing, China
| | - Xiaoke Di
- Department of Radiotherapy, Jiangsu Provincial People’s Hospital, Nanjing, China
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Shivaram S, Gao H, Qin S, Liu D, Weinshilboum RM, Wang L. Cytochrome P450 Transcriptional Regulation by Testis-Specific Y-Encoded-Like Protein: Identification of Novel Upstream Transcription Factors. Drug Metab Dispos 2023; 51:1-7. [PMID: 36153008 PMCID: PMC9832376 DOI: 10.1124/dmd.122.000945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 07/05/2022] [Accepted: 07/05/2022] [Indexed: 01/14/2023] Open
Abstract
Cytochrome P450s (CYPs) display significant inter-individual variation in expression, much of which remains unexplained by known CYP single-nucleotide polymorphisms (SNPs). Testis-specific Y-encoded-like proteins (TSPYLs) are transcriptional regulators for several drug-metabolizing CYPs including CYP3A4 However, transcription factors (TFs) that might influence CYP expression through an effect on TSPYL expression are unknown. Therefore, we studied regulators of TSPYL expression in hepatic cell lines and their possible SNP-dependent variation. Specifically, we identified candidate TFs that might influence TSPYL expression using the ENCODE ChIPseq database. Subsequently, the expression of TSPYL1/2/4 as well as that of selected CYP targets for TSPYL regulation were assayed in hepatic cell lines before and after knockdown of TFs that might influence CYP expression through TSPYL-dependent mechanisms. Those results were confirmed by studies of TF binding to TSPYL1/2/4 gene promoter regions. In hepatic cell lines, knockdown of the REST and ZBTB7A TFs resulted in decreased TSPYL1 and TSPYL4 expression and increased CYP3A4 expression, changes reversed by TSPYL1/4 overexpression. Potential binding sites for REST and ZBTB7A on the promoters of TSPYL1 and TSPYL4 were confirmed by chromatin immunoprecipitation. Finally, common SNP variants in upstream binding sites on the TSPYL1/4 promoters were identified and luciferase reporter constructs confirmed SNP-dependent modulation of TSPYL1/4 gene transcription. In summary, we identified REST and ZBTB7A as regulators of the expression of TSPYL genes which themselves can contribute to regulation of CYP expression and-potentially-of drug metabolism. SNP-dependent modulation of TSPYL transcription may contribute to individual variation in both CYP expression and-downstream-drug response phenotypes. SIGNIFICANCE STATEMENT: Testis-specific Y-encoded-like proteins (TSPYLs) are transcriptional regulators of cytochrome P450 (CYP) gene expression. Here, we report that variation in TSPYL expression as a result of the effects of genetically regulated TSPYL transcription factors is an additional factor that could result in downstream variation in CYP expression and potentially, as a result, variation in drug biotransformation.
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Affiliation(s)
- Suganti Shivaram
- Division of Clinical Pharmacology, Department of Molecular Pharmacology and Therapeutics, Mayo Clinic, Rochester, Minnesota
| | - Huanyao Gao
- Division of Clinical Pharmacology, Department of Molecular Pharmacology and Therapeutics, Mayo Clinic, Rochester, Minnesota
| | - Sisi Qin
- Division of Clinical Pharmacology, Department of Molecular Pharmacology and Therapeutics, Mayo Clinic, Rochester, Minnesota
| | - Duan Liu
- Division of Clinical Pharmacology, Department of Molecular Pharmacology and Therapeutics, Mayo Clinic, Rochester, Minnesota
| | - Richard M Weinshilboum
- Division of Clinical Pharmacology, Department of Molecular Pharmacology and Therapeutics, Mayo Clinic, Rochester, Minnesota
| | - Liewei Wang
- Division of Clinical Pharmacology, Department of Molecular Pharmacology and Therapeutics, Mayo Clinic, Rochester, Minnesota
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4
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Nguyen T, Gao H, Liu D, Philips TJ, Ye Z, Lee JH, Shi GX, Copenhaver K, Zhang L, Wei L, Yu J, Zhang H, Barath A, Luong M, Zhang C, Gaspar-Maia A, Li H, Wang L, Ordog T, Weinshilboum R. Glucocorticoids unmask silent non-coding genetic risk variants for common diseases. Nucleic Acids Res 2022; 50:11635-11653. [PMID: 36399508 PMCID: PMC9723631 DOI: 10.1093/nar/gkac1045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 10/26/2022] [Indexed: 11/19/2022] Open
Abstract
Understanding the function of non-coding genomic sequence variants represents a challenge for biomedicine. Many diseases are products of gene-by-environment interactions with complex mechanisms. This study addresses these themes by mechanistic characterization of non-coding variants that influence gene expression only after drug or hormone exposure. Using glucocorticoid signaling as a model system, we integrated genomic, transcriptomic, and epigenomic approaches to unravel mechanisms by which variant function could be revealed by hormones or drugs. Specifically, we identified cis-regulatory elements and 3D interactions underlying ligand-dependent associations between variants and gene expression. One-quarter of the glucocorticoid-modulated variants that we identified had already been associated with clinical phenotypes. However, their affected genes were 'unmasked' only after glucocorticoid exposure and often with function relevant to the disease phenotypes. These diseases involved glucocorticoids as risk factors or therapeutic agents and included autoimmunity, metabolic and mood disorders, osteoporosis and cancer. For example, we identified a novel breast cancer risk gene, MAST4, with expression that was repressed by glucocorticoids in cells carrying the risk genotype, repression that correlated with MAST4 expression in breast cancer and treatment outcomes. These observations provide a mechanistic framework for understanding non-coding genetic variant-chemical environment interactions and their role in disease risk and drug response.
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Affiliation(s)
- Thanh Thanh L Nguyen
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic; Rochester, MN, USA
- Mayo Clinic Graduate School of Biomedical Sciences, Mayo Clinic; Rochester, MN, USA
| | - Huanyao Gao
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic; Rochester, MN, USA
| | - Duan Liu
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic; Rochester, MN, USA
| | - Trudy Janice Philips
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic; Rochester, MN, USA
| | - Zhenqing Ye
- Department of Health Sciences Research, Mayo Clinic; Rochester, MN, USA
- Current affiliation: Greehey Children's Cancer Research Institute, University of Texas Health San Antonio; San Antonio, TX 78229, USA
| | - Jeong-Heon Lee
- Epigenomics Program, Center for Individualized Medicine, Mayo Clinic; Rochester, MN, USA
| | - Geng-xian Shi
- Epigenomics Program, Center for Individualized Medicine, Mayo Clinic; Rochester, MN, USA
| | - Kaleigh Copenhaver
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic; Rochester, MN, USA
| | - Lingxin Zhang
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic; Rochester, MN, USA
| | - Lixuan Wei
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic; Rochester, MN, USA
| | - Jia Yu
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic; Rochester, MN, USA
| | - Huan Zhang
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic; Rochester, MN, USA
| | | | - Maggie Luong
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic; Rochester, MN, USA
| | - Cheng Zhang
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic; Rochester, MN, USA
| | - Alexandre Gaspar-Maia
- Epigenomics Program, Center for Individualized Medicine, Mayo Clinic; Rochester, MN, USA
- Department of Laboratory Medicine and Pathology, Division of Experimental Pathology and Lab Medicine, Mayo Clinic; Rochester, MN, USA
| | - Hu Li
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic; Rochester, MN, USA
| | - Liewei Wang
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic; Rochester, MN, USA
| | - Tamas Ordog
- Epigenomics Program, Center for Individualized Medicine, Mayo Clinic; Rochester, MN, USA
- Department of Physiology and Biomedical Engineering, Mayo Clinic; Rochester, MN, USA
- Division of Gastroenterology and Hepatology, Department of Medicine, Mayo Clinic; Rochester, MN, USA
| | - Richard M Weinshilboum
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic; Rochester, MN, USA
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5
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Fasching PA, Liu D, Scully S, Ingle JN, Lyra PC, Rack B, Hein A, Ekici AB, Reis A, Schneeweiss A, Tesch H, Fehm TN, Heinrich G, Beckmann MW, Ruebner M, Huebner H, Lambrechts D, Madden E, Shen J, Romm J, Doheny K, Jenkins GD, Carlson EE, Li L, Fridley BL, Cunningham JM, Janni W, Monteiro ANA, Schaid DJ, Häberle L, Weinshilboum RM, Wang L. Identification of Two Genetic Loci Associated with Leukopenia after Chemotherapy in Patients with Breast Cancer. Clin Cancer Res 2022; 28:3342-3355. [PMID: 35653140 PMCID: PMC9357161 DOI: 10.1158/1078-0432.ccr-20-4774] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 01/20/2022] [Accepted: 05/27/2022] [Indexed: 02/04/2023]
Abstract
PURPOSE To identify molecular predictors of grade 3/4 neutropenic or leukopenic events (NLE) after chemotherapy using a genome-wide association study (GWAS). EXPERIMENTAL DESIGN A GWAS was performed on patients in the phase III chemotherapy study SUCCESS-A (n = 3,322). Genotyping was done using the Illumina HumanOmniExpress-12v1 array. Findings were functionally validated with cell culture models and the genotypes and gene expression of possible causative genes were correlated with clinical treatment response and prognostic outcomes. RESULTS One locus on chromosome 16 (rs4784750; NLRC5; P = 1.56E-8) and another locus on chromosome 13 (rs16972207; TNFSF13B; P = 3.42E-8) were identified at a genome-wide significance level. Functional validation revealed that expression of these two genes is altered by genotype-dependent and chemotherapy-dependent activity of two transcription factors. Genotypes also showed an association with disease-free survival in patients with an NLE. CONCLUSIONS Two loci in NLRC5 and TNFSF13B are associated with NLEs. The involvement of the MHC I regulator NLRC5 implies the possible involvement of immuno-oncological pathways.
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Affiliation(s)
- Peter A Fasching
- Department of Gynecology and Obstetrics, University Breast Center for Franconia, Erlangen University Hospital, Friedrich-Alexander University Erlangen-Nürnberg, Comprehensive Cancer Center Erlangen EMN, Erlangen, Germany
| | - Duan Liu
- Division of Clinical Pharmacology, Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, Minnesota
| | - Steve Scully
- Division of Clinical Pharmacology, Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, Minnesota
| | - James N Ingle
- Division of Medical Oncology, Mayo Clinic, Rochester, Minnesota
| | - Paulo C Lyra
- Biotechnology/RENORBIO Program, Federal University of Espírito Santo, Vitória, Espírito Santo, Brazil
| | - Brigitte Rack
- Department of Gynecology and Obstetrics, Ulm University Hospital, Ulm, Germany
| | - Alexander Hein
- Department of Gynecology and Obstetrics, University Breast Center for Franconia, Erlangen University Hospital, Friedrich-Alexander University Erlangen-Nürnberg, Comprehensive Cancer Center Erlangen EMN, Erlangen, Germany
| | - Arif B Ekici
- Institute of Human Genetics, Erlangen University Hospital, Friedrich-Alexander University Erlangen-Nürnberg, Erlangen, Germany
| | - Andre Reis
- Institute of Human Genetics, Erlangen University Hospital, Friedrich-Alexander University Erlangen-Nürnberg, Erlangen, Germany
| | - Andreas Schneeweiss
- National Center for Tumor Diseases, Division of Gynecologic Oncology, Heidelberg University Hospital and German Cancer Research Center, Heidelberg, Germany
| | - Hans Tesch
- Onkologie Bethanien, Frankfurt am Main, Germany
| | - Tanja N Fehm
- Department of Gynecology and Obstetrics, Düsseldorf University Hospital, Heinrich Heine University, Düsseldorf, Germany
| | - Georg Heinrich
- Schwerpunktpraxis für Gynäkologische Onkologie, Fürstenwalde, Germany
| | - Matthias W Beckmann
- Department of Gynecology and Obstetrics, University Breast Center for Franconia, Erlangen University Hospital, Friedrich-Alexander University Erlangen-Nürnberg, Comprehensive Cancer Center Erlangen EMN, Erlangen, Germany
| | - Matthias Ruebner
- Department of Gynecology and Obstetrics, University Breast Center for Franconia, Erlangen University Hospital, Friedrich-Alexander University Erlangen-Nürnberg, Comprehensive Cancer Center Erlangen EMN, Erlangen, Germany
| | - Hanna Huebner
- Department of Gynecology and Obstetrics, University Breast Center for Franconia, Erlangen University Hospital, Friedrich-Alexander University Erlangen-Nürnberg, Comprehensive Cancer Center Erlangen EMN, Erlangen, Germany
| | - Diether Lambrechts
- VIB Center for Cancer Biology, VIB and Laboratory for Translational Genetics, KU Leuven, Leuven, Belgium
| | - Ebony Madden
- Division of Genomic Medicine, National Human Genome Research Institute, Bethesda, Maryland
| | - Jess Shen
- Centre for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Jane Romm
- McKusick-Nathans Department of Genetic Medicine, Center for Inherited Disease Research, Johns Hopkins University, Baltimore, Maryland
| | - Kim Doheny
- McKusick-Nathans Department of Genetic Medicine, Center for Inherited Disease Research, Johns Hopkins University, Baltimore, Maryland
| | - Gregory D Jenkins
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota
| | - Erin E Carlson
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota
| | - Liang Li
- Division of Clinical Pharmacology, Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, Minnesota
- Department of Oncology, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Tiantan Xili, Beijing, China
| | - Brooke L Fridley
- Department of Biostatistics and Bioinformatics, Moffitt Cancer Center, Tampa, Florida
| | - Julie M Cunningham
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Wolfgang Janni
- Department of Gynecology and Obstetrics, Ulm University Hospital, Ulm, Germany
| | - Alvaro N A Monteiro
- Cancer Epidemiology Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Daniel J Schaid
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota
| | - Lothar Häberle
- Department of Gynecology and Obstetrics, University Breast Center for Franconia, Erlangen University Hospital, Friedrich-Alexander University Erlangen-Nürnberg, Comprehensive Cancer Center Erlangen EMN, Erlangen, Germany
- Department of Gynecology and Obstetrics, Unit of Biostatistics, Erlangen University Hospital, Friedrich-Alexander University Erlangen-Nürnberg, Erlangen, Germany
| | - Richard M Weinshilboum
- Division of Clinical Pharmacology, Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, Minnesota
| | - Liewei Wang
- Division of Clinical Pharmacology, Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, Minnesota
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Watzky M, Huard S, Juricek L, Dairou J, Chauvet C, Coumoul X, Letessier A, Miotto B. Hexokinase 2 is a transcriptional target and a positive modulator of AHR signalling. Nucleic Acids Res 2022; 50:5545-5564. [PMID: 35609998 PMCID: PMC9178003 DOI: 10.1093/nar/gkac360] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 04/20/2022] [Accepted: 05/16/2022] [Indexed: 12/14/2022] Open
Abstract
The aryl hydrocarbon receptor (AHR) regulates the expression of numerous genes in response to activation by agonists including xenobiotics. Although it is well appreciated that environmental signals and cell intrinsic features may modulate this transcriptional response, how it is mechanistically achieved remains poorly understood. We show that hexokinase 2 (HK2) a metabolic enzyme fuelling cancer cell growth, is a transcriptional target of AHR as well as a modulator of its activity. Expression of HK2 is positively regulated by AHR upon exposure to agonists both in human cells and in mice lung tissues. Conversely, over-expression of HK2 regulates the abundance of many proteins involved in the regulation of AHR signalling and these changes are linked with altered AHR expression levels and transcriptional activity. HK2 expression also shows a negative correlation with AHR promoter methylation in tumours, and these tumours with high HK2 expression and low AHR methylation are associated with a worse overall survival in patients. In sum, our study provides novel insights into how AHR signalling is regulated which may help our understanding of the context-specific effects of this pathway and may have implications in cancer.
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Affiliation(s)
- Manon Watzky
- Université Paris Cité, Institut Cochin, INSERM, U1016, CNRS, UMR8104, F-75014 Paris, France
| | - Solène Huard
- Université Paris Cité, Institut Cochin, INSERM, U1016, CNRS, UMR8104, F-75014 Paris, France
| | - Ludmila Juricek
- METATOX, T3S, Toxicologie Environnementale, Cibles thérapeutiques, Signalisation cellulaire et Biomarqueurs, INSERM UMR-S1124, F-75006 Paris, France
| | - Julien Dairou
- Université Paris Cité, UFR des Sciences Fondamentales et Biomédicales, Paris, France.,Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, CNRS, UMR 8601, Université Paris Cité, F-75006 Paris, France
| | - Caroline Chauvet
- METATOX, T3S, Toxicologie Environnementale, Cibles thérapeutiques, Signalisation cellulaire et Biomarqueurs, INSERM UMR-S1124, F-75006 Paris, France.,Université Paris Cité, UFR des Sciences Fondamentales et Biomédicales, Paris, France
| | - Xavier Coumoul
- METATOX, T3S, Toxicologie Environnementale, Cibles thérapeutiques, Signalisation cellulaire et Biomarqueurs, INSERM UMR-S1124, F-75006 Paris, France.,Université Paris Cité, UFR des Sciences Fondamentales et Biomédicales, Paris, France
| | - Anne Letessier
- Université Paris Cité, Institut Cochin, INSERM, U1016, CNRS, UMR8104, F-75014 Paris, France
| | - Benoit Miotto
- Université Paris Cité, Institut Cochin, INSERM, U1016, CNRS, UMR8104, F-75014 Paris, France
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7
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Mo Z, Li P, Cao Z, Zhang S. A Comprehensive Pan-Cancer Analysis of 33 Human Cancers Reveals the Immunotherapeutic Value of Aryl Hydrocarbon Receptor. Front Immunol 2021; 12:564948. [PMID: 34290693 PMCID: PMC8287657 DOI: 10.3389/fimmu.2021.564948] [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: 05/23/2020] [Accepted: 06/18/2021] [Indexed: 12/29/2022] Open
Abstract
Background Previous studies have reported the potential of aryl hydrocarbon receptor (AhR) in cancer immunotherapy. However, the mechanisms underpinning its therapeutic value have yet to be comprehensively investigated. Thus, this research aimed to explore the underlying association between AhR and cancer immunotherapy in 33 human cancers. Methods The gene expression data and clinical characteristics of 33 cancers were retrieved from The Cancer Genome Atlas database. The immunotherapeutic cohorts included GSE67501 and GSE78220 as well as IMvigor210, which were obtained from the Gene Expression Omnibus database and included in a previously published study respectively. Clinical parameters, including patient age, gender, survival, and tumor stage were analyzed to assess the prognostic value of AhR. The activity of AhR was generated by single sample gene set enrichment analysis and used to evaluate the difference between the AhR transcriptome and protein expression level. To better understand the role of AhR in cancer immunotherapy, the correlation between AhR and tumor microenvironment, as well as its relation to immune processes/elements, such as immune cell infiltration, immune inhibitors and stimulators, and the major histocompatibility complex were analyzed. The relevant underlying pathways associated with AhR signaling in cancer were also explored. Furthermore, the correlation between AhR and two immunotherapeutic biomarkers (tumor mutational burden and microsatellite instability) was investigated. Finally, the relationship between AhR and immunotherapeutic response was explored using three independent immunotherapeutic cohorts. Results Although AhR was not closely associated with age (5/33), gender (3/33), or tumor stage (3/21) in any of the studied human cancers, it exhibited potential prognostic value for predicting patient survival. Consistency has been observed between AhR activity and expression in some cancers (7/33). Generally, AhR presented a robust correlation with immune cell infiltration, immune modulators, and immunotherapeutic markers. Moreover, high AhR expression was significantly related to immune-relevant pathways. However, no significant correlation was observed between AhR and the immunotherapeutic response. Conclusions This research investigated the immunotherapeutic value of AhR in 33 human cancers, providing evidence regarding the function of AhR and its role in clinical treatment. However, considering that a bioinformatics approach was adopted, the current results are preliminary and require further validation.
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Affiliation(s)
- Zhuomao Mo
- Department of Traditional Chinese Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Pan Li
- Department of Traditional Chinese Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Zhirui Cao
- Department of Traditional Chinese Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Shijun Zhang
- Department of Traditional Chinese Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
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8
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Watzky M, de Dieuleveult M, Letessier A, Saint-Ruf C, Miotto B. Assessing the consequences of environmental exposures on the expression of the human receptor and proteases involved in SARS-CoV-2 cell-entry. ENVIRONMENTAL RESEARCH 2021; 195:110317. [PMID: 33069705 PMCID: PMC7560643 DOI: 10.1016/j.envres.2020.110317] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 09/09/2020] [Accepted: 10/07/2020] [Indexed: 05/06/2023]
Abstract
The role of environmental condition on the infection by the novel pathogenic SARS-CoV-2 virus remains uncertain. In here, exploiting a large panel of publicly available genome-wide data, we investigated whether the human receptor ACE2 and human proteases TMPRSS2, FURIN and CATHEPSINs (B, L and V), which are involved in SARS-CoV-2 cell entry, are transcriptionally regulated by environmental cues. We report that more than 50 chemicals modulate the expression of ACE2 or human proteases important for SARS-CoV-2 cell entry. We further demonstrate that transcription factor AhR, which is commonly activated by pollutants, binds to the promoter of TMPRSS2 and enhancers and/or promoters of Cathepsin B, L and V encoding genes. Our exploratory study documents an influence of environmental exposures on the expression of genes involved in SARS-CoV-2 cell entry. These results could be conceptually and medically relevant to our understanding of the COVID-19 disease, and should be further explored in laboratory and epidemiologic studies.
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Affiliation(s)
- Manon Watzky
- Université de Paris, Institut Cochin, INSERM, U1016, CNRS, UMR8104, F-75014, PARIS, France
| | - Maud de Dieuleveult
- Université de Paris, Institut Cochin, INSERM, U1016, CNRS, UMR8104, F-75014, PARIS, France
| | - Anne Letessier
- Université de Paris, Institut Cochin, INSERM, U1016, CNRS, UMR8104, F-75014, PARIS, France
| | - Claude Saint-Ruf
- Université de Paris, Institut Cochin, INSERM, U1016, CNRS, UMR8104, F-75014, PARIS, France
| | - Benoit Miotto
- Université de Paris, Institut Cochin, INSERM, U1016, CNRS, UMR8104, F-75014, PARIS, France.
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9
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Liu D, Nguyen TTL, Gao H, Huang H, Kim DC, Sharp B, Ye Z, Lee JH, Coombes BJ, Ordog T, Wang L, Biernacka JM, Frye MA, Weinshilboum RM. TCF7L2 lncRNA: a link between bipolar disorder and body mass index through glucocorticoid signaling. Mol Psychiatry 2021; 26:7454-7464. [PMID: 34535768 PMCID: PMC8872993 DOI: 10.1038/s41380-021-01274-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Revised: 07/21/2021] [Accepted: 08/19/2021] [Indexed: 02/08/2023]
Abstract
Bipolar disorder (BD) and obesity are highly comorbid. We previously performed a genome-wide association study (GWAS) for BD risk accounting for the effect of body mass index (BMI), which identified a genome-wide significant single-nucleotide polymorphism (SNP) in the gene encoding the transcription factor 7 like 2 (TCF7L2). However, the molecular function of TCF7L2 in the central nervous system (CNS) and its possible role in the BD and BMI interaction remained unclear. In the present study, we demonstrated by studying human induced pluripotent stem cell (hiPSC)-derived astrocytes, cells that highly express TCF7L2 in the CNS, that the BD-BMI GWAS risk SNP is associated with glucocorticoid-dependent repression of the expression of a previously uncharacterized TCF7L2 transcript variant. That transcript is a long non-coding RNA (lncRNA-TCF7L2) that is highly expressed in the CNS but not in peripheral tissues such as the liver and pancreas that are involved in metabolism. In astrocytes, knockdown of the lncRNA-TCF7L2 resulted in decreased expression of the parent gene, TCF7L2, as well as alterations in the expression of a series of genes involved in insulin signaling and diabetes. We also studied the function of TCF7L2 in hiPSC-derived astrocytes by integrating RNA sequencing data after TCF7L2 knockdown with TCF7L2 chromatin-immunoprecipitation sequencing (ChIP-seq) data. Those studies showed that TCF7L2 directly regulated a series of BD risk genes. In summary, these results support the existence of a CNS-based mechanism underlying BD-BMI genetic risk, a mechanism based on a glucocorticoid-dependent expression quantitative trait locus that regulates the expression of a novel TCF7L2 non-coding transcript.
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Affiliation(s)
- Duan Liu
- grid.66875.3a0000 0004 0459 167XDepartment of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN USA
| | - Thanh Thanh Le Nguyen
- grid.66875.3a0000 0004 0459 167XDepartment of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN USA ,grid.66875.3a0000 0004 0459 167XGraduate School of Biomedical Sciences, Mayo Clinic, Rochester, MN USA
| | - Huanyao Gao
- grid.66875.3a0000 0004 0459 167XDepartment of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN USA
| | - Huaizhi Huang
- grid.66875.3a0000 0004 0459 167XDepartment of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN USA ,grid.66875.3a0000 0004 0459 167XGraduate School of Biomedical Sciences, Mayo Clinic, Rochester, MN USA
| | - Daniel C. Kim
- grid.66875.3a0000 0004 0459 167XDepartment of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN USA
| | - Brenna Sharp
- grid.66875.3a0000 0004 0459 167XDepartment of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN USA
| | - Zhenqing Ye
- grid.66875.3a0000 0004 0459 167XDivision of Computational Biology, Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN USA
| | - Jeong-Heon Lee
- grid.66875.3a0000 0004 0459 167XDepartment of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN USA
| | - Brandon J. Coombes
- grid.66875.3a0000 0004 0459 167XDivision of Computational Biology, Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN USA
| | - Tamas Ordog
- grid.66875.3a0000 0004 0459 167XDepartment of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN USA ,grid.66875.3a0000 0004 0459 167XDivision of Gastroenterology and Hepatology, Department of Internal Medicine, Mayo Clinic, Rochester, MN USA
| | - Liewei Wang
- grid.66875.3a0000 0004 0459 167XDepartment of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN USA
| | - Joanna M. Biernacka
- grid.66875.3a0000 0004 0459 167XDivision of Computational Biology, Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN USA ,grid.66875.3a0000 0004 0459 167XDepartment of Psychiatry and Psychology, Mayo Clinic, Rochester, MN USA
| | - Mark A. Frye
- grid.66875.3a0000 0004 0459 167XDepartment of Psychiatry and Psychology, Mayo Clinic, Rochester, MN USA
| | - Richard M. Weinshilboum
- grid.66875.3a0000 0004 0459 167XDepartment of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN USA
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10
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Xi XX, Wang HL, Chen T, Dai JR, Hou SY, Chen YG. Prognostic value of preoperative serum bilirubin levels in ovarian cancer. Am J Transl Res 2020; 12:2267-2280. [PMID: 32509218 PMCID: PMC7269994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 04/30/2020] [Indexed: 06/11/2023]
Abstract
Bilirubin is a promising prognostic factor for non-liver disease-related deaths in various cancers. We investigated the association between preoperative serum bilirubin levels and oncological outcomes in patients with ovarian cancer. We retrospectively analyzed the clinical data of 282 patients with epithelial ovarian carcinoma (EOC), and grouped them according to optimal threshold values of total bilirubin (TBIL), direct bilirubin (DBIL), and indirect bilirubin (IBL) measured by receiver operating characteristic curve analysis. Univariate and multivariate Cox proportional hazards regression analyses were used to evaluate various parameters that might affect overall survival (OS) and progression-free survival (PFS) in patients with EOC. The optimal cutoff values for TBIL, DBIL, and IBIL levels were 9.65 µmol/L, 2.95 µmol/L, and 6.75 µmol/L, respectively. Increased TBIL, DBIL, and IBIL levels correlated with the serum carbohydrate antigen (CA)-125 levels, International Federation of Gynecology and Obstetrics stage, and pathological differentiation (all P<0.05). Univariate analysis revealed longer OS and PFS in patients with high TBIL (≥9.65 µmol/L) and IBIL (≥6.75 µmol/L) levels (P<0.05). Multivariate analysis showed that patients with high IBIL levels (≥6.75 µmol/L) had significantly longer OS and PFS than those with low IBIL levels (<6.75 µmol/L) [hazard ratio (HR) = 0.333, 95% confidence interval (CI): 0.123~0.904, P<0.05; HR = 1.814, 95% CI: 1.169~2.816, P<0.05]. Therefore, IBIL is a potential independent prognostic factor for OS and PFS in patients with EOC. The higher the IBL level, the better the prognosis of patients with EOC.
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Affiliation(s)
- Xiao-Xue Xi
- Department of Obstetrics and Gynaecology, The First Affiliated Hospital of Soochow UniversitySuzhou 215006, China
- Department of Obstetrics and Gynaecology, Suzhou Hospital Affiliated to Nanjing Medical University (Suzhou Municipal Hospital)Suzhou 215002, China
| | - Hui-Lin Wang
- Department of Obstetrics and Gynaecology, Suzhou Hospital Affiliated to Nanjing Medical University (Suzhou Municipal Hospital)Suzhou 215002, China
| | - Ting Chen
- Department of Obstetrics and Gynaecology, Suzhou Hospital Affiliated to Nanjing Medical University (Suzhou Municipal Hospital)Suzhou 215002, China
| | - Jian-Rong Dai
- Department of Obstetrics and Gynaecology, Suzhou Hospital Affiliated to Nanjing Medical University (Suzhou Municipal Hospital)Suzhou 215002, China
| | - Shun-Yu Hou
- Department of Obstetrics and Gynaecology, Suzhou Hospital Affiliated to Nanjing Medical University (Suzhou Municipal Hospital)Suzhou 215002, China
| | - You-Guo Chen
- Department of Obstetrics and Gynaecology, The First Affiliated Hospital of Soochow UniversitySuzhou 215006, China
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