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Principal Investigator: Daniel Menendez Rendon
Organization: NATIONAL INSTITUTE OF ENVIRONMENTAL HEALTH SCIENCES
Fiscal Year: 2020
Award: $17,940
Funding agency: National Institute of Environmental Health Sciences
p53 is central to human DNA repair, damage checkpoints and many aspects of human biology. Most cancers are altered for p53 function. Although the guardian of the genome p53 has been extensively studied, much about its function and its targets remains unknown. IDENTIFYING p53 TARGETS. Identifying the universe of p53 direct transcriptional targets is clinically relevant, especially since many of these may have therapeutic value. There is considerable variation in p53 dependent expression across targeted genes leading to differences in p53-mediated biological consequences, due in part to variation in target response element (RE) sequence. We have focused on RE functionality, i.e., the ability of REs to support transactivation by p53 in human cells in culture and ex vivo. Several studies have used genome-wide, next-generation sequencing approaches to identify p53 binding sites in the human genome. We developed a rigorous method for reanalyzing all the raw data from the individual ChIP-seq studies and associated gene expression using a single analysis workflow, then combining information using a common set of criteria. Our approach revealed a large p53 genome-wide cistrome composed of >900 genes directly targeted by p53. CHARACTERIZATION OF THE P53 HUMAN CISTROME IN RESPONSE TO ENVIRONMENTAL STRESSORS. Using a common analysis pipeline, we analyzed 41 data sets from genome-wide ChIP-seq studies of which 16 have associated gene expression data, including our primary data in normal human lymphocytes. The resulting extensive analysis, accessible at the p53 Binding And Expression Resource (BAER) hub via the UCSC browser, provides a robust platform to characterize p53 binding throughout the human genome including its direct influence on gene expression (i.e., cistrome) and underlying mechanisms. This approach led to our identification of more than 700 novel p53 candidates involved in the classical roles ascribed to p53 function, as well as in processes not immediately related to classical p53 outcomes such as the immune response. Using the p53 BAER hub together with our various gene expression datasets we have 1) expanded the p53 transcriptome in DNA repair and nucleic acid metabolism transactions in different human cancer and primary cells with different p53 functional status and 2) identified new autoregulatory loops in the p53 pathway through the analysis of the p53- interactome withp53-cistrome.THE p53 IMMUNE CISTROME. Through our meta-analysis of the p53 transcriptional network following stresses in many cell types, including lymphocytes, monocytes and blood derived macrophages from healthy participants treated with p53 activating drugs, we have identified a p53 Immune Associated Cistrome (p53IAC). These p53 direct targets, consists of 70 genes directly involved in cellular immune and inflammatory processes, several interleukins, membrane receptors and various viral/bacterial restriction factors. Additionally, we found that activation of wild type p53 as well as many tumor-associated p53 mutants modulates and changes the expression profile of two major innate immune gene families, the TLR (Toll-like Receptor) family and the A3 (APOBEC3) family that are, respectively, pathogen sensors and sentinels against viral infections. We have described this p53 influence on immune responses as the p53/immune axis. THE INFLUENCE OF p53 ON HUMAN IMMUNE RESPONSES DURING VIRAL INFECTIONS. We demonstrated that a SNP (rs3761624; also referred to as the TLR8-p53G/A SNP) in a p53RE could lead to p53-dependent enhanced expression of TLR8, which is involved in virus detection. This SNP affect the level of inflammatory responses in lymphocytes from healthy donors are challenged with the cognate ligand for this receptor. We found this SNP was positively associated with the severity of respiratory syncytial virus (RSV) disease in infants (as described in our 2019 publication in Journal of Clinical Investigations). Using isogenic p53 proficient and p53 null cell lines we detected that activation of p53 by RSV leads to upregulation of several A3 genes and led us to identify A3G as a novel restriction factor against RSV. We have expanded the p53-TLR8-immune axis concept to human immunodeficiency virus (HIV) infection with support that we obtained from the Office of AIDS Research, using an ex-vivo model of human healthy T lymphocytes. In a blind design study, we are using the NIEHS Environmental Polymorphism Registry cohort, to recruit healthy participants on the basis of the TLR8 rs3761624 genotypes. Then isolated CD4+ T lymphocytes for each donor are pretreated with vehicle (DMSO) or p53 activating drug Nutlin and then infected with HIV. We detected the appearance of two clear groups, non-responsive and responsive for TLR8 expression after Nutlin treatment. For those samples where the induction of TLR8 expression is more than 2 fold, a 30-50% reduction in HIV infectivity was observed when compared to the donors with less than 2 fold or no TLR8 induction. Projecting from this work, we have proposed that the rs rs3761624 SNP, with a worldwide ethnic frequency varying from 25-75%, is a good candidate for a functional biomarker of differences in response to COVID19, including ethnicity and gender, and opens up additional approaches to treatments and targets. Based on our efforts with RSV, there are several directions that should be pursued. One immediate direction has been be to determine the relationship between the SNP and severity in COVID-19 infected people. There are several opportunities for mechanistic studies as well as interventions. Using our p53IAC dataset, we identified around 30 well known HIV-1 host restriction factors that are transcriptional responsive to p53 activation. Among this genes are A3G, A3H, SAMHD1, TRIM5, HERC5, TRIM5, MARCH2, MX1, TSG101 PRK and ZAP. In collaboration with Johns Hopkins School of Public Health, we identified 263 HIV-1 seroconverts in the Multicenter AIDS Cohort Study (MACS) previously genotyped for TP53 SNP rs1042522 and TLR8 SNP rs37646880, which is in high linkage disequilibrium with TLR8-p53RE SNP. A preliminary analysis showed that especially TP53 codon 72 variant, may be associated with a lower risk of developing AIDS but the presence of both protective alleles (TP53 rs1042522=GG and TLR8 rs37646880=A) might convey an overall 65% reduction in the risk of AIDS. CANCER-ASSOCIATED p53 MUTANTS. With inclusion of immune response-related TLR and A3 genes into the p53 network, we found that also tumor associated p53 mutants have the potential to modulate the transcriptional response of these genes. We are pursuing the identification of synthetic lethal (SL) genes with genome-wide siRNA-based screens, that when reduced in expression in p53 mutant cells cause death or reduced growth in cells treated (or untreated) with anticancer agents. We have identified several SL targets for two of the most frequent tumor-associated p53 mutants (R175H and R273H) in the presence of anticancer drug etoposide as well as for the WT p53 and p53 null conditions. We have found that drug mediated inhibition of ATR in combination with etoposide is an SL target in a p53 mutant specific manner (R273H and p53 null) and impacts Topoisomerase-mediated enzymatic activities.
This project involves research on human coronavirus, novel coronavirus, COVID-19, Severe Acute Respiratory Syndrome coronavirus disease, SARS coronavirus, SARS-coronavirus-2, SARS-cov-2, SARS-cov2, SARS-related coronavirus 2, Severe acute respiratory syndrome coronavirus 2, SARS-Associated Coronavirus, SARS-cov, or SARS-Related Coronavirus.
Terms: <2019 novel coronavirus><2019-nCoV><AIDS><AIDS Virus><Acquired Immune Deficiency><Acquired Immune Deficiency Syndrome><Acquired Immune Deficiency Syndrome Virus><Acquired Immuno-Deficiency Syndrome><Acquired Immunodeficiency Syndrome><Acquired Immunodeficiency Syndrome Virus><Acquired Immunologic Deficiency Syndrome><Address><Affect><Anti-Cancer Agents><Antineoplastic Agents><Antineoplastic Drugs><Antineoplastics><Antioncogene Protein p53><Appearance><Basal Transcription Factor><Basal transcription factor genes><Binding><Binding Sites><Biological><Biological Markers><Blood><Blood Reticuloendothelial System><Blood monocyte><CD4 Cells><CD4 Positive T Lymphocytes><CD4 T cells><CD4 helper T cell><CD4 lymphocyte><CD4+ T-Lymphocyte><CD4-Positive Lymphocytes><CEB1 Gene><COVID-19><COVID19><Cancer Drug><Cancers><Cause of Death><Cell Body><Cell Line><CellLine><Cells><Cellular Tumor Antigen P53><Cessation of life><ChIP Sequencing><ChIP-seq><Chromosomes><CoV emergence><Codon><Codon Nucleotides><Collaborations><Combining Site><DMSO><DNA Damage><DNA Damage Repair><DNA Injury><DNA Repair><DNA damage check point><DNA damage check point response><DNA damage checkpoint><DNA damage checkpoint response><DNA damage response, signal transduction resulting in cell cycle arrest><Data><Data Set><Dataset><Death><Demasorb><Demeso><Dimethyl Sulfoxide><Dimethylsulphinyl><Dimethylsulphoxide><Disease><Disorder><Domoso><Dromisol><Drugs><EPEG><Eposide><Ethnic Origin><Ethnicity><Etoposide><Evaluation><Evolution><Expression Profiling><Family><Frequencies><Gender><Gene Expression><Gene Family><Gene Transcription><General Transcription Factor Gene><General Transcription Factors><Generalized Growth><Genes><Genetic Alteration><Genetic Change><Genetic Polymorphism><Genetic Transcription><Genetic defect><Genome><Genotype><Goals><Growth><HCoV><HERC5><HERC5 Gene><HIV><Homolog of Yeast Vacuolar Protein Sorting 23><Human><Human Biology><Human Cell Line><Human Genome><Human Immunodeficiency Viruses><Human Volunteers><Immune><Immune response><Immunes><Immunity><Immunological response><Individual><Infant><Inflammation><Inflammatory><Inflammatory Response><Interleukins><Intermediary Metabolism><Intervention><Intervention Strategies><Journals><LAV-HTLV-III><LOC51191><Lastet><Lead><Lethal Genes><Ligands><Linkage Disequilibrium><Lymphadenopathy-Associated Virus><Lymphocyte><Lymphocytic><Magazine><Malignant Neoplasms><Malignant Tumor><Marrow monocyte><Mediating><Medication><Membrane><Meta-Analysis><Metabolic Processes><Metabolism><Methods><Modern Man><Molecular Interaction><Mutation><NGS Method><NGS system><NIEHS><National Institute of Environmental Health Sciences><Neoplastic Disease Chemotherapeutic Agents><Null Cells><Null Lymphocytes><Oncoprotein p53><Outcome><P53><Participant><Pathway interactions><Pb element><Pharmaceutic Preparations><Pharmaceutical Preparations><Phenotype><Phosphoprotein P53><Phosphoprotein pp53><Process><Protein TP53><Protein p53><Public Health Schools><Publications><RNA Expression><Reactive Site><Receptor Protein><Registries><Research><Research Design><Research Resources><Resources><Respiratory syncytial virus><Response Elements><Risk><Role><SARS><SARS Virus><SARS corona virus><SARS coronavirus><SARS coronavirus disease><SARS-Associated Coronavirus><SARS-CoV><SARS-CoV disease><SARS-CoV-2><SARS-CoV2><SARS-Related Coronavirus><SARS-associated coronavirus 2><SARS-coronavirus-2><SARS-related coronavirus 2><Sampling><Scientific Publication><Sentinel><Severe Acute Respiratory Syndrome><Severe Acute Respiratory Syndrome CoV disease><Severe Acute Respiratory Syndrome Virus><Severe Acute Respiratory Syndrome corona virus><Severe Acute Respiratory Syndrome coronavirus><Severe Acute Respiratory Syndrome coronavirus disease><Severe acute respiratory syndrome coronavirus 2><Severities><Short interfering RNA><Small Interfering RNA><Strains Cell Lines><Stress><Study Type><System><T-Cells><T-Lymphocyte><T4 Cells><T4 Lymphocytes><TLR protein><TLR8><TLR8 gene><TP53><TP53 gene><TRIM5><TRIM5 gene><TRIM5alpha><TRP53><TSG101><TSG101 gene><The Multi-center AIDS Cohort Study><The Multicenter AIDS Cohort Study><Therapeutic><Tissue Growth><Toll-Like Receptor 8><Toll-Like Receptor Family Gene><Toll-like receptors><Topoisomerase><Transact><Transactivation><Transcription><Transcription Factor Proto-Oncogene><Transcription factor genes><Translating><Tumor Protein p53><Tumor Protein p53 Gene><Tumor-Specific Treatment Agents><Unscheduled DNA Synthesis><Up-Regulation><Upregulation><VPS23><Variant><Variation><Vepesid><Viral><Viral Diseases><Virus Diseases><Virus-HIV><Work><Wuhan coronavirus><analysis pipeline><anti-cancer drug><anticancer agent><anticancer drug><base><bio-markers><biologic marker><biological adaptation to stress><biomarker><blind><cell type><chemotherapy><chromatin immunoprecipitation-sequencing><clinical investigation><clinical relevance><clinically relevant><cohort><corona virus disease 2019><coronavirus disease 2019><coronavirus emergence><cultured cell line><drug/agent><emergent CoV><emergent coronavirus><emerging CoV><emerging coronavirus><entire genome><environmental stressor><full genome><functional status><genome analysis><genome mutation><genome scale><genome-wide><genomewide><global gene expression><global transcription profile><heavy metal Pb><heavy metal lead><host response><human CoV><human DNA><human corona virus><human coronavirus><human model><human whole genome><immunoresponse><interventional strategy><lymph cell><macrophage><malignancy><membrane structure><model of human><monocyte><mutant><nCoV><neoplasm/cancer><new CoV><new coronavirus><next gen sequencing><next generation sequencing><nextgen sequencing><novel><novel CoV><novel coronavirus><nucleic acid metabolism><ontogeny><p53 Antigen><p53 Genes><p53 Tumor Suppressor><pathogen><pathway><polymorphism><protective allele><protective variant><reaction; crisis><receptor><recruit><repair><repaired><response><screening><sensor><severe acute respiratory syndrome-CoV><siRNA><social role><stress response><stress; reaction><study design><thymus derived lymphocyte><trans-activation><transcription factor><transcriptome><tumor><tumor susceptibility gene 101><viral detection><viral infection><virus detection><virus infection><virus-induced disease><whole genome>