title: TNF-α modulates genome-wide redistribution of ΔNp63α/TAp73 and NF-κB cREL interactive binding on TP53 and AP-1 motifs to promote an oncogenic gene program in squamous cancer.
abstract: The Cancer Genome Atlas (TCGA) network study of 12 cancer types (PanCancer 12) revealed frequent mutation of TP53, and amplification and expression of related TP63 isoform ΔNp63 in squamous cancers. Further, aberrant expression of inflammatory genes and TP53/p63/p73 targets were detected in the PanCancer 12 project, reminiscent of gene programs comodulated by cREL/ΔNp63/TAp73 transcription factors we uncovered in head and neck squamous cell carcinomas (HNSCCs). However, how inflammatory gene signatures and cREL/p63/p73 targets are comodulated genome wide is unclear. Here, we examined how the inflammatory factor tumor necrosis factor-α (TNF-α) broadly modulates redistribution of cREL with ΔNp63α/TAp73 complexes and signatures genome wide in the HNSCC model UM-SCC46 using chromatin immunoprecipitation sequencing (ChIP-seq). TNF-α enhanced genome-wide co-occupancy of cREL with ΔNp63α on TP53/p63 sites, while unexpectedly promoting redistribution of TAp73 from TP53 to activator protein-1 (AP-1) sites. cREL, ΔNp63α and TAp73 binding and oligomerization on NF-κB-, TP53- or AP-1-specific sequences were independently validated by ChIP-qPCR (quantitative PCR), oligonucleotide-binding assays and analytical ultracentrifugation. Function of the binding activity was confirmed using TP53-, AP-1- and NF-κB-specific REs or p21, SERPINE1 and IL-6 promoter luciferase reporter activities. Concurrently, TNF-α regulated a broad gene network with cobinding activities for cREL, ΔNp63α and TAp73 observed upon array profiling and reverse transcription-PCR. Overlapping target gene signatures were observed in squamous cancer subsets and in inflamed skin of transgenic mice overexpressing ΔNp63α. Furthermore, multiple target genes identified in this study were linked to TP63 and TP73 activity and increased gene expression in large squamous cancer samples from PanCancer 12 TCGA by CircleMap. PARADIGM inferred pathway analysis revealed the network connection of TP63 and NF-κB complexes through an AP-1 hub, further supporting our findings. Thus, inflammatory cytokine TNF-α mediates genome-wide redistribution of the cREL/p63/p73, and AP-1 interactome, to diminish TAp73 tumor suppressor function and reciprocally activate NF-κB and AP-1 gene programs implicated in malignancy.
authors.affiliation: Tumor Biology Section, Head and Neck Surgery Branch, National Institute on Deafness and Other Communication Disorders, NIH, Bethesda, Maryland, USA.
authors.forename: H
authors.initials: H
authors.lastname: Si
authors.affiliation: Tumor Biology Section, Head and Neck Surgery Branch, National Institute on Deafness and Other Communication Disorders, NIH, Bethesda, Maryland, USA.|Orthopaedic Center, Zhujiang Hospital Guangzhou, Guangdong, China.
authors.forename: H
authors.initials: H
authors.lastname: Lu
authors.affiliation: Tumor Biology Section, Head and Neck Surgery Branch, National Institute on Deafness and Other Communication Disorders, NIH, Bethesda, Maryland, USA.
authors.forename: X
authors.initials: X
authors.lastname: Yang
authors.affiliation: Tumor Biology Section, Head and Neck Surgery Branch, National Institute on Deafness and Other Communication Disorders, NIH, Bethesda, Maryland, USA.
authors.forename: A
authors.initials: A
authors.lastname: Mattox
authors.affiliation: Tumor Biology Section, Head and Neck Surgery Branch, National Institute on Deafness and Other Communication Disorders, NIH, Bethesda, Maryland, USA.
authors.forename: M
authors.initials: M
authors.lastname: Jang
authors.affiliation: Tumor Biology Section, Head and Neck Surgery Branch, National Institute on Deafness and Other Communication Disorders, NIH, Bethesda, Maryland, USA.
authors.forename: Y
authors.initials: Y
authors.lastname: Bian
authors.affiliation: Department of Chemistry and Biochemistry, University of California, San Diego, CA, USA.
authors.forename: E
authors.initials: E
authors.lastname: Sano
authors.affiliation: Instituto de Química, Universidad Nacional Autónoma de México (UNAM), Circuito Exterior, Ciudad Universitaria, Mexico City, MÉXICO.
authors.forename: H
authors.initials: H
authors.lastname: Viadiu
authors.affiliation: LKS Faculty of Medicine and School of Biomedical Sciences, LKS Faculty of Medicine and Center of Genome Sciences, The University of Hong Kong, Hong Kong, China.
authors.forename: B
authors.initials: B
authors.lastname: Yan
authors.affiliation: Buck Institute for Research on Aging, Novato, CA, USA.
authors.forename: C
authors.initials: C
authors.lastname: Yau
authors.affiliation: Department of Biomolecular Engineering, Center for Biomolecular Sciences and Engineering, University of California, Santa Cruz, Santa Cruz, CA, USA.
authors.forename: S
authors.initials: S
authors.lastname: Ng
authors.affiliation: Tumor Biology Section, Head and Neck Surgery Branch, National Institute on Deafness and Other Communication Disorders, NIH, Bethesda, Maryland, USA.
authors.forename: S K
authors.initials: SK
authors.lastname: Lee
authors.affiliation: Department of Biochemistry, State University of New York at Buffalo, Center for Excellence in Bioinformatics and Life Sciences, Buffalo, New York, USA.
authors.forename: R-A
authors.initials: RA
authors.lastname: Romano
authors.affiliation: Cancer Genetics Branch, National Cancer Institute, Bethesda, Maryland, USA.
authors.forename: S
authors.initials: S
authors.lastname: Davis
authors.affiliation: Cancer Genetics Branch, National Cancer Institute, Bethesda, Maryland, USA.
authors.forename: R L
authors.initials: RL
authors.lastname: Walker
authors.affiliation: Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AK, USA.
authors.forename: W
authors.initials: W
authors.lastname: Xiao
authors.affiliation: Biodata Mining and Discovery Section, National Institute of Arthritis, Musculoskeletal and Skin Diseases, Bethesda, Maryland, USA.
authors.forename: H
authors.initials: H
authors.lastname: Sun
authors.affiliation: Clinical Immunology Section, National Eye Institute, NIH, Bethesda, Maryland, USA.|State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China.
authors.forename: L
authors.initials: L
authors.lastname: Wei
authors.affiliation: Department of Biochemistry, State University of New York at Buffalo, Center for Excellence in Bioinformatics and Life Sciences, Buffalo, New York, USA.
authors.forename: S
authors.initials: S
authors.lastname: Sinha
authors.affiliation: Buck Institute for Research on Aging, Novato, CA, USA.
authors.forename: C C
authors.initials: CC
authors.lastname: Benz
authors.affiliation: Department of Biomolecular Engineering, Center for Biomolecular Sciences and Engineering, University of California, Santa Cruz, Santa Cruz, CA, USA.
authors.forename: J M
authors.initials: JM
authors.lastname: Stuart
authors.affiliation: Cancer Genetics Branch, National Cancer Institute, Bethesda, Maryland, USA.
authors.forename: P S
authors.initials: PS
authors.lastname: Meltzer
authors.affiliation: Tumor Biology Section, Head and Neck Surgery Branch, National Institute on Deafness and Other Communication Disorders, NIH, Bethesda, Maryland, USA.
authors.forename: C
authors.initials: C
authors.lastname: Van Waes
authors.affiliation: Tumor Biology Section, Head and Neck Surgery Branch, National Institute on Deafness and Other Communication Disorders, NIH, Bethesda, Maryland, USA.
authors.forename: Z
authors.initials: Z
authors.lastname: Chen
mesh_terms: D001665:Binding Sites; D002294:Carcinoma, Squamous Cell / Q000235:genetics* / Q000378:metabolism*; D002471:Cell Transformation, Neoplastic / Q000235:genetics / Q000378:metabolism; D016000:Cluster Analysis; D016384:Consensus Sequence; D020869:Gene Expression Profiling; D015972:Gene Expression Regulation, Neoplastic; D006801:Humans; D008954:Models, Biological; D016328:NF-kappa B / Q000378:metabolism*; D059372:Nucleotide Motifs; D011401:Promoter Regions, Genetic; D011485:Protein Binding; D021381:Protein Transport; D012045:Regulatory Sequences, Nucleic Acid; D020218:Response Elements; D015398:Signal Transduction; D018808:Transcription Factor AP-1 / Q000378:metabolism*; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism*; D024363:Transcription Initiation Site; D015533:Transcriptional Activation; D014409:Tumor Necrosis Factor-alpha / Q000378:metabolism*; D000072160:Tumor Protein p73 / Q000235:genetics / Q000378:metabolism*; D016159:Tumor Suppressor Protein p53 / Q000378:metabolism*; D025521:Tumor Suppressor Proteins / Q000235:genetics / Q000378:metabolism*
chemical_list: D016328:NF-kappa B; C115051:TP63 protein, human; D018808:Transcription Factor AP-1; D014157:Transcription Factors; D014409:Tumor Necrosis Factor-alpha; D000072160:Tumor Protein p73; D016159:Tumor Suppressor Protein p53; D025521:Tumor Suppressor Proteins