RÉSUMÉ
Background: Reportedly, nasopharyngeal carcinoma (NPC) patients with MHC I Class aberration are prone to poor survival outcomes, which indicates that the deficiency of tumor neoantigens might represent a mechanism of immune surveillance escape in NPC. Methods: To clearly delineate the landscape of neoantigens in NPC, we performed DNA and RNA sequencing on paired primary tumor, regional lymph node metastasis and distant metastasis samples from 26 patients. Neoantigens were predicted using pVACseq pipeline. Subtype prediction model was built using random forest algorithm. Results: Portraying the landscape of neoantigens in NPC for the first time, we found that the neoantigen load of NPC was above average compared to that of other cancers in The Cancer Genome Atlas program. While the quantity and quality of neoantigens were similar among primary tumor, regional lymph node metastasis and distant metastasis samples, neoantigen depletion was more severe in metastatic sites than in primary tumors. Upon tracking the clonality change of neoantigens, we found that neoantigen reduction occurred during metastasis. Building a subtype prediction model based on reported data, we observed that subtype I lacked T cells and suffered from severe neoantigen depletion, subtype II highly expressed immune checkpoint molecules and suffered from the least neoantigen depletion, and subtype III was heterogenous. Conclusions: These results indicate that neoantigens are conducive to the guidance of clinical treatment, and personalized therapeutic vaccines for NPC deserve deeper basic and clinical investigations to make them feasible in the future.
Sujet(s)
Antigènes néoplasiques/immunologie , Cancer du nasopharynx/secondaire , Tumeurs du rhinopharynx/immunologie , Adulte , Antigènes néoplasiques/génétique , ADN tumoral/génétique , ADN viral/analyse , ADN viral/génétique , Femelle , Antigènes HLA/génétique , Antigènes HLA/immunologie , Herpèsvirus humain de type 4/génétique , Humains , Mutation de type INDEL , Inhibiteurs de points de contrôle immunitaires/usage thérapeutique , Estimation de Kaplan-Meier , Métastase lymphatique/immunologie , Mâle , Adulte d'âge moyen , Cancer du nasopharynx/immunologie , Cancer du nasopharynx/thérapie , Cancer du nasopharynx/virologie , Tumeurs du rhinopharynx/génétique , Tumeurs du rhinopharynx/thérapie , Tumeurs du rhinopharynx/virologie , Polymorphisme de nucléotide simple , Survie sans progression , ARN tumoral/génétique , Récepteurs aux antigènes des cellules T/immunologie , Échappement de la tumeur à la surveillance immunitaire , Microenvironnement tumoral/immunologie , Infections à virus oncogènes/virologieRÉSUMÉ
The genetic events occurring in recurrent nasopharyngeal carcinoma (rNPC) are poorly understood. Here, we performed whole-genome and whole-exome sequencing in 55 patients with rNPC and 44 primarily diagnosed NPC (pNPC), with 7 patients having paired rNPC and pNPC samples. Previously published pNPC exome data were integrated for analysis. rNPC and pNPC tissues had similar mutational burdens, however, the number of clonal mutations was increased in rNPC samples. TP53 and three NF-κB pathway components (TRAF3, CYLD, and NFKBIA) were significantly mutated in both pNPC and rNPC. Notably, mutations in TRAF3, CYLD, and NFKBIA were all clonal in rNPC, however, 55.6% to 57.9% of them were clonal in pNPC. In general, the number of clonal mutations in NF-κB pathway-associated genes was significantly higher in rNPC than in pNPC. The NF-κB mutational clonality was selected and/or enriched during NPC recurrence. The amount of NF-κB translocated to the nucleus in samples with clonal NF-κB mutants was significantly higher than that in samples with subclonal NF-κB mutants. Moreover, the nuclear abundance of NF-κB protein was significantly greater in pNPC samples with locoregional relapse than in those without relapse. Furthermore, high nuclear NF-κB levels were an independent negative prognostic marker for locoregional relapse-free survival in pNPC. Finally, inhibition of NF-κB enhanced both radiosensitivity and chemosensitivity in vitro and in vivo. In conclusion, NF-κB pathway activation by clonal mutations plays an important role in promoting the recurrence of NPC. Moreover, nuclear accumulation of NF-κB is a prominent biomarker for predicting locoregional relapse-free survival. SIGNIFICANCE: This study uncovers genetic events that promote the progression and recurrence of nasopharyngeal carcinoma and has potential prognostic and therapeutic implications.See related commentary by Sehgal and Barbie, p. 5915.
Sujet(s)
Carcinomes , Cancer du nasopharynx , Tumeurs du rhinopharynx , Humains , Mutation , Facteur de transcription NF-kappa B/génétique , Récidive tumorale localeRÉSUMÉ
Rationale: Epstein-Barr virus (EBV) is associated with multiple malignancies with expression of viral oncogenic proteins and chronic inflammation as major mechanisms contributing to tumor development. A less well-studied mechanism is the integration of EBV into the human genome possibly at sites which may disrupt gene expression or genome stability. Methods: We sequenced tumor DNA to profile the EBV sequences by hybridization-based enrichment. Bioinformatic analysis was used to detect the breakpoints of EBV integrations in the genome of cancer cells. Results: We identified 197 breakpoints in nasopharyngeal carcinomas and other EBV-associated malignancies. EBV integrations were enriched at vulnerable regions of the human genome and were close to tumor suppressor and inflammation-related genes. We found that EBV integrations into the introns could decrease the expression of the inflammation-related genes, TNFAIP3, PARK2, and CDK15, in NPC tumors. In the EBV genome, the breakpoints were frequently at oriP or terminal repeats. These breakpoints were surrounded by microhomology sequences, consistent with a mechanism for integration involving viral genome replication and microhomology-mediated recombination. Conclusion: Our finding provides insight into the potential of EBV integration as an additional mechanism mediating tumorigenesis in EBV associated malignancies.
Sujet(s)
ADN viral/analyse , Infections à virus Epstein-Barr/complications , Génome humain , Herpèsvirus humain de type 4/génétique , Tumeurs/virologie , Intégration virale , ADN viral/génétique , Locus génétiques , Humains , Analyse de séquence d'ADNRÉSUMÉ
Epstein-Barr virus (EBV)-associated epithelial cancers, including nasopharyngeal carcinoma (NPC) and approximately 10% of gastric cancers, termed EBVaGC, represent 80% of all EBV-related malignancies. However, the exact role of EBV in epithelial cancers remains elusive. Here, we report that EBV functions in vasculogenic mimicry (VM). Epithelial cancer cells infected with EBV develop tumor vascular networks that correlate with tumor growth, which is different from endothelial-derived angiogenic vessels and is VEGF-independent. Mechanistically, activation of the PI3K/AKT/mTOR/HIF-1α signaling cascade, which is partly mediated by LMP2A, is responsible for EBV-induced VM formation. Both xenografts and clinical samples of NPC and EBVaGC exhibit VM histologically, which are correlated with AKT and HIF-1α activation. Furthermore, although anti-VEGF monotherapy shows limited effects, potent synergistic antitumor activities are achieved by combination therapy with VEGF and HIF-1α-targeted agents. Our findings suggest that EBV creates plasticity in epithelial cells to express endothelial phenotype and provides a novel EBV-targeted antitumor strategy.
Sujet(s)
Cellules épithéliales/anatomopathologie , Cellules épithéliales/virologie , Herpèsvirus humain de type 4/physiologie , Tumeurs du rhinopharynx/vascularisation , Tumeurs du rhinopharynx/virologie , Néovascularisation pathologique/anatomopathologie , Animaux , Axitinib/pharmacologie , Axitinib/usage thérapeutique , Lignée cellulaire tumorale , Femelle , Analyse de profil d'expression de gènes , Génome viral , Herpèsvirus humain de type 4/génétique , Sous-unité alpha du facteur-1 induit par l'hypoxie/métabolisme , Souris de lignée BALB C , Souris nude , Moutardes/pharmacologie , Moutardes/usage thérapeutique , Tumeurs du rhinopharynx/traitement médicamenteux , Tumeurs du rhinopharynx/génétique , Néovascularisation pathologique/génétique , Phénylpropionates/pharmacologie , Phénylpropionates/usage thérapeutique , Phosphatidylinositol 3-kinases/métabolisme , Protéines proto-oncogènes c-akt/métabolisme , Transduction du signal , Sérine-thréonine kinases TOR/métabolisme , Facteur de croissance endothéliale vasculaire de type A/antagonistes et inhibiteurs , Facteur de croissance endothéliale vasculaire de type A/métabolisme , Protéines de la matrice virale/métabolismeRÉSUMÉ
Epstein-Barr virus (EBV) is a human cancer-related virus closely associated with lymphoid and epithelial malignancies, and EBV glycoprotein B (gB) plays an essential role in viral entry into both B cells and epithelial cells by promoting cell-cell fusion. EBV gB is exclusively modified with high-mannose-linked N-glycans and primarily localizes to the endoplasmic reticulum (ER) with low levels on the plasma membrane (PM). However, the mechanism through which gB is regulated within host cells is largely unknown. Here, we report the identification of F-box only protein 2 (FBXO2), an SCF ubiquitin ligase substrate adaptor that preferentially binds high-mannose glycans and attenuates EBV infectivity by targeting N-glycosylated gB for degradation. gB possesses seven N-glycosylation sites, and FBXO2 directly binds to these high-mannose moieties through its sugar-binding domain. The interaction promotes the degradation of glycosylated gB via the ubiquitin-proteasome pathway. Depletion of FBXO2 not only stabilizes gB but also promotes its transport from the ER to the PM, resulting in enhanced membrane fusion and viral entry. FBXO2 is expressed in epithelial cells but not B cells, and EBV infection up-regulates FBXO2 levels. In summary, our findings highlight the significance of high-mannose modification of gB and reveal a novel host defense mechanism involving glycoprotein homeostasis regulation.
Sujet(s)
Protéines du cycle cellulaire/métabolisme , Infections à virus Epstein-Barr/métabolisme , Protéines F-box/métabolisme , Interactions hôte-parasite/physiologie , Protéines de tissu nerveux/métabolisme , Protéines de l'enveloppe virale/métabolisme , Animaux , Herpèsvirus humain de type 4/métabolisme , Herpèsvirus humain de type 4/pathogénicité , HumainsRÉSUMÉ
The management of advanced nasopharyngeal carcinoma (NPC) remains a challenge. The ubiquitous nature of Epstein-Barr virus (EBV) infection in nonkeratinizing NPC has forced us to investigate novel drugs for NPC in the presence of EBV. In this study, we performed a small-scale screening of a library of compounds that target epigenetic regulators in paired EBV-positive and EBV-negative NPC cell lines. We found that bromodomain and extra-terminal (BET) inhibitor JQ1 preferentially inhibits the growth of EBV-positive NPC cells. JQ1 induces apoptosis, decreases cell proliferation and enhances the radiosensitivity in NPC cells, especially EBV-positive cells. Significantly, JQ1-induced cell death is c-Myc-dependent. Notably, RNA-seq analysis demonstrated that JQ1 represses TP63, TP53 and their targets. JQ1 also lessens the expression of PD-L1 in NPC. Moreover, the high potency of JQ1 in NPC cells was further confirmed in vivo in CNE2-EBV+ tumor-bearing mice. These findings indicate that JQ1 is a promising therapeutic candidate for advanced NPC.
Sujet(s)
Azépines/usage thérapeutique , Infections à virus Epstein-Barr/traitement médicamenteux , Infections à virus Epstein-Barr/métabolisme , Cancer du nasopharynx/traitement médicamenteux , Cancer du nasopharynx/métabolisme , Tumeurs du rhinopharynx/traitement médicamenteux , Tumeurs du rhinopharynx/métabolisme , Protéines/antagonistes et inhibiteurs , Protéines/métabolisme , Protéines proto-oncogènes c-myc/métabolisme , Triazoles/usage thérapeutique , Animaux , Cycle cellulaire/effets des médicaments et des substances chimiques , Cycle cellulaire/génétique , Lignée cellulaire tumorale , Survie cellulaire/effets des médicaments et des substances chimiques , Survie cellulaire/génétique , Femelle , Technique d'immunofluorescence , Régulation de l'expression des gènes tumoraux/effets des médicaments et des substances chimiques , Humains , Immunohistochimie , Souris , Souris de lignée BALB C , Souris nudeRÉSUMÉ
Genetic susceptibility underlies the pathogenesis of cancer. We and others have previously identified a novel susceptibility gene TNFRSF19, which encodes an orphan member of the TNF receptor superfamily known to be associated with nasopharyngeal carcinoma (NPC) and lung cancer risk. Here, we show that TNFRSF19 is highly expressed in NPC and is required for cell proliferation and NPC development. However, unlike most of the TNF receptors, TNFRSF19 was not involved in NFκB activation or associated with TRAF proteins. We identified TGFß receptor type I (TßRI) as a specific binding partner for TNFRSF19. TNFRSF19 bound the kinase domain of TßRI in the cytoplasm, thereby blocking Smad2/3 association with TßRI and subsequent signal transduction. Ectopic expression of TNFRSF19 in normal epithelial cells conferred resistance to the cell-cycle block induced by TGFß, whereas knockout of TNFRSF19 in NPC cells unleashed a potent TGFß response characterized by upregulation of Smad2/3 phosphorylation and TGFß target gene transcription. Furthermore, elevated TNFRSF19 expression correlated with reduced TGFß activity and poor prognosis in patients with NPC. Our data reveal that gain of function of TNFRSF19 in NPC represents a mechanism by which tumor cells evade the growth-inhibitory action of TGFß.Significance:TNFRSF19, a susceptibility gene for nasopharyngeal carcinoma and other cancers, functions as a potent inhibitor of the TGFß signaling pathway.Graphical Abstract: http://cancerres.aacrjournals.org/content/canres/78/13/3469/F1.large.jpg Cancer Res; 78(13); 3469-83. ©2018 AACR.
Sujet(s)
Carcinogenèse/anatomopathologie , Cancer du nasopharynx/anatomopathologie , Tumeurs du rhinopharynx/anatomopathologie , Récepteur de type I du facteur de croissance transformant bêta/métabolisme , Récepteurs aux facteurs de nécrose tumorale/métabolisme , Adolescent , Adulte , Sujet âgé , Biopsie , Lignée cellulaire tumorale , Études de cohortes , Femelle , Techniques de knock-down de gènes , Humains , Mâle , Adulte d'âge moyen , Partie nasale du pharynx/anatomopathologie , Phosphorylation , Récepteurs aux facteurs de nécrose tumorale/génétique , Transduction du signal , Protéine Smad2/métabolisme , Protéine Smad-3/métabolisme , Facteur de croissance transformant bêta/métabolisme , Régulation positive , Jeune adulteRÉSUMÉ
Despite advances in the development of radiation against nasopharyngeal carcinoma (NPC), the management of advanced NPC remains a challenge. Smac mimetics are designed to neutralize inhibitor of apoptosis (IAP) proteins, thus reactivating the apoptotic program in cancer cells. In this study, we investigated the effect of a novel bivalent Smac mimetic APG-1387 in NPC. In vitro, APG-1387 in combination with TNF-α potently decreased NPC cell viability by inducing apoptosis in majority of NPC cell lines. The in vitro antitumor effect was RIPK1-dependent, whereas it was independent on IAPs, USP11, or EBV. Of note, the inhibition of NF-κB or AKT pathway rendered resistant NPC cells responsive to the treatment of APG-1387/TNF-α. In vivo, APG-1387 displayed antitumor activity as a single agent at well-tolerated doses, even in an in vitro resistant cell line. In summary, our results demonstrate that APG-1387 exerts a potent antitumor effect on NPC. These findings support clinical evaluation of APG-1387 as a potential treatment for advanced NPC.