Comparison of cell response to chromatin and DNA damage

DNA-targeting drugs are widely used for anti-cancer treatment. Many of these drugs cause different types of DNA damage, i.e. alterations in the chemical structure of DNA molecule. However, molecules binding to DNA may also interfere with DNA packing into chromatin. Interestingly, some molecules do not cause any changes in DNA chemical structure but interfere with DNA binding to histones and nucleosome wrapping. This results in histone loss from chromatin and destabilization of nucleosomes, a phenomenon that we call chromatin damage. Although the cellular response to DNA damage is well-studied, the consequences of chromatin damage are not. Moreover, many drugs used to study DNA damage also cause chromatin damage, therefore there is no clarity on which effects are caused by DNA or chromatin damage. In this study, we aimed to clarify this issue. We treated normal and tumor cells with bleomycin, nuclease mimicking drug which cut predominantly nucleosome-free DNA and therefore causes DNA damage in the form of DNA breaks, and CBL0137, which causes chromatin damage without direct DNA damage. We describe similarities and differences between the consequences of DNA and chromatin damage. Both agents were more toxic for tumor than normal cells, but while DNA damage causes senescence in both normal and tumor cells, chromatin damage does not. Both agents activated p53, but chromatin damage leads to the accumulation of higher levels of unmodified p53, which transcriptional activity was similar to or lower than that of p53 activated by DNA damage. Most importantly, we found that while transcriptional changes caused by DNA damage are limited by p53-dependent activation of a small number of p53 targets, chromatin damage activated many folds more genes in p53 independent manner.

Human Immunodeficiency Virus Is Associated With Poor Overall Survival Among Patients With Head and Neck Cancer

BACKGROUND

Head and neck squamous cell cancer (HNSCC) occurs at higher rates among persons with HIV (PWH). This study compares the impact of sociodemographic and clinicopathologic characteristics on outcomes among PWH-HNSCC compared with HNSCC patients without HIV.

METHODS

Patient data from HNSCC individuals were collected at a single academic hospital center between 2002 and 2018. Forty-eight patients with HIV (HIV-HNSCC) and 2894 HNSCC patients without HIV were included. Multivariate analysis determined predictors of survival using Cox proportional hazards regression model. HIV-positive and -negative tumors were analyzed by quantitative immunofluorescence for expression of CD4, CD8, CD20 and PD-L1.

RESULTS

HIV-HNSCC patients had a lower median overall survival than HNSCC patients without HIV (34 [18-84] vs 94 [86-103] months; P < .001). In multivariate analysis that included age, sex, race/ethnicity, stage, site, tobacco use, time to treatment initiation, and insurance status, HIV was an independent predictor of poorer survival, with a hazard ratio of 1.98 (95% CI: 1.32-2.97; P < .001). PWH with human papillomavirus (HPV)-positive oropharyngeal tumors also had worse prognosis than HPV-positive oropharyngeal tumors in the population without HIV (P < .001). The tumor microenvironment among HIV-HNSCC patients revealed lower intratumoral CD8 infiltration among HIV+ HPV+ tumors compared with HIV- HPV+ tumors (P = .04).

CONCLUSIONS

HIV-HNSCC patients had worse prognosis than the non-HIV population, with HIV being an independent predictor of poor clinical outcomes when accounting for important sociodemographic and clinicopathologic factors. Our findings highlight differences in tumor biology that require further detailed characterization in large cohorts and increased inclusion of PWH in immunotherapy trials.

Abstract 3735: Regulation of HPV gene expression by 5-azacytidine treatment in head and neck cancer

Human papillomavirus (HPV) causes approximately 80% of head and neck squamous cell carcinoma (HNSCC) in the oropharynx, and its incidence is now higher than uterine cervical cancer in the US. The CDC estimates that this common sexually transmitted disease accounts for nearly 13,000 HPV+ HNSCC patients per year in the United States. Despite having a higher cure rate than HPV- HNSCC, the recurrence rate is approximately 30%. These patients have few therapeutic options since resistance to treatment arises from all known therapeutic modalities. Initial therapy for HPV+ HNSCC is aggressive and often results in negative lifelong side effects. The substantial recurrence rate and high morbidity of primary therapy suggest the need for new treatments. Global genome hypermethylation in HPV+ HNSCC, compared to HPV-, prompted our lab to explore demethylation as a therapeutic option. 5-azacytidine (5-aza) and 5-aza-2′-deoxycytidine (decitabine) are synthetic cytidine analogs that cause DNA demethylation by trapping methyltransferases to chromatin. These demethylating agents are FDA approved for the treatment of myelodysplasia and acute myeloid leukemia. Recently, we found that HPV+ HNSCC cells are more sensitive than HPV- cells to 5-aza, that low doses of 5-aza delayed HPV+ xenograft tumor growth, and that HPV+ tumor samples from patients treated with 5-aza in a window trial had increased apoptosis. We also observed a marked downregulation of HPV gene expression after 5-aza. Decreased HPV E6 expression, followed by reactivation of tumor suppressor p53, induced p53-dependent apoptosis in HPV+ HNSCC. Thus, decreased expression of HPV genes is an important component of 5-aza-associated toxicity toward HPV+ HNSCC; therefore, we further explored mechanisms through which demethylation negatively regulates the expression of HPV genes. First, we determined that 5-aza regulates transcription of HPV genes, but not the stability of HPV transcripts. Second, we found that transcriptional regulation of HPV genes after 5-aza depends on the proto-oncogene JunB, a component of the transcription factor Activator Protein 1 (AP-1). Moreover, our experiments revealed that clonogenic survival of HPV+ head and neck cancer cells is dependent on JunB expression. In summary, our study provides an improved mechanistic understanding of the regulation of HPV gene transcription in HNSCC and identifies a novel HPV+ HNSCC dependency on JunB, potentially providing a basis for a new rational targeted therapy.

Citation Format: Hina Rehmani, Natalia Isaeva, Wendell G. Yarbrough. Regulation of HPV gene expression by 5-azacytidine treatment in head and neck cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3735.

Impact of HIV infection on clinical outcomes among people diagnosed with head and neck cancer

e18080

Background: Incidence of non-AIDS-defining cancers, including head and neck cancer (HNC), is rising among people with HIV (PWH) in the combination antiretroviral therapy (cART) era. The following study compares demographics, clinical outcomes, and the tumor microenvironment of HIV+ and Uninfected HNC patients at a single institution. Methods: Yale Tumor Registry query identified 3,356 HNC patients from 2002 to 2018 for analysis, including 50 PWH. In addition, quantitative immunofluorescence (QIF) was performed on tumor tissue from 22 PWH and 75 matched Uninfected patients. HPV status was based on p16 staining done universally among oropharyngeal squamous cell carcinomas (OPSCC) after 2010. Results: PWH were younger at cancer presentation compared to Uninfected patients (55.5 vs. 62.0, p < 0.001), with differences in race/ethnicity and insurance status (p < 0.001 for both). Biologic sex, tobacco use, alcohol consumption, anatomic site, stage at presentation, stage-specific treatment, and time to initiation of treatment were comparable between HIV+ and Uninfected cohorts. 89% of the PWH were on cART, with 79% achieving viral loads ≤200 copies/mL and a median CD4 count of 341 cells/mm³. Median survival among PWH was 39.1 months, compared to 100.8 months among Uninfected patients (p < 0.001). In a multivariate (MV) analysis that included age, sex, race/ethnicity, tobacco use, anatomic site, stage, time to treatment initiation and insurance status, HIV was an independent predictor of poor outcome (HR 1.88 with 95% CI: 1.25-2.81). Difference in survival was noted particularly in early stage (stages 0, I, II) cancer, with a median survival of 73.8 months in PWH compared to 141.9 months in Uninfected patients (p = 0.001). Survival was comparable among late stage (stages III, IV) HNC patients. Among PWH, increased HIV viral load was associated with poor outcome in a MV analysis (p = 0.03). Among HPV-associated OPSCC, PWH had decreased survival compared to Uninfected patients (p < 0.001). In our study of the tumor microenvironment by QIF, tumors of PWH had lower tumoral CD8 T cell infiltration (p = 0.04) and lower PD-L1 expression in tumor, stroma, and combined compartments (CPS) (p = 0.01, p = 0.03, and p = 0.01, respectively) compared to Uninfected patients. Conclusions: In our single institution study, HNC patients living with HIV experienced decreased overall survival, with HIV serving as an independent predictor of poor outcome in a multivariate analysis which included insurance status and treatment approaches. Difference in outcome was significant among early stage tumors and among HPV+ OPSCC. CD8 T cell infiltration and PD-L1 expression, both associated with improved outcomes in the general population, are decreased within the TME of PWH. Our data suggest that HIV-associated HNC is associated with poorer outcomes and highlight differences in tumor biology that require further detailed characterization in large cohorts.

Abstract P133: NF-κB and NRF2 pathways dysregulation is associated with improved outcomes in HPV-associated head and neck cancer

This study aims to better understand the mechanisms of HPV carcinogenesis. Additionally, it helps to improve therapeutic personalization, identify new therapeutic targets in cancer, and aids in understanding the role of NF-κB in HPV-driven carcinogenesis, HPV biology, and tumor response to therapy. The incidence of HPV-associated (HPV+) head and neck cancer (HNSCC) is increasing rapidly, however, the mechanisms of HPV-driven carcinogenesis in head and neck cancers have not been thoroughly investigated. The relatively favorable prognosis of HPV+ HNSCC, along with severe side-effects seen in patients due to radiotherapy, it is pertinent to develop de-intensification strategies. However, a reliable prognostic biomarker is a limiting factor for clinical trials aiming to decrease the morbidity of therapy for HPV+ HNSCC through treatment de-escalation. Using molecular characteristics of HPV+ HNSCC and based on the presence or absence of NF-κB activating mutations in TCGA head and neck cancer cohort, we developed an NF-kB activity classifier and identified two intrinsic subtypes of HPV+ HNSCCs. The subtype harboring mutations in NF-κB regulators is associated with activated NF-κB, maintenance of episomal HPV, and improved patient survival. Identification of a subtype of HPV+ HNSCC with active NF-κB, improved survival, and absence of HPV genome integration, suggested that these tumors were driven by a distinct or alternative mechanism of oncogenesis that is dependent on episomal HPV and NF-κB activity, while classical HPV-driven carcinogenesis relies on increased expression of HPV E6 and E7 oncogenes occurring upon HPV genome integration and loss of HPV E2.However, it is not yet known why this subset of tumors with overactive NF-κB displays better survival. An interesting finding from our study was that these tumors with increased NF-κB activity had reduced NRF2 signaling.NRF2 has been associated with resistance to treatment and significant downregulation of NRF2 signaling in the subtype of HPV+ HNSCC with active NF-κB may contribute to increased treatment sensitivity and improved patient survival. Preliminary experiments confirmed that baseline and inducible (with small molecule NRF2 activator or radiation treatment) NRF2 transcriptional activity is downregulated in HPV-positive head and neck cancer cells with deleted CYLD or TRAF3 and activated NF-κB, and that this effect is most likely independent of NRF2 degradation mediated by Cul3. Moreover, expression of major NRF2 targets was decreased in HPV+ HNSCC cells harboring constitutively active NF-κB. Finding an inverse correlation between NF-κB and NRF2 activities suggests that inhibition of NRF2 in NF-κB active HPV+ HNSCCs drives their sensitivity to radiation and that NF-κB regulates NRF2 transcriptional activity in HPV+ HNSCC. This project uncovers the role of NF-κB in HPV-driven head and neck cancer etiology. Our novel NF-κB activity RNA classifier or mutations in NF-κB pathway distinguishing the 2 subtypes of HPV+ HNSCC may serve as prognostic biomarkers to help clinicians with therapeutic decisions.

Citation Format: Aditi Kothari, Travis Parke Schrank, Wendell Gray Yarbrough, Natalia Isaeva. NF-κB and NRF2 pathways dysregulation is associated with improved outcomes in HPV-associated head and neck cancer [abstract]. In: Proceedings of the AACR-NCI-EORTC Virtual International Conference on Molecular Targets and Cancer Therapeutics; 2021 Oct 7-10. Philadelphia (PA): AACR; Mol Cancer Ther 2021;20(12 Suppl):Abstract nr P133.