Omics analysis of the regulatory role of APOBEC in the immune microenvironment of head and neck squamous cell carcinoma with different HPV status
Objective: To investigate the differences in apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like (APOBEC) between human papillomavirus (HPV)-positive and HPV-negative head and neck squamous cell carcinoma (HNSCC) patients, analyze its association with the immune microenvironment and the cGAS-STING pathway, and evaluate its predictive value for immunotherapy efficacy. Methods: Whole-exome sequencing data from HNSCC patients (from September 2017 to March 2020 at the Third Affiliated Hospital of Kunming Medical University) were collected for somatic mutation profiling. APOBEC enrichment scores were calculated and integrated with differentially expressed genes (DEGs) to perform Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis and Gene Set Enrichment Analysis (GSEA). Single-cell RNA sequencing (scRNA-seq) data were utilized to validate the relationship between APOBEC3 expression, immune cell composition, and cGAS-STING module activity. Furthermore, an immunotherapy cohort was analyzed to evaluate the association of APOBEC3 family gene expression with immune checkpoint genes and therapeutic outcomes. Results: APOBEC mutational signatures were prevalent in both HPV-negative and HPV-positive HNSCC patients, but their driving patterns differed significantly: HPV-positive patients were dominated by APOBEC3A mutations, whereas the HPV-negative group exhibited a synergistic effect of multiple family members, including APOBEC3A/3B/3C/3D/3F. Pathway analysis indicated that in HPV-negative HNSCC, APOBEC activity was significantly associated with the enhancement of the cGAS-STING pathway, interferon response, and inflammatory response. Single-cell analysis confirmed that tumors with high APOBEC3 expression had richer immune cell infiltration, and the activities of four functional modules of the cGAS-STING pathway (cGAS-STING, NF-κB, interferon stimulation, and antigen presentation) were significantly upregulated. In the immunotherapy cohort, patients with high APOBEC3 expression exhibited higher expression of immune checkpoint molecules, and their treatment response rates were significantly superior to those in the low-expression group. Conclusions: APOBEC exhibits distinct driving mechanisms in HNSCC depending on HPV status. Its activity is closely related to cGAS-STING pathway activation, enhanced immune infiltration, and improved immunotherapy efficacy, suggesting potential predictive and therapeutic value.
- # HPV-negative Head And Neck Squamous Cell Carcinoma
- # HPV-positive Patients
- # HPV-negative Head And Neck Squamous Cell Carcinoma Patients
- # Immunotherapy Cohort
- # Expression Of Immune Checkpoint Molecules
- # Human Papillomavirus Status
- # cGAS-STING Pathway
- # Neck Squamous Cell Carcinoma
- # APOBEC Mutational Signatures
- # Differences In Apolipoprotein
- Peer Review Report
- 10.7554/elife.82705.sa1
- Jan 13, 2023
Multi-omic profiling of tumor-infiltrating T cells provides new insights into the differences in the effectiveness of CDK4 inhibitor between human papillomavirus (HPV)-positive and HPV-negative head and neck squamous cell carcinoma patients.
- Peer Review Report
- 10.7554/elife.82705.sa0
- Jan 13, 2023
Multi-omic profiling of tumor-infiltrating T cells provides new insights into the differences in the effectiveness of CDK4 inhibitor between human papillomavirus (HPV)-positive and HPV-negative head and neck squamous cell carcinoma patients.
- Research Article
- 10.1158/1538-7755.disp14-ia18
- Sep 30, 2015
- Cancer Epidemiology, Biomarkers & Prevention
IA18: Tumor suppressor gene silencing by somatic mutations and promoter methylation leads to genomic instability in head and neck squamous cell carcinoma
- Research Article
12
- 10.1002/ijc.32623
- Aug 26, 2019
- International Journal of Cancer
There have been hints that nonviral cancer antigens are differentially expressed in human papillomavirus (HPV)-positive and HPV-negative head and neck squamous cell carcinoma (HNSCC). Antibody responses (AR) to cancer antigens may be used to indirectly determine cancer antigen expression in the tumor using a noninvasive and tissue-saving liquid biopsy. Here, we set out to characterize AR to a panel of nonviral cancer antigens in HPV-positive and HPV-negative HNSCC patients. A fluorescent microbead multiplex serology to 29 cancer antigens (16 cancer-testis antigens, 5 cancer-retina antigens and 8 oncogenes) and 29 HPV-antigens was performed in 382 HNSCC patients from five independent cohorts (153 HPV-positive and 209 HPV-negative). AR to any of the cancer antigens were found in 272/382 patients (72%). The ten most frequent AR were CT47, cTAGE5a, c-myc, LAGE-1, MAGE-A1, -A3, -A4, NY-ESO-1, SpanX-a1 and p53. AR to MAGE-A3, MAGE-A9 and p53 were found at significantly different prevalences by HPV status. An analysis of AR mean fluorescent intensity values uncovered remarkably different AR clusters by HPV status. To identify optimal antigen selections covering a maximum of patients with ≤10 AR, multiobjective optimization revealed distinct antigen selections by HPV status. We identified that AR to nonviral antigens differ by HPV status indicating differential antigen expression. Multiplex serology may be used to characterize antigen expression using serum or plasma as a tissue-sparing liquid biopsy. Cancer antigen panels should address the distinct antigen repertoire of HPV-positive and HPV-negative HNSCC.
- Research Article
- 10.1158/1538-7445.am2022-3718
- Jun 15, 2022
- Cancer Research
Histone modifications play important role in regulating the function and structure of chromatin. Abnormal histone methylation is often detected during tumor development and progression. NSD1, NSD2, and NSD3 are key histone methyltransferases (HMTs) that catalyze lysine 36 dimethylation (K36me2) at histone H3. Inactivating NSD1 mutations are frequent in head neck squamous cell carcinoma (HNSCC) commonly occur in HPV-negative oropharyngeal (OP) carcinoma and laryngeal carcinomas (LC), and define a novel prognostic subtype in LC, where they associate with dramatically improved overall and progression-free survival. Here, we explored the biological impact of the loss of function of NSD1 in head neck squamous carcinoma (HNSCC). First, we discovered that HNSCC cells with a damaging mutation in NSD1 have reduced K36me2 methylation levels relative to NSD1 wild-type HNSCC cells. Second, we also found slower cell proliferation in NSD1 mutant cell line (SCC4) in comparison with other NSD1 WT cell lines. To further investigate the biologic impact of NSDs, we knocked down NSD1 and NSD2 with shRNA in different histologic subtypes of HNSCC cell lines (JHU011, JHU022, Cal27, and FaDu cell lines). We discovered that depletion of NSD1 and NSD2 results in a reduction of K36me2 and a significant decrease in cell proliferation and clonogenic formation in HNSCC, but not in lung cancer cells. Next, we performed a flow cytometry-based assay and found that NSD1/NSD2 depletion in HNSCC cells causes a significant increase in apoptosis level. We also probed for gene expression and signaling in HNSCC cells following NSD1 depletion using RNA sequencing and reverse protein phase array (RPPA) approaches. From a list of RPPA candidate targets of NSD1, we confirmed the decrease in the protein and mRNA level of Phosphatidylinositol-5-Phosphate 4-Kinase Type 2 Beta (PIP4K2B), but not other members of this family (PIP4K2A and PIP4K2C). PIP4K2B may regulate the ratio of lipid messengers PI5P and PI(4,5)P2 (substrate and reaction product, respectively). The level of phosphorylation of mitogen-activated kinase p70S6 was also decreased under NSD1 knockdown. PIP4K2B siRNA depletion has also led to a significant decrease in HNSCC proliferation. Taken together, this data supports the idea that NSD1 is required for HNSCC cell proliferation via PIP4K2B. Downstream signaling, gene expression effects, and possible cell cycle regulation by NSD enzymes remain to be investigated in more detail. Further, NSDs might be attractive targets for drug development, and targeting NSD1/NSD2 enzymes may be a new strategy for improving outcomes in HNSCC patients. Citation Format: Iuliia Topchu, Rajendra Pangeni, Igor Bychkov, Petr Makhov, John Karanicolas, Jindan Yu, Erica Golemis, Jochen Lorch, Yanis Boumber. NSD histone methyltransferases drive cell proliferation in HPV-negative head and neck squamous cell carcinoma (HNSCC) [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 3718.
- Research Article
18
- 10.1002/path.4953
- Oct 6, 2017
- The Journal of Pathology
The success of programmed cell death 1 (PD-1) inhibition in achieving a clinical response in a subset of head and neck squamous cell carcinoma (HNSCC) patients emphasizes the need to better understand the immunobiology of HNSCC. Immunophenotyping was performed for 30 HCSCC patients [16 human papillomavirus (HPV)-positive; 14 HPV-negative] on matched tissue from the primary tumour site, locally metastatic cervical lymph nodes (LNs), uninvolved local cervical LNs, and peripheral blood. CD4+ and CD8+ T-cell lymphocytes obtained from tissue were analysed for expression levels of the inhibitory receptors PD-1, TIM-3 and CTLA-4. Next-generation sequencing of the T-cell receptor (TCR) β chain was performed on patients (n = 9) to determine receptor repertoire diversity and for clonality analysis. HPV-negative HNSCC patients, particularly those with stage IV disease, had significantly higher proportions of CD8+ T cells expressing CTLA-4 in tumour tissue (P = 0.0013) and in peripheral blood (P = 0.0344) than HPV-positive patients, as well as higher expression levels of TIM-3+ PD-1+ CD8+ T cells (P = 0.0072) than controls. For all patients, PD-1 expression on CD8+ T cells-particularly in HPV-negative HNSCC cases-strongly correlated (r = 0.63, P = 0.013) with tumour size at the primary site. The top CD8+ TCR clones from tumour tissue significantly overlapped with circulating peripheral blood TCR clones (r = 0.946), and HPV-positive patients had frequently expanded TCR clones that were more hydrophobic-and potentially more immunogenic-than those from HPV-negative patients. Collectively, our findings demonstrate, for the first time, that high-stage HPV-negative HNSCC patients with primary tumours at different sites in the head and neck have elevated peripheral CTLA-4+ CD8+ T-cell levels, that tumour-familiar CD8+ T cells are detectable in peripheral blood from HNSCC patients, and that TCRs from HPV-positive HNSCC patients potentially recognize distinctly immunogenic cognate antigens. However, our findings are preliminary, and need to be further confirmed in a larger patient cohort; also, how these factors affect patient response to immunotherapy needs to be determined. Copyright © 2017 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
- Research Article
- 10.1158/1538-7445.am2012-4499
- Apr 15, 2012
- Cancer Research
Introduction: HPV-negative head and neck squamous cell carcinomas (HNSCC) represent a subset of head and neck cancers with poor response to treatment and worse prognosis compared to HPV-positive HNSCC. In our prior pre-clinical experiments with HNSCC cell lines, we demonstrated that copy number loss of ATM as a marker for loss of distal chromosome 11q loss leads to defectiveγ-H2AX focus formation, increased chromosomal instability, and reduced sensitivity to ionizing radiation. We hypothesize that in HPV-negative HNSCC, ATM loss is a biomarker for poor outcome. Methods: We performed a single center, retrospective analysis of 42 HNSCC patients to determine if ATM loss is associated with poor overall survival in HPV-negative HNSCC. We performed fluorescence in situ hybridization using probes to cyclin D1 (CCND1) and ATM to assess copy number changes in paraffin sections from HNSCC tumors. Disease-specific survival was defined as time from the date of tissue procurement (surgery or biopsy) until death from disease (HNSCC). Patients who were alive at last follow-up or had died from causes unrelated to their disease were censored. Disease-specific survival by ATM loss status was estimated by the Kaplan-Meier method and tested for a difference by a two-tailed log rank test. Three covariates, age, T stage and N stage were investigated and the effect of ATM loss upon disease-specific survival was assessed with proportional hazards regression by adjusting for these covariates as needed to determine if ATM loss could be considered independently associated with cancer mortality. Results and Conclusions: HPV-negative HNSCC patients with ATM copy number loss have a median disease-specific survival of only 19 months compared to 65 months for patients without ATM loss (log rank p = .0401). We investigated whether the association between ATM loss and disease-specific survival was due to the confounding influence of other clinical variables. Age and T stage were modestly associated with survival, but neither covariate was correlated with ATM loss. We estimated the hazard ratio for ATM loss alone and conditional upon age and T stage was unchanged (.040 alone vs .047 adjusting for age and T stage). Therefore, distal 11q loss, marked by copy number loss of ATM appears to increase the risk of disease-specific mortality independently of age, N stage and T stage. Our results demonstrate that ATM loss in HPV-negative HNSCC may be prognostic of poor outcome and novel therapeutic strategies may be required in this subset of patients. Further studies to elucidate the mechanisms of distal 11q loss and study potential treatment options are underway in our laboratory. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 4499. doi:1538-7445.AM2012-4499
- Research Article
26
- 10.1186/s41199-019-0042-3
- Jul 8, 2019
- Cancers of the Head & Neck
BackgroundCompared to HPV-negative head and neck squamous cell carcinomas (HNSCCs), HPV-positive HNSCCs are associated with a favorable prognosis in part due to their improved treatment sensitivity. Inactivating mutations in NSD1 were shown to be a favorable prognostic biomarker in laryngeal cancers. Here, we characterize NSD1 mutations from the expanded The Cancer Genome Atlas (TCGA) HNSCC cohort (n = 522) and examine their prognostic implications based on HPV status of the tumor. We also begin to examine if NSD1 regulates response to platinum-based drugs and other DNA-damaging agents.MethodsTCGA HNSCC samples were segregated by HPV and NSD1 mutations using cBioPortal and patient survival was determined. Pathogenicity of mutations was predicted using UMD-Predictor. NSD1-depleted cell lines were established by transfection with control or shRNAs against NSD1, followed by puromycin selection, and confirmed by qRT-PCR. Cell sensitivity to DNA damaging agents was assessed using short-term proliferation and long-term clonogenic survival assays.ResultsAmong 457 HPV(−) tumors, 13% contained alterations in the NSD1 gene. The majority (61.3%) of NSD1 gene alterations in HPV(−) specimens were truncating mutations within or before the enzymatic SET domain. The remaining alterations included homozygous gene deletions (6.7%), missense point mutations (30.7%) and inframe deletions (1.3%). UMD-Predictor categorized 18 of 23 missense point mutations as pathogenic. For HPV(+) HNSCC (n = 65), 6 NSD1 mutations, comprised of two truncating (33%) and 4 missense point (66%) mutations, were identified. Three of the 4 missense point mutations were predicted to be pathogenic or probably pathogenic by UMD-Predictor. Kaplan-Meier survival analysis determined significantly improved survival of HPV(−) HNSCC patients whose tumors harbored NSD1 gene alterations, as compared to patients with wild-type NSD1 tumors. Interestingly, the survival effect of NSD1 mutations observed in HPV-negative HNSCC was reversed in HPV(+) tumors. Proliferation and clonogenic survival of two HPV(−) cell lines stably expressing control or NSD1 shRNAs showed that NSD1-depleted cells were more sensitive to cisplatin and carboplatin, but not to other DNA damaging drugs.ConclusionsGenetic alterations in NSD1 hold potential as novel prognostic biomarkers in HPV(−) head and neck cancers. NSD1 mutations in HPV(+) cancers may also play a prognostic role, although this effect must be examined in a larger cohort. NSD1 downregulation results in improved sensitivity to cisplatin and carboplatin, but not to other DNA-damaging agents, in epithelial cells. Increased sensitivity to platinum-based chemotherapy agents associated with NSD1 depletion may contribute to improved survival in HPV(−) HNSCCs. Further studies are needed to determine mechanisms through which NSD1 protects HPV(−) HNSCC cells from platinum-based therapy, as well as confirmation of NSD1 effect in HPV(+) HNSCC.
- Research Article
30
- 10.3389/fonc.2021.688615
- Sep 24, 2021
- Frontiers in Oncology
ObjectiveTo investigate the impact of the human papillomavirus (HPV) status on head and neck squamous cell carcinoma (HNSCC) arising from different anatomic subsites.MethodsHNSCC patients with known HPV status from the Surveillance, Epidemiology, and End Results (SEER) database between 2010–2015 were included in our analysis. Patients were classified into three categories of HNSCC according to Site recode ICD-O-3/WHO 2008 and Primary Site-labeled, namely, oropharynx, hypopharynx, and nasopharynx. Logistic regression model was conducted to evaluate the relationship between patient characteristics and HPV status. Kaplan-Meier methods and COX regression analysis were used to analyze survival data.ResultsA total of 9,943 HNSCC patients with known HPV status from the SEER database were enrolled, with 6,829 (68.7%) HPV-positive patients. HPV-positive and HPV-negative HNSCC were distinct and had different clinical and socioeconomic features (all P < 0.001). Primary sites, socioeconomical factors (age, sex, marital status, and race), and pathological features (TNM stage and grade) were closely related with HPV status (all P < 0.001). HPV-positive status was a favorable prognostic marker in HNSCC patients with cancers of the oropharynx and hypopharynx (all P < 0.001), but was not in nasopharyngeal carcinoma patients (P = 0.843). A total of 8,933 oropharyngeal carcinoma (OPC) and 558 hypopharyngeal carcinoma (HPC) patients were divided into the training and validation cohorts with a ratio of 1:1. Significant prognostic factors of the OS yielded by multivariate COX analysis in the training cohort were integrated to construct nomograms for OPC and HPC patients. The prognostic models showed a good discrimination with a C-index of 0.79 ± 0.007 and 0.73 ± 0.023 in OPC and HPC, respectively. Favorable calibration was reflected by the calibration curves. Additionally, corresponding risk classification systems for OPC and HPC patients based on the nomograms were built and could perfectly classify patients into low-risk, intermediated-risk, high-risk groups. OS in the three risk groups was accurately differentiated and showed a good discrimination.ConclusionHPV positivity was associated with an improved survival in HNSCC patients with cancers of the oropharynx and hypopharynx. Nomograms and corresponding risk classification systems were constructed to assist clinicians in evaluating the survival of OPC and HPC patients.
- Research Article
4
- 10.1016/j.neo.2025.101178
- May 16, 2025
- Neoplasia (New York, N.Y.)
Differential prognostic association of systemic inflammatory biomarkers on survival outcomes in head and neck squamous cell carcinoma patients by human papillomavirus status
- Research Article
3
- 10.1016/j.neo.2025.101241
- Oct 19, 2025
- Neoplasia (New York, N.Y.)
Promiscuous activation of growth factor receptors drives sustained MAP kinase signaling, which reinforces oncogene addiction in HPV-negative head and neck squamous cell carcinoma (HNSCC). This feature promotes invasive growth, complicating surgical resection and contributing to high rates of local relapse and poor patient outcomes. Current treatment strategies for locally advanced or non-resectable tumors targeting single growth factor receptors offer limited therapeutic benefit, underscoring the need for alternative targets. Using patient-derived tumor organoid (PDO) models of invasive HNSCC, we demonstrate that FER, a non-receptor tyrosine kinase that correlates with poor survival in HNSCC patients, is essential for growth factor receptor dependent invasive growth in Collagen-I extracellular matrix (ECM) networks. In this setting, FER promotes phosphorylation of EGFR-Y1068 and MET-Y1234/5. Additionally, FER controls ligand-dependent endocytic transport velocity, demonstrating a multifactorial regulation of proximal GFR activation during HNSCC invasion. Finally, genetic loss of function experiments or a FER-specific PROteolysis-TArgeting Chimera (PROTAC) strategy in PDO-based xenograft mouse models, demonstrate that FER is essential for invasive growth and metastasis of HNSCC. In sum, we propose that FER is an indiscriminate regulator of proximal GFR activation in HNSCC, a mechanism that may foster oncogene addition, thereby leading to invasive growth and metastasis. Based on its oncogenic roles and correlations with poor patient prognosis, we nominate FER as a potential candidate for targeted clinical intervention of HNSCC.
- Research Article
21
- 10.1002/cncr.32610
- Nov 13, 2019
- Cancer
Head and neck squamous cell carcinoma (HNSCC) is one of the most frequently diagnosed cancers worldwide. LOXL2 demonstrates alternative splicing events in patients with human papillomavirus (HPV)-negative HNSCC. The current study explored the role of a dominant LOXL2 variant in HPV-negative HNSCC. Expression of the LOXL2 variant was analyzed using The Cancer Genome Atlas cohorts and validated using quantitative reverse transcriptase-polymerase chain reaction in a separate primary tumor set. The authors defined the effect of LOXL2 splice variants in assays for cell proliferation using a cell viability assay and colony formation assay. Cell migration and invasion were examined using a cell scratch assay and transwell cell migration and invasion assay in LOXL2 splice variant gain and loss of expression cells. Western blot analysis and gene set enrichment analysis were used to explore the potential mechanism of the LOXL2 splice variant in HPV-negative HNSCC. Expression of a novel LOXL2 variant was found to be upregulated in The Cancer Genome Atlas HPV-negative HNSCC, and confirmed in the separate primary tumor validation set. Analyses of loss and gain of function demonstrated that this LOXL2 variant enhanced proliferation, migration, and invasion in HPV-negative HNSCC cells and activated the FAK/AKT pathway. A total of 837 upregulated and 820 downregulated genes and 526 upregulated and 124 downregulated pathways associated with LOXL2 variant expression were identified using gene set enrichment analysis, which helped in developing a better understanding of the networks activated by this LOXL2 variant in patients with HPV-negative HNSCC. The novel LOXL2 variant can promote the progression of HPV-negative HNSCC, in part through FAK/AKT pathway activation, which may provide a new potential therapeutic target among patients with HPV-negative HNSCC.
- Research Article
22
- 10.1002/lary.25587
- Sep 7, 2015
- The Laryngoscope
Although several imaging characteristics of human papillomavirus (HPV)-related head and neck squamous cell carcinoma (HNSCC) have been reported, imaging features of nodal metastasis and influence to outcomes have not been well studied thus far. The purpose of the study was to investigate the imaging characteristics of nodal metastasis by HPV status in HNSCC and to clarify whether those findings influence the outcomes. Retrospective review. Computed tomography and magnetic resonance imaging for initial staging on 139 patients of HNSCC with known HPV status were retrospectively reviewed. We investigated imaging characteristics of the nodal metastasis including the presence of extracapsular spread (ECS), and also investigated the influence of nodal metastasis characteristics to outcomes by HPV status. Two-year actuarial control and survival rates were estimated using the Kaplan-Meier product-limit method (P < 0.05). Eighty-eight patients with nodal metastasis were identified and outcome information was available for 78 patients. Nodal metastasis was significantly more common in HPV-positive patients compared to HPV-negative patients (75% vs. 54%, P = 0.009). HPV-positive patients showed a higher prevalence of ECS compared to HPV-negative patients (77% vs. 56%, P = 0.041). The prevalence of disease recurrence was more common in HPV-negative patients (67% vs. 13%, P < 0.0001), and it was independent of the presence of ECS in nodal metastasis. Nodal metastases were significantly more common in HPV-positive HNSCC, whereas the prevalence of disease recurrence was greater in HPV-negative HNSCC. Although ECS was noted in the majority of the HPV-positive patients with nodal metastasis, rates of recurrence were lower compared to HPV-negative patients. 4.
- Research Article
1
- 10.1158/1538-7445.am2023-4756
- Apr 4, 2023
- Cancer Research
Members of the NSD protein family (NSD1, NSD2, and NSD3) are histone methyltransferases (HMTs) that catalyze lysine 36 dimethylation (K36me2) at histone H3. H3K36 modifications play an important role in regulating the function and structure of chromatin, affecting transcription, replication, and repair. Abnormal H3K36 methylation is often detected during tumor development and progression. Inactivating NSD1 mutations are frequent in head and neck squamous cell carcinoma (HNSCC). They commonly occur in HPV-negative oropharyngeal (OP) and laryngeal (LC) carcinomas, and define a prognostic subtype in LC, associated with significantly improved overall and progression-free survival. Notably, the SCC4 cell line, carrying a damaging mutation in the NSD1 gene demonstrated reduced dimethylation level of H3K36 compared to NSD1 wild-type HNSCC counterparts. To explore the biological impact of the NSD1/NSD2 loss of function in HNSCC, we established cell lines with doxycycline-inducible shRNA knockdown of NSD1 and NSD2 in the set of HNSCC cell lines originating from different sites (JHU011, JHU022, Cal27, and FaDu cell lines). The depletion of NSD1 and NSD2 led to reduction of K36me2, significant decrease in cell growth as measured by cell titer blue (CTB) and clonogenic assays. NSD1/NSD2 depletion in these HNSCC cells also caused a significant increase in apoptosis. Gene Set Enrichment Analysis (GSEA) of RNA-seq for NSD1 wt versus knockdown cells indicates that NSD1 knockdown reduced expression of E2F target genes. Among the E2F transcription factor family, E2F2 gene expression was significantly decreased in all NSD1 knockdown cell lines. NSD1 knockdown also activated gene pathways related to autophagy and response to starvation. NSD1 knockdown reduced the levels of autophagy initiation gene ULK1 at both mRNA and protein levels. We also probed for protein signaling in HNSCC cells following NSD1 depletion using a reverse protein phase array (RPPA) approach, and validated Phosphatidylinositol-5-Phosphate 4-Kinase Type 2 Beta (PIP4K2B), but not other members of this family (PIP4K2A and PIP4K2C), as NSD1-regulated. PIP4K2B was regulated at the mRNA level by NSD1 as well. The CHIP-qPCR assay demonstrated the loss of H3K36me2 at the promoter of the PIP4K2B gene in NSD1 knockdown cells, suggesting direct regulation by NSD1. Moreover, PIP4K2B siRNA depletion has also led to a significant decrease in HNSCC proliferation, which suggests that the NSD1 may regulate proliferative activity through PIP4K2B. Taken together, while this data supports the suggestion that NSD histone methyltransferases have multiple downstream targets, the underlying mechanism remain to be investigated in more detail. Further, NSD proteins are attractive targets for drug development for improving treatment strategies for HNSCC. Citation Format: Iuliia Topchu, Igor Bychkov, Petr Makhov, Evgeny Izumchenko, John Karanicolas, Jindan Yu, Jochen Lorch, Yanis Boumber. NSD1/2 histone methyltransferases regulate cell growth in HPV-negative head and neck squamous cell carcinoma (HNSCC). [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4756.
- Research Article
2
- 10.1158/1538-7445.am2023-6284
- Apr 4, 2023
- Cancer Research
Human Papilloma Virus (HPV)-negative head and neck squamous cell carcinoma (HNSCC) is the sixth most common cancer type in the world and its outcomes are mostly unchanged for the past few decades, especially for HPV-negative HNSCC. The TCGA recently revealed a plethora of genetic alterations in chromatin modifiers in HPV-negative HNSCC, including protein lysine methyltransferases which methylate lysine residues on histone tails and regulate gene expression. One of these enzymes, SUV420H1, is known to trimethylate H4K20 and is recurrently amplified in approximately 6% of HPV-negative HNSCC tumors (TCGA). It has also been found to be significantly overexpressed in multiple HNSCC cell lines compared with normal keratinocytes. This study aims to investigate whether SUV420H1 has oncogenic activity and could be a novel therapeutic target in HPV-negative HNSCC. To evaluate the effect of SUV420H1 depletion on HPV-negative HNSCC cell lines, siRNA-mediated knockdown was performed in four SUV420H1 overexpressing HPV-negative HNSCC cell lines, and MTT assays showed significantly reduced cell viability by approximately 80-90% after 12 days of siRNA treatment. Colony formation assays, cell cycle analysis and apoptosis assays are ongoing, and these assays are planned in SUV420H1 CRISPR KO cell lines. Gene Set Enrichment Analysis in 434 HPV-negative HNSCC tumors (TCGA) showed significant enrichment of immune signatures, EMT, cell cycle and apoptosis pathways. Ongoing experiments aim to investigate the effects of SUV420H1 knockdown on the global histone methylome, and to identify direct downstream targets of SUV420H1 through combined genome-wide mapping of SUV420H1 using CUT&RUN assays and RNA-seq in HPV-negative HNSCC cell lines. Syngeneic and xenograft mouse models are also planned to evaluate the effect of SUV420H1 depletion on flank tumor growth in vivo. These studies may elucidate the oncogenic effects and mechanisms of SUV420H1, and may provide evidence to support SUV420H1 as a potential novel target in the treatment of HPV-negative HNSCC tumors with SUV420H1 amplification or overexpression. Citation Format: Arfa Moshiri, Hui Cheng, Sohyoung Kim, Vassiliki Saloura. SUV420H1 as a novel target in HPV-negative head and neck squamous cell carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 6284.