MAPK pathway mutations affect one-fifth of head and neck squamous cell carcinoma (HNSCC). Unexpectedly, MAPK pathway aberrations are associated with remarkably long patient survival, even among patients with TP53 mutations (median ∼14 yr). We explored underlying outcome-favoring mechanisms with omics followed by preclinical models. Strikingly, multiple hotspot and non-hotspot MAPK mutations (A/BRAF, HRAS, MAPK1, and MAP2K1/2) all abrogated ErbB3 activation, a well-established HNSCC progression signal. Inhibitor studies functionally defined ERK activity negatively regulating phospho-ErbB3 in MAPK-mutants. Furthermore, pan-pathway immunoprofiling investigations identified MAPK-mutant tumors as the only “CD8+ T-cell–inflamed” tumors inherently bearing high-immunoreactive, constitutive cytolytic tumor microenvironments. Immunocompetent MAPK-mutant HNSCC models displayed active cell death and massive CD8+ T-cell recruitment in situ. Consistent with CD8+ T-inflamed phenotypes, MAPK-mutant HNSCC patients, independent of tumor-mutational burden, survived 3.3–4 times longer than WT patients with anti-PD1/PD-L1 immunotherapies. Similar prognosticity was noted in pan-cancers. We uncovered clinical, signaling, and immunological uniqueness of MAPK-mutant HNSCC with potential biomarker utilities predicting favorable patient survival.

Germline CYLD mutation is associated with the development of a rare inheritable syndrome, called the CYLD cutaneous syndrome. Patients with this syndrome are distinctly presented with multiple tumors in the head and neck region, which can grow in size and number over time. Some of these benign head and neck tumors can turn into malignancies in some individuals. CYLD has been identified to be the only tumor suppressor gene reported to be associated with this syndrome thus far. Here, we summarize all reported CYLD germline mutations associated with this syndrome, as well as the reported paired somatic CYLD mutations of the developed tumors. Interestingly, whole-exome sequencing (WES) studies of multiple cancer types also revealed CYLD mutations in many human malignancies, including head and neck cancers and several epithelial cancers. Currently, the role of CYLD mutations in head and neck carcinogenesis and other cancers is poorly defined. We hope that this timely review of recent findings on CYLD genetics and animal models for oncogenesis can provide important insights into the mechanism of head and neck tumorigenesis.

RAC1 is a small GTPase with known oncogenicity. Mutations of RAC1 are highly relevant to melanoma. Yet, little is known about RAC1 aberrations in other human cancers, including HNSCC. Pan-cancer analysis of 32 cancer types from the TCGA reveals that RAC1 mutations only affect 12/32 cancer types and HNSCC is the 2nd most frequently affected (2.64%; 14/510 cases), after melanoma (4.59%, 22/479 cases). 28/34 cancer types harbor RAC1 copy number alterations, including HNSCC (2.08% cases, all are amplifications). Among all 14 HNSCC-associated RAC1 mutations found in the TCGA cohort, RAC1 p.A159V mutation (residing in the highly conserved G5 Box of RAC1) appears to be particularly prevalent in HNSCC (6/14 cases), suggesting a likely mutant-specific role in HNSCC. HNSCC patients with somatic RAC1 aberrations [gene amplification/copy number gain/hotspot mutations (p.P29, p.K116 and p.A159)] have poorer overall survival (OS)(P=4.555e-5; median survival of 30.91 months vs 68.43 months) and disease-free survival (DFS) (P=5.49e-5; 27.89 months vs unreached median) vs. RAC1-unaltered HNSCC patients. RAC1-mutated tumors are also associated with a higher rate of TP53 mutation (P=2.07e-6), and a lower rate of HPV infection (P=7.397e-6; 7.7% vs. 87.2%; Fisher’s Exact test). Further, RAC1-altered patients are of more advanced T clinical staging (T3/4 vs T1/2; P=0.0312) and with more gross/microscopic extension (P=0.0111; 59/119 vs 54/201). These evidences strongly suggest that HNSCC with RAC1 aberrations are more aggressive and may serve as a prognostic biomarker for HNSCC. To further elucidate the biological function of RAC1 mutations in HNSCC, we analyzed the mutational profile of RAC1-mutated HNSCC tumors which showed enriched mutations of 3 tumor suppressor genes: FAT1, FAT4 and CSMD3 (P=0.0001, P=0.0038 and P=0.0467 respectively). Gene set enrichment analysis (GSEA) of RAC1-mutated HNSCC also demonstrates significant dysregulation of immune-related gene sets (vs. RAC1-WT tumors) including increased interleukin-6 (IL-6) production (P<0.0001), a pro-tumorigenic inflammatory cytokine known to be involved in HNSCC tumorigenesis and progression. A previous study showed that overexpression of RAC1 activating mutation (p.V12) could upregulate IL-6 production in a cervical cancer model, HeLa, which is supportive of a RAC1/IL-6 axis in HNSCC. This is further supported by our RNAseq finding that RAC1-mutated HNSCC tumors do have significant upregulation of MYD88 (P=0.0436), a gene that has been shown to induce IL-6 secretion in HNSCC cells. Subsequent Tumor Immune Estimation Resource (TIMER) analysis shows that RAC1-mutated HNSCC primary tumors have higher infiltrating neutrophil levels than RAC1-WT tumors (P=0.019). Our findings may uncover a novel tumorigenic mechanism by RAC1 mutations in HNSCC, first linking IL-6 dysregulation to an oncogene mutation in HNSCC. Citation Format: Hoi Lam Ngan, Yuchen Liu, Peony Hiu Yan Poon, Vivian Wai Yan Lui. RAC1 genomic aberrations as predictive biomarkers for head and neck squamous cell carcinoma (HNSCC) [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 4033.

Immunocompetent metastatic head and neck cancer (HNC) models, although scarce, can help understanding cancer progression and therapy responses in vivo. Their comprehensive genome characterizations are essential for translational research. We first exome-sequenced the two most widely used spontaneous metastatic immunocompetent models, namely AT-84 and SCC VII, followed by comprehensive genomic analyses with three prior-sequenced models (MOC2, MOC2-10, and 4MOSC2), together with patient tumors for utility assessment. AT-84 and SCC VII bear high HNC tumor resemblance regarding mutational signatures—Trp53, Fanconi anemia, and MAPK and PI3K pathway defects. Collectively, the five models harbor genetic aberrations across 10 cancer hallmarks and 14 signaling pathways and machineries (metabolic, epigenetic, immune evasion), to extents similar in patients. Immune defects in HLA-A (H2-Q10, H2-Q4, H2-Q7, and H2-K1), Pdcd1, Tgfb1, Il2ra, Il12a, Cd40, and Tnfrsf14 are identified. Invasion/metastatic genome analyses first highlight potential druggable ERBB4 and KRAS mutations, for advanced/metastatic oral cavity cancer, as well as known metastasis players (Muc5ac, Trem3, Trp53, and Ttn) frequently captured by all models. Notable immunotherapy and precision druggable targets (Pdcd1, Erbb4, Fgfr1, H/Kras, Jak1, and Map2k2) and three druggable hubs (RTK family, MAPK, and DNA repair pathways) are frequently represented by these models. Immunocompetent metastatic HNC models are worth developing to address therapy- and invasion/metastasis-related questions in host immunity contexts.

We previously showed the MAPK pathway can be mutationally activated, and may implicate drug sensitivity in HNSCC [1]. Here, we report that RNA expression of several MAPK pathway components may be associated with HNSCC patients' outcome based on the US-TCGA Provisional data. We found that loss of DUSP4, a negative regulator of MAPK pathway, was correlated with poor overall survival (OS; P=0.0286) and disease free survival (DFS) in HNSCC (0.00150; median progression time = 38.11 vs. 71.22 months in DUSP4-unaltered patients) which can potentially be explained by activation of oncogenic MAPK pathway upon DUSP4 underexpression. Interestingly, we identified a group of HNSCC patients with homozygous loss and mRNA downregulation of MAPK pathway scaffold protein components (GRB2, SHC2 and SHC3) with significantly poorer DFS (P=0.000871). RPPA analysis showed a trend of decreased protein expression level of phospho-RAFs, downstream of scaffold proteins, decreased MEKs and MAPKs, supportive of an overall decreased MAPK pathway signaling in this subset of patients. Unexpectedly, downregulation (homozygous deletion/ RNA expression less than 2 SD) of multiple MAPK pathway components which normally support activation of the pathway: RAF1 (9%), MAPK1 (3%) and RPS6KA1 (1.9%) was found to be significantly associated with poorer DFS (P=6.643x10^-5) with median time to progression of 18.17 months vs. 71.22 months in the unaltered group. Subsequent proteomic analysis of the respective patient tumors from the TCGA cohort (N=357 with RPPA data) showed that these patient tumors had elevated levels of E2F1 protein expression (P=0.0146), along with increase FOXM1 expression (P=8.499x10^-4), which is known to drive cell cycle progression [2]. As E2F1 is involved in cell survival upon DNA damage [3], it is likely that upregulation of E2F1 protein expression may enable cancer cells to survive after DNA insults by radiotherapy or chemotherapy, and contributes to disease relapse. Acknowledgements: VWYL is funded by the Research Grant Council, Hong Kong (#17114814, General Research Fund), Theme-based Research Scheme (T12-401/13-R), and the Start-up Fund from the School of Biomedical Sciences, Faculty of Medicine, the Chinese University of Hong Kong. Reference: 1. Van Allen, E.M., et al., Genomic Correlate of Exceptional Erlotinib Response in Head and Neck Squamous Cell Carcinoma. JAMA Oncol, 2015. 1(2): p. 238-44. 2. Barger, C.J., et al., Genetic determinants of FOXM1 overexpression in epithelial ovarian cancer and functional contribution to cell cycle progression. Oncotarget, 2015. 6(29): p. 27613-27. 3. Berton, T.R., et al., Regulation of epidermal apoptosis and DNA repair by E2F1 in response to ultraviolet B radiation. Oncogene, 2005. 24(15): p. 2449-60. Citation Format: Hoi Lam Ngan, Vivian W.Y. Lui. Potential clinical significance of downregulation of MAPK pathway components mRNA expression in head and neck squamous cell carcinoma (HNSCC) [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 5712. doi:10.1158/1538-7445.AM2017-5712