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.

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.

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.

The annual incidence of head and neck squamous cell carcinoma (HNSCC) is ~0.88 million worldwide (IARC, WHO 2018). Despite great success of precision medicine in major cancers such as lung cancer and breast cancers, there are limited precision therapies for HNSCC. We previously reported an HNSCC patient whose tumor harbored a somatic MAPK1 p.E322K mutation demonstrating exceptional clinical response to erlotinib, an EGFR inhibitor. Subsequent laboratory investigation confirmed the ability of MAPK1 p.E322K to hyperactivate EGFR, thus causing erlotinib sensitivity in HNSCC models, both in vitro and in vivo. Here, we sequenced 105 tumors from Hong Kong (HK) HNSCC patients by next-generation sequencing (NGS) on MAPK1 gene and we found a 5.71% rate (6/105 tumors) of MAPK1 somatic mutation in HK-HNSCC. This rate appears to be relatively higher than the 1.75% (9/521 tumors) rate in the US-TCGA HNSCC cohort (P=0.0288). Apart from the MAPK1 p.E322K mutation found in the US-TCGA HNSCC cohort, we identified novel MAPK1 p.R135K and p.D321N mutations in our HK cohort which were absent in the US TCGA HNSCC. Pan-cancer mapping of MAPK1 somatic mutations revealed that MAPK1 p.R135K and p.D321N mutations are also recurrent hotspot mutation in TCGA pan-cancers (32 cancer types). Strikingly, based on the X-ray crystallography of the human MAPK1 protein, R135 and D321 amino acid residues both reside on the same kinase interaction motif (KIM) domain as E322 (all are within a 13Å distance in 3D). Thus, we further investigated if MAPK1 p.R135K and p.D321N mutations might function similarly as MAPK1 p.E322K mutant in terms of their abilities to drive HNSCC growth, and erlotinib sensitivity in HNSCC models. We employed the same FaDu retroviral infection method to study these mutations as we did previously, and we found that MAPK1 p.D321N (P<0.0001) was a driver for HNSCC proliferation, while MAPK1 p.R135K was not (all vs. MAPK1-wildtype). Subsequent in vivo erlotinib treatment experiments with xenografts bearing these mutants and MAPK1-wildtype showed that MAPK1 p.D321N tumors demonstrated heightened sensitivity to erlotinib with marked reduction of tumor size, tumor cell positivity, as well as membranous pEGFR expression when compared to vehicle treatment (P=0.0037). Whereas MAPK1 p.R135K tumors only showed a trend for erlotinib sensitivity (P=0.0646), with reduction in membranous p-EGFR expression by erlotinib in the tumors. Thus, MAPK1 p.D321N mutation confers erlotinib-sensitivity in HNSCC system. Further clinical investigation is warranted to further explore the relationship between various MAPK1 mutations and erlotinib sensitivity in HNSCC patients. Citation Format: Hoi Lam Ngan, Peony Hiu Yan Poon, Yu-Xiong Su, Jason Yik Kuen Chan, Kwok-Wai Lo, Chun Kit Yeung, Yuchen Liu, Eileen Wong, Hui Li, Chin Wang Lau, Wenying Piao, Vivian Wai Yan Lui. MAPK1 p.D321N mutation confers sensitive to erlotinib in head and neck squamous cell carcinoma (HNSCC) [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 1792.

Anaplastic lymphoma kinase (ALK) is a receptor tyrosine kinase (RTK) that is frequently translocated in anaplastic large cell lymphoma (ALCL) and non-small cell lung cancer (NSCLC), etc. Gain-of-function mutations, largely mutations associated with resistance to ALK inhibitors, have been identified in neuroblastoma, colon adenocarcinoma and prostate adenocarcinoma, etc. Pan-cancer analysis of whole-exome sequencing data of >25 cancer types showed a mutational rate ranging from 0-9.4% across pan-cancers (www.cbioportal.org). In cancers of the head and neck, the potential role of ALK on precision treatment has been demonstrated in an Asian head and neck sarcomatoid carcinoma patient bearing an ALK aberration (Kim et al., 2015). In this study, we sought to examine the mutational rates of ALK in the US-TCGA HNSCC Provisional cohort, in a small Asian HNSCC cohort, as well as in Nasopharyngeal carcinoma (NPC, an Asian-prevalent HNC). Analysis of the whole-exome sequencing (WES) data of the US-TCGA HNSCC Provisional cohort (N=527; largely Caucasian ethnicity, 85.6%; www.cbioportal.org) revealed a somatic mutation rate of 4.0% (21 out of 527 patients, with 18 non-synonymous and 3 synonymous mutations) and a gene amplification rate of 0.4% (2 out of 522 tumors with copy number change data available). In contrast, the Asian prevalent Epstein-Barr Virus-associated NPC (N=102 micro-dissected tumors with paired blood samples analyzed by WES), no somatic ALK mutation was identified. Using a small Asian HNSCC cohort (N=16), next-generation sequencing (NGS) analysis with an ALK exon coverage of ~90% revealed no somatic ALK mutation, but the presence of Asian-predilected SNPs with unknown clinical or biological significance. Lastly, ALK protein expression, analyzed by Western blotting, was found to be low or largely undetectable in 25 Asian HNSCC tumors analyzed thus far. Yet, we cannot exclude the possibility of focal ALK expression in HNSCC tumors, which can be largely obscured by Western blotting. In conclusion, somatic mutation of ALK appears to be rare events in Asian HNSCC and EBV-associated Nasopharyngeal carcinoma. Acknowledgements: VWYL receives funding supports from the Research Grant Council, Hong Kong (General Research Fund: #1711484, #17121616; Theme-based Research: T12-401/13-R) and the Hong Kong Cancer Fund, Hong Kong. KWL receives funding from the Research Grant Council (Theme-based Research: T12-401/13-R), Hong Kong. WP is supported by Faculty Postdoctoral Fellowship Scheme from the Faculty of Medicine, Chinese University of Hong Kong. JYKC receives funding support by the Dr Stanley Ho Medical Foundation. Reference Kim, S. M., Kim, M. J., Jung, H. A., Sun, J. M., Choi, Y. L., Ko, Y. H., . . . Ahn, M. J. (2015) Presence of anaplastic lymphoma kinase translocation in sarcomatoid carcinoma of head and neck and treatment effect of crizotinib: A case series. Head Neck, 37(5), E66-69 Citation Format: Wenying Piao, Peony Hiu Yan Poon, Lan Wang, Chin Wang Lau, Jason Ying Kuen Chan, Yuxiong Su, Amy Bik Wan Chan, Hoi Lam Ngan, Kwok Wai Lo, Vivian Wai Yan Lui. Somatic mutation and overexpression of anaplastic lymphoma kinase (ALK) are uncommon events in Asian head and neck cancers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 5347.

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

RAC1 is a Rho GTPase well-identified as an oncogene overexpressed in various cancer types. RAC1 amplification or gain account for ~40% of head and neck squamous cell carcinoma (HNSCC) while mutation of RAC1 occurs at ~3% according to TCGA-HNSCC cohort. HNSCC patients with RAC1 aberrations, including RAC1 mutations and amplification or gain, are associated with poor overall and disease-free survival in HNSCC. Significantly higher tumor mutational burden is observed in RAC1-mutated group (p=0.0336) or in RAC1-amplified/gain group (p=0.0109) vs. wildtype patients in TCGA-HNSCC cohort. As increases in TMB are often associated with immune cell infiltration in cancers, we hypothesized that RAC1 aberrations impact the tumor immune microenvironment (TIME) of HNSCC, potentially contributing to disease progression.PD-L1 (CD274) is an important immunosuppressive immune checkpoint molecule expressed in tumor cells. Here, we first reported that ectopic overexpression of RAC1 p.P29S and p.A159V mutations in a human HNSCC cell line (PECAPJ41 clone D2, ATCC, USA) could cause upregulation of PD-L1 at both mRNA (by RNA-seq) and protein levels (by Western blotting), first demonstrating a direct effect of RAC1 mutations on potential HNSCC TIME modulation via PD-L1. Furthermore, by tumor immune estimation resources (TIMER) analysis, we found that RAC1-mutated tumors have significantly higher level of neutrophils immune infiltration of 38.63% (p=0.027) compared to the wildtype tumors. From the CIBERSORTx analysis, M2 Macrophages was significantly increased by 40.42% in RAC1-mutated tumors vs wildtype in the TCGA-HNSCC cohort (p=0.031). We also validated this finding by immunofluorescent staining of PD-L1 and M2 Macrophages in immunocompetent mouse HNSCC xenografts models expressing RAC1 p.P29S and p.A159V mutations as compared to controls. Our in silico, in vitro and in vivo findings first uncover an important role of RAC1 aberrations in HNSCC TIME immunosuppression by regulating PD-L1 expression, neutrophil and M2 macrophages infiltrations. Clinical activities of PD-L1 inhibitors in RAC1-mutated HNSCC patients worth future investigations. Acknowledgement: This research is funded by the General Research Fund (Ref. No.:14168517) and the Research Impact Fund (Ref. No.: R4015-19) from the Research Grants Council in Hong Kong. VWYL is supported by Start-up Fund, Georgia Cancer Center, Medical College of Georgia at Augusta University. Citation Format: Helen Hoi Yin Chan, Yuchen Liu, Hoi Lam Ngan, Vivian Wai Yan Lui. RAC1 aberrations in head and neck cancer affect immune microenvironments. [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 3628.