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Studies of the immune landscape led to breakthrough trials of programmed death-1 (PD-1) inhibitors for recurrent/metastatic head and neck squamous cell carcinoma therapy. This study investigated the timing, influence of somatic copy-number alterations (SCNAs), and clinical implications of PD-L1 and immune-cell patterns in oral precancer (OPC).The authors evaluated spatial CD3, CD3/8, and CD68 density (cells/mmEpithelial, but not CD68 immune-cell, PD-L1 expression was detected in 28% of OPCs, correlated with immune-cell infiltration, 9p21.3 loss of heterozygosity (LOH), and inferior oral cancer-free survival (OCFS), notably in OPCs with low CD3/8 cell density, dysplasia, and/or 9p21.3 LOH. High CD3/8 cell density in dysplastic lesions predicted better OCFS and eliminated the excess risk associated with prior oral cancer and dysplasia. PD-L1 and CD3/8 patterns revealed inferior OCFS in PD-L1 high intrinsic induction and dysplastic immune-cold subgroups.This report provides spatial insight into the immune landscape and drivers of OPCs, and a publicly available immunogenomic data set for future precancer interrogation. The data suggest that 9p21.3 LOH triggers an immune-hot inflammatory phenotype; whereas increased 9p deletion size encompassing CD274 at 9p24.1 may contribute to CD3/8 and PD-L1 depletion during invasive transition. The inferior OCFS in PD-L1-high, immune-cold OPCs support the development of T-cell recruitment strategies.

Supplementary Material 9 from Gene Expression Profiling Predicts the Development of Oral Cancer

Perspectives on this Article from Objective Detection and Delineation of Oral Neoplasia Using Autofluorescence Imaging

Supplementary Material 5 from Gene Expression Profiling Predicts the Development of Oral Cancer

Supplementary Text - PDF file 435K, This file contains supplementary methods, figure legends for supplementary figures S1-S5, descriptions for supplementary tables S1-S14, legends for supplementary methods figures SM1-SM15, supplementary references 1-7, and supplementary methods figures SM1-SM15

Supplementary Material 3 from Gene Expression Profiling Predicts the Development of Oral Cancer

Supplementary Material 7 from Gene Expression Profiling Predicts the Development of Oral Cancer

The p53 (TP53) tumor suppressor is the most frequently mutated gene in human cancers. Restoring expression of wild-type p53 has led to tumor growth suppression in a variety of tumor models that are p53 deficient. Other mechanisms, for example, upregulation of Mdm2, exist in tumors to inactivate the p53 pathway. Mdm2, an E3 ubiquitin ligase that targets p53 for proteasomal degradation, is present at high levels in many tumors with wild-type p53. In this study, the effects of restoring p53 activity were probed in Mdm2-overexpressing tumors genetically using animal models. Here, it was demonstrated that elevated levels of Mdm2 and decreased levels of p53 act additively to dampen p53 activity in DNA damage response and tumor development. Our data further indicate that restoration of wild-type p53 expression in Mdm2-overexpressing angiosarcomas results in tumor stasis and regression in some cases. Finally, it was determined that restored p53 suppressed cell proliferation but did not elicit apoptosis in the Mdm2-overexpressing angiosarcomas.Implications: Restoration of wild-type p53 expression in Mdm2-overexpressing tumors suppresses tumor growth, which represents a potential clinical strategy to treat tumors with high levels of Mdm2.Visual Overview: http://mcr.aacrjournals.org/content/12/6/901/F1.large.jpg.Mol Cancer Res; 12(6); 901–11. ©2014 AACR.

Supplementary Figures PDF - file 648K, This file contains supplementary figures S1-S5. Figure S1 has additional copy number analysis. Figure S2 expands on the integration of gene expression and copy number analysis. Figures S3-S4 provide additional data on the function and mechanism of activated NOTCH1 expression in cell lines. Figure S5 shows inhibition of CASP8 promotes tumorigenesis

Recent reports have shown limited anticancer therapeutic efficacy of insulin-like growth factor receptor (IGF-1R)-targeted monoclonal antibodies (mAb), but the resistance mechanisms have not been completely identified. Because cooperation between epidermal growth factor receptor (EGFR) and IGF-IR could cause resistance to inhibitors of individual receptor tyrosine kinases, we investigated the involvement of EGFR signaling in resistance to IGF-1R mAb and the underlying mechanisms of action. Most head and neck squamous cell carcinoma (HNSCC) tissues had coexpression of total and phosphorylated IGF-1R and EGFR at high levels compared with paired adjacent normal tissues. Treatment with cixutumumab (IMC-A12), a fully humanized IgG1 mAb, induced activation of Akt and mTOR, resulting in de novo synthesis of EGFR, Akt1, and survivin proteins and activation of the EGFR pathway in cixutumumab-resistant HNSCC and non–small cell lung cancer (NSCLC) cells. Targeting mTOR and EGFR pathways by treatment with rapamycin and cetuximab (an anti-EGFR mAb), respectively, prevented cixutumumab-induced expression of EGFR, Akt, and survivin and induced synergistic antitumor effects in vitro and in vivo. These data show that resistance to IGF-1R inhibition by mAbs is associated with Akt/mTOR-directed enhanced synthesis of EGFR, Akt1, and survivin. Our findings suggest that Akt/mTOR might be effective targets to overcome the resistance to IGF-1R mAbs in HNSCC and NSCLC. Mol Cancer Ther; 10(12); 2437–48. ©2011 AACR.

The survival of patients with oral squamous cell carcinoma (OSCC) has not changed significantly in several decades, leading clinicians and investigators to search for promising molecular targets. To this end, we conducted comprehensive genomic analysis of gene expression, copy number, methylation, and point mutations in OSCC. Integrated analysis revealed more somatic events than previously reported, identifying four major driver pathways (mitogenic signaling, Notch, cell cycle, and TP53) and two additional key genes (FAT1, CASP8). The Notch pathway was defective in 66% of patients, and in follow-up studies of mechanism, functional NOTCH1 signaling inhibited proliferation of OSCC cell lines. Frequent mutation of caspase-8 (CASP8) defines a new molecular subtype of OSCC with few copy number changes. Although genomic alterations are dominated by loss of tumor suppressor genes, 80% of patients harbored at least one genomic alteration in a targetable gene, suggesting that novel approaches to treatment may be possible for this debilitating subset of head and neck cancers.Significance: This is the first integrated genomic analysis of OSCC. Only through integrated multiplatform analysis was it possible to identify four key pathways. We also discovered a new disease subtype associated with CASP8 and HRAS mutation. Finally, many candidate targetable events were found and provide hope for future genomically driven therapeutic strategies. Cancer Discov; 3(7); 770–81. ©2013 AACR.See related commentary by Iglesias-Bartolome et al., p. 722This article is highlighted in the In This Issue feature, p. 705

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PDF file - 354K, Figure S1. Tumor-free survival curves of the Mdm2Tg p53Neo/Neo and Mdm2Tg p53Neo/Neo CreER mice. Figure S2. Analysis of p53Neo recombination in tamoxifen-treated Mdm2Tg p53Neo/Neo CreER tumors. Figure S3. Initial tumor volumes of the Mdm2Tg p53Neo/Neo and Mdm2Tg p53Neo/Neo CreER angiosarcomas. Figure S4. p53 target gene p21 expression in tamoxifen-treated spontaneous Mdm2Tg p53Neo/Neo and Mdm2Tg p53Neo/Neo CreER angiosarcomas. Figure S5. PCR analysis of p53Neo allele recombination upon tamoxifen treatment in transplanted Mdm2Tg p53Neo/Neo CreER angiosarcomas. Figure S6. Effects of tamoxifen on the Mdm2Tgp53Neo/Neo angiosarcomas. Table S1. List of Mdm2Tg p53Neo/Neo and Mdm2Tg p53Neo/Neo CreER angiosarcomas monitored in the MRI study.

DNA promoter methylation of tumor suppressor genes and global DNA hypomethylation are common features of head and neck cancers. Our goal was to identify early DNA methylation changes in oral premalignant lesions (OPL) that may serve as predictive markers of developing oral squamous cell carcinoma (OSCC). Using high-throughput DNA methylation profiles of 24 OPLs, we found that the top 86 genes differentially methylated between patients who did or did not develop OSCC were simultaneously hypermethylated, suggesting that a CpG island methylation phenotype may occur early during OSCC development. The vast majority of the 86 genes were nonmethylated in normal tissues and hypermethylated in OSCC versus normal mucosa. We used pyrosequencing in a validation cohort of 44 patients to evaluate the degree of methylation of AGTR1, FOXI2, and PENK promoters CpG sites that were included in the top 86 genes and of LINE1 repetitive element methylation, a surrogate of global DNA methylation. A methylation index was developed by averaging the percent methylation of AGTR1, FOXI2, and PENK promoters; patients with a high methylation index had a worse oral cancer–free survival (P = 0.0030). On the other hand, patients with low levels of LINE1 methylation had a significantly worse oral cancer–free survival (P = 0.0153). In conclusion, AGTR1, FOXI2, and PENK promoter methylation and LINE1 hypomethylation may be associated with an increased risk of OSCC development in patients with OPLs. Cancer Prev Res; 8(11); 1027–35. ©2015 AACR.

Leukoplakia is the most common premalignant lesion of the oral cavity. Epidermal growth factor receptor (EGFR) abnormalities are associated with oral tumorigenesis and progression. We hypothesized that EGFR expression and gene copy number changes are predictors of the risk of an oral premalignant lesion (OPL) progressing to oral squamous cell carcinoma (OSCC). A formalin-fixed, paraffin-embedded OPL biopsy specimen was collected from each of 162 patients in a randomized controlled clinical trial. We assessed EGFR expression by immunohistochemistry with two methods: a semiquantitative analysis (145 evaluable specimens) and an automated quantitative analysis (127 evaluable specimens). EGFR gene copy number was assessed by fluorescence in situ hybridization (FISH) in a subset of 49 OPLs with high EGFR expression defined by the semiquantitative analysis. We analyzed EGFR abnormalities for associations with OSCC development. High EGFR expression occurred in 103 (71%) of the 145 OPLs and was associated with a nonsignificantly higher risk of OSCC (P = 0.10). Twenty (41%) of 49 OPLs assessed by FISH had an increased EGFR gene copy number (FISH-positive). Patients with FISH-positive lesions had a significantly higher incidence of OSCC than did patients with FISH-negative (a normal copy number) lesions (P = 0.0007). Of note, 10 of 11 OSCCs that developed at the site of the examined OPL were in the FISH-positive group, leaving only one FISH-negative OPL that did so (P < 0.0001). Our data indicate that an increased EGFR gene copy number is common in and associated with OSCC development in patients with OPLs expressing high EGFR, particularly OSCC developing at the site of a high-expression OPL; they also suggest that EGFR inhibitors may prevent oral cancer in patients with OPLs having an increased EGFR gene copy number. Cancer Prev Res; 3(7); 800–9. ©2010 AACR.

Supplementary Material 2 from Gene Expression Profiling Predicts the Development of Oral Cancer

Supplementary Material 4 from Gene Expression Profiling Predicts the Development of Oral Cancer

Supplementary Figure 1: Flow-chart describing the selection of 86 candidate genes. Supplementary Figure 2: Promoter methylation of 62/86 candidate genes in head and neck cancer, normal mucosa and blood. Supplementary Figure 3: Promoter methylation of 13/86 candidate genes in normal tissues. Supplementary Fig. 4: Hierarchical clustering of paired normal, dysplastic lesions and carcinomas (in situ or invasive) collected from 10 patients (3), using methylation profiles of 60/86 of our candidate genes. Supplementary Figure 5: (A) Hierarchical cluster analysis of oral squamous cell carcinoma and oral normal mucosa using candidate genes expression profiles. Supplementary Figure 6: Correlation of the percentage methylation of AGTR1.

Supplementary Table 1: Description of the studies used for the in silico validation of the candidate genes in terms of number of samples analyzed, platform used and number of overlapping genes between our candidate gene list and the genes analyzed on the platform (HN: head and neck; SCC: squamous cell carcinoma). Supplementary Table 2: List of cell lines in which the level of promoter methylation of AGTR1, FOXI2, HOXA9, PENK and ZIC1 were evaluated (HNSCC: head and neck squamous cell carcinoma). Supplementary Table 3: Univariate Cox proportional hazards model for all other available variables. Supplementary table 4: Multi-covariable Cox Model analysis including histology (hyperplasia or dysplasia).

Perspective on this Article from Epidermal Growth Factor Receptor Expression and Gene Copy Number in the Risk of Oral Cancer

Perspective on this Article from Phase II Randomized, Placebo-Controlled Trial of Green Tea Extract in Patients with High-Risk Oral Premalignant Lesions

Supplementary Tables 1-4 from Epidermal Growth Factor Receptor Expression and Gene Copy Number in the Risk of Oral Cancer

Supplementary Material 6 from Gene Expression Profiling Predicts the Development of Oral Cancer

SupplementaryFigureS1. Quantification of the immunohistochemistry shown in Figure 3A. The graphs represent comparative analyses of the staining for the indicated proteins between low-and high-grade lesions in the control and anti-PD1 treatment groups. Supplementary Figure S2. Quantification of the immunohistochemistry shown in Figure 3B. The graphs represent comparative analyses of the staining for the indicated proteins between low-and high-grade lesions in the control and anti-PD1 treatment groups. Supplementary Figure S3. Quantification o fthe (A-C) immunohistochemistry and (D) TUNEL assay shown in Figure 4.

Supplementary Material 1 from Gene Expression Profiling Predicts the Development of Oral Cancer

The majority of TP53 missense mutations identified in cancer patients are in the DNA-binding domain and are characterized as either structural or contact mutations. These missense mutations exhibit inhibitory effects on wild-type p53 activity. More importantly, these mutations also demonstrate gain-of-function (GOF) activities characterized by increased metastasis, poor prognosis, and drug resistance. To better understand the activities by which TP53 mutations, identified in Li–Fraumeni syndrome, contribute to tumorigenesis, we generated mice harboring a novel germline Trp53R245W allele (contact mutation) and compared them with existing models with Trp53R172H (structural mutation) and Trp53R270H (contact mutation) alleles. Thymocytes from heterozygous mice showed that all three hotspot mutations exhibited similar inhibitory effects on wild-type p53 transcription in vivo, and tumors from these mice had similar levels of loss of heterozygosity. However, the overall survival of Trp53R245W/+ and Trp53R270H/+ mice, but not Trp53R172H/+ mice, was significantly shorter than that of Trp53+/− mice, providing strong evidence for p53-mutant–specific GOF contributions to tumor development. Furthermore, Trp53R245W/+ and Trp53R270H/+ mice had more osteosarcoma metastases than Trp53R172H/+ mice, suggesting that these two contact mutants have stronger GOF in driving osteosarcoma metastasis. Transcriptomic analyses using RNA sequencing data from Trp53R172H/+, Trp53R245W/+, and Trp53R270H/+ primary osteosarcomas in comparison with Trp53+/– indicated that GOF of the three mutants was mediated by distinct pathways. Thus, both the inhibitory effect of mutant over wild-type p53 and GOF activities of mutant p53 contributed to tumorigenesis in vivo. Targeting p53 mutant–specific pathways may be important for therapeutic outcomes in osteosarcoma. Significance: p53 hotspot mutants inhibit wild-type p53 similarly but differ in their GOF activities, with stronger tumor-promoting activity in contact mutants and distinct protein partners of each mutant driving tumorigenesis and metastasis.

Supplemental Figures S1-S2 and Methods. Figure S1: Mutation types and number by previous radiation treatment. Figure S2: Copy number alterations.

Supplementary Table from Pilot Phase II Trial of Neoadjuvant Immunotherapy in Locoregionally Advanced, Resectable Cutaneous Squamous Cell Carcinoma of the Head and Neck

Supplementary Table S1. Significant expression differences between AR and control siRNAs treatment in RET981 cell. Supplementary Table S2. PCR Primer information

Supplemental Table S5: mutation annotation file.

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Purpose: The objectives of this study were to determine the incidence of the MYB-NFIB fusion in salivary adenoid cystic carcinoma (ACC), to establish the clinicopathologic significance of the fusion, and to analyze the expression of MYB in ACCs in the context of the MYB-NFIB fusion.Experimental Design: We did an extensive analysis involving 123 cancers of the salivary gland, including primary and metastatic ACCs, and non-ACC salivary carcinomas. MYB-NFIB fusions were identified by reverse transcriptase-PCR (RT-PCR) and sequencing of the RT-PCR products, and confirmed by fluorescence in situ hybridization. MYB RNA expression was determined by quantitative RT-PCR and protein expression was analyzed by immunohistochemistry.Results: The MYB-NFIB fusion was detected in 28% primary and 35% metastatic ACCs, but not in any of the non-ACC salivary carcinomas analyzed. Different exons in both the MYB and NFIB genes were involved in the fusions, resulting in expression of multiple chimeric variants. Notably, MYB was overexpressed in the vast majority of the ACCs, although MYB expression was significantly higher in tumors carrying the MYB-NFIB fusion. The presence of the MYB-NFIB fusion was significantly associated (P = 0.03) with patients older than 50 years of age. No correlation with other clinicopathologic markers, factors, and survival was found.Conclusions: We conclude that the MYB-NFIB fusion characterizes a subset of ACCs and contributes to MYB overexpression. Additional mechanisms may be involved in MYB overexpression in ACCs lacking the MYB-NFIB fusion. These findings suggest that MYB may be a specific novel target for tumor intervention in patients with ACC. Clin Cancer Res; 16(19); 4722–31. ©2010 AACR.

1 supplementary method, 3 supplementary tables and 7 supplementary figures

Ligand independent AR activation and AR downstream target genes expression in SDC cell lines.

Tumors and Metastasis in KRas+/LA1;Dicer+/2SD mice

Supplementary Figure S1. Association between age, number of mutations and smoking status.

Purpose: Aggressive cutaneous squamous cell carcinoma (cSCC) is often a disfiguring and lethal disease. Very little is currently known about the mutations that drive aggressive cSCC.Experimental Design: Whole-exome sequencing was performed on 39 cases of aggressive cSCC to identify driver genes and novel therapeutic targets. Significantly, mutated genes were identified with MutSig or complementary methods developed to specifically identify candidate tumor suppressors based upon their inactivating mutation bias.Results: Despite the very high-mutational background caused by UV exposure, 23 candidate drivers were identified, including the well-known cancer-associated genes TP53, CDKN2A, NOTCH1, AJUBA, HRAS, CASP8, FAT1, and KMT2C (MLL3). Three novel candidate tumor suppressors with putative links to cancer or differentiation, NOTCH2, PARD3, and RASA1, were also identified as possible drivers in cSCC. KMT2C mutations were associated with poor outcome and increased bone invasion.Conclusions: The mutational spectrum of cSCC is similar to that of head and neck squamous cell carcinoma and dominated by tumor-suppressor genes. These results improve the foundation for understanding this disease and should aid in identifying and treating aggressive cSCC. Clin Cancer Res; 20(24); 6582–92. ©2014 AACR.

Fig. S1. Difference in mean age and in mean tumor size among subtypes. Fig. S2. Genes effected by putative somatic Mobile Elements Insertions (MEI) events. Fig. S3. Rearrangements leading to potential fusion events. Fig. S4. Mutational hotspots in CIC (SLC25A1) and MUC16 genes. Fig. S5. Contribution of known somatic mutation signatures into mutational processes. Fig. S6. Genes effected by frequent germline alterations. Fig. S7. Association of patient's age (A) and each subtype (B) with survival. Fig. S8. Association of each type of structural variations (SVs) and overall survival. Fig. S9. CCDC58 mutation associated with worse survival.

Purpose: The inhibition of c-Src results in a striking reduction in cancer cell invasion, but the effect on cell survival is modest. Defining mechanisms that limit apoptosis following c-Src inhibition could result in an ideal therapeutic approach that both inhibits invasion and leads to apoptosis. In this regard, we discovered a novel feedback loop that results in STAT3 reactivation following sustained c-Src inhibition. Here we define the mechanism underlying this feedback loop and examine the effect of inhibiting it in vivo.Experimental Design: We measured levels and activity of pathway components using PCR, Western blotting, and kinase assays following their manipulation using both molecular and pharmacologic approaches. We used a heterotransplant animal model in which human oral squamous cancer is maintained exclusively in vivo.Results: Following c-Src inhibition, STAT5 is durably inhibited. The inhibition of STAT5A, but not STAT5B, subsequently reduces the expression of suppressors of cytokine signaling 2 (SOCS2). SOCS2 inhibits Janus kinase 2 (Jak2) activity and Jak2–STAT3 binding. SOCS2 expression is necessary for STAT3 inhibition by c-Src inhibitors. Overexpression of SOCS2 is adequate to prevent STAT3 reactivation and to enhance the cytotoxic effects of c-Src inhibition. Likewise, the combination of Jak and c-Src inhibitors led to significantly more apoptosis than either agent alone in vivo.Conclusions: To our knowledge, ours is the first study that fully defines the mechanism underlying this feedback loop, in which sustained c-Src inhibition leads to diminished SOCS2 expression via sustained inhibition of STAT5A, allowing activation of Jak2 and STAT3, Jak2–STAT3 binding, and survival signals. Clin Cancer Res; 18(1); 127–39. ©2011 AACR.

Supplementary Figure S1. Global chromosomal rearrangements in ACCs. Supplementary Figure S2. Shared mutated genes in ACC with MYB-/MYBL1-NFIB fusions and Non-fusion. Supplementary Figure. S3. Characterization of MYBL1-NFIB fusion transcripts. Supplementary Figure S4. (A-E) Nucleotide and Amino acid of MYBL1-NFIB fusion genes. Supplementary Figure S5. Characterization of MYBL1-YTHDF3 fusion transcripts. Supplementary Figure S6. Characterization of MYBL1 truncations. Supplementary Figure S7. Analysis of NFIB fusions at the 5'end of the gene. Supplementary Figure S8. Kaplan-Meier survival curves of ACCs patients.

Supplemental Tables S1-S4 and S6-S13. Supplemental Table S1: Summary of Patient Characteristics. Supplemental Table S2: Patient Characteristics and Key Mutations. Supplemental Table S3: Tumor purity and ploidy calculations. Supplemental Table S4: Sequencing Coverages. Supplemental Table S6: Allele fraction analysis. Supplemental Table S7: MutSig analysis. Supplemental Table S8: IntOGen mutational significance analysis. Supplemental Table S9: Chi-square mutational significance analysis. Supplemental Table S10: Multinomial mutational significance analysis. Supplemental Table S11: Kappa analysis for gene-gene associations. Supplemental Table S12: ABSOLUTE copy number analysis segmentation data. Supplemental Table S13: Clinical and mutation associations.

Supplementary Figure S1. Distribution of RET981 cell line. Supplementary Figure S2. Detection of AR splice variants in SDCs. Supplementary Figure S3. Cleaved PARP increased by AR siRNAs.

Purpose: Salivary duct carcinoma overexpresses epidermal growth factor receptor (EGFR) and HER-2, although the underlying mechanisms remain undefined. Because of the potential utilization of these markers as treatment targets, we evaluated protein and gene status by several techniques to determine complementary value.Experimental Design: A tissue microarray of 66 salivary duct carcinomas was used for immunohistochemical analysis of HER-2 and EGFR expression (semiquantitatively evaluated into a three-tiered system), and fluorescence in situ hybridization for gene copy number, and chromosomes 7 and 17 ploidy status. Sequencing of exons 18, 19, and 21 of the EGFR gene for mutations was carried out.Result: For EGFR, 46 (69.7%) of the 66 tumors showed some form of EGFR expression (17 at 3+, 17 at 2+, 12 at 1+) but none gene amplification. Five (9.4%) of 53 tumors showed mutations in exon 18 (n = 3) and exon 19 (n = 2). Polysomy of chromosome 7 (average >2.5 copies/cell) was detected in 15 (25.0%) of 60 tumors (6 at 3+, 5 at 2+, 2 at 1+, 2 at 0+ expression) and correlated with poor 3-year survival (P = 0.015). For HER-2, 17 (25.8%) of 66 tumors expressed HER-2 (10 at 3+, 3 at 2+, 4 at 1+). Eight tumors showed HER-2 gene amplification (6 at 3+, 1 at 1+, 1 at 0+ protein expression). Chromosome 17 polysomy was found in 8 (15.7%) of 51 tumors; two had HER-2 expression (3+, 1+).Conclusion: Our study shows that salivary duct carcinomas (a) harbor EGFR gene mutations in a subset of tumors that may guide therapy, (b) pursue an aggressive clinical course in cases with chromosome 7 polysomy and high EGFR expression, and (c) with HER-2 gene amplification and protein high expression, may be selected for targeted therapy. Clin Cancer Res; 16(8); 2266–74. ©2010 AACR.