Abstract Adenoid cystic carcinoma (AdCC) is a slow-growing salivary gland malignancy that relapses frequently. AdCCs of the submandibular gland exhibit unique differences in prognosis and treatment ...response to adjuvant radiotherapy compared to other sites, yet the role of tumor anatomic subsite on gene expression and tumor immune microenvironment (TIME) composition remains unclear. We used 87 samples, including 48 samples (27 AdCC and 21 normal salivary gland tissue samples) from 4 publicly available AdCC RNA sequencing datasets, a validation set of 33 minor gland AdCCs, and 39 samples from an in-house cohort (30 AdCC and 9 normal salivary gland samples). RNA sequencing data were used for single sample gene set enrichment analysis and TIME deconvolution. Quantitative PCR and multiplex immunofluorescence were performed on the in-house cohort. Wilcoxon rank-sum, nonparametric equality-of-medians tests and linear regression models were used to evaluate tumor subsite differences. AdCCs of different anatomic subsites including parotid, submandibular, sublingual, and minor salivary glands differed with respect to expression of several key tumorigenic pathways. Among the three major salivary glands, the reactive oxygen species (ROS)/nuclear factor erythroid 2-related factor 2 (NRF2) pathway signature was significantly underexpressed in AdCC of submandibular compared to parotid and sublingual glands while this association was not observed among normal glands. Additionally, the NRF2 pathway, whose expression was associated with favorable overall survival, was overexpressed in AdCCs of parotid gland compared to minor and submandibular glands. The TIME deconvolution identified differences in CD4 + T cell populations between AdCC of major and minor glands and natural killer (NK) cells among AdCC of minor, submandibular, and parotid glands while plasma cells were enriched in normal submandibular glands compared to other normal gland controls. Our data reveal key molecular differences in AdCC of different anatomic subsites. The ROS and NRF2 pathways are underexpressed in submandibular and minor AdCCs compared to parotid gland AdCCs, and NRF2 pathway expression is associated with favorable overall survival. The CD4 + T, NK, and plasma cell populations also vary by tumor subsites, suggesting that the observed submandibular AdCC tumor-intrinsic pathway differences may be responsible for influencing the TIME composition and survival differences.
Background
Human papillomavirus–positive (HPV+) squamous cell carcinoma of the oropharynx (OPSCC) is the most prevalent HPV‐associated malignancy in the United States. Favorable treatment outcomes ...have led to increased interest in treatment de‐escalation to reduce treatment morbidity as well as the development of prognostic markers to identify appropriately low‐risk patients. Intratumoral genomic heterogeneity and copy number alteration burden have been demonstrated to be predictive of poor outcomes in many other cancers; therefore, we sought to determine whether intratumor heterogeneity and genomic instability are associated with poor outcomes in HPV+ OPSCC.
Methods
Tumor heterogeneity estimates were made based on targeted exome sequencing of 45 patients with HPV+ OPSCC tumors. Analysis of an additional cohort of HPV+ OPSCC tumors lacking matched normal sequencing allowed copy number analysis of 99 patient tumors.
Results
High intratumorally genomic heterogeneity and high numbers of copy number alterations were strongly associated with worse recurrence‐free survival. Tumors with higher heterogeneity and frequent copy number alterations were associated with loss of distal 11q, which encodes key genes related to double‐strand break repair, including ATM and MRE11A.
Conclusions
Both intratumor genomic heterogeneity and high‐burden copy number alterations are strongly associated with poor recurrence‐free survival in patients with HPV+ OPSCC. The drivers of genomic instability and heterogeneity in these tumors remains to be elucidated. However, 11q loss and defective DNA double‐strand break repair have been associated with genomic instability in other solid tumors. Copy number alteration burden and intratumoral heterogeneity represent promising avenues for risk stratification of patients with HPV+OPSCC.
Molecular markers are needed to determine which human papillomavirus (HPV)‐positive patients with squamous cell carcinoma of the oropharynx (OPSCC) are best served by reduced intensity treatment, which has the potential to reduce severe treatment‐related morbidity. We demonstrate that 11q‐related copy number variant burden and heterogeneity are highly associated with poor recurrence‐free survival in patients with HPV‐positive OPSCC and may have potential as translational biomarkers.
Squamous cell carcinoma of the head and neck (HNSCC) accounts for more than 300,000 deaths worldwide per year as a consequence of tumor cell invasion of adjacent structures or metastasis. LIM-only ...protein 4 (LMO4) and LIM-domain binding protein 1 (LDB1), two directly interacting transcriptional adaptors that have important roles in normal epithelial cell differentiation, have been associated with increased metastasis, decreased differentiation, and shortened survival in carcinoma of the breast. Here, we implicate two LDB1-binding proteins, single-stranded binding protein 2 (SSBP2) and 3 (SSBP3), in controlling LMO4 and LDB1 protein abundance in HNSCC and in regulating specific tumor cell functions in this disease. First, we found that the relative abundance of LMO4, LDB1, and the two SSBPs correlated very significantly in a panel of human HNSCC cell lines. Second, expression of these proteins in tumor primaries and lymph nodes involved by metastasis were concordant in 3 of 3 sets of tissue. Third, using a Matrigel invasion and organotypic reconstruct assay, CRISPR/Cas9-mediated deletion of LDB1 in the VU-SCC-1729 cell line, which is highly invasive of basement membrane and cellular monolayers, reduced tumor cell invasiveness and migration, as well as proliferation on tissue culture plastic. Finally, inactivation of the LDB1 gene in these cells decreased growth and vascularization of xenografted human tumor cells in vivo. These data show that LMO4, LDB1, and SSBP2 and/or SSBP3 regulate metastasis, proliferation, and angiogenesis in HNSCC and provide the first evidence that SSBPs control LMO4 and LDB1 protein abundance in a cancer context.
Human papillomavirus-positive (HPV+) squamous cell carcinoma of the oropharynx (OPSCC) is the most prevalent HPV-associated malignancy in the United States and is primarily caused by HPV subtype 16 ...(HPV16). Favorable treatment outcomes have led to increasing interest in treatment deescalation to reduce treatment-related morbidity. Prognostic biomarkers are needed to identify appropriately low-risk patients for reduced treatment intensity. Targeted DNA sequencing including all HPV16 open reading frames was performed on tumors from 104 patients with HPV16+ OPSCC treated at a single center. Genotypes closely related to the HPV16-A1 reference were associated with increased numbers of somatic copy-number variants in the human genome and poor recurrence-free survival (RFS). Genotypes divergent from HPV16-A1 were associated with favorable RFS. These findings were independent of tobacco smoke exposure. Total RNA sequencing was performed on a second independent cohort of 89 HPV16+ OPSCC cases. HPV16 genotypes divergent from HPV16-A1 were again validated in this independent cohort, to be prognostic of improved RFS in patients with moderate (less than 30 pack-years) or low (no more than 10 pack-years) of tobacco smoke exposure. In summary, we show in two independent cohorts that viral sequence divergence from the HPV16-A1 reference is correlated with improved RFS in patients with moderate or low tobacco smoke exposure.
HPV16 genotype is a potential biomarker that could be easily adopted to guide therapeutic decision-making related to deescalation therapy.
Human papillomavirus (HPV) is associated with a subset of head and neck squamous cell carcinoma (HNSCC). Between 15% and 35%
of HNSCCs harbor HPV DNA. Demographic and exposure differences between ...HPV-positive (HPV + ) and negative (HPV − ) HNSCCs suggest that HPV + tumors may constitute a subclass with different biology, whereas clinical differences have also been observed. Gene expression
profiles of HPV + and HPV − tumors were compared with further exploration of the biological effect of HPV in HNSCC. Thirty-six HNSCC tumors were analyzed
using Affymetrix Human 133U Plus 2.0 GeneChip and for HPV by PCR and real-time PCR. Eight of 36 (22%) tumors were positive
for HPV subtype 16. Statistical analysis using Significance Analysis of Microarrays based on HPV status as a supervising variable
resulted in a list of 91 genes that were differentially expressed with statistical significance. Results for a subset of these
genes were verified by real-time PCR. Genes highly expressed in HPV + samples included cell cycle regulators (p16 INK4A , p18, and CDC7) and transcription factors (TAF7L, RFC4, RPA2, and TFDP2). The microarray data were also investigated by mapping
genes by chromosomal location (DIGMAP). A large number of genes on chromosome 3q24-qter had high levels of expression in HPV + tumors. Further investigation of differentially expressed genes may reveal the unique pathways in HPV + tumors that may explain the different natural history and biological properties of these tumors. These properties may be
exploited as a target of novel therapeutic agents in HNSCC treatment.
Abstract
Background
In rural states, travel burden for complex cancer care required for head and neck squamous cell carcinoma (HNSCC) may affect patient survival, but its impact is unknown.
Methods
...Patients with HPV‐negative HNSCC were retrospectively identified from a statewide, population‐based study. Euclidian distance from the home address to the treatment center was calculated for radiation therapy, surgery, and chemotherapy. Multivariable Cox proportional hazards models were used to examine the risk of 5‐year mortality with increasing travel quartiles.
Results
There were 936 patients with HPV‐negative HNSCC with a mean age of 60. Patients traveled a median distance of 10.2, 11.1, and 10.9 miles to receive radiation therapy, surgery, and chemotherapy, respectively. Patients in the fourth distance quartile were more likely to live in a rural location (
p
< 0.001) and receive treatment at an academic hospital (
p
< 0.001). Adjusted overall survival (OS) improved proportionally to distance traveled, with improved OS remaining significant for patients who traveled the furthest for care (third and fourth quartile by distance). Relative to patients in the first quartile, patients in the fourth had a reduced risk of mortality with radiation (HR 0.59, 95% CI 0.42–0.83;
p
= 0.002), surgery (HR 0.47, 95% CI 0.30–0.75;
p
= 0.001), and chemotherapy (HR 0.56, 95% CI 0.35–0.91;
p
= 0.020).
Conclusion
For patients in this population‐based cohort, those traveling greater distances for treatment of HPV‐negative HNSCC had improved OS. This analysis suggests that the benefits of coordinated, multidisciplinary care may outweigh the barriers of travel burden for these patients.
Abstract To facilitate development of CSC-targeting therapies, we analyzed publicly available breast cancer datasets to identify genes co-expressed with SOX10, a neural crest marker, and PROM1/CD133, ...a common CSC marker. The conserved SOX10/PROM1 gene signature that we characterized supports the existence in basal breast cancers of SOX10+/CD133+ cells with neural stem-like features exposing clinically relevant CSC markers and signaling networks. Background We previously characterized in salivary adenoid cystic carcinoma (ACC) a novel population of CSC marked by co-expression of two stemness genes, SOX10 and CD133. We also reported that in ACC and basal-like breast carcinoma (BBC), a triple-negative breast cancer subtype, expression of SOX10 similarly demarcates a highly conserved gene signature enriched with neural stem cell genes. Based on these findings, we hypothesized that BBC may be likewise driven by SOX10+/CD133+ cells with neural stem cell properties. Methods To validate our hypothesis on clinical data, we used a novel approach to meta-analysis that merges gene expression data from independent breast cancer studies and ranks genes by statistical significance of their co-expression with the gene of interest. Genes that showed strong association with both CD133/PROM1 and SOX10 were validated across different platforms and datasets and analyzed for enrichment with genes involved in neurogenesis. Results We identified in clinical breast cancer datasets a highly conserved SOX10/PROM1 gene signature that contains neural stem cell markers common for Schwann cells, ACC, BBC, and melanoma. Identification of TRIM2, TRIM29, MPZL2, KCNN4, and VTCN1/B7-H4 within this signature provides insight into molecular mechanisms of CSC maintenance. Conclusion Our results suggest that BBC is driven by SOX10+/CD133+ cells that express NSC-specific markers and share molecular similarities with CSC of neural crest origin. Our study provides clinically relevant information on possible drivers of these cells that may facilitate development of CSC-targeting therapies against this cancer distinguished with poor prognosis and resistance to conventional therapies.
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