Noncanonical HPV carcinogenesis drives radiosensitization of head and neck tumors.

We analyzed transcriptional data from 104 HPV+ (Human papillomavirus) HNSCC (head and neck squamous cell carcinoma) tumors together with two publicly available sources to identify highly robust transcriptional programs (modules) which could be detected consistently despite heterogeneous sequencing and quantification methodologies. Among 22 modules identified, we found a single module that naturally subclassifies HPV+ HNSCC tumors based on a bimodal pattern of gene expression, clusters all atypical features of HPV+ HNSCC biology into a single subclass, and predicts patient outcome in four independent cohorts. The subclass-defining gene set was strongly correlated with Nuclear factor kappa B (NF-κB) target expression. Tumors with high expression of this NF-κB module were rarely associated with activating PIK3CA alterations or viral integration, and also expressed higher levels of HPHPV E2 and had decreased APOBEC mutagenesis. Alternatively, they harbored inactivating alterations of key regulators of NF-κB, TNF receptor associated factor 3 (TRAF3), and cylindromatosis (CYLD), as well as retinoblastoma protein (RB1). HPV+ HNSCC cells in culture with experimental depletion of TRAF3 or CYLD displayed increased expression of the subclass-defining genes, as well as robust radio-sensitization, thus recapitulating both the tumor transcriptional state and improved treatment response observed in patient data. Across all gene sets investigated, methylation to expression correlations were the strongest for the subclass-defining, NF-κB-related genes. Increased tumor-infiltrating CD4+ T cells and increased Estrogen receptors alpha (ERα) expression were identified in NF-κB active tumors. Based on the relatively high rates of cure in HPV+ HNSCC, deintensification of therapy to reduce treatment-related morbidity is being studied at many institutions. Tumor subclassification based on oncogenic subtypes may help guide the selection of therapeutic intensity or modality for patients with HPV+ HNSCC.

Plasmacytoma of the Head and Neck: Case Series and Review of the Literature.

Solitary plasmacytoma is a rare neoplasm characterized by localized proliferation of monoclonal plasma cells and is classified as solitary bone or solitary extramedullary plasmacytoma. Here, we present two rare cases of plasmacytoma of the head and neck. The first is a 78-year-old male who presented with a 3-month history of epistaxis and progressive obstruction of the right nasal passage. Computerized tomography (CT) imaging revealed a mass in the right nasal cavity with destruction to the maxillary sinus. An excisional biopsy was performed revealing anaplastic plasmacytoma. The second is a 64-year-old male with a past medical history significant for prostate cancer who presented with a 2-month history of left ear pain and progressive non-tender temporal swelling. A PET/CT revealed a highly avid, destructive, and lytic left temporal mass with no other evidence of distant disease. A left temporal craniectomy and infratemporal fossa dissection revealed plasma cell dyscrasia with monoclonal lambda in situ hybridization. Although plasmacytomas are uncommon tumors of the head and neck, they may mimic other entities that require different treatment. Prompt and accurate diagnosis is critical for appropriate therapeutic decisions and prognosis.

Characterizing Adverse Events of Biologic Treatment of T2 Disease: A Disproportionality Analysis of the FDA Adverse Event Reporting System.

INTRODUCTION: Over the last 3 years, the FDA has approved dupilumab, omalizumab, and mepolizumab for the treatment of CRSwNP; however, adverse events of these biologics have not been described in post-marketing surveillance trials. By utilizing the FDA Adverse Event Reporting System (FAERS), this study describes and compares biologic-associated adverse events in T2 disease. METHODS: This case-non-case study assessed disproportionate reporting rates using reporting odds ratios (RORs). RORs and p values for biologic-associated AEs were categorized and compared among dupilumab, omalizumab, and mepolizumab. This analysis included AEs associated with all treatment indications. Relative AE rates and outcomes were calculated. RESULTS: There were a total of 112,560, 24,428, and 18,741 unique AE reports associated with dupilumab, omalizumab, and mepolizumab, respectively. Omalizumab had the strongest association with anaphylaxis (ROR = 20.80, 95% confidence interval [CI]: 18.58, 23.29). Dupilumab had large relative proportions and positive signals in the ophthalmologic category (7.76%, ROR = 6.20, 95% CI: 6.06, 6.35), such as with blurry vision (ROR = 3.80, CI: 3.52, 4.12) and visual impairment (ROR = 1.98, CI: 1.80, 2.19). Dupilumab was the only biologic associated with injection-site reactions (7.98%, ROR = 8.17, 95% CI: 7.98, 8.37). DISCUSSION/CONCLUSION: This is the first large-scale comparative analysis of the AE profiles of dupilumab, omalizumab, and mepolizumab. Our data suggest possible relations between dupilumab and ophthalmologic and injection-site AEs. Omalizumab was the only biologic with a positive anaphylaxis signal. This FAERS investigation suggests important AE differences among these biologics.

On the association analysis of CNV data: a fast and robust family-based association method.

BACKGROUND: Copy number variation (CNV) is known to play an important role in the genetics of complex diseases and several methods have been proposed to detect association of CNV with phenotypes of interest. Statistical methods for CNV association analysis can be categorized into two different strategies. First, the copy number is estimated by maximum likelihood and association of the expected copy number with the phenotype is tested. Second, the observed probe intensity measurements can be directly used to detect association of CNV with the phenotypes of interest. RESULTS: For each strategy we provide a statistic that can be applied to extended families. The computational efficiency of the proposed methods enables genome-wide association analysis and we show with simulation studies that the proposed methods outperform other existing approaches. In particular, we found that the first strategy is always more efficient than the second strategy no matter whether copy numbers for each individual are well identified or not. With the proposed methods, we performed genome-wide CNV association analyses of hematological trait, hematocrit, on 521 Korean family samples. CONCLUSIONS: We found that statistical analysis with the expected copy number is more powerful than the statistic with the probe intensity measurements regardless of the accuracy of the estimation of copy numbers.

Visualization of haplotype sharing patterns in pedigree samples.

OBJECTIVES: A particular approach to the visualization of descent of founder DNA copies in a pedigree has been suggested, which helps to understand haplotype sharing patterns among subjects of interest. However, the approach does not provide the information in an ideal format to show haplotype sharing patterns. Therefore, we aimed to find an efficient way to visualize such sharing patterns and to demonstrate that our tool provides useful information for finding an informative subset of subjects for a sequence study. METHODS: The visualization package, SharedHap, computes and visualizes a novel metric, the SharedHap proportion, which quantifies haplotype sharing among a set of subjects of interest. We applied SharedHap to simulated and real pedigree datasets to illustrate the approach. RESULTS: SharedHap successfully represents haplotype sharing patterns that contribute to linkage signals in both simulated and real datasets. Using the visualizations we were also able to find ideal sets of subjects for sequencing studies. CONCLUSIONS: Our novel metric that can be computed using the SharedHap package provides useful information about haplotype sharing patterns among subjects of interest. The visualization of the SharedHap proportion provides useful information in pedigree studies, allowing for a better selection of candidate subjects for use in further sequencing studies.

The Surprising Effect of Priming on SNOT-22 Results.

BACKGROUND: Priming is a psychological phenomenon where subconscious cues in the environment impact our behavioral responses in certain situations. Well studied in the worlds of business, marketing, and even politics, it is unclear how the priming phenomenon impacts patient perception of their own disease state nor how they report that perception using tools like the Sinonasal Outcomes Test (SNOT-22), used to measure that perception in chronic rhinosinusitis. OBJECTIVE: To determine the impact of positive or negative priming on self-reported patient perception of their chronic rhinosinusitis disease using the SNOT-22 disease-specific quality of life instrument. METHODS: Single-blind, randomized, prospective cohort pilot study of 206 consecutive adult patients with a clinical diagnosis of chronic rhinosinusitis presenting to a university rhinology clinic. Patients were randomized to receive "positive priming" (103) or "negative priming" (103) by reading a passage about the positive or negative aspects of chronic sinusitis and its treatment respectively. Patients were then asked to fill out the SNOT-22 and results between the two groups were compared. RESULTS: The negative priming group had a higher median SNOT-22 score of 49 [IQR = 39] compared to the positive priming groups' score of 22 [IQR = 27], p < 0.0001), a difference of nearly three times the minimal clinical impactful difference (MCID). This effect was consistent regardless of age or sex of the patient. Subgroup analysis revealed a greater impact when priming was performed by the senior male attending regardless of patient age or sex (p < 0.001), while priming performed by the younger female research fellow had greater impact on older patients (>59 years, p = 0.001) and female patients (p = 0.003). CONCLUSIONS: Priming impacts how patient's perceive their chronic rhinosinusitis as determined by the SNOT-22. It is imperative that the rhinologist understand this when using this instrument in research applications and in clinical decision-making for patients.

"Left on their own": Left-handedness among rhinologists and otolaryngology trainees.

KEY POINTS: Left-hand-dominant (LHD) respondents reported higher rates of training difficulties because of handedness differences. LHD respondents cited particular difficulty with functional endoscopic sinus surgery. Both LHD and right-hand-dominant respondents perceived a need for laterality-specific training during residency.

Inheritance model introduces differential bias in CNV calls between parents and offspring.

Copy Number Variation (CNV) is increasingly implicated in disease pathogenesis. CNVs are often identified by statistical models applied to data from single nucleotide polymorphism panels. Family information for samples provides additional information for CNV inference. Two modes of PennCNV (the Joint-call and Posterior-call), which are some of the most well-developed family-based CNV calling methods, use a "Joint-model" as a main component. This models all family members' CNV states together with Mendelian inheritance. Methods based on the Joint-model are used to infer CNV calls of cases and controls in a pedigree, which may be compared to each other to test an association. Although benefits from the Joint-model have been shown elsewhere, equality of call rates in parents and offspring has not been evaluated previously. This can affect downstream analyses in studies that compare CNV rates in cases vs. controls in pedigrees. In this paper, we show that the Joint-model can introduce different CNV call rates among family members in the absence of a true difference. We show that the Joint-model may analytically introduce differential CNV calls because of asymmetry of the model. We demonstrate these differential call rates using single-marker simulations. We show that call rates using the two modes of PennCNV also differ between parents and offspring in one multimarker simulated dataset and two real datasets. Our results advise need for caution in use of the Joint-model calls in CNV association studies with family-based datasets.

Effects of health insurance on racial disparity in osteoporosis medication adherence.

OBJECTIVE: To explore whether racial disparity in osteoporosis drug therapy maintenance varies by health insurance coverage status. DESIGN: Longitudinal observation study. SETTING: Cleveland Clinic Health System (Cleveland, OH) from January 2006 to December 2009. PATIENTS: 3,901 black and white female Medicare beneficiaries starting osteoporosis drug therapy. INTERVENTION: Analysis of the health system's integrated electronic medical records. MAIN OUTCOME MEASURES: Drug therapy adherence (medication possession ratio ≥80%) for more than 12 of 15 surveillance units and occurrence of extended nonadherence gaps for at least two surveillance units in a row. RESULTS: Among patients with supplementary health insurance (n = 2,278), no difference was observed for drug therapy adherence ( P = 0.17) and extended nonadherence gaps ( P = 0.53) between black and white participants. When patients did not have supplementary health insurance (n = 1,623), blacks (36% [95% CI 28-47]) were less likely to adhere to drug therapy than whites (47% [38-57]; odds ratio [OR] 0.34 [95% CI 0.09-0.92], P = 0.004). Blacks (25% [19-32]) also were more likely to have an extended nonadherence gap episode than whites (18% [11-26]; OR 2.42 [1.13-3.50], P = 0.03). CONCLUSION: Similar to previous research on racial disparity in health services, racial disparity in osteoporosis drug therapy maintenance between black and white female older patients existed when supplementary health insurance was not affordable.

Relationships among advance directives, principal diagnoses, and discharge outcomes in critically ill older adults.

OBJECTIVE: The purpose of this study was to determine the relationships among advance directive status, principal diagnoses, and the discharge outcomes in community-dwelling, critically ill older adults. METHOD: Using administrative and clinical data (n = 1673), multinomial logit regressions were used to examine the relationships among advance directive status, principal diagnoses, and discharge outcomes (in-hospital deaths, hospice discharges, and transition to institutions). RESULTS: In the overall sample, the adjusted probability of in-hospital deaths with advance directives (12%) was lower than that without advance directives (17%; odds ratio [OR] = 0.56; p = 0.007) and the adjusted probability of hospice discharges with advance directives (11%) was higher than that without advance directives (7%; OR = 1.96; p = 0.03). Subgroup analysis showed that the magnitude of the abovementioned changes was aggregated when their principal diagnoses were a group of diseases with more difficult prognostication (circulatory and respiratory diseases) and more potential for reversibility (infectious diseases). By contrast, the magnitude of the abovementioned findings was diminished with other principal diagnoses. On the other hand, the presence of advance directives did not make a contribution to transition from communities to institutions. SIGNIFICANCE OF RESULTS: Significantly fewer in-hospital deaths in addition to higher hospice discharges were observed with any advance directives in community-dwelling, critically ill older adults. The magnitude of these findings was aggregated when their principal diagnoses were a group of diseases with more difficult prognostication (circulatory and respiratory diseases) and more potential for reversibility (infectious diseases). By contrast, the magnitude of these findings was diminished with other principal diagnoses.

Time to treatment patterns of head and neck cancer patients before and during the Covid-19 pandemic.

OBJECTIVES: The delivery of healthcare has changed significantly over the past decades. This study analyzes the clinicodemographic factors and treatment patterns of head and neck squamous cell carcinoma (HNSCC) patients between 2004 and 2020. MATERIALS AND METHODS: Retrospective cohort analysis of HNSCC patients from the National Cancer Data Base from 2004 to 2020. RESULTS: A total of 164,290 patients were included. Increased times from diagnosis to definitive surgery (TTS) were seen across all facility types (academic centers, AC; non-academic centers, NAC) between 2004 and 2019, with NAC affected more. TTS < 15 days (RR = 1.05, 95%CI:1.05-1.09) and > 75 days (1.07, 95%CI:1.05-1.09) were associated with increased mortality risk. This association was more prominent among HPV + HNSCC (RR = 1.45; 95%CI:1.18-1.78). Treatment in AC was associated with a decreased mortality risk (RR = 0.94, 95%CI:0.93-0.95). Despite the universal increase in wait times from 2004 to 2019, short-term mortality was significantly decreased from 2016 to 2019, relative to 2004-2007 (3-month mortality: RR = 0.77, 95%CI:0.70-0.85; 12-month mortality: RR = 0.80, 95%CI:0.77-0.84). Wait times decreased in 2020. CONCLUSIONS: TTS increased between 2004 and 2019, with NAC affected more. However, despite longer wait times, short-term survival increased significantly. Very short (<15 days) and very long (>75 days) TTS were associated with increased mortality risk. Patients with HPV + HNSCC have the highest increase among those treated > 75 days from diagnosis. Treatment at AC was associated with improved survival, which could be explained by the presence of multidisciplinary teams and subspecialists that may be less available at NAC. The 2021 NCDB data are required for a comprehensive analysis of wait times in 2020.

Granulomatosis With Polyangiitis Presenting as an Infratemporal Fossa Mass.

Granulomatosis with polyangiitis is a rare autoimmune disease that affects small to medium-sized blood vessels throughout the body. Here, we present a case of an infratemporal mass that was the result of granulomatosis with polyangiitis. A 51-year-old male presented to the emergency department due to right cheek and facial pain that he had been experiencing for 2 to 3 months. An MRI revealed a mass within the right infratemporal and pterygopalatine fossae extending into the inferior right orbital fissure along the maxillary division of the trigeminal nerve (V2) and the vidian nerve causing concern for malignancy. Histology from an endoscopic biopsy demonstrated multiple arteries with luminal obliteration with non-necrotizing granulomas. The patient was started on steroids and immunosuppressive therapy, which improved his symptoms and decreased the size of the residual mass. This case illustrates the need for laboratory testing, imaging, and biopsy of the involved tissue in cases where GPA is suspected to prevent treatment delays that could lead to the destruction of vital organs.

Characteristics of olfactory dysfunction in patients with long-haul covid-19.

Background: A subset of individuals suffering from Coronavirus Disease 2019 (COVID-19) will experience ongoing symptoms that last longer than three months (i.e., long-haul COVID). This includes olfactory dysfunction (OD), which is currently estimated to occur in 1-63.5% of patients at one-year post-infection. However, OD in individuals with long-haul COVID-19 is poorly understood, and there is little information regarding how initial SARS-CoV-2 variants correlate with long-haul symptoms. In this study, we investigated the prevalence and severity of OD in patients with long-haul COVID-19 and investigated how OD severity varied with SARS-CoV-2 variants. Methods: Patients were recruited from the University of North Carolina-Chapel Hill COVID Recovery Clinic. Each patient completed the University of Pennsylvania Smell Identification Test (UPSIT). The dominant strain at the time of infection was determined using the date of COVID-19 diagnosis, and Centers for Disease Control and Prevention, World Health Organization, and North Carolina Department of Health and Human Services databases. Results: Nearly 85% of patients with long-haul COVID-19 reported some degree of OD, which persisted in some patients for two or more years from the date of the initial infection. There was no association between the time since COVID-19 infection and severity of OD. No difference was detected between OD in patients with long-haul COVID-19 based on the dominant variant at the time of infection (p=0.0959). Conclusion: A vast majority of patients with long-haul COVID-19 had some degree of ongoing olfactory complications, although the severity of symptoms was not dependent on the dominant SARS-CoV-2 variant at the time of infection.

Histologic characterization of primary ciliary dyskinesia chronic rhinosinusitis.

KEY POINTS: We present the largest cohort of structured histopathology reports on primary ciliary dyskinesia-related chronic rhinosinusitis (PCD-CRS). Despite endoscopic differences, PCD-CRS and cystic fibrosis-related chronic rhinosinusitis (CF-CRS) had similar structured histopathology reports. Compared to healthy patients and those with idiopathic chronic rhinosinusitis without nasal polyps, patients with PCD-CRS had an increased neutrophil count.

Sinonasal quality of life in primary ciliary dyskinesia.

KEY POINTS: Our findings suggest that primary ciliary dyskinesia (PCD)-related chronic rhinosinusitis (CRS) has a more significant impact on quality of life than CRS without nasal polyps and cystic fibrosis (CF). PCD and CF have similar mucociliary clearance defects, yet sinonasal symptom severity varies between the two.

Direct Comparison of HPV16 Viral Genomic Integration, Copy Loss, and Structural Variants in Oropharyngeal and Uterine Cervical Cancers Reveal Distinct Relationships to E2 Disruption and Somatic Alteration.

Squamous cell carcinoma of the oropharynx caused by HPV type 16 (HPV16+ OPSCC) is the most common HPV-associated malignancy in the USA and has many molecular differences from uterine cervical squamous cell carcinoma (UCSCC). Our understanding of HPV oncogenesis relied on studies of UCSCC revealing a consensus model reliant on HPV integration with a loss of E2. Here, we compare patterns of HPV integration in UCSCC and OPSCC by analysis of affinity capture sequencing of the HPV16 genome in 104 OPSCC and 44 UCSCC tumors. These cohorts were contemporaneously sequenced using an identical strategy. Integration was identified using discordant read pair clustering and assembly-based approaches. Viral integration sites, structural variants, and copy losses were examined. While large-scale deep losses of HPV16 genes were common in UCSCC and were associated with E2 loss, deep copy losses of the HPV16 genome were infrequent in HPV16+ OPSCC. Similarly, structural variants within HPV16 favored E2 loss in UCSCC but not OPSCC. HPV16 integration sites were non-random, with recurrent integration hot-spots identified. OPSCC tumors had many more integration sites per tumor when compared to UCSCC and had more integration sites in genomic regions with high gene density. These data show that viral integration and E2 disruption are distinct in UCSCC and OPSCC. Our findings also add to growing literature suggesting that HPV tumorigenesis in OPSCC does not follow the model developed based on UCSCC.

Single-marker and two-marker association tests for unphased case-control genotype data, with a power comparison.

In case-control single nucleotide polymorphism (SNP) data, the allele frequency, Hardy Weinberg Disequilibrium, and linkage disequilibrium (LD) contrast tests are three distinct sources of information about genetic association. While all three tests are typically developed in a retrospective context, we show that prospective logistic regression models may be developed that correspond conceptually to the retrospective tests. This approach provides a flexible framework for conducting a systematic series of association analyses using unphased genotype data and any number of covariates. For a single stage study, two single-marker tests and four two-marker tests are discussed. The true association models are derived and they allow us to understand why a model with only a linear term will generally fit well for a SNP in weak LD with a causal SNP, whatever the disease model, but not for a SNP in high LD with a non-additive disease SNP. We investigate the power of the association tests using real LD parameters from chromosome 11 in the HapMap CEU population data. Among the single-marker tests, the allelic test has on average the most power in the case of an additive disease, but for dominant, recessive, and heterozygote disadvantage diseases, the genotypic test has the most power. Among the four two-marker tests, the Allelic-LD contrast test, which incorporates linear terms for two markers and their interaction term, provides the most reliable power overall for the cases studied. Therefore, our result supports incorporating an interaction term as well as linear terms in multi-marker tests.

Phase uncertainty in case-control association studies.

The possible evidence for association comprises three types of information: differences between cases and controls in allele frequencies, in parameters for Hardy-Weinberg disequilibrium (HWD), and in parameters for linkage disequilibrium (LD). LD between marker and disease alleles results in a difference in at least one of the three types of parameters [Won and Elston, 2008]. However, the parameters for LD require knowledge about phase, which is usually unknown, making the LD contrast test without modification infeasible in practice. Methods for handling phase uncertainty are: (1) the most probable haplotype pair for each individual can be considered as the true phase; (2) a weighted average of haplotypes can be used; (3) we can consider the composite LD, which does not require any information about phase. We compare these methods to handle phase uncertainty in terms of validity and efficiency, and the effect on them of HWD in the population, at the same time confirming results for the three types of information. When the LD between markers is high, the LD contrast test that uses a weighted average of haplotypes or the most probable haplotypes to calculate the LD is recommended, but otherwise the LD contrast test that uses the composite LD is recommended. We conclude that, even though the difference in allele frequencies is usually the most informative test except in the case of a recessive disease, the LD contrast test can be more powerful if the markers are dense enough.

Differential effects of N-linked glycosylation of Vstm5 at multiple sites on surface expression and filopodia formation.

V-set and transmembrane domain-containing protein 5 (Vstm5), a newly characterized small membrane glycoprotein, can induce membrane protrusions in various cells. Vstm5 can modulate both the position and complexity of central neurons by altering their membrane morphology and dynamics. In this study, we investigated the significance of glycosylation in the expression and function of Vstm5. Four N-linked glycosylation sites (Asn43, Asn87, Asn101, and Asn108) are predicted to be located in the extracellular N-terminus of mouse Vstm5. Although all four sites were glycosylated, their functional roles may not be identical. N-glycosylation at multiple sites affects differentially the function of Vstm5. Glycosylation at individual sites not only played essential roles in surface expression of Vstm5 but also in the formation of neuronal dendritic filopodia. These results indicate that N-linked glycosylation at multiple sites plays important roles by differentially influencing the expression, targeting, and biological activity of Vstm5.