Smoking initiation is followed by the early acquisition of epigenetic change in cervical epithelium: a longitudinal study

Global DNA methylation changes in rock pigeon (Columba livia) as a sentinel species due to polycyclic aromatic hydrocarbons exposure in Tehran (Iran) as a megacity

Global DNA methylation, as an epigenetic modifications, can be a promising genomic marker for monitoring the contaminants and predicting their adverse health effects. The study aims to assess the effects of 16 PAH concentration on the altered DNA methylation levels in the kidney and liver of rock pigeon (Columba livia), as a sentinel species, from Tehran megacity as well as 40 days benzo(a)pyrene in vitro exposure: (0.1, 2.5, 5, 7.5, and 10 mg kg^-1 bw). Data indicated that the total LMW-PAH (low molecular weight PAHs) group (120.22, 121.34, 103.69, and 128.79 ng g^-1 dw in liver, kidney, skin, and muscle, respectively) in the Tehran samples have higher levels than the other PAHs groups. In addition, the DNA methylation level had negative relation with the total amount of PAHs in liver and kidney. A comparatively higher global DNA hypomethylation (by 8.65% in liver and 3.76% in kidney) was observed in birds exposed to B(a)P. Our results lead us to suggest that DNA hypomethylation in liver and kidney associated with the B(a)P may be useful biomarker discovery (more than the amount of PAH concentration in different tissues of C. livia) in urban areas. In conclusion, based on the overall results assessed, DNA methylation changes in pigeon may show a new target pathway for evaluation of environmental health.

Associations of P16INK4a promoter hypermethylation with squamous intra-epithelial lesion, cervical cancer and their clinicopathological features: a meta-analysis

To assess the associations of P16INK4a methylation status with low-grade squamous intra-epithelial lesion (LSIL), high-grade squamous intra-epithelial lesion (HSIL), cervical cancer (CC) and their clinicopathological features, a meta-analysis with 29 eligible studies was conducted. Pooled odds ratios (ORs) with their 95% confidence intervals (CIs) were estimated to assess the strength of the associations. Heterogeneity, sensitivity of pooled results and publication bias were also evaluated. Overall, there was an increasing trend of P16INK4a hypermethylation rates among LSIL (21.4%), HSIL (30.9%) and CC (35.0%) specimens. P16INK4a hypermethylation was significantly associated with the increased risk of LSIL, HSIL and CC, with the pooled ORs of 3.26 (95% CI: 1.86-5.71), 5.80 (95% CI: 3.80-8.84) and 12.17 (95% CI: 5.86-25.27), respectively. A significant association was also found between P16INK4a hypermethylation and smoking habit (OR = 3.88, 95% CI: 2.13-7.08). Taken together, meta-analysis results support P16INK4a hypermethylation as an epigenetic marker for the progression of cervical carcinogenesis.

The dynamics of smoking-related disturbed methylation: a two time-point study of methylation change in smokers, non-smokers and former smokers

Background

The evidence for epigenome-wide associations between smoking and DNA methylation continues to grow through cross-sectional studies. However, few large-scale investigations have explored the associations using observations for individuals at multiple time-points. Here, through the use of the Illumina 450K BeadChip and data collected at two time-points separated by approximately 7 years, we investigate changes in methylation over time associated with quitting smoking or remaining a former smoker, and those associated with continued smoking.

Results

Our results indicate that after quitting smoking the most rapid reversion of altered methylation occurs within the first two decades, with reversion rates related to the initial differences in methylation. For 52 CpG sites, the change in methylation from baseline to follow-up is significantly different for former smokers relative to the change for never smokers (lowest p-value 3.61 x 10^-39 for cg26703534, gene AHRR). Most of these sites’ respective regions have been previously implicated in smoking-associated diseases. Despite the early rapid change, dynamism of methylation appears greater in former smokers vs never smokers even four decades after cessation. Furthermore, our study reveals the heterogeneous effect of continued smoking: the methylation levels of some loci further diverge between smokers and non-smokers, while others re-approach. Though intensity of smoking habit appears more significant than duration, results remain inconclusive.

Conclusions

This study improves the understanding of the dynamic link between cigarette smoking and methylation, revealing the continued fluctuation of methylation levels decades after smoking cessation and demonstrating that continuing smoking can have an array of effects. The results can facilitate insights into the molecular mechanisms behind smoking-induced disturbed methylation, improving the possibility for development of biomarkers of past smoking behavior and increasing the understanding of the molecular path from exposure to disease.

Electronic supplementary material

The online version of this article (10.1186/s12864-017-4198-0) contains supplementary material, which is available to authorized users.

Alcohol and nicotine codependence-associated DNA methylation changes in promoter regions of addiction-related genes

Altered DNA methylation in addiction-related genes may modify the susceptibility to alcohol or drug dependence (AD or ND). We profiled peripheral blood DNA methylation levels of 384 CpGs in promoter regions of 82 addiction-related genes in 256 African Americans (AAs) (117 cases with AD-ND codependence and 139 controls) and 196 European Americans (103 cases with AD-ND codependence and 93 controls) using Illumina's GoldenGate DNA methylation array assays. AD-ND codependence-associated DNA methylation changes were analyzed using linear mixed-effects models with consideration of batch effects and covariates age, sex, and ancestry proportions. Seventy CpGs (in 41 genes) showed nominally significant associations (P < 0.05) with AD-ND codependence in both AAs and EAs. One CpG (HTR2B cg27531267) was hypomethylated in AA cases (P = 7.2 × 10^-5), while 17 CpGs in 16 genes (including HTR2B cg27531267) were hypermethylated in EA cases (5.6 × 10^-9 ≤ P ≤ 9.5 × 10^-5). Nevertheless, 13 single nucleotide polymorphisms (SNPs) nearby HTR2B cg27531267 and the interaction of these SNPs and cg27531267 did not show significant effects on AD-ND codependence in either AAs or EAs. Our study demonstrated that DNA methylation changes in addiction-related genes could be potential biomarkers for AD-ND co-dependence. Future studies need to explore whether DNA methylation alterations influence the risk of AD-ND codependence or the other way around.

HPV infection and p16 promoter methylation as predictors of ASC-US/LSIL progression

BACKGROUND

Although patients found to have atypical squamous cells of undetermined significance (ASC-US) and low-grade squamous intraepithelial lesions (LSILs) on Papanicolaou (Pap) testing are treated conservatively, 5.2% to 18.8% of them progress to high-grade squamous intraepithelial lesions (HSILs). The objective of the current study was to identify predictors of progression to HSIL and determine what percentage of ASC-US/LSIL cases harbor cervical intraepithelial neoplasia of grade 2 or higher.

METHODS

The current study included 381 consecutive cases with ASC-US/LSIL. After the exclusion of 87 cases because of a history of dysplasia or loss to follow-up, 165 cases with follow-up cytology were used to analyze predictive factors of progression to HSIL, and 129 cases that underwent immediate tissue biopsy were subjected to correlation analysis between cytology and histology. Disease regression was defined as a reversion to normal or benign cellular changes, disease persistence as maintenance at ASC-US/LSIL, and disease progression as progression to HSIL. Data regarding clinical parameters were obtained from medical records. Methylation-specific polymerase chain reaction was performed using cytology samples to evaluate methylation of the p16 promoter.

RESULTS

Of 165 cases, 131 (79.4%) regressed, 23 (13.9%) were persistent, and 11 cases (6.7%) progressed. Human papillomavirus infection was more common in women with disease progression than in those with disease regression or persistence (P = .033). Promoter methylation of p16 in the cytology sample was more common in cases that progressed (5 of 6 cases) than in cases that regressed (0 of 8 cases). Twenty-three of 129 cases (17.8%) were found to harbor cervical intraepithelial neoplasia of grade 2 or higher on immediate tissue biopsy.

CONCLUSIONS

Human papillomavirus infection and p16 promoter methylation might be valuable surrogate markers of disease progression from ASC-US/LSIL to HSIL.

Epigenetic changes in neurology: DNA methylation in multiple sclerosis

INTRODUCTION

Epigenetics is defined as the study of the mechanisms that regulate gene expression without altering the underlying DNA sequence. The best known is DNA methylation. Multiple Sclerosis (MS) is a disease with no entirely known etiology, in which it is stated that the involvement of environmental factors on people with a genetic predisposition, may be key to the development of the disease. It is at this intersection between genetic predisposition and environmental factors where DNA methylation may play a pathogenic role.

DEVELOPMENT

A literature review of the effects of environmental risk factors for the development of MS can have on the different epigenetic mechanisms as well as the implication that such changes have on the development of the disease.

CONCLUSION

Knowledge of epigenetic modifications involved in the pathogenesis of MS, opens a new avenue of research for identification of potential biomarkers, as well as finding new therapeutic targets.

Evaluation of INK4A promoter methylation using pyrosequencing and circulating cell-free DNA from patients with hepatocellular carcinoma

BACKGROUND

Hyper-methylation of CpG dinucleotides in the promoter region of inhibitor of cyclin-dependent kinase 4A (INK4A) has been reported in 60%-80% of hepatocellular carcinoma (HCC). As INK4A promoter hypermethylation event occurs early in HCC progression, the quantification of INK4A promoter methylation in blood sample may represent a useful biomarker for non-invasive diagnosis and prediction of response to therapy.

METHODS

We examined INK4A promoter methylation using circulating cell-free DNA (ccfDNA) in a total of 109 serum specimens, including 66 HCC and 43 benign chronic liver diseases. Methylation of the individual seven CpG sites was examined using pyrosequencing.

RESULTS

Our results showed that there were significantly higher levels of methylated INK4A in HCC specimens than controls and that the seven CpG sites had different levels of methylation and might exist in different PCR amplicons. The area under receiver operating characteristic (ROC) curve was 0.82, with 65.3% sensitivity and 87.2% specificity at 5% (LOD), 39.0% sensitivity and 96.5% specificity at 7% LOD, and 20.3% sensitivity and 98.8% specificity at 10% LOD, respectively.

CONCLUSIONS

Our results support additional studies incorporating INK4A methylation testing of ccfDNA to further validate the diagnostic, predictive, and prognostic characteristics of this biomarker in HCC patients. The knowledge of the existence of epi-alleles should help improve assay design to maximize detection.

Visualizing Europe's demographic scars with coplots and contour plots

We present two enhancements to existing methods for visualizing vital statistics data. Data from the Human Mortality Database were used and vital statistics from England and Wales are used for illustration. The simpler of these methods involves coplotting mean age of death with its variance, and the more complex of these methods is to present data as a contour plot. The coplot method shows the effect of the 20th century's epidemiological transitions. The contour plot method allows more complex and subtle age, period and cohort effects to be seen. The contour plot shows the effects of broad improvements in public health over the 20th century, including vast reductions in rates of childhood mortality, reduced baseline mortality risks during adulthood and the postponement of higher mortality risks to older ages. They also show the effects of the two world wars and the 1918 influenza pandemic on men of fighting age, women and children. The contour plots also show a cohort effect for people born around 1918, suggesting a possible epigenetic effect of parental exposure to the pandemic which shortened the cohort's lifespan and which has so far received little attention. Although this article focuses on data from England and Wales, the associated online appendices contain equivalent visualizations for almost 50 series of data available on the Human Mortality Database. We expect that further analyses of these visualizations will reveal further insights into global public health.

Pathophysiology of tobacco smoke exposure: recent insights from comparative and redox proteomics

First-hand and second-hand tobacco smoke are causally linked to a huge number of deaths and are responsible for a broad spectrum of pathologies such as cancer, cardiovascular, respiratory, and eye diseases as well as adverse effects on female reproductive function. Cigarette smoke is a complex mixture of thousands of different chemical species, which exert their negative effects on macromolecules and biochemical pathways, both directly and indirectly. Many compounds can act as oxidants, pro-inflammatory agents, carcinogens, or a combination of these. The redox behavior of cigarette smoke has many implications for smoke related diseases. Reactive oxygen and nitrogen species (both radicals and non-radicals), reactive carbonyl compounds, and other species may induce oxidative damage in almost all the biological macromolecules, compromising their structure and/or function. Different quantitative and redox proteomic approaches have been applied in vitro and in vivo to evaluate, respectively, changes in protein expression and specific oxidative protein modifications induced by exposure to cigarette smoke and are overviewed in this review. Many gel-based and gel-free proteomic techniques have already been used successfully to obtain clues about smoke effects on different proteins in cell cultures, animal models, and humans. The further implementation with other sensitive screening techniques could be useful to integrate the comprehension of cigarette smoke effects on human health. In particular, the redox proteomic approach may also help identify biomarkers of exposure to tobacco smoke useful for preventing these effects or potentially predictive of the onset and/or progression of smoking-induced diseases as well as potential targets for therapeutic strategies.

Alcohol and the methylome: design and analysis considerations for research using human samples

BACKGROUND

A growing number of studies in human samples have sought to determine whether chronic alcohol use and alcohol use disorders (AUDs) may be associated with epigenetic factors, such as DNA methylation. We review the extant literature in light of some of the challenges that currently affect the design and interpretation of epigenetic research in human samples.

METHOD

A literature search was used to identify studies that have examined DNA methylation in relation to alcohol use or AUDs in human samples (through July 2013). A total of 22 studies were identified.

RESULTS

Associations with quantitative or diagnostic phenotypes of alcohol use or AUDs have been reported for several genes. However, all studies to date have relied on relatively small samples and cross-sectional study designs. Additionally, attempts to replicate results have been rare. More generally, research progress is hampered by several issues, including limitations of the technologies used to assess DNA methylation, tissue- and cell-specificity of methylation patterns, the difficulties of relating observed methylation differences at a given locus to a functional effect, and limited knowledge about the molecular mechanisms underlying the effects of alcohol on DNA methylation.

CONCLUSIONS

Although we share the optimism that epigenetics may lead to new insights into the etiology and pathophysiology of AUDs, the methodological and scientific challenges associated with conducting methylomic research in human samples need to be carefully considered when designing and evaluating such studies.

Distinct loci in the CHRNA5/CHRNA3/CHRNB4 gene cluster are associated with onset of regular smoking

Neuronal nicotinic acetylcholine receptor (nAChR) genes (CHRNA5/CHRNA3/CHRNB4) have been reproducibly associated with nicotine dependence, smoking behaviors, and lung cancer risk. Of the few reports that have focused on early smoking behaviors, association results have been mixed. This meta-analysis examines early smoking phenotypes and SNPs in the gene cluster to determine: (1) whether the most robust association signal in this region (rs16969968) for other smoking behaviors is also associated with early behaviors, and/or (2) if additional statistically independent signals are important in early smoking. We focused on two phenotypes: age of tobacco initiation (AOI) and age of first regular tobacco use (AOS). This study included 56,034 subjects (41 groups) spanning nine countries and evaluated five SNPs including rs1948, rs16969968, rs578776, rs588765, and rs684513. Each dataset was analyzed using a centrally generated script. Meta-analyses were conducted from summary statistics. AOS yielded significant associations with SNPs rs578776 (beta = 0.02, P = 0.004), rs1948 (beta = 0.023, P = 0.018), and rs684513 (beta = 0.032, P = 0.017), indicating protective effects. There were no significant associations for the AOI phenotype. Importantly, rs16969968, the most replicated signal in this region for nicotine dependence, cigarettes per day, and cotinine levels, was not associated with AOI (P = 0.59) or AOS (P = 0.92). These results provide important insight into the complexity of smoking behavior phenotypes, and suggest that association signals in the CHRNA5/A3/B4 gene cluster affecting early smoking behaviors may be different from those affecting the mature nicotine dependence phenotype.

Cigarette smoke induces epithelial to mesenchymal transition and increases the metastatic ability of breast cancer cells

Background

Recent epidemiological studies demonstrate that both active and involuntary exposure to tobacco smoke increase the risk of breast cancer. Little is known, however, about the molecular mechanisms by which continuous, long term exposure to tobacco smoke contributes to breast carcinogenesis because most previous studies have focused on short term treatment models. In this work we have set out to investigate the progressive transforming effects of tobacco smoke on non-tumorigenic mammary epithelial cells and breast cancer cells using in vitro and in vivo models of chronic cigarette smoke exposure.

Results

We show that both non-tumorigenic (MCF 10A, MCF-12A) and tumorigenic (MCF7) breast epithelial cells exposed to cigarette smoke acquire mesenchymal properties such as fibroblastoid morphology, increased anchorage-independent growth, and increased motility and invasiveness. Moreover, transplantation experiments in mice demonstrate that treatment with cigarette smoke extract renders MCF 10A cells more capable to survive and colonize the mammary ducts and MCF7 cells more prone to metastasize from a subcutaneous injection site, independent of cigarette smoke effects on the host and stromal environment. The extent of transformation and the resulting phenotype thus appear to be associated with the differentiation state of the cells at the time of exposure. Analysis by flow cytometry showed that treatment with CSE leads to the emergence of a CD44^hi/CD24^low population in MCF 10A cells and of CD44⁺ and CD49f ⁺ MCF7 cells, indicating that cigarette smoke causes the emergence of cell populations bearing markers of self-renewing stem-like cells. The phenotypical alterations induced by cigarette smoke are accompanied by numerous changes in gene expression that are associated with epithelial to mesenchymal transition and tumorigenesis.

Conclusions

Our results indicate that exposure to cigarette smoke leads to a more aggressive and transformed phenotype in human mammary epithelial cells and that the differentiation state of the cell at the time of exposure may be an important determinant in the phenotype of the final transformed state.

Benzo[a]pyrene decreases global and gene specific DNA methylation during zebrafish development

DNA methylation is important for gene regulation and is vulnerable to early-life exposure to environmental contaminants. We found that direct waterborne benzo[a]pyrene (BaP) exposure at 24μg/L from 2.5 to 96hpf to zebrafish embryos significantly decreased global cytosine methylation by 44.8% and promoter methylation in vasa by 17%. Consequently, vasa expression was significantly increased by 33%. In contrast, BaP exposure at environmentally relevant concentrations did not change CpG island methylation or gene expression in cancer genes such as ras-association domain family member 1 (rassf1), telomerase reverse transcriptase (tert), c-jun, and c-myca. Similarly, BaP did not change gene expression of DNA methyltransferase 1 (dnmt1) and glycine N-methyltransferase (gnmt). While total DNMT activity was not affected, GNMT enzyme activity was moderately increased. In summary, BaP is an epigenetic modifier for global and gene specific DNA methylation status in zebrafish larvae.

Epigenetics and personalized medicine: prospects and ethical issues

As scientific knowledge about gene-environment interactions and the role of epigenetic factors in gene expression grows, new possibilities for personalized medicine may be opened up. In particular, the associations that have been demonstrated between epigenetic markers and certain diseases are an exciting development for personalized medicine. These advances also create new ethical challenges, regarding causal and moral responsibility, due to unique characteristics of how epigenetic effects regulate gene expression, are established and may change over the course of a person's life. This article examines the ethical implications of integrating epigenetic knowledge into personalized medicine.

Chronic opioid use is associated with increased DNA methylation correlating with increased clinical pain

Environmentally caused changes in chromosomes that do not alter the DNA sequence but cause phenotypic changes by altering gene transcription are summarized as epigenetics. A major epigenetic mechanism is methylation or demethylation at CpG-rich DNA islands. DNA methylation triggered by drugs has largely unexplored therapeutic consequences. Here we report increased methylation at a CpG rich island in the OPRM1 gene coding for μ-opioid receptors and at a global methylation site (LINE-1) in leukocytes of methadone-substituted former opiate addicts compared with matched healthy controls. Higher DNA methylation associated with chronic opioid exposure was reproduced in an independent cohort of opioid-treated as compared to non-opioid-treated pain patients. This suggests that opioids may stimulate DNA methylation. The OPRM1 methylation had no immediate effect on μ-opioid receptor transcription and was not associated with opioid dosing requirements. However, the global DNA methylation at LINE-1 was significantly correlated with increased chronic pain. This suggests inhibitory effects on the transcription of still unspecified nocifensive gene products. It further implies that opioids may be causally associated with increased genome-wide DNA methylation, although currently there is no direct evidence of this. This has phenotypic consequences for pain and may provide a new, epigenetics-associated mechanism of opioid-induced hyperalgesia. The results indicate a potential influence of opioid analgesics on the patients' epigenome. They emphasize the need for reliable and cost-effective screening tools and may imply that high-throughput screening for lead compounds in artificial expression systems may not provide the best tools for identifying new pain medications.

Epigenetic changes in patients with multiple sclerosis

Epigenetic changes influence gene expression without altering the DNA sequence. DNA methylation, histone modification and microRNA-associated post-transcriptional gene silencing are three key epigenetic mechanisms. Multiple sclerosis (MS) is a disease of the CNS with both inflammatory and neurodegenerative features. Although studies on epigenetic changes in MS only began in the past decade, a growing body of literature suggests that epigenetic changes may be involved in the development of MS, possibly by mediating the effects of environmental risk factors, such as smoking, vitamin D deficiency and Epstein-Barr virus infection. Such studies are also beginning to deliver important insights into the pathophysiology of MS. For example, inflammation and demyelination in relapsing-remitting MS may be related to the increased differentiation of T cells toward a T-helper 17 phenotype, which is an important epigenetically regulated pathophysiological mechanism. In progressive MS, other epigenetically regulated mechanisms, such as increased histone acetylation and citrullination of myelin basic protein, might exacerbate the disease course. In this Review, we summarize current knowledge on the role of epigenetic changes in the pathophysiology of MS.

Epigenetics and miRNAs in the diagnosis and treatment of multiple sclerosis

The risk of developing multiple sclerosis (MS) depends on both genetic and environmental factors. Although the genetic susceptibility to MS has been investigated in great detail, reports describing epigenetic changes in the context of MS have only recently appeared. Epigenetic changes to DNA influence gene expression without altering the underlying DNA sequence. DNA methylation, histone modification, and miRNA-associated silencing are the three most important epigenetic mechanisms that influence gene expression. In this review, we summarize recent studies investigating epigenetic changes and miRNA as biomarkers for diagnosing MS and predicting disease course or treatment response. We also discuss how the current studies address important clinical questions and how future studies could be designed to best inform clinical practice.

Aberrant DNA methylation in cervical carcinogenesis

Persistent infection with high-risk types of human papillomavirus(HPV) is known to cause cervical cancer; however, additional genetic and epigenetic alterations are required for progression from precancerous disease to invasive cancer. DNA methylation is an early and frequent molecular alteration in cervical carcinogenesis. In this review, we summarize DNA methylation within the HPV genome and human genome and identify its clinical implications. Methylation of the HPV long control region (LCR) and L1 gene is common during cervical carcinogenesis and increases with the severity of the cervical neoplasm. The L1 gene of HPV16 and HPV18 is consistently hypermethylated in invasive cervical cancers and can potentially be used as a clinical marker of cancer progression. Moreover, promoters of tumor suppressor genes (TSGs) involved in many cellular pathways are methylated in cervical precursors and invasive cancers. Some are associated with squamous cell carcinomas, and others are associated with adenocarcinomas. Identification of methylated TSGs in Pap smear could be an adjuvant test in cervical cancer screening for triage of women with high-risk HPV, atypical squamous cells of undetermined significance, or low grade squamous intraepithelial lesion (LSIL). However, consistent panels must be validated for this approach to be translated to the clinic. Furthermore, reversion of methylated TSGs using demethylating drugs may be an alternative anticancer treatment, but demethylating drugs without toxic carcinogenic and mutagenic properties must be identified and validated.

Susceptibility to cervical cancer: an overview

Cervical cancer is the second most common cancer in females worldwide. It is well-established that Human Papillomavirus (HPV) infections play a critical role in the development of cervical cancer. However, a large number of women infected with oncogenic HPV types will never develop cervical cancer. Thus, there are several external environment and genetic factors involved in the progression of a precancerous lesion to invasive cancer. In this review article, we addressed possible susceptible phenotypes to cervical cancer, focusing on host genome and HPV DNA variability, multiple HPV infections, co-infection with other agents, circulating HPV DNA and lifestyle.

Discrimination of 'driver' and 'passenger' HPV in tonsillar carcinomas by the polymerase chain reaction, chromogenic in situ hybridization, and p16(INK4a) immunohistochemistry

Human papillomavirus (HPV) positive tonsillar squamous cell carcinoma (TSCC) is associated with a favorable clinical outcome. However, the HPV detected in a given tumor may be causal (driver HPV) or an incidental bystander (passenger HPV). There is a need to discriminate these forms of HPV in TSCCs to understand their impact on HPV as a biomarker for use in TSCC patient management. This study has compared the polymerase chain reaction (PCR), chromogenic in situ hybridization (CISH), and p16(INK4a) immunohistochemistry in the assessment of HPV status in TSCC. Archival specimens of TSCC from thirty patients were investigated. HPV was detected by PCR in 25/30 (83.3%) tumors; HPV16 (70.0%) and HPV52 (6.7%) were the most common types. HPV was corroborated by CISH in 22/25 (88.0%) specimens; integrated HPV was implicated by the presence of punctate signals in each of these cases. p16(INK4a) staining was found in 20/22 (90.9%) HPV PCR positive samples; two PCR/CISH HPV positive cases were p16(INK4a) negative and two HPV negative samples were p16(INK4a) positive. These data suggest that a minority of HPV positive TSCCs are positive for passenger HPV and that two or more assays may be required for diagnosing driver HPV status. Further studies are required to exam whether oropharyngeal tumors positive for passenger HPV have a less favorable prognosis than tumors that are driver HPV positive. The clinical significance of TSCCs that test HPV negative/p16(INK4a) positive, PCR and CISH HPV positive/p16 (INK4a) negative, or PCR HPV positive/p16 (INK4a) and CISH negative, also requires further investigation.