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Background Mucous membrane pemphigoid (MMP) is an uncommon bullous disease typically involving the oral cavity. The most commonly used laboratory test for the diagnosis of MMP is direct immunofluorescence (DIF) on fresh perilesional tissue; however, the sensitivity of this test may be hampered by technical difficulties. Immune-serological investigations can also be employed to render a diagnosis. The purpose of this paper was to present an evaluation of diagnostic testing for MMP within an Oral Medicine Unit in UK. Methods A retrospective analysis of the medical records was undertaken for patients who had undergone biopsy and DIF testing from January 2016 to December 2018. Parameters analysed included clinical presentation, histopathological features, DIF, salt-split skin indirect immunofluorescence, ELISA anti-BP180 and BP 230 and HLA-DQB1*03:01 findings. Results Thirty patients (23 females and 7 males, mean age 66.8 years old) were diagnosed with MMP through a combination of histopathology and serological testing. Sixteen patients (53%) were DIF positive, whereas in 14 (47%), MMP diagnosis was achieved using immune-serologic tests. HLA DQB1*03:01 status was undertaken in 15 DIF-positive and 12 DIF-negative patients, and HLA DQB1*03:01 was found in 73% and 58% of the cases, respectively. Conclusions This service evaluation has shown that when DIF is informative, it remains the gold standard technique for diagnosis of MMP. However, we have also highlighted the value of serological testing for increasing diagnostic yield for patients with suspected MMP and the potential for HLA DQB1*03:01 as an adjunctive test for the evaluation of MMP.

High-quality histopathology is essential for the success of clinical trials. Histopathologists have a detailed understanding of tumour biology and mechanisms of disease, as well as practical knowledge of optimal tissue handling and logistical service requirements for study delivery, such as biomarker evaluation, tissue acquisition and turnaround times. As such, histopathologist input is essential throughout every stage of research and clinical trials, from concept development and study design to trial delivery, analysis and dissemination of results. Patient recruitment to trials takes place among all healthcare settings, meaning that histopathologists make an invaluable contribution to clinical trials as part of their routine day-to-day work that often goes unrecognised. More complex evaluation of surgical specimens in the neoadjuvant setting and ever-expanding minimum data sets add to the workload of every histopathologist, not just academic pathologists in tertiary centres. This is occurring against a backdrop of increasing workload pressures and a worldwide shortage of histopathologists and biomedical scientists. Providing essential histopathology support for trials at grassroots level requires funding for adequate resources including histopathologist time, education and training, biomedical scientist and administrative support and greater recognition of the contribution made by histopathology. This paper will discuss the many ways in which histopathologists are involved in clinical trials and the challenges faced in meeting the additional demands posed by trial participation and potential ways to address this, with a special emphasis on the UK model and the Cellular-Molecular Pathology Initiative (CM-Path).

Trans-oral robotic surgery (TORS) was approved by the FDA in 2009 and over the past decade head and neck surgeons have adopted the technology for the benefit of their patients. Whilst the surgical methods have evolved, there has been little consideration about the pathological assessment of the specimens and a lack of understanding around the oncological principles that underpin minimally invasive surgical techniques in the head and neck region. This article will highlight the issues encountered during the reporting of TORS specimens. The challenges include identifying anatomical boundaries, block selection, assessment of resection margins, the use of intra-operative frozen sections, the assessment of tongue base mucosectomies for patients with head and neck cancer of unknown primary, and TORS for recurrent disease. The article will conclude with emerging innovations, including i-Knife, narrow band imaging and the potential of step serial sections to identify sub-clinical HPV-related oropharyngeal squamous cell carcinomas.

Tetelan ikan tuna merupakan salah satu hasil samping dari produksi tuna loin, memiliki nilai ekonomisrendah dan dapat diolah menjadi berbagai produk diversifikasi salah satunya adalah ikan kering blok. Ikankering blok dibuat dengan memberikan garam dan asap cair pada tetelan dan kemudian dikeringkan.Tujuan penelitian ini adalah menentukan efek penambahan asap cair terhadap profil asam lemak dari ikantuna kering blok. Perlakuan yang digunakan adalah penambahan asap cair (2%) dan tanpa penambahanasap cair. Produk ikan tuna kering blok mengandung asam lemak jenuh (SFA) 12 jenis, asam lemak takjenuh tunggal (MUFA) 6 jenis, dan asam lemak tak jenuh jamak (PUFA) 9 jenis. Jumlah asam lemak jenuh(SFA) pada ikan tuna kering blok tanpa dan dengan penambahan asap cair adalah 19,94% dan 21,29%, asamlemak tak jenuh tunggal (MUFA) adalah 9,35% dan 11,77% dan asam lemak tak jenuh jamak (PUFA) adalah14,45% dan 16,04%.

The 1000 Genomes Project (TGP) is a foundational resource that serves the biomedical community as a standard reference cohort for human genetic variation. There are now seven public versions of these genomes. The TGP Consortium produced the first by mapping its final data release against human reference sequence GRCh37, then "lifted over" these genomes to the improved reference sequence (GRCh38) when it was released, and remapped the original data to GRCh38 with two similar pipelines. As best-practice quality validation, the pipelines that generated these versions were benchmarked against the Genome In A Bottle Consortium's "platinum quality" genome (NA12878). The New York Genome Center recently released the results of independently resequencing the cohort at greater depth (30×), a phased version informed by the inclusion of related individuals, and independently remapped the original variant calls to GRCh38. We performed a cross-comparison evaluation of all seven versions using genome fingerprinting, which supports ultrafast genome comparison even across reference versions. We noted multiple issues, including discrepancies in cohort membership, disagreement on the overall level of variation, evidence of substandard pipeline performance on specific genomes and in specific regions of the genome, cryptic relationships between individuals, inconsistent phasing, and annotation distortions caused by the history of the reference genome itself. We therefore recommend global quality assessment by rapid genome comparisons, alongside benchmarking as part of best-practice quality assessment of large genome datasets. Our observations also help inform the decision of which version to use, to support analyses by individual researchers.

This study reports oncological outcomes of transoral robotic surgery (TORS) and neck dissection (ND) alone for head and neck squamous cell carcinoma (HNSCC) and aims to analyse the influence of resection margins on local recurrence rates.Fifty-one patients treated with curative intent for HNSCC, with TORS and ND alone between 2013 and 2019 at two tertiary centres were included in this observational multi-centre prospective cohort study. Oncological outcomes are reported on 47 patients for whom the aim was to treat with TORS and ND alone; this excluded four patients who were recommended adjuvant radiotherapy based on resective pathology but did not receive treatment. Local control is the primary endpoint; disease specific, progression free and overall survival are secondary outcomes.With a median follow up of 43 months, estimated outcomes at 3 years (n = 47) were as follows: local control 92%, progression free survival 80%, disease specific survival 94%, and overall survival 84%. Presence of a positive margin on the main specimen was the only statistically significant predictor of local recurrence on univariate Cox regression analysis. Time dependent receiver operating characteristic curve identified margins of 1.1 mm as a threshold for local control, with area under the curve 0.788 (95% CI 0.616-0.960), indicating a good classifier.This is the first UK surgery alone series reporting mature oncological outcomes following TORS and ND. Positive margins on the resected specimen are the strongest predictor of local recurrence, with conventional definitions of "close margins" having no impact.

Introduction Clinical management of oral potentially malignant disorders relies on accurate histopathological assessment of the presence and grade of oral epithelial dysplasia. Whilst adjunctive laboratory tests have provided useful prognostic information, none are in widespread clinical use. This study was performed to assess the clinical utility of two contemporary oral epithelial dysplasia grading systems. Methods Patients were identified from a clinical database. Oral epithelial dysplasia grading was performed by three oral and maxillofacial pathologists blinded to clinical outcome using the WHO 2017 system and a binary classification. The primary outcome measure was the development of oral squamous cell carcinoma, termed 'malignant transformation'. Results 131 cases satisfied the inclusion criteria, of which 23 underwent malignant transformation. There was substantial inter-rater agreement between the study pathologists for both grading systems, measured using kappa statistics (κ = 0.753-0.784). However, there was only moderate agreement between the consensus WHO 2017 dysplasia grade for the study against the original grade assigned by a pool of six pathologists in the context of the clinical service (κ = 0.491). Higher grade categories correlated with an increased risk of developing cancer using both grading systems. Conclusion This study demonstrates that the WHO 2017 and binary grading systems are reproducible between calibrated pathologists and that consensus reporting is likely to improve the consistency of grading. The WHO and binary systems were prognostically comparable. We recommend that institutions implement consensus oral epithelial dysplasia grading and prospectively audit the effectiveness of risk stratifying their patients with oral potentially malignant disorders. (249 words).

Longitudinal multi-omics measurements are highly valuable in studying heterogeneity in health and disease phenotypes. For thousands of people, we have collected longitudinal multi-omics data. To analyze, interpret and visualize this extremely high-dimensional data, we use the Pareto Task Inference (ParTI) method. We find that the clinical labs data fall within a tetrahedron. We then use all other data types to characterize the four archetypes. We find that the tetrahedron comprises three wellness states, defining a wellness triangular plane, and one aberrant health state that captures aspects of commonality in movement away from wellness. We reveal the tradeoffs that shape the data and their hierarchy, and use longitudinal data to observe individual trajectories. We then demonstrate how the movement on the tetrahedron can be used for detecting unexpected trajectories, which might indicate transitions from health to disease and reveal abnormal conditions, even when all individual blood measurements are in the norm., Longitudinal multi-omics measurements are highly valuable in studying heterogeneity in health and disease phenotypes. Here, the authors apply Pareto Task Inference to analyze the clinical lab tests of 3094 individuals and find three wellness states, and one aberrant health state defining this cohort.

Aggregation and accumulation of amyloid-β (Aβ) is a defining feature of Alzheimer’s disease (AD) pathology. To study microglial responses to Aβ, we applied exogenous Aβ peptide, in either oligomeric or fibrillar conformation, to primary mouse microglial cultures and evaluated system level transcriptional changes and then compared these to transcriptomic changes in the brains of CRND8 APP mice. We find that primary microglial cultures have rapid and massive transcriptional change to in response to Aβ. Transcriptomic responses to oligomeric or fibrillar Aβ in primary microglia, though partially overlapping, are distinct and are not recapitulated in vivo where Aβ progressively accumulates. Furthermore, though classic immune mediators show massive transcriptional changes in the primary microglial cultures, these changes are not observed in the mouse model. Together, these data extend previous studies which demonstrate that microglia responses ex vivo are poor proxies for in vivo responses. Finally, these data demonstrate the potential utility of using microglia as biosensors of different aggregate conformation, as the transcriptional responses to oligomeric and fibrillar Aβ can be distinguished.

Oropharyngeal squamous cell carcinoma (OPSCC) is an increasing world health problem with a more favorable prognosis for patients with human papillomavirus (HPV)-positive tumors compared to those with HPV-negative OPSCC. How HPV confers a less aggressive phenotype, however, remains undefined. We demonstrated that HPV-positive OPSCC cells display reduced macroautophagy/autophagy activity, mediated by the ability of HPV-E7 to interact with AMBRA1, to compete with its binding to BECN1 and to trigger its calpain-dependent degradation. Moreover, we have shown that AMBRA1 downregulation and pharmacological inhibition of autophagy sensitized HPV-negative OPSCC cells to the cytotoxic effects of cisplatin. Importantly, semi-quantitative immunohistochemical analysis in primary OPSCCs confirmed that AMBRA1 expression is reduced in HPV-positive compared to HPV-negative tumors. Collectively, these data identify AMBRA1 as a key target of HPV to impair autophagy and propose the targeting of autophagy as a viable therapeutic strategy to improve treatment response of HPV-negative OPSCC. Abbreviations: AMBRA1: autophagy and beclin 1 regulator 1; CDDP: cisplatin (CDDP); FFPE: formalin-fixed paraffin-embedded (FFPE); HNC: head and neck cancers (HNC); HPV: human papillomavirus (HPV); hrHPV: high risk human papillomavirus (hrHPV); OCSCC: oral cavity squamous carcinomas (OCSSC); OPSCC: oropharyngeal squamous cell carcinoma (OPSCC); OS: overall survival (OS); qPCR: quantitative polymerase chain reaction; RB1: RB transcriptional corepressor 1; ROC: receiver operating characteristic curve (ROC).

Single molecule biomarkers are used extensively in head and neck pathology for diagnosis and increasingly for prognosis. Companion markers for therapy such as PDL-1 and NTRK are now finding applications in head and neck cancer care. Immunohistochemistry is an attractive option because of its rapid turnaround time and convenience but molecular testing is often necessary for validation. This chapter will focus on some selected biomarkers being developed for translational purposes. Adoptive T cell therapies are being trialled for head and neck cancer and have limited efficacy currently. Identification of biomarkers as targets is an attractive option for development, and the use of molecular sequencing to identify individual neo-antigens is a promising way forward for precision medicine approaches including adoptive T cell therapies.

Although several oropharyngeal cancer (OPC) susceptibility loci have been identified, most previous studies lacked detailed information on human papillomavirus (HPV) status. We conduct a genome-wide analysis by HPV16 serology status in 4,002 oral cancer cases (OPC and oral cavity cancer (OCC)) and 5,256 controls. We detect four susceptibility loci pointing to a distinct genetic predisposition by HPV status. Our most notable finding in the HLA region, that is now confirmed to be specific of HPV(+)OPC risk, reveal two independent loci with strong protective effects, one refining the previously reported HLA class II haplotype association. Antibody levels against HPV16 viral proteins strongly implicate the protective HLA variants as major determinants of humoral response against L1 capsid protein or E6 oncoprotein suggesting a natural immune response against HPV(+)OPC promoted by HLA variants. This indicates that therapeutic vaccines that target E6 and attenuate viral response after established HPV infections might protect against HPV(+)OPC., Genetic susceptibility loci for oropharyngeal cancer have been reported but these studies have not always examined human papillomavirus (HPV) status. Here, the authors perform genome-wide analysis taking into account HPV16 serology status and report two independent loci in the HLA region, suggesting the protective role of HLA variants against HPV infection.

Introduction Passive immunotherapies targeting Aβ continue to be evaluated as Alzheimer’s disease (AD) therapeutics, but there remains debate over the mechanisms by which these immunotherapies work. Besides the amount of preexisting Aβ deposition and the type of deposit (compact or diffuse), there is little data concerning what factors, independent of those intrinsic to the antibody, might influence efficacy. Here we (i) explored how constitutive priming of the underlying innate activation states by Il10 and Il6 might influence passive Aβ immunotherapy and (ii) evaluated transcriptomic data generated in the AMP-AD initiative to inform how these two cytokines and their receptors’ mRNA levels are altered in human AD and an APP mouse model. Methods rAAV2/1 encoding EGFP, Il6 or Il10 were delivered by somatic brain transgenesis to neonatal (P0) TgCRND8 APP mice. Then, at 2 months of age, the mice were treated bi-weekly with a high-affinity anti-Aβ1–16 mAb5 monoclonal antibody or control mouse IgG until 6 months of age. rAAV mediated transgene expression, amyloid accumulation, Aβ levels and gliosis were assessed. Extensive transcriptomic data was used to evaluate the mRNA expression levels of IL10 and IL6 and their receptors in the postmortem human AD temporal cortex and in the brains of TgCRND8 mice, the later at multiple ages. Results Priming TgCRND8 mice with Il10 increases Aβ loads and blocks efficacy of subsequent mAb5 passive immunotherapy, whereas priming with Il6 priming reduces Aβ loads by itself and subsequent Aβ immunotherapy shows only a slightly additive effect. Transcriptomic data shows that (i) there are significant increases in the mRNA levels of Il6 and Il10 receptors in the TgCRND8 mouse model and temporal cortex of humans with AD and (ii) there is a great deal of variance in individual mouse brain and the human temporal cortex of these interleukins and their receptors. Conclusions The underlying immune activation state can markedly affect the efficacy of passive Aβ immunotherapy. These results have important implications for ongoing human AD immunotherapy trials, as they indicate that underlying immune activation states within the brain, which may be highly variable, may influence the ability for passive immunotherapy to alter Aβ deposition.

BACKGROUND: This study was undertaken to develop and validate a gene expression signature that characterises oral potentially malignant disorders (OPMD) with a high risk of undergoing malignant transformation. METHODS: Patients with oral epithelial dysplasia at one hospital were selected as the ‘training set’ (n = 56) whilst those at another hospital were selected for the ‘test set’ (n = 66). RNA was extracted from formalin-fixed paraffin-embedded (FFPE) diagnostic biopsies and analysed using the NanoString nCounter platform. A targeted panel of 42 genes selected on their association with oral carcinogenesis was used to develop a prognostic gene signature. Following data normalisation, uni- and multivariable analysis, as well as prognostic modelling, were employed to develop and validate the gene signature. RESULTS: A prognostic classifier composed of 11 genes was developed using the training set. The multivariable prognostic model was used to predict patient risk scores in the test set. The prognostic gene signature was an independent predictor of malignant transformation when assessed in the test set, with the high-risk group showing worse prognosis [Hazard ratio = 12.65, p = 0.0003]. CONCLUSIONS: This study demonstrates proof of principle that RNA extracted from FFPE diagnostic biopsies of OPMD, when analysed on the NanoString nCounter platform, can be used to generate a molecular classifier that stratifies the risk of malignant transformation with promising clinical utility.

Human Papilloma Virus (HPV) is a major risk factor for the development of oropharyngeal cancer. Automatic detection of HPV in digitized pathology tissues using in situ hybridisation (ISH) is a difficult task due to the variability and complexity of staining patterns as well as the presence of imaging and staining artefacts. This paper proposes an intelligent image analysis framework to determine HPV status in digitized samples of oropharyngeal cancer tissue micro-arrays (TMA). The proposed pipeline mixes handcrafted feature extraction with a deep learning for epithelial region segmentation as a preliminary step. We apply a deep central attention learning technique to segment epithelial regions and within those assess the presence of regions representing ISH products. We then extract relevant morphological measurements from those regions which are then input into a supervised learning model for the identification of HPV status. The performance of the proposed method has been evaluated on 2009 TMA images of oropharyngeal carcinoma tissues captured with a ×20 objective. The experimental results show that our technique provides around 91% classification accuracy in detecting HPV status when compared with the histopatholgist gold standard. We also tested the performance of end-to-end deep learning classification methods to assess HPV status by learning directly from the original ISH processed images, rather than from the handcrafted features extracted from the segmented images. We examined the performance of sequential convolutional neural networks (CNN) architectures including three popular image recognition networks (VGG-16, ResNet and Inception V3) in their pre-trained and trained from scratch versions, however their highest classification accuracy was inferior (78%) to the hybrid pipeline presented here.

Background: Oral potentially malignant disorders are a clinical conundrum as there are no reliable methods to predict their behaviour. We combine conventional oral epithelial dysplasia grading with DNA ploidy analysis to examine the validity of this approach to risk assessment in a cohort of patients with known clinical outcomes. Methods: Sections from diagnostic biopsies were assessed for oral epithelial dysplasia using the WHO grading system, and DNA ploidy analysis was performed using established methods. Patients reviewed for a minimum of 5 years who did not develop oral squamous cell carcinoma were classified as “non-transforming” cases. Patients that developed oral squamous cell carcinoma ≥ 6 months after the initial diagnostic biopsy were classified as having “malignant transformation.” Results: Ninety cases were included in the study. Seventy cases yielded informative DNA ploidy results. Of these 70 cases, 31 progressed to cancer. Oral epithelial dysplasia grading and DNA ploidy status were both significantly associated with clinical outcome (P < 0.05). Severe dysplasia had a hazard ratio of 3.50 (CI: 1.46, 8.45; P = 0.005) compared to cases with mild dysplasia. Aneuploidy had a hazard ratio of 2.09 (CI: 1.01, 4.32; P = 0.046) compared to cases with a diploid/tetraploid status. Receiver operating characteristic analysis gave an area under the curve of 0.617 for DNA ploidy status and 0.688 when DNA ploidy status was combined with dysplasia grading. Conclusion: Our findings suggest that combining dysplasia grading with DNA ploidy status has clinical utility which could be used to develop novel management algorithms.

Typically, HPV-related cancers are sexually transmitted, however, the natural history of HPV-related oropharyngeal squamous cell carcinoma (OPSCC) is unclear. HPV16 transmission has been reported previously between five couples with OPSCC. We report the clinico-pathological features of a further four couples with HPV-related OPSCC and compare them with the published cases.We identified four couples in long-term heterosexual relationships that all had HPV-related OPSCC. The couples were treated at three UK hospitals and presented between 2009 and 2015. HPV tests included p16 immunohistochemistry, high-risk HPV DNA in-situ hybridisation and Roche Cobas HPV test. DNA sequencing was used to determine the HPV variant.The four couples represented2% of patients with HPV-related OPSCC at the three contributing hospitals (8 of 457 consecutive patients). The couples' tumours all contained HPV16. The mean age was 63 years old (range 52-72 years). The interval between the index cancer and the partner's cancer was 16, 24, 26 and 64 months respectively. The majority of patients had Stage I disease (UICC TNM8). Six of eight patients are disease free, one patient is alive with disease and there was one death from loco-regional recurrence.This report highlights the occurrence of HPV-related OPSCC in heterosexual couples and raises the possibility of transmission of HPV16. Despite increasing prevalence of HPV-related OPSCC and increased awareness of the disease, there is a paucity of couples with the disease, suggesting either under-reporting or that the development of OPSCC following HPV transmission between couples is a rare event.

Diagnostic tonsillectomy is rarely an oncologic operation owing to close or positive margins. The standard of care is for further treatment to the primary site, typically with adjuvant radiotherapy. 14 patients with close or positive margins following a diagnostic tonsillectomy underwent transoral robotic surgery (TORS) and lateral oropharyngectomy; five patients with the longest follow-up had their excision specimens examined with a step serial sectioning technique (SSS). Conventional histopathological examination of the TORS resection specimens did not demonstrate residual carcinoma in 13 patients, confirmed by examination using SSS in 5 patients. There were no post-operative complications or long-term functional deficit. Seven patients received surgery alone with 100% overall and disease specific survival, respectively (median follow-up 27.5 months; range 5.2–50.4). This prospective study suggests that TORS lateral oropharyngectomy alone is an oncologically safe treatment when close or positive margins are identified on diagnostic tonsillectomy in HPV-positive SCC.

Head and neck cancer (HNC) is a preventable malignancy that continues to cause substantial morbidity and mortality worldwide. Using data from the ARCAGE and Rome studies, we investigated the main predictors of survival after larynx, hypopharynx and oral cavity (OC) cancers. We used the Kaplan-Meier method to estimate overall survival, and Cox proportional models to examine the relationship between survival and sociodemographic and clinical characteristics. 604 larynx, 146 hypopharynx and 460 OC cancer cases were included in this study. Over a median follow-up time of 4.6 years, nearly 50% (n = 586) of patients died. Five-year survival was 65% for larynx, 55% for OC and 35% for hypopharynx cancers. In a multivariable analysis, we observed an increased mortality risk among older (≥71 years) versus younger (≤50 years) patients with larynx/hypopharynx combined (LH) and OC cancers [HR = 1.61, 95% CI 1.09-2.38 (LH) and HR = 2.12, 95% CI 1.35-3.33 (OC)], current versus never smokers [HR = 2.67, 95% CI 1.40-5.08 (LH) and HR = 2.16, 95% CI 1.32-3.54 (OC)] and advanced versus early stage disease at diagnosis [IV versus I, HR = 2.60, 95% CI 1.78-3.79 (LH) and HR = 3.17, 95% CI 2.05-4.89 (OC)]. Survival was not associated with sex, alcohol consumption, education, oral health, p16 expression, presence of HPV infection or body mass index 2 years before cancer diagnosis. Despite advances in diagnosis and therapeutic modalities, survival after HNC remains low in Europe. In addition to the recognized prognostic effect of stage at diagnosis, smoking history and older age at diagnosis are important prognostic indicators for HNC.

Exogenous amyloid beta peptides cause distinct transcriptomic responses in microglia cultures that are not fully replicated in an amyloid mouse model or identified microglial subpopulations in vivo., Aggregation and accumulation of amyloid-β (Aβ) is a defining feature of Alzheimer’s disease pathology. To study microglial responses to Aβ, we applied exogenous Aβ peptide, in either oligomeric or fibrillar conformation, to primary mouse microglial cultures and evaluated system-level transcriptional changes and then compared these with transcriptomic changes in the brains of CRND8 APP mice. We find that primary microglial cultures have rapid and massive transcriptional change in response to Aβ. Transcriptomic responses to oligomeric or fibrillar Aβ in primary microglia, although partially overlapping, are distinct and are not recapitulated in vivo where Aβ progressively accumulates. Furthermore, although classic immune mediators show massive transcriptional changes in the primary microglial cultures, these changes are not observed in the mouse model. Together, these data extend previous studies which demonstrate that microglia responses ex vivo are poor proxies for in vivo responses. Finally, these data demonstrate the potential utility of using microglia as biosensors of different aggregate conformation, as the transcriptional responses to oligomeric and fibrillar Aβ can be distinguished.

Mapping network analysis in cells and tissues can provide insights into metabolic adaptations to changes in external environment, pathological conditions, and nutrient deprivation. Here, we reconstructed a genome-scale metabolic network of the rat liver that will allow for exploration of systems-level physiology. The resulting in silico model (iRatLiver) contains 1,882 reactions, 1,448 metabolites, and 994 metabolic genes. We then used this model to characterize the response of the liver’s energy metabolism to a controlled perturbation in diet. Transcriptomics data were collected from the livers of Sprague Dawley rats at 4 or 14 days of being subjected to 15%, 30%, or 60% diet restriction. These data were integrated with the iRatLiver model to generate condition-specific metabolic models, allowing us to explore network differences under each condition. We observed different pathway usage between early and late time points. Network analysis identified several highly connected “hub” genes (Pklr, Hadha, Tkt, Pgm1, Tpi1, and Eno3) that showed differing trends between early and late time points. Taken together, our results suggest that the liver’s response varied with short- and long-term diet restriction. More broadly, we anticipate that the iRatLiver model can be exploited further to study metabolic changes in the liver under other conditions such as drug treatment, infection, and disease.

Background: Determination of human papillomavirus (HPV) status has become clinically relevant for patient stratification under UICC TNM8 staging. Within the United Kingdom, a combination of p16 IHC and HPV DNA-ISH is recommended for classifying HPV status. This study will assess a series of clinically applicable second-line molecular tests to run in combination with p16 IHC to optimally determine HPV status. Methods: The ability of HPV RNA-ISH, HPV DNA-ISH, and HPV DNA-PCR to identify p16-positive/HPV-positive patients was investigated in a population-based oropharyngeal squamous cell carcinoma (OPSCC) cohort of patients diagnosed in Northern Ireland from 2000 to 2011. Results: Only 41% of the Northern Irish OPSCC patient population was associated with HPV-driven carcinogenesis. Both ISH assays were more specific than the DNA-PCR assay (100% and 95% vs. 67%) and were less likely to be affected by preanalytic factors such as increasing block age. A pooled HPV genotype probe for RNA-ISH was found to be the most accurate molecular assay assessed (95% accuracy) when compared with p16 positivity. Conclusions: Our study demonstrates the advantage of tissue-based molecular assays when determining HPV status in retrospective samples. Specifically, we demonstrate the enhanced sensitivity and specificity of ISH techniques compared with PCR-based methodology when working with formalin-fixed paraffin-embedded tissue, and found HPV RNA-ISH to be the most effective assay for determining HPV status. Impact: As p16 IHC is a relatively inexpensive, accessible, and sensitive test for stratifying patients by HPV status, this study finds that more patients would benefit from first-line p16 IHC followed by specific HPV testing using HPV RNA-ISH to confirm HPV status.

The 1000 Genomes Project (TGP) is a foundational resource which serves the biomedical community as a standard reference cohort for human genetic variation. There are now seven public versions of these genomes. The TGP Consortium produced the first by mapping its final data release against human reference sequence GRCh37, then “lifted over’’ these genomes to the improved reference sequence (GRCh38) when it was released, and remapped the original data to GRCh38 with two similar pipelines. As ‘best practice’ quality validation, the pipelines that generated these versions were benchmarked against the Genome In A Bottle Consortium’s ‘platinum quality’ genome (NA12878). The New York Genome Center recently released the results of independently resequencing the cohort at greater depth (30X), a phased version informed by the inclusion of related individuals, and independently remapped the original variant calls to GRCh38. We evaluated all seven versions using genome fingerprinting, which supports ultrafast genome comparison even across reference versions. We noted multiple issues including discrepancies in cohort membership, disagreement on the overall level of variation, evidence of substandard pipeline performance on specific genomes and in specific regions of the genome, cryptic relationships between individuals, inconsistent phasing, and annotation distortions caused by the history of the reference genome itself. We therefore recommend global quality assessment by rapid genome comparisons, using genome fingerprints and other metrics, alongside benchmarking as part of ‘best practice’ quality assessment of large genome datasets. Our observations also help inform the decision of which version to use, to support analyses by individual researchers.

Background The incidence of human papillomavirus (HPV)-positive oropharyngeal cancer, a disease affecting younger patients, is rapidly increasing. Cetuximab, an epidermal growth factor receptor inhibitor, has been proposed for treatment de-escalation in this setting to reduce the toxicity of standard cisplatin treatment, but no randomised evidence exists for the efficacy of this strategy. Methods We did an open-label randomised controlled phase 3 trial at 32 head and neck treatment centres in Ireland, the Netherlands, and the UK, in patients aged 18 years or older with HPV-positive low-risk oropharyngeal cancer (non-smokers or lifetime smokers with a smoking history of

109 Background: Trials in human papilloma virus associated oropharyngeal squamous cell carcinoma (HPVOPSCC), substituting cetuximab (CETUX) for cisplatin (CIS) with radiotherapy (RT), resulted in decreased efficacy without improved toxicity or symptom burden. We reported that high intratumoral immune cell (ITIC) CD103 expression (> 30%), a marker of tissue-resident memory T cells, is associated with better prognosis in unselected patients with HPVOPSCC treated with CIS/RT. In this study our aim was to determine whether low risk HPVOPSCC patients treated with CETUX/RT with high CD103 have a superior prognosis. Methods: TROG 12.01 and De-ESCALaTE are randomised multicentre trials that compared 70Gy RT/CETUX with 70Gy RT/CIS (weekly in TROG 12.01, 3-weekly in De-ESCALaTE) in patients with HPVOPSCC, low risk by Ang criteria: AJCC 7th Stage III (excluding T1-2N1) or stage IV (excluding N2b-c if smoking history > 10 pack years and/or distant metastases). In TROG 12.01 T4 and/or N3 patients were also excluded. Eligible patients required tumor samples available for immune cell quantification on immunohistochemistry. Data from the two trials were pooled, with analyses performed in eligible randomised patients who commenced treatment. The primary endpoint was failure-free survival (FFS) in patients receiving CETUX/ RT comparing CD103 ITIC > 30% (high) vs. < 30% (low). High/low CD103 were compared using Cox model adjusting for age, stage and trial. Results: Samples for CD103 testing were available in 159/182 patients on TROG 12.01 and 145/334 on De-ESCALaTE. ITIC CD103 expression was high in 26% of patients. The median follow-up was 3.2 years. The 3 -year failure-free survival rates in patients treated with CETUX/RT were 92% (95% CI: 78-97%) in high CD103 and 74% (95% CI: 64-82%) in low CD103, adjusted HR 0.25 (95% CI: 0.14-0.44); p < 0.001. The 3 -year overall survival (OS) in patients treated with CETUX/RT were 100% in high CD103 and 86% (95% CI: 76-92%) in low CD103, p < 0.001. Superior FFS in the high CD103 group was independent of stage. In patients treated with CIS/RT there was no significant difference in FFS (3-year 86% in high CD103 and 90% in low CD103; p = 0.55) or in OS (3-year 100% in high CD103 and 95% in low CD103; p = 0.14). The increase in failures in the low CD103 patients treated with CETUX/RT was evenly split between distant and locoregional failures. Conclusions: ITIC CD103 separates CETUX/RT treated low risk HPVOPSCC into excellent and poor prognosis subgroups. In a low risk population CIS/RT achieves excellent outcomes in both high and low ITIC CD103 groups. The high ITIC CD103 population is a rational target for future de-intensification trials.

Author(s): Wilmanski, Tomasz; Diener, Christian; Rappaport, Noa; Patwardhan, Sushmita; Wiedrick, Jack; Lapidus, Jodi; Earls, John C; Zimmer, Anat; Glusman, Gustavo; Robinson, Max; Yurkovich, James T; Kado, Deborah M; Cauley, Jane A; Zmuda, Joseph; Lane, Nancy E; Magis, Andrew T; Lovejoy, Jennifer C; Hood, Leroy; Gibbons, Sean M; Orwoll, Eric S; Price, Nathan D | Abstract: In the version of this article initially published, NIAMS grant R01AR061445 was not included in the Acknowledgements. The error has been corrected in the HTML and PDF versions of the article.

Background Intraoperative analysis of sentinel lymph nodes would enhance the care of early-stage oral squamous cell carcinoma (OSCC). We determined the frequency and extent of cytokeratin 19 (CK19) expression in OSCC primary tumours and surrounding tissues to explore the feasibility of a “clinic-ready” intraoperative diagnostic test (one step nucleic acid amplification—OSNA, sysmex). Methods Two cohorts were assembled: cohort 1, OSCC with stage and site that closely match cases suitable for sentinel lymph node biopsy (SLNB); cohort 2, HNSCC with sufficient fresh tumour tissue available for the OSNA assay (>50 mg). CK19 assays included qRT-PCR, RNA in situ hybridisation (ISH), and immunohistochemistry (IHC), as well as OSNA. Results CK19 mRNA expression was detected with variable sensitivity, depending on method, in 60–80% of primary OSCC tumours, while protein expression was observed in only 50% of tumours. Discordance between different techniques indicated that OSNA was more sensitive than qRT-PCR or RNA-ISH, which in turn were more sensitive than IHC. OSNA results showed CK19 expression in 80% of primary cases, so if used for diagnosis of lymph node metastasis would lead to a false-negative result in 20% of patients with cervical lymph node metastases. Conclusions OSNA in its current form is not suitable for use in OSCC SLNB due to inadequate expression of the CK19 target in all case. However, the same assay technology would likely be very promising if applied using a more ubiquitous squamous epithelial target. Electronic supplementary material The online version of this article (doi:10.1245/s10434-016-5337-6) contains supplementary material, which is available to authorized users.

Background: Oral squamous cell carcinoma (OSCC) is a global healthcare problem associated with poor clinical outcomes. Early detection is key to improving patient survival. OSCC may be preceded by clinically recognizable lesions, termed oral potentially malignant disorders (OPMD). As histologic assessment of OPMD does not accurately predict their clinical behavior, biomarkers are required to detect cases at risk of malignant transformation. Epidermal growth factor receptor gene copy number (EGFR GCN) is a validated biomarker in lung non–small cell carcinoma. We examined EGFR GCN in OPMD and OSCC to determine its potential as a biomarker in oral carcinogenesis. Methods: EGFR GCN was examined by in situ hybridization (ISH) in biopsies from 78 patients with OPMD and 92 patients with early-stage (stages I and II) OSCC. EGFR ISH signals were scored by two pathologists and a category assigned by consensus. The data were correlated with patient demographics and clinical outcomes. Results: OPMD with abnormal EGFR GCN were more likely to undergo malignant transformation than diploid cases. EGFR genomic gain was detected in a quarter of early-stage OSCC, but did not correlate with clinical outcomes. Conclusion: These data suggest that abnormal EGFR GCN has clinical utility as a biomarker for the detection of OPMD destined to undergo malignant transformation. Prospective studies are required to verify this finding. It remains to be determined if EGFR GCN could be used to select patients for EGFR-targeted therapies. Impact: Abnormal EGFR GCN is a potential biomarker for identifying OPMD that are at risk of malignant transformation. Cancer Epidemiol Biomarkers Prev; 25(6); 927–35. ©2016 AACR.

Background The contemporary treatment of oropharyngeal squamous cell carcinoma (SCC) is an area of debate. We report outcomes of a minimally invasive approach involving transoral laser microsurgery (TLM). Methods A consecutive series of patients (n = 153) undergoing primary TLM for oropharyngeal SCC from 2006 to 2013 was studied. Human papillomavirus (HPV) status was determined by p16 immunohistochemistry and high-risk HPV DNA in situ hybridization. Survival analyses were evaluated using Kaplan–Meier statistics. Results Tumor subsites included tonsil (n = 94; 61.5%), tongue base (n = 38; 24.8%), and soft palate (n = 21; 13.7%), with the majority being American Joint Committee on Cancer (AJCC) stage III/IVa (n = 124; 81.0%) and HPV-positive (n = 101; 66.0%). Three-year overall survival (OS), disease-specific survival (DSS), and disease-free survival (DFS) were 84.5%, 91.7%, and 78.2%, respectively. HPV-positivity portended favorable oncologic outcomes. One-year gastrostomy tube (G-tube) dependency was 1.3%. Conclusion To the best of our knowledge, this is the largest single-center TLM oropharyngeal SCC series to date. Our data suggest that TLM +/− postoperative radiotherapy (PORT) results in at least as good oncologic outcomes as chemoradiotherapy (CRT), while conferring swallowing function advantages. © 2016 Wiley Periodicals, Inc. Head Neck , 2016 © 2016 Wiley Periodicals, Inc. Head Neck 38:1263–1270, 2016

This is the official guideline endorsed by the specialty associations involved in the care of head and neck cancer patients in the UK. Although much commoner in the eastern hemisphere, with an age-standardised incidence rate of 0.39 per 100 000 population, cancers of the nasopharynx form one of the rarer subsites in the head and neck.1 This paper provides recommendations on the work up and management of nasopharyngeal cancer based on the existing evidence base for this condition.Recommendations• Patients with nasopharyngeal carcinoma (NPC) should be assessed with rigid and fibre-optic nasendoscopy. (R)• Nasopharyngeal biopsies should be preferably carried out endoscopically. (R)• Multislice computed tomographic (CT) scan of head, neck and chest should be carried out in all patients and magnetic resonance imaging (MRI) where appropriate to optimise staging. (R)• Radiotherapy (RT) is the mainstay for the radical treatment for NPC. (R)• Concurrent chemoradiotherapy offers significant improvement in overall survival in stage III and IV diseases. (R)• Surgery should only be used to obtain tissue for diagnosis and to deal with otitis media with effusion. (R)• Radiation therapy is the treatment of choice for stage I and II disease. (R)• Intensity modulated radiation therapy techniques should be employed. (R)• Concurrent chemotherapy with radiation therapy is the treatment of choice for stage III and IV disease. (R)• Patients with NPC should be followed-up and assessed with rigid and/or fibre-optic nasendoscopy. (G)• Positron emission tomography–computed tomography (PET–CT), CT or MRI scan should be carried out at three months from completion of treatment to assess response. (R)• Multislice CT scan of head, neck and chest should be carried out in all patients and MRI scan whenever possible and specially in advanced cases with suspected recurrence. (R)• Surgery in form of nasopharyngectomy should be considered as a first line treatment of residual or recurrent disease at the primary site. (R)• Neck dissection remains the treatment of choice for residual or metastatic neck disease whenever possible. (R)• Re-irradiation should be considered as a second line of treatment in recurrent disease. (R)

Objectives The incidence of human papillomavirus (HPV)-positive head and neck cancer, particularly oropharyngeal, has been increasing rapidly. Understanding of this disease, and modelling of suitable therapeutics, requires sustainable cell cultures, yet they remain limited in number and of variable origin. A comprehensive understanding of these resources is therefore of great importance. Materials and Methods Viral gene expression assays and pathological testing methods were used in the six currently available HPV-positive cell lines derived from head and neck (H&N) subsites, two HPV-negative H&N and two cervical carcinoma cell lines. A 2D migration assay monitored cell movement, speed and pattern of migration. Results All six H&N and two cervical cell lines were confirmed HPV-positive by gold standard testing, yet variability between tests was apparent. Although migration was not significantly different between cell lines, each demonstrated unique migration patterns. Conclusion Patient-derived cancer cells, arising as a consequence of natural oncogenic processes rather than in vitro manipulation, are essential for understanding cancer biology. We have characterised the available HPV-positive H&N cell lines and provided clear evidence of a persisting viral oncogenic driver in each, as such supporting their ongoing use as a model of HPV-positive H&N cancer. Importantly, we also highlight a need for caution to be exercised when translating future in vitro findings associated with these lines particularly in the context of oropharyngeal cancer given irregularities in tumour provenance (origin site and clinicopathological features).

Background TNM8 staging for oropharyngeal squamous cell carcinomas (OPSCC) surrogates p16 immunohistochemistry for HPV testing. Patients with p16+ OPSCC may lack HPV aetiology. Here, we evaluate the suitability of TNM8 staging for guiding prognosis in such patients. Methods HPV status was ascertained using p16 immunohistochemistry and high-risk HPV RNA and DNA in situ hybridisation. Survival by stage in a cohort of OPSCC patients was evaluated using TNM7/TNM8 staging. Survival of p16+/HPV− patients was compared to p16 status. Results TNM8 staging was found to improve on TNM7 (log rank p = 0·0190 for TNM8 compared with p = 0·0530 for TNM7) in p16+ patients. Patients who tested p16+ but were HPV− (n = 20) had significantly reduced five-year survival (33%) compared to p16+ patients (77%) but not p16− patients (35%). Cancer stage was reduced in 95% of p16+/HPV− patients despite having a mortality rate twice (HR 2.66 [95% CI: 1.37–5.15]) that of p16+/HPV+ patients under new TNM8 staging criteria. Conclusion Given the significantly poorer survival of p16+/HPV− OPSCCs, these data provide compelling evidence for use of an HPV-specific test for staging classification. This has particular relevance in light of potential treatment de-escalation that could expose these patients to inappropriately reduced treatment intensity as treatment algorithms evolve.

Pre-trial radiotherapy quality assurance (RTQA) for the SPARC trial of preoperative pancreas SBRT highlighted overgenerous target contouring. We aimed to assess for improvement following a training workshop and appraise the effectiveness of a novel web-conferencing format for on-trial RTQA.

Scale invariance is a common property of physical laws and a key concept in perspective drawing, which aims to provide a meaningful two-dimensional representation of a more complex, three-dimensional scene. Here we describe Scale Invariant Geometric Data Analysis (SIGDA), a new, general exploratory data analysis (EDA) method based on normalization of data to scale invariance. We discuss similarities and differences between SIGDA and two widely-used EDA methods, Correspondence Analysis (CA) and Principal Components Analysis (PCA). We then illustrate SIGDA’s ability to analyze and visualize population structure relationships within the data that inspired its development: genetic marker data, in which context PCA is considered a standard method. We show that SIGDA provides significant advantages over PCA of the same data, including: (a) robust detection and separation of a larger number of population axes, leading to (b) better separation of annotated populations; (c) separation of an independent allele frequency axis interpretable as a proxy for allele age, (d) visualization of marker flow between populations (populationhistory), and (d) robust detection and visualization of relationships between closely-related individuals and among family groups. Although this illustration focuses on a specific task, SIGDA is a general-purpose EDA method and derives its advantages from its novel approach to fundamental issues in data analysis, rather than clever sampling or other task-specific methodology.One Sentence SummaryWe illustrate the advantages of Scale Invariant Geometric Data Analysis (SIGDA), a new exploratory data analysis method similar to PCA, by applying SIGDA to derive detailed, robust visualizations of the complex history of human population structure from a large sample of single nucleotide variants.

This special communication describes activities, products, and lessons learned from a recent hackathon that was funded by the National Center for Advancing Translational Sciences via the Biomedical Data Translator program (‘Translator’). Specifically, Translator team members self-organized and worked together to conceptualize and execute, over a five-day period, a multi-institutional clinical research study that aimed to examine, using open clinical data sources, relationships between sex, obesity, diabetes, and exposure to airborne fine particulate matter among patients with severe asthma. The goal was to develop a proof of concept that this new model of collaboration and data sharing could effectively produce meaningful scientific results and generate new scientific hypotheses. Three Translator Clinical Knowledge Sources, each of which provides open access (via Application Programming Interfaces) to data derived from the electronic health record systems of major academic institutions, served as the source of study data. Jupyter Python notebooks, shared in GitHub repositories, were used to call the knowledge sources and analyze and integrate the results. The results replicated established or suspected relationships between sex, obesity, diabetes, exposure to airborne fine particulate matter, and severe asthma. In addition, the results demonstrated specific differences across the three Translator Clinical Knowledge Sources, suggesting cohort- and/or environment-specific factors related to the services themselves or the catchment area from which each service derives patient data. Collectively, this special communication demonstrates the power and utility of intense, team-oriented hackathons and offers general technical, organizational, and scientific lessons learned.

Whilst dental healthcare professionals naturally focus on assessment of the teeth and the supporting tissues, they also have an important role in assessing the whole oro-facial complex and the neck. Assessment of the neck is particularly important, not least, because it contains the regional lymph nodes that are involved in immune surveillance of the head and neck region. The neck also contains the major salivary glands: the sub­mandibular gland and the tail of the parotid gland. Mid-line structures include the hyoid bone, larynx, and trachea, along with the thyroid gland and parathyroid glands. The assessment of these anatomical structures should form part of the routine clinical examination. The dis­covery of an abnormality in the neck, which may not have been noticed by the patient, may expedite the diagnosis of significant disease and facilitate a timely intervention. A through understanding of the anatomy of the neck is essential and informs the clinical examination. It is also important to understand the concept of the anatomical levels that map out the lymph node groups of the neck (Chapter 1; Fig. 1.2). Accurate assessment of the neck is usually best achieved by a combination of visual inspection and palpation, with the patient in a slightly reclined position, the clinician standing behind the patient. Any lumps, e.g. enlarged lymph nodes, are described by anatomical site, size, consistency (cystic, soft, rubbery, hard), whether the lump is mobile or fixed to the underlying tissue, and if palpation elic­its pain or discomfort. The combination of these parameters will help to formulate the differential diagnosis; for example, an isolated hard lump that is fixed to underlying structures is likely to represent meta­static cancer, whereas, bilateral soft lumps that are mobile and painful to palpation are likely to represent lymphadenitis as a consequence of systemic infection. Ultrasound examination can be used to ascertain important informa­tion about a neck lump such as the site (precise anatomical location, superficial or deep), size, consistency (solid or cystic), and multi-focality. Doppler settings can help to establish the vascularity of a lesion and its proximity to major vessels.

A sound understanding of clinical oral pathology is essential if a dental clinician is to navigate successfully through clinical guidelines, make timely referrals to specialists, and provide good care for patients. This new edition of Soames' & Southam's Oral Pathology provides a clear and friendly guide for students, practitioners, and the whole dental team. Thoroughly updated for today's clinical practice, this textbook covers 'must-know' oral pathology and integrates key aspects of oral medicine. It begins by explaining the principles of clinical assessment, the synthesis of a differential diagnosis, and the selection of further investigations including laboratory tests. Ten chapters bring this theory to life by looking at the clinical and pathological features of a wide range of common oral diseases including oral cancer, salivary gland disorders, and diseases of the jaws. Two new chapters address skin diseases affecting the oro-facial region and neck lumps. A final chapter highlights the importance of clinical oral pathology in the context of systemic human disease. New radiology content includes examples of cross-sectional imaging. Photomicrographs have been replaced with carefully selected images to illustrate key pathological features. Each chapter includes key points boxes and tables to aid learning. Written by experts in both oral pathology and oral medicine, this new edition is a must-have for dentistry students, and those working in the field, providing current and trustworthy information.

The most common oral diseases are dental caries and periodontal dis­ease. The diagnosis and treatment of these diseases are the focus of the majority of dentists, dental therapists, and dental hygien­ists. Nevertheless, it is the responsibility of the dental healthcare pro­fessional to provide a holistic approach to management that ensures both good oral and general health for their patients. A broad knowledge of the range of diseases that affect the oral cavity is essential and also an appreciation that oral disease may be the first sign of an underlying systemic disease. Before this knowledge can be applied, the clinician must obtain an accurate patient history and undertake a systematic clinical examination. These key clinical skills underpin both medicine and dentistry, and are an absolute requirement to formulate a differ­ential diagnosis. The use of imaging modalities and laboratory tests are often required to reach a definitive diagnosis, and it is the justification and informed choice of these additional investigations that will facili­tate a timely and accurate diagnosis. Following diagnosis, appropriate treatment can be instituted, the ideal outcome being a return to health or control of the patient’s symptoms in recalcitrant chronic diseases. Obtaining a clear and precise clinical history is essential. The clinician must listen carefully to the information conveyed by the patient and then use direct questioning to collect additional data to construct an accurate picture of the patient’s problem. This can be a significant challenge and requires excellent communication skills to build a good patient–clinician relationship. The most common presenting problems relate to pain or the development of a lesion: swelling, lump, ulcer, or white/red patch. To establish a comprehensive pain history, the features listed in Table 1.1 should be addressed. Obtaining an accurate history for a lesion is dependent on the patient noticing the abnormality in the first instance and, as a consequence, the information may be rather vague; however, it is important to ascertain the key points listed in Table 1.2. A comprehensive medical history (Box 1.1) will identify any concur­rent disease that may be relevant to the presenting oral condition (Chapter 10) and highlight any issues relating to proposed medical or surgical interventions.