Standardisation of labial salivary gland histopathology in clinical trials in primary Sjögren's syndrome

Labial salivary gland (LSG) biopsy is used in the classification of primary Sjögren's syndrome (PSS) and in patient stratification in clinical trials. It may also function as a biomarker. The acquisition of tissue and histological interpretation is variable and needs to be standardised for use in clinical trials. A modified European League Against Rheumatism consensus guideline development strategy was used. The steering committee of the ad hoc working group identified key outstanding points of variability in LSG acquisition and analysis. A 2-day workshop was held to develop consensus where possible and identify points where further discussion/data was needed. These points were reviewed by a subgroup of experts on PSS histopathology and then circulated via an online survey to 50 stakeholder experts consisting of rheumatologists, histopathologists and oral medicine specialists, to assess level of agreement (0–10 scale) and comments. Criteria for agreement were a mean score ≥6/10 and 75% of respondents scoring ≥6/10. Thirty-nine (78%) experts responded and 16 points met criteria for agreement. These points are focused on tissue requirements, identification of the characteristic focal lymphocytic sialadenitis, calculation of the focus score, identification of germinal centres, assessment of the area of leucocyte infiltration, reporting standards and use of prestudy samples for clinical trials. We provide standardised consensus guidance for the use of labial salivary gland histopathology in the classification of PSS and in clinical trials and identify areas where further research is required to achieve evidence-based consensus

Genomic analysis to assess disease progression and recurrence in patients with oral squamous cell carcinoma: – a preliminary study

We studied the progression from dysplasia to invasive carcinoma and subsequent second primaries or locoregional recurrences in 11 patients with recurrent squamous cell carcinoma (SCC). Between one and six samples were sequenced/patient. DNA samples were prepared, and libraries multiplexed to between 40 and 80 samples/lane of an Illumina HiSeq 3000 and sequenced with 2 × 100 bp paired end sequencing. Copy number data were generated by CNAnorm (Bioconductor package). Samples of recurrent SCC showed unique patterns of descent when compared with earlier samples from the primary tumour, and three main patterns emerged. In four patients there was convincing evidence that the later lesion was descended directly from cells from the first, and in a further four there were no detectable genomic events between the two lesions. Three patients had some shared events between the early and later lesions, but although there were enough differences to deduce that the two lesions had a shared ancestor, they were not directly descended from each other. We present the patients’ characteristics in detail, including the overall survival in each group. There was a distinct genomic pattern after a second episode of SCC in all the groups. A larger study that uses similar methods and a longer duration could provide reliable conclusions with respect to survival. With the use of new techniques, genomic data can be available to clinical teams during the planning of treatment

A scenario-specific nexus modelling toolkit to identify trade-offs in the promotion of sustainable irrigated agriculture in Ecuador, a Belt and Road country

Increased demand for food due to development and population growth has prompted irrigated agriculture expansion, posing enhanced global challenges to water, energy, and food security. To confront these challenges, an approach that considers the water-energy-food-environment nexus can address multidimensional trade-offs that complicate the efficient use of resources and the achievement of Sustainable Development Goals. In order to provide insights into solutions to these challenges for a specific case, this study develops a modelling toolkit that integrates biophysical and socioeconomic aspects of nexus components in the context of agro-export and irrigation expansion in Ecuador, a Belt and Road Country. The nexus toolkit is applied to agricultural-development scenarios defined in participatory workshops and incorporates a water resources model, a lifecycle environmental assessment, and a socioeconomic analysis. The modelling exercise is constructed around specific scenario-determined land use patterns in the Santa Elena peninsula of Ecuador. Agriculture in the peninsula is water-limited, relying on delivery infrastructure and transfers from a neighbouring catchment. Impacts on nexus components are analysed for ten crops under two potential land-use scenarios: a substantial increase in irrigated area due to investment in irrigation infrastructure; and a substantial shift in land use towards export crops. The two have distinct impact on water and energy use, global warming potential, freshwater eutrophication, terrestrial acidification, and fine particulate matter formation. The results provide insights into future water and energy resource challenges and environmental and socioeconomic trade-offs associated with likely changes in irrigation expansion. The results for scenarios show that, for example, banana production has the greatest environmental impacts (e.g. a 519% increase in global warming potential and 452% increase in fine particulate matter forma for scenario 2), primarily due to water and energy requirements, despite the crop being mainly produced organically. In addition, total net income and labour demand increase (net income increases by 43% and 217% under scenarios 1 and 2, respectively) due to a larger crop area and crop intensification. Scale effects on labour demand are mainly due to labour intensity of maize in Ecuador, which is disadvantaged in the crop export scenario (an unexpected result). However, expanding irrigated areas would also increase total water and energy demand for irrigation, global warming potential, and freshwater eutrophication. This type of information enables stakeholders and decision-makers to design policies that achieve equitable and sustainable agricultural production, water use, and economic growth.Natural Environment Research Council (NERC): NE/R015759/

Next-generation sequencing analysis for detecting human papillomavirus in oral verrucous carcinoma

Purpose The aetiology of oral verrucous carcinoma is unknown whilst human papillomavirus ‘involvement’ remains contentious. Dubiety can be attributed to varied detection procedures and difficulties in defining ‘gold-standard’ histological criteria for diagnosing ‘verrucous’ lesions. Their paucity also hampers investigation. Design We aimed to analyse oral verrucous lesions for HPV subtype genomes using ‘next generation sequencing’ for the detection of papilloma virus sequences, identifying subtypes and computing viral loads. We identified a total of 78 oral verrucous cases [62 carcinomas and 16 hyperplasias]. DNA was extracted from all and sequenced at a coverage between 2.5 and 13%. Findings An HPV-16 sequence was detected in one carcinoma and one hyperplasia, and an HPV-2 sequence was detected in one carcinoma out of the 78 cases, with viral loads of 2.24, 8.16 and 0.33 viral genomes per cell respectively. Practical implications Our results indicate no conclusive human papilloma virus involvement in oral verrucous carcinoma or hyperplasia

Next-generation sequencing for simultaneous determination of human papillomavirus load, subtype, and associated genomic copy number changes in tumors

Human papillomavirus (HPV) infection in cases of squamous cell carcinoma of the oropharynx is a powerful predictive and prognostic biomarker. We describe how the use of next-generation sequencing can provide a novel method for the detection of HPV in DNA isolated from formalin-fixed paraffin-embedded tissues. Using this methodology in a cohort of 44 head and neck tumors, we identified the samples that contained HPV sequences, the viral subtype involved, and a direct readout of viral load. Specificity of HPV detection by sequencing compared to traditional detection methods using either PCR or p16 immunohistochemistry was 100%. Sensitivity was 50% when either compared to PCR [confidence interval (CI) = 29% to 71%] or 75% when compared to p16 (CI = 47% to 91%). In addition, we demonstrate the ability of next-generation sequencing to detect other HPV subtypes that would not have been detected by traditional methods, and we demonstrated the ability to apply this method to any tumor and any virus in a panel of eight human cancer cell lines. This methodology also provides a tumor genomic copy number karyogram, and in the samples analyzed here, a lower level of chromosome instability was detected in HPV-positive tumors compared to HPV-negative tumors, as observed in previous studies. Thus, the use of next-generation sequencing for the detection of HPV provides a multiplicity of data with clinical significance in a single test

Standardisation of labial salivary gland histopathology in clinical trials in primary Sjögren's syndrome

Labial salivary gland (LSG) biopsy is used in the classification of primary Sjögren's syndrome (PSS) and in patient stratification in clinical trials. It may also function as a biomarker. The acquisition of tissue and histological interpretation is variable and needs to be standardised for use in clinical trials. A modified European League Against Rheumatism consensus guideline development strategy was used. The steering committee of the ad hoc working group identified key outstanding points of variability in LSG acquisition and analysis. A 2-day workshop was held to develop consensus where possible and identify points where further discussion/data was needed. These points were reviewed by a subgroup of experts on PSS histopathology and then circulated via an online survey to 50 stakeholder experts consisting of rheumatologists, histopathologists and oral medicine specialists, to assess level of agreement (0-10 scale) and comments. Criteria for agreement were a mean score ≥6/10 and 75% of respondents scoring ≥6/10. Thirty-nine (78%) experts responded and 16 points met criteria for agreement. These points are focused on tissue requirements, identification of the characteristic focal lymphocytic sialadenitis, calculation of the focus score, identification of germinal centres, assessment of the area of leucocyte infiltration, reporting standards and use of prestudy samples for clinical trials. We provide standardised consensus guidance for the use of labial salivary gland histopathology in the classification of PSS and in clinical trials and identify areas where further research is required to achieve evidence-based consensus. © 2016 BMJ Publishing Group Limited

Standardisation of labial salivary gland histopathology in clinical trials in primary Sjögren's syndrome

Labial salivary gland (LSG) biopsy is used in the classification of primary Sjögren's syndrome (PSS) and in patient stratification in clinical trials. It may also function as a biomarker. The acquisition of tissue and histological interpretation is variable and needs to be standardised for use in clinical trials. A modified European League Against Rheumatism consensus guideline development strategy was used. The steering committee of the ad hoc working group identified key outstanding points of variability in LSG acquisition and analysis. A 2-day workshop was held to develop consensus where possible and identify points where further discussion/data was needed. These points were reviewed by a subgroup of experts on PSS histopathology and then circulated via an online survey to 50 stakeholder experts consisting of rheumatologists, histopathologists and oral medicine specialists, to assess level of agreement (0-10 scale) and comments. Criteria for agreement were a mean score ≥6/10 and 75% of respondents scoring ≥6/10. Thirty-nine (78%) experts responded and 16 points met criteria for agreement. These points are focused on tissue requirements, identification of the characteristic focal lymphocytic sialadenitis, calculation of the focus score, identification of germinal centres, assessment of the area of leucocyte infiltration, reporting standards and use of prestudy samples for clinical trials. We provide standardised consensus guidance for the use of labial salivary gland histopathology in the classification of PSS and in clinical trials and identify areas where further research is required to achieve evidence-based consensus. © 2016 BMJ Publishing Group Limited