Abstract 1926: Machine learning-enhanced image and spatial analytic pipelines for imaging mass cytometry applied to the TRACERx non-small cell lung cancer study

Introduction: High dimensional imaging approaches such as imaging mass cytometry (IMC) are becoming widely used in cancer research. Such methods allow simultaneous observation of many cell types and their functional states and can provide valuable spatial information on cancer disease states when applied to clinical tissue samples. For example, in-situ immune and tumor cell interactions can be interrogated in their spatial context within the tumor microenvironment (TME). Analysis methods for the resultant complex data are not well formalized, and bespoke methods are usually required to fully capitalize on the underlying richness of information made available by IMC. Deep learning [DL] approaches, while highly accurate for other imaging modalities, have been slow to be adopted in IMC, as public resources for deep learning tasks in IMC are not abundant.

Methods: We developed multiple DL and ML-based analysis pipelines for the following tasks in IMC data processing: [1] nucleus and necrotic tissue segmentation, [2] quantitative nuclear and cellular morphometry, [3] identification of cell type-specific niches. We applied these protocols to images and derived single cell spatial data from the TRACERx IMC cohort (n=81 non-small cell lung cancer patients, 561 images).

Results: [1] We created a 120 image, 46,000+ labelled nucleus segmentation dataset for IMC data with representative images from lung adenocarcinoma, squamous cell carcinoma and other tissues. We achieved state-of-the-art performance in nuclear instance segmentation using a custom U-net++ neural network architecture trained using this dataset, which we benchmarked against traditional image processing methods, as well as publicly available deep learning architectures. Subsequently, we exploited transfer learning to retrain this model on a restricted dataset of labelled necrotic domains, which produced predictions in good agreement with independent pathologist assessment. [2] We developed an IMC morphometry pipeline utilizing ML-informed partitions of nuclear and cellular shape descriptors through which we performed cell-type specific morphometric characterization of all mapped cells in the non-small cell lung cancer TME, and which enabled a comparative analysis of the morphometries of each distinct cellular phenotype. [3] We established a high throughput density-based spatial clustering pipeline capable of identifying locally enriched niches of a given cell type of interest, as well as probing the composition and phenotypes of other cells within these niches.

Conclusions: These approaches enhanced the quality as well as the breadth of spatial information derivable from TRACERx IMC data. Applying such tools to other clinical and pre-clinical datasets can improve our understanding of the spatial organization of cells both in non-small cell lung cancer and other cancer types.

Citation Format: Alastair Magness, Katey Enfield, Mihaela Angelova, Emma Colliver, Emer Daly, Kristiana Grigoriadis, Claudia Lee, Oriol Pich, Philip Hobson, Dina Levi, Takahiro Karasaki, David Moore, Julian Downward, Erik Sahai, Mariam Jamal-Hanjani, Charles Swanton, TRACERx Consortium. Machine learning-enhanced image and spatial analytic pipelines for imaging mass cytometry applied to the TRACERx non-small cell lung cancer study [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1926.

Abstract 3609: Defining extrinsic and intrinsic mechanisms of immune evasion in TRACERx using imaging mass cytometry

Introduction: The relationship between the evolving cancer genome and its tumor microenvironment (TME) is poorly understood. TRACERx has examined the intrinsic mechanisms of immune escape in non-small cell lung cancer. Here, we applied imaging mass cytometry (IMC) to address the contribution of extrinsic mechanisms in the context of intrinsic mechanisms and genomic features such as neoantigen burden.

Methods: We applied two 35-antibody IMC panels to the treatment naïve multiregion TRACERx cohort (n=81 patients, 221 regions), and developed an IMC analysis pipeline to study T cell differentiation states, cancer associated fibroblasts, vasculature, and innate and adaptive immunity. Identities and functional states were assigned to over 4 million cells and their positions were mapped within tumor and stromal compartments.

Results: We identified four distinct TMEs according to the local densities of lymphoid and myeloid cells: high infiltrate, stroma TIL enriched, myeloid enriched, and low infiltrate. We confirmed frequent intratumor TME heterogeneity, previously inferred from RNA sequencing. In high and stroma TIL enriched TMEs, we found the balance of effector and suppressor cells either favoured an exhausted (exhausted T cells and Tregs, n=16, 26.7%), suppressed (effector T cells and suppressive macrophages, n=31, 51.6%) or effector phenotype (high M1:M2, n=13, 21.6%). Tregs within exhausted TMEs neighboured effector and exhausted T cells, whereas effector T cells were nearest tumor cells within effector TMEs. Cell-type specific checkpoint molecule expression favoured specific compartments and TMEs. For example, the highest density of intratumoral PDL1+ M2-macrophages was observed within high infiltrate regions. Complementary intrinsic and extrinsic immune evasion mechanisms were identified, including immune avoiding architectures and stromal barriers as spatial mechanisms of evasion. Tumor cells were found to express lactate transporter, MCT4, in high infiltrate environments. Neoantigen burden associated with immune cell densities in a histology-specific manner. In lung adenocarcinoma, neoantigen burden was associated with a high infiltrate TME and suppressive myeloid populations such as M2-macrophages. In squamous cell carcinoma, we observed significant associations with CD8+ T cells, including exhausted populations, specifically in tumors lacking HLALOH.

Conclusions: IMC allowed for the identification of spatial mechanisms of immune evasion that, when combined with intrinsic mechanisms, provided a more complete understanding of how lung tumors escape immune predation. By visualising single cells in their native context, we observed various immunosuppressive TMEs that defined high infiltrate tumors. Histology-specific relationships between immune cells and neoantigen burden point to different immune pressures, which may influence tumor evolution.

Citation Format: Katey Enfield, Emma Colliver, Mihaela Angelova, Alastair Magness, Claudia Lee, Kristiana Grigoriadis, Oriol Pich, Clare Puttick, Dina Levi, Philip Hobson, David Moore, Takahiro Karasaki, Selvaraju Veeriah, TRACERx Consortium, Mariam Jamal-Hanjani, Nicholas McGranahan, Erik Sahai, Julian Downward, Crispin Hiley, Charles Swanton. Defining extrinsic and intrinsic mechanisms of immune evasion in TRACERx using imaging mass cytometry [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3609.

Abstract 6113: Spatially resolved biomarker detection on single cells in TRACERx using multiplex imaging

Introduction. Studying cell-to-cell variation within the tumour’s native context is crucial for fully understanding tumour heterogeneity and its impact on disease progression and therapy response. Tumour cells and their surrounding stromal cells can be spatially profiled using multiplex imaging with a growing number of detectable proteins. The methods currently used for identification of cell phenotypes from multiplex imaging data have been initially developed for cells in suspension. Therefore, more accurate and robust approaches are required to account for spatial signal overlap and to automatically detect the presence of biomarkers in spatial proteomics.

Methods. We performed imaging mass cytometry on 221 tumour and adjacent normal regions from 81 untreated, non-small cell lung cancer patients in the TRACERx study. Two antibody panels with 35 markers were applied to include a range of phenotypic, functional, and structural biomarkers. Single cells were segmented using deep learning-based approaches, and the measured biomarker intensities per cell were further used to identify cell types and functional states.

Results. We developed a computational approach optimised for spatial proteomics for identification of cell types and functional states and automated detection of the presence of biomarkers on single cells. First, we demonstrated that current approaches for cell phenotyping lack reproducibility with subsampling and can produce ambiguous clusters of cells from different cell types. Using a multi-tiered analytical approach in combination with statistical tools, we showed reproducibility between technical and biological replicates. We estimated the performance using orthogonal measurements from flow cytometry and immunohistochemistry from matched tumour samples. This approach has been automated with a scalable and portable Nextflow-based implementation.

Conclusions. We developed a streamlined approach that overcame limitations of current methods and quantified single-cell biomarker presence using multiplex imaging with TRACERx. Implemented as open-source, portable and customisable, this pipeline for spatially resolved TME characterisation will allow the study of drug targets expression within their spatial context for a better understanding of therapy efficacy.

Citation Format: Mihaela Angelova, Katey Enfield, Alastair Magness, Emma Colliver, Masako Shimato, Claudia Lee, David A. Moore, Febe Van Maldegem, Philip Hobson, Dina Levi, James L. Reading, Crispin T. Hiley, Julian Downward, Erik Sahai, Charles Swanton. Spatially resolved biomarker detection on single cells in TRACERx using multiplex imaging [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 6113.

Functional antibody and T cell immunity following SARS-CoV-2 infection, including by variants of concern, in patients with cancer: the CAPTURE study

Patients with cancer have higher COVID-19 morbidity and mortality. Here we present the prospective CAPTURE study, integrating longitudinal immune profiling with clinical annotation. Of 357 patients with cancer, 118 were SARS-CoV-2 positive, 94 were symptomatic and 2 died of COVID-19. In this cohort, 83% patients had S1-reactive antibodies and 82% had neutralizing antibodies against wild type SARS-CoV-2, whereas neutralizing antibody titers against the Alpha, Beta and Delta variants were substantially reduced. S1-reactive antibody levels decreased in 13% of patients, whereas neutralizing antibody titers remained stable for up to 329 days. Patients also had detectable SARS-CoV-2-specific T cells and CD4+ responses correlating with S1-reactive antibody levels, although patients with hematological malignancies had impaired immune responses that were disease and treatment specific, but presented compensatory cellular responses, further supported by clinical recovery in all but one patient. Overall, these findings advance the understanding of the nature and duration of the immune response to SARS-CoV-2 in patients with cancer.

Inhibition of protein N-myristoylation blocks Plasmodium falciparum intraerythrocytic development, egress and invasion

We have combined chemical biology and genetic modification approaches to investigate the importance of protein myristoylation in the human malaria parasite, Plasmodium falciparum. Parasite treatment during schizogony in the last 10 to 15 hours of the erythrocytic cycle with IMP-1002, an inhibitor of N-myristoyl transferase (NMT), led to a significant blockade in parasite egress from the infected erythrocyte. Two rhoptry proteins were mislocalized in the cell, suggesting that rhoptry function is disrupted. We identified 16 NMT substrates for which myristoylation was significantly reduced by NMT inhibitor (NMTi) treatment, and, of these, 6 proteins were substantially reduced in abundance. In a viability screen, we showed that for 4 of these proteins replacement of the N-terminal glycine with alanine to prevent myristoylation had a substantial effect on parasite fitness. In detailed studies of one NMT substrate, glideosome-associated protein 45 (GAP45), loss of myristoylation had no impact on protein location or glideosome assembly, in contrast to the disruption caused by GAP45 gene deletion, but GAP45 myristoylation was essential for erythrocyte invasion. Therefore, there are at least 3 mechanisms by which inhibition of NMT can disrupt parasite development and growth: early in parasite development, leading to the inhibition of schizogony and formation of “pseudoschizonts,” which has been described previously; at the end of schizogony, with disruption of rhoptry formation, merozoite development and egress from the infected erythrocyte; and at invasion, when impairment of motor complex function prevents invasion of new erythrocytes. These results underline the importance of P. falciparum NMT as a drug target because of the pleiotropic effect of its inhibition.

Understanding the essential factors needed for malaria parasite development could help us find new therapeutic targets. This study reveals that N-myristoylation is a posttranslational modification of proteins essential for the parasites’ growth and their invasion of red blood cells.

Characterisation of tumour microenvironment remodelling following oncogene inhibition in preclinical studies with imaging mass cytometry

Mouse models are critical in pre-clinical studies of cancer therapy, allowing dissection of mechanisms through chemical and genetic manipulations that are not feasible in the clinical setting. In studies of the tumour microenvironment (TME), multiplexed imaging methods can provide a rich source of information. However, the application of such technologies in mouse tissues is still in its infancy. Here we present a workflow for studying the TME using imaging mass cytometry with a panel of 27 antibodies on frozen mouse tissues. We optimise and validate image segmentation strategies and automate the process in a Nextflow-based pipeline (imcyto) that is scalable and portable, allowing for parallelised segmentation of large multi-image datasets. With these methods we interrogate the remodelling of the TME induced by a KRAS G12C inhibitor in an immune competent mouse orthotopic lung cancer model, highlighting the infiltration and activation of antigen presenting cells and effector cells.

Functional antibody and T-cell immunity following SARS-CoV-2 infection, including by variants of concern, in patients with cancer: the CAPTURE study

Patients with cancer have higher COVID-19 morbidity and mortality. Here we present the prospective CAPTURE study (NCT03226886) integrating longitudinal immune profiling with clinical annotation. Of 357 patients with cancer, 118 were SARS-CoV-2-positive, 94 were symptomatic and 2 patients died of COVID-19. In this cohort, 83% patients had S1-reactive antibodies, 82% had neutralizing antibodies against WT, whereas neutralizing antibody titers (NAbT) against the Alpha, Beta, and Delta variants were substantially reduced. Whereas S1-reactive antibody levels decreased in 13% of patients, NAbT remained stable up to 329 days. Patients also had detectable SARS-CoV-2-specific T cells and CD4+ responses correlating with S1-reactive antibody levels, although patients with hematological malignancies had impaired immune responses that were disease and treatment-specific, but presented compensatory cellular responses, further supported by clinical. Overall, these findings advance the understanding of the nature and duration of immune response to SARS-CoV-2 in patients with cancer.

Preexisting and de novo humoral immunity to SARS-CoV-2 in humans

Zoonotic introduction of novel coronaviruses may encounter preexisting immunity in humans. Using diverse assays for antibodies recognizing SARS-CoV-2 proteins, we detected preexisting humoral immunity. SARS-CoV-2 spike glycoprotein (S)-reactive antibodies were detectable using a flow cytometry-based method in SARS-CoV-2-uninfected individuals and were particularly prevalent in children and adolescents. They were predominantly of the immunoglobulin G (IgG) class and targeted the S2 subunit. By contrast, SARS-CoV-2 infection induced higher titers of SARS-CoV-2 S-reactive IgG antibodies targeting both the S1 and S2 subunits, and concomitant IgM and IgA antibodies, lasting throughout the observation period. SARS-CoV-2-uninfected donor sera exhibited specific neutralizing activity against SARS-CoV-2 and SARS-CoV-2 S pseudotypes. Distinguishing preexisting and de novo immunity will be critical for our understanding of susceptibility to and the natural course of SARS-CoV-2 infection.

Preexisting and de novo humoral immunity to SARS-CoV-2 in humans

Zoonotic introduction of novel coronaviruses may encounter preexisting immunity in humans. Using diverse assays for antibodies recognizing SARS-CoV-2 proteins, we detected preexisting humoral immunity. SARS-CoV-2 spike glycoprotein (S)-reactive antibodies were detectable using a flow cytometry-based method in SARS-CoV-2-uninfected individuals and were particularly prevalent in children and adolescents. They were predominantly of the immunoglobulin G (IgG) class and targeted the S2 subunit. By contrast, SARS-CoV-2 infection induced higher titers of SARS-CoV-2 S-reactive IgG antibodies targeting both the S1 and S2 subunits, and concomitant IgM and IgA antibodies, lasting throughout the observation period. SARS-CoV-2-uninfected donor sera exhibited specific neutralizing activity against SARS-CoV-2 and SARS-CoV-2 S pseudotypes. Distinguishing preexisting and de novo immunity will be critical for our understanding of susceptibility to and the natural course of SARS-CoV-2 infection.

Adapting to the Coronavirus Pandemic: Building and Incorporating a Diagnostic Pipeline in a Shared Resource Laboratory

In March 2020, with lockdown due to the coronavirus pandemic underway, the Francis Crick Institute (the Crick) regeared its research laboratories into clinical testing facilities. Two pipelines were established, one for polymerase chain reaction and the other for Serology. This article discusses the Cricks Flow Cytometry Science Technology Platform (Flow STP) role in setting up the Serology pipeline. Pipeline here referring to the overarching processes in place to facilitate the receipt of human sera through to a SARs‐CoV‐2 enzyme‐linked immunosorbent assay result. We examine the challenges that had to be overcome by a research laboratory to incorporate clinical diagnostics and the processes by which this was achieved. It describes the governance required to run the service, the design of the standard operating procedures (SOPs) and pipeline, the setting up of the assay, the validation required to show the robustness of the pipeline and reporting the results of the assay. Finally, as the lockdown started to ease in June 2020, it examines how this new service affects the daily running of the Flow STP. © 2020 The Authors. Cytometry Part A published by Wiley Periodicals LLC on behalf of International Society for Advancement of Cytometry.

Comparative analysis of three laboratory based serological assays for SARS-CoV-2 in an Australian cohort

Many unanswered questions remain regarding the role of SARS-CoV-2 serological assays in this unfolding COVID-19 pandemic. These include their utility for the diagnosis of acute SARS-CoV-2 infection, past infection or exposure, correlation with immunity and the effective duration of immunity. This study examined the performance of three laboratory based serological assays, EUROIMMUN Anti-SARS-CoV-2 IgA/IgG, MAGLUMI 2000 Plus 2019-nCov IgM/IgG and EDI Novel Coronavirus (COVID-19) IgM/IgG immunoassays. We evaluated 138 samples from a reference non-infected population and 71 samples from a cohort of 37 patients with SARS-CoV-2 confirmed positive by RT-PCR. The samples were collected at various intervals of 0-45 days post symptoms onset (PSO). Specificity and sensitivity of these assays was 60.9%/71.4% (IgA) and 94.2%/63.3% (IgG) for EUROIMMUN; 98.5%/18.4% (IgM) and 97.8%/53.1% (IgG) for MAGLUMI; and 94.9%/22.5% (IgM) and 93.5%/57.1% (IgG) for EDI, respectively. When samples collected ≥14 days PSO were considered, the sensitivities were 100.0 and 100.0%; 31.0 and 82.8%; 34.5 and 57.1%, respectively. Using estimated population prevalence of 0.1, 1, and 10%, the positive predictive value of all assays remained low. The EUROIMMUN Anti-SARS-CoV-2 IgA lacked specificity for acute diagnosis and all IgM assays offered poor diagnostic utility. Seroconversion can be delayed although all patients had seroconverted at 28 days in our cohort with the EUROIMMUN Anti-SARS-CoV-2 IgG. Despite this, with specificity of only 94% this assay would not be satisfactory for seroprevalence studies in the general Australian population given this is likely to be currently <1%.

Abstract A160: Deep immunoprofiling of mouse lung cancer models in steady state and upon drug treatment

With the advancement of immunotherapies for lung cancer, it has become apparent how insufficient our knowledge is surrounding the interactions between the tumor and the immune system. In particular in the context of combining immunotherapy with conventional chemotherapy or novel targeted therapies, it is of the utmost importance that we understand the effects that those therapies have on the tumor immune infiltrate and how that would counteract or synergize with immunotherapy. We have used multiplex flow cytometry to characterise the basal tumor immune infiltrate of various spontaneous and orthogonous syngeneic mouse models for lung cancer, with different levels of immunogenicity. With imaging mass cytometry, visualizing and quantifying &gt;30 markers simultaneously in mouse tumor tissue sections, we studied the localization and interactions of the immune cells within and surrounding the tumors. This has highlighted the level to which tumors are regulating their microenvironment, actively excluding all potential effector cells while attracting protumoral myeloid cells, and how this is amplified as the tumors progress. We have observed differences between the various models and seen how the tumors make adaptations when they are intrinsically more immunogenic. Furthermore, we have started to address how these balances are perturbed by various immune and chemotherapies in short- and long-term experiments and preliminary data will be presented.

Citation Format: Febe van Maldegem, Karishma Valand, Victoria Tsang, Edurne Mugarza, Deborah Caswell, Philip Hobson, Julian Downward. Deep immunoprofiling of mouse lung cancer models in steady state and upon drug treatment. [abstract]. In: Proceedings of the Fourth CRI-CIMT-EATI-AACR International Cancer Immunotherapy Conference: Translating Science into Survival; Sept 30-Oct 3, 2018; New York, NY. Philadelphia (PA): AACR; Cancer Immunol Res 2019;7(2 Suppl):Abstract nr A160.

Cross-sectional biomonitoring study of pesticide exposures in Queensland, Australia, using pooled urine samples

A range of pesticides are available in Australia for use in agricultural and domestic settings to control pests, including organophosphate and pyrethroid insecticides, herbicides, and insect repellents, such as N,N-diethyl-meta-toluamide (DEET). The aim of this study was to provide a cost-effective preliminary assessment of background exposure to a range of pesticides among a convenience sample of Australian residents. De-identified urine specimens stratified by age and sex were obtained from a community-based pathology laboratory and pooled (n = 24 pools of 100 specimens). Concentrations of urinary pesticide biomarkers were quantified using solid-phase extraction coupled with isotope dilution high-performance liquid chromatography-tandem mass spectrometry. Geometric mean biomarker concentrations ranged from <0.1 to 36.8 ng/mL for organophosphate insecticides, <0.1 to 5.5 ng/mL for pyrethroid insecticides, and <0.1 to 8.51 ng/mL for all other biomarkers with the exception of the DEET metabolite 3-diethylcarbamoyl benzoic acid (4.23 to 850 ng/mL). We observed no association between age and concentration for most biomarkers measured but noted a "U-shaped" trend for five organophosphate metabolites, with the highest concentrations observed in the youngest and oldest age strata, perhaps related to age-specific differences in behavior or physiology. The fact that concentrations of specific and non-specific metabolites of the organophosphate insecticide chlorpyrifos were higher than reported in USA and Canada may relate to differences in registered applications among countries. Additional biomonitoring programs of the general population and focusing on vulnerable populations would improve the exposure assessment and the monitoring of temporal exposure trends as usage patterns of pesticide products in Australia change over time.

Concentrations of phthalates and DINCH metabolites in pooled urine from Queensland, Australia

Dialkyl phthalate esters (phthalates) are ubiquitous chemicals used extensively as plasticizers, solvents and adhesives in a range of industrial and consumer products. 1,2-Cyclohexane dicarboxylic acid, diisononyl ester (DINCH) is a phthalate alternative introduced due to a more favourable toxicological profile, but exposure is largely uncharacterised. The aim of this study was to provide the first assessment of exposure to phthalates and DINCH in the general Australian population. De-identified urine specimens stratified by age and sex were obtained from a community-based pathology laboratory and pooled (n=24 pools of 100). Concentrations of free and total species were measured using online solid phase extraction isotope dilution high performance liquid chromatography tandem mass spectrometry. Concentrations ranged from 2.4 to 71.9ng/mL for metabolites of di(2-ethylhexyl)phthalate, and from <0.5 to 775ng/mL for all other metabolites. Our data suggest that phthalate metabolites concentrations in Australia were at least two times higher than in the United States and Germany; and may be related to legislative differences among countries. DINCH metabolite concentrations were comparatively low and consistent with the limited data available. Ongoing biomonitoring among the general Australian population may help assess temporal trends in exposure and assess the effectiveness of actions aimed at reducing exposures.

DG Connect Funded Projects on Information and Communication Technologies (ICT) for Old Age People: Beyond Silos, CareWell and SmartCare

Information and communication technologies (ICT) are promising for the long-term care of older and frequently frail people. These innovations can improve health outcomes, quality of life and efficiency of care processes, while supporting independent living. However, they may be disruptive innovations. As all European member states are facing an increasing complexity of health and social care, good practices in ICT should be identified and evaluated. Three projects funded by DG CNECT are related to Active and Healthy Ageing (AHA) and frailty: (i) BeyondSilos, dealing with independent living and integrated services, (ii) CareWell, providing integrated care coordination, patient empowerment and home support and (iii) SmartCare, proposing a common set of standard functional specifications for an ICT platform enabling the delivery of integrated care to older patients. The three projects described in this paper provide a unique pan-European research field to further study implementation efforts and outcomes of new technologies. Below, based on a description of the projects, the authors display four domains that are in their views fundamental for in-depth exploration of heterogeneity in the European context: 1. Definition of easily transferable, high level pathways with solid evidence-base; 2. Change management in implementing ICT enabled integrated care; 3. Evaluation and data collection methodologies based on existing experience with MAST and MEDAL methodologies; and 4. Construction of new models for delivery of health and social care. Understanding complementarity, synergies and differences between the three unique projects can help to identify a more effective roll out of best practices within a varying European context.

Use of pooled samples to assess human exposure to parabens, benzophenone-3 and triclosan in Queensland, Australia

Parabens, benzophenone-3 and triclosan are common ingredients used as preservatives, ultraviolet radiation filters and antimicrobial agents, respectively. Human exposure occurs through consumption of processed food and use of cosmetics and consumer products. The aim of this study was to provide a preliminary characterisation of exposure to selected personal care product chemicals in the general Australian population. De-identified urine specimens stratified by age and sex were obtained from a community-based pathology laboratory and pooled (n=24 pools of 100). Concentrations of free and total (sum of free plus conjugated) species of methyl, ethyl, propyl and butyl paraben, benzophenone-3 and triclosan were quantified using isotope dilution tandem mass spectrometry; with geometric means 232, 33.5, 60.6, 4.32, 61.5 and 87.7ng/mL, respectively. Age was inversely associated with paraben concentration, and females had concentrations approximately two times higher than males. Total paraben and benzophenone-3 concentrations are significantly higher than reported worldwide, and the average triclosan concentration was more than one order of magnitude higher than in many other populations. This study provides the first data on exposure of the general Australian population to a range of common personal care product chemical ingredients, which appears to be prevalent and warrants further investigation.

Intrinsic properties of germinal center-derived B cells promote their enhanced class switching to IgE

Background

Research on the origins and development of human IgE‐expressing (IgE⁺) cells is required for understanding the pathogenesis of allergy and asthma. These studies have been thwarted by the rarity of IgE⁺ cells in vivo and the low frequency of class switch recombination (CSR) to IgE ex vivo. To determine the main source of IgE⁺ cells, we investigated the relation between the phenotypic composition of tonsil B cells and the CSR to IgE ex vivo.

Methods

Human tonsil B cells were analyzed by flow cytometry (FACS) and cultured with IL‐4 and anti‐CD40 to induce CSR to IgE. Naïve, germinal center (GC), early GC (eGC), and memory tonsil B cells were isolated by FACS, and their capacities for IL‐4 and anti‐CD40 signaling, cell proliferation, and de novo class switching to IgE were analyzed by RT‐PCR and FACS.

Results

B cells from different tonsils exhibited varying capacities for CSR to IgE ex vivo. This was correlated with the percentage of eGC B cells in the tonsil at the outset of the culture. Despite relatively poor cell viability, eGC and GC B‐cell cultures produced the highest yields of IgE⁺ cells compared to naïve and memory B‐cell cultures. The main factors accounting for this result were the strength of IL‐4R and CD40 signaling and relative rates of cell proliferation.

Conclusions

This study shows that the maturation state of tonsil B cells determines their capacity to undergo class switching to IgE ex vivo, with the GC‐derived B cells yielding the highest percentage of IgE⁺ cells.

The effect of ongoing blood loss on human serum concentrations of perfluorinated acids

Perfluorinated alkyl acids (PFAAs) have been detected in serum at low concentrations in background populations. Higher concentrations haven been observed in adult males compared to females, with a possible explanation that menstruation offers females an additional elimination route. In this study, we examined the significance of blood loss as an elimination route of PFAAs. Pooled serum samples were collected from individuals undergoing a medical procedure involving ongoing blood withdrawal called venesection. Concentrations from male venesection patients were approximately 40% lower than males in the general population for perfluorohexane sulfonate (PFHxS), perfluorooctane sulfonate (PFOS) and perfluorooctanoic acid (PFOA). A simple pharmacokinetic model was used to test the hypothesis that blood loss could explain why adult males have higher concentrations of PFAAs than females, and why males undergoing venesections had lower concentrations compared to males in the general population. The model application generally supported these hypotheses showing that venesection might reduce blood serum concentrations by 37% (PFOA) and 53% (PFOS) compared to the observed difference of 44% and 37%. Menstruation was modeled to show a 22% reduction in PFOA serum concentrations compared to a 24% difference in concentrations between males and females in the background population. Uncertainties in the modeling and the data are identified and discussed.

Decline in perfluorooctane sulfonate and perfluorooctanoate serum concentrations in an Australian population from 2002 to 2011

Some perfluoroalkyl and polyfluoroalkyl substances (PFASs) have become widespread pollutants detected in human and wildlife samples worldwide. The main objective of this study was to assess temporal trends of PFAS concentrations in human blood in Australia over the last decade (2002-2011), taking into consideration age and sex trends. Pooled human sera from 2002/03 (n=26); 2008/09 (n=24) and 2010/11 (n=24) from South East Queensland, Australia were obtained from de-identified surplus pathology samples and compared with samples collected previously from 2006/07 (n=84). A total of 9775 samples in 158 pools were available for an assessment of PFASs. Stratification criteria included sex and age: <16 years (2002/03 only); 0-4 (2006/07, 2008/09, 2010/11); 5-15 (2006/07, 2008/09, 2010/11); 16-30; 31-45; 46-60; and >60 years (all collection periods). Sera were analyzed using on-line solid-phase extraction coupled to high-performance liquid chromatography-isotope dilution-tandem mass spectrometry. Perfluorooctane sulfonate (PFOS) was detected in the highest concentrations ranging from 5.3-19.2 ng/ml (2008/09) to 4.4-17.4 ng/ml (2010/11). Perfluorooctanoate (PFOA) was detected in the next highest concentration ranging from 2.8-7.3 ng/ml (2008/09) to 3.1-6.5 ng/ml (2010/11). All other measured PFASs were detected at concentrations <1 ng/ml with the exception of perfluorohexane sulfonate which ranged from 1.2-5.7 ng/ml (08/09) and 1.4-5.4 ng/ml (10/11). The mean concentrations of both PFOS and PFOA in the 2010/11 period compared to 2002/03 were lower for all adult age groups by 56%. For 5-15 year olds, the decrease was 66% (PFOS) and 63% (PFOA) from 2002/03 to 2010/11. For 0-4 year olds the decrease from 2006/07 (when data were first available for this age group) was 50% (PFOS) and 22% (PFOA). This study provides strong evidence for decreasing serum PFOS and PFOA concentrations in an Australian population from 2002 through 2011. Age trends were variable and concentrations were higher in males than in females. Global use has been in decline since around 2002 and hence primary exposure levels are expected to be decreasing. Further biomonitoring will allow assessment of PFAS exposures to confirm trends in exposure as primary and eventually secondary sources are depleted.

Bisphenol A exposure is not associated with area-level socioeconomic index in Australian children using pooled urine samples

Bisphenol A (BPA) is used extensively in food-contact materials and has been detected routinely in populations worldwide; this exposure has been linked to a range of negative health outcomes in humans. There is some evidence of an association between BPA and different socioeconomic variables which may be the result of different dietary patterns. The aim of this study was to conduct a preliminary investigation of the association between BPA and socioeconomic status in Australian children using pooled urine specimens and an area-level socioeconomic index. Surplus pathology urine specimens collected from children aged 0-15 years in Queensland, Australia, as samples of convenience (n=469), were pooled by age, sex and area-level socioeconomic index (n=67 pools) and analysed for total BPA using online solid-phase extraction LC-MS/MS. Concentration ranged from 1.08 to 27.4 ng/ml with geometric mean 2.57 ng/ml, and geometric mean exposure was estimated as 70.3 ng/kg d(-1). Neither BPA concentration nor excretion was associated with age or sex, and the authors found no evidence of an association with socioeconomic status. These results suggest that BPA exposure is not associated with socioeconomic status in the Australian population due to relatively homogenous exposures in Australia, or that the socioeconomic gradient is relatively slight in Australia compared with other OECD countries.

Age-related trends in urinary excretion of bisphenol A in Australian children and adults: evidence from a pooled sample study using samples of convenience

Bisphenol A (BPA or 4,4'-(propane-2,2-diyl)diphenol) is a chemical intermediate in the production of polycarbonate and epoxy resins, and is used in a wide range of applications. BPA has attracted significant attention in the past decade due to its frequency of detection in human populations worldwide, and has demonstrated animal toxicity and potential impact on human health, particularly during critical periods of development. The aim of this study was to perform a preliminary assessment of age-related trends in urinary concentration and to estimate daily excretion of BPA in Australian children (aged >0 to <5 yr) and adults (≥15 to <75 yr). This was achieved using 79 samples pooled by age and gender, created from 868 individual samples of convenience collected as part of routine, community-based pathology testing. Total BPA was analyzed using online solid phase extraction (SPE)-liquid chromatography tandem mass spectrometry (LC-MS/MS) and detected in all samples with a range of 0.65-265 ng/ml. No significant differences were observed between males and females. A urine flow model was constructed from published values and was used to provide an estimate of daily excretion per unit body weight for each pooled sample. The daily excretion estimates ranged from 26.2 to 18,200 ng/kg-d for children, and from 20.1 to 165 ng/kg-d for adults. Urinary concentrations and estimated excretion rates were inversely associated with age, and estimated daily excretion in infants and young children was significantly higher than in adults (geometric mean: 107 and 47.0 ng/kg-d, respectively). Higher excretion of BPA in children may be explained by their higher food consumption relative to body weight compared to adults and adolescents, and may also reflect alternative exposure pathways and sources.

High resolution analysis of the chromatin landscape of the IgE switch region in human B cells

Antibodies are assembled by a highly orchestrated series of recombination events during B cell development. One of these events, class switch recombination, is required to produce the IgG, IgE and IgA antibody isotypes characteristic of a secondary immune response. The action of the enzyme activation induced cytidine deaminase is now known to be essential for the initiation of this recombination event. Previous studies have demonstrated that the immunoglobulin switch regions acquire distinct histone modifications prior to recombination. We now present a high resolution analysis of these histone modifications across the IgE switch region prior to the initiation of class switch recombination in primary human B cells and the human CL-01 B cell line. These data show that upon stimulation with IL-4 and an anti-CD40 antibody that mimics T cell help, the nucleosomes of the switch regions are highly modified on histone H3, accumulating acetylation marks and tri-methylation of lysine 4. Distinct peaks of modified histones are found across the switch region, most notably at the 5′ splice donor site of the germline (I) exon, which also accumulates AID. These data suggest that acetylation and K4 tri-methylation of histone H3 may represent marks of recombinationally active chromatin and further implicates splicing in the regulation of AID action.

Magnetic resonance imaging in rectal cancer downstaged using neoadjuvant chemoradiation: accuracy of prediction of tumour stage and circumferential resection margin status

OBJECTIVE

The aim was to examine the accuracy of magnetic resonance imaging (MRI) in predicting circumferential resection margin (CRM) involvement, T- and N-stage in patients with locally advanced carcinoma of the rectum, who had undergone long-course downstaging chemoradiation (CRT).

METHOD

Patients with rectal cancer were selected for long-course downstaging CRT if their tumour was considered to threaten (< or = 1 mm) or involve the CRM on MRI. Eighty such patients had a repeat MRI at a median of 6 weeks post-CRT followed by surgical excision soon thereafter. The findings on the post-CRT MRI were compared with histological examination of the surgical specimen.

RESULTS

For CRM involvement, post-CRT restaging MRI had an accuracy of 81% (65/80) a sensitivity of 54% (7/13), a specificity of 87% (58/67), a positive predictive value of 44% (7/16) and a negative predictive value of 91% (58/64). Accuracy for T- and N-staging was 43% (34/80) and 78% (62/80), respectively. 38% of T-stages were overstaged and 20% understaged. 4% of N-stages were overstaged and 19% understaged. The 13 patients with histological positive CRM had worse clinical outcomes than the 67 patients with negative CRM in terms of disease-free survival (relative risk of reduced DFS 4.6, P = 0.001) and overall survival (relative risk of death 3.6, P = 0.016).

CONCLUSION

Magnetic resonance imaging has good specificity and negative predictive value for predicting an uninvolved CRM post downstaging CRT in locally advanced rectal cancer although sensitivity and positive predictive value for an involved CRM were unsatisfactory. The shortcomings of MRI stem from poor differentiation of viable tumour from posttreatment changes and inability to identify small nodal and tumour deposits. Clinical correlates in this group of patients have confirmed the importance of achieving a clear CRM at surgery.

Recent developments in molecular therapeutic approaches for rheumatoid arthritis

Rheumatoid arthritis is a debilitating systemic autoimmune disease characterized by chronic synovial inflammation, which results in the progressive destruction of diseased joints. Advances in understanding the disease pathogenesis have led to the clinical introduction of biological inhibitors of inflammation or articular destruction. However, frequency of administration, cost and systemic side effects have driven efforts to develop gene therapeutic transfer strategies. This article reviews recent progress in the application of viral and non-viral vectors to target therapeutic genes for in vivo delivery.

Mucosal immunization with DNA vaccines

DNA vaccines represent a new approach to the control of infectious disease. Both cellular and humoral immune responses are induced without the attendant concerns associated with live, attenuated vaccines. The vast majority of DNA vaccines are delivered by parental routes, which rarely elicit immune responses at the mucosal epithelia, the primary sites of pathogen transmission. In view of the importance of mucosal and regional lymph node immunity in the control of pathogens transmitted across the mucosal epithelia, a number of groups, including our own, have developed immunization strategies that target plasmid DNA to mucosal inductive sites associated with the lymphoid tissues of the respiratory, gastrointestinal, and genital tracts. Here, we describe the procedures for the formulation and delivery of plasmid DNA to mucosal inductive tissues and address the theoretical basis to selection of particular mucosal locations for the induction of effective immune responses.

Measuring the impact of Parkinson's disease with the Parkinson's Disease Quality of Life questionnaire

OBJECTIVES

To assess the validity of the Parkinson's Disease Quality of Life (PDQL) questionnaire, a patient-specific multi-dimensional quality of life measure, in a community-based sample of patients with Parkinson's disease (PI)) using standardized measures of disease severity, depressive symptomatology and cognitive function.

DESIGN

A group of 194 patients with probable PD were randomly selected from a community-based register and were invited to self-complete the 37-item PDQL. Disease severity was measured by the disease-specific Webster scale, cognition by the CAMCOG neuropsychological test and depressive symptomatology by the self-report 15-item GDS-15 geriatric depression scale.

RESULTS

A total of 136 patients returned completed PDQL questionnaires. Significant differences (P < 0.05) emerged between the pooled PDQL score of patients grouped on the basis of disease severity. Depressive symptoms and cognition were also associated with poorer perceived quality of life as measured by the PDQL.

CONCLUSIONS

The results of this study are indicative of the validity of the PDQL as an important additional measurement which reflects the impact of PD from the patient perspective. It shows poorer quality of life to be associated with increasing age, disease severity more severe depressive symptomatology and impaired cognitive functioning. However, the responsiveness of this instrument in the evaluation of care in PD remains to be determined.

Accuracy of diagnosis in patients with presumed Parkinson's disease

OBJECTIVES

to study the diagnostic accuracy for parkinsonism and Parkinson's disease in a community-based sample of subjects on anti-parkinsonian medication.

METHODS

computerized prescribing records in general practice were used to create a community-based disease register for Parkinson's disease. Subjects were examined to establish the likely diagnosis using recommended clinical diagnostic criteria.

RESULTS

of 402 cases, parkinsonism was confirmed in 74% and clinically probable Parkinson's disease in 53%. The commonest causes of misdiagnosis were essential tremor, Alzheimer's disease and vascular pseudo-parkinsonism. Over one-quarter of subjects did not benefit from anti-parkinsonian medication.

CONCLUSIONS

there is difficulty in diagnosing parkinsonism and Parkinson's disease in elderly subjects and we suggest early referral of those suspected of having parkinsonism for specialist assessment.

The detection of dementia and cognitive impairment in a community population of elderly people with Parkinson's disease by use of the CAMCOG neuropsychological test

AIM

To assess cognitive function in elderly subjects with clinically probable Parkinson's disease (PD).

METHODS

A community sample of 126 patients with probable PD completed the CAMCOG, which is the cognitive section of the Cambridge Examination for Mental Disorders, and the Mini-Mental State Examination (MMSE). The performance of the CAMCOG and the MMSE in detecting dementia in this subject group was compared with the results of applying the DSM-IV criteria for dementia to this population.

RESULTS

A total of 44% of the group met DSM-IV criteria for dementia, which is higher than most previous prevalence figures for dementia in PD. The CAMCOG was more sensitive than the MMSE in detecting cognitive impairment and more specific than the MMSE in detecting dementia as defined by DSM-IV criteria. Poorer performance on the CAMCOG was related to gender, social class and age (P<0.05). Among subjects with PD, those with dementia, as defined by DSM-IV criteria, were significantly older, had greater depressive symptomatology and had greater motor deficits. A greater proportion of the group with dementia were living in residential care (P<0.05).

CONCLUSION

The CAMCOG appears to be a useful screening instrument for dementia and cognitive impairment in PD. Furthermore, it may prove helpful in detecting those with PD who may be at risk of developing dementia and in longitudinal studies of cognitive function in PD.

Use of the GDS-15 geriatric depression scale as a screening instrument for depressive symptomatology in patients with Parkinson's disease and their carers in the community

OBJECTIVES

To assess the level of depressive symptomatology in a community based group of patients with Parkinson's disease (PD) and their carers and to investigate the patient characteristics that might predict carer distress.

METHODS

The GDS-15 geriatric depression scale was used to measure self-rated depressive symptoms in a group of 132 subjects with clinically probable PD randomly selected from a community-based disease register. Disease severity was assessed by the Webster scale and cognitive function by the CAMCOG test. Carers of the patients, who in this study were all spouses, were also asked to complete the GDS-15.

RESULTS

A total of 64% of our group of patients and 34% of carers scored within the 'depressed' range on the GDS-15. Patients with high levels of depressive symptoms tended to have more severe disease, disease of longer duration and more impaired cognitive function. The GDS score of the carer was best predicted by the GDS score of the patient being cared for. Less than 10% of patients and carers were being treated with antidepressant medication.

CONCLUSIONS

This community-based study confirms the high level of depressive symptoms in PD suggested by hospital- and clinic-based studies. Depression in patients appears to be related to disease severity and cognitive impairment. An important determinant of carer distress and mood disorder, as reflected by the GDS score, appears to be the level of depression expressed by the patient being cared for. Despite high levels of depressive symptoms in both patients and carers, very few subjects were in receipt of antidepressant drug therapy.

Can practice guidelines safely reduce hospital length of stay? Results from a multicenter interventional study

BACKGROUND

Although practice guidelines about appropriate lengths of stay have been widely promulgated, their effects on patient outcomes are not clear. Our objective was to study the effects of length of stay practice guidelines on patient outcomes.

PATIENTS AND METHODS

We performed a prospective, nonrandomized, interventional trial in six geographically distributed hospitals, among consecutively hospitalized "low-risk" patients with total hip replacement, hip fracture, or knee replacement. Case managers provided physicians with patient risk information based on guideline recommendations. We measured length of stay, compliance with recommended guideline length of stay, health status, hospital readmission rates, return to emergency department, return to work and recreation, and patient satisfaction.

RESULTS

A total of 560 patients were included in the study. For patients with knee replacement, there was a statistically significant increase in practice guideline compliance (27% baseline versus 53% intervention, P <0.0001) and reduction in length of stay (5.2 days versus 4.6 days, P <0.001) when compared with the baseline period. For hip replacement patients, there similarly was an increase in practice guideline compliance (66% baseline versus 82% intervention, P = 0.01) and reduction in length of stay (5.1 days versus 4.8 days, P = 0.03). Significant reductions in length of stay were not observed for patients recovering after hip fracture despite a significant increase in guideline compliance. There were few statistically significant changes in patient outcomes related to reductions in lengths of stay, including health status, hospital readmission rates, return to emergency department, return to work and recreation, and patient satisfaction. For patients undergoing hip replacement, very short lengths of stay (shorter than the guideline recommendation) were associated with an increased rate of discharging patients to nursing homes and rehabilitation facilities (21% versus 7%, P = 0.01), and hip fracture patients with very short lengths of stay required more visits to the doctor after discharge (56% versus 25%, P = 0.04).

CONCLUSION

Reductions in lengths of stay were most often associated with no significant change in patient outcomes. However, very short lengths of stay were associated with increased intensity of care following discharge for patients undergoing hip surgery, indicating possible cost shifting (the cost incurred by transferring patients to rehabilitation facilities may have been greater than had the patients remained in the acute care hospital for an additional 1 or 2 days and been sent directly home). These results emphasize the importance of monitoring the effects of cost containment and other systematic efforts to change patient care at the local level.