Precision-guided treatment in high-risk pediatric cancers.

Recent research showed that precision medicine can identify new treatment strategies for patients with childhood cancers. However, it is unclear which patients will benefit most from precision-guided treatment (PGT). Here we report consecutive data from 384 patients with high-risk pediatric cancer (with an expected cure rate of less than 30%) who had at least 18 months of follow-up on the ZERO Childhood Cancer Precision Medicine Program PRecISion Medicine for Children with Cancer (PRISM) trial. A total of 256 (67%) patients received PGT recommendations and 110 (29%) received a recommended treatment. PGT resulted in a 36% objective response rate and improved 2-year progression-free survival compared with standard of care (26% versus 12%; P = 0.049) or targeted agents not guided by molecular findings (26% versus 5.2%; P = 0.003). PGT based on tier 1 evidence, PGT targeting fusions or commenced before disease progression had the greatest clinical benefit. Our data show that PGT informed by comprehensive molecular profiling significantly improves outcomes for children with high-risk cancers. ClinicalTrials.gov registration: NCT03336931.

Real-world utilisation of SARS-CoV-2 rapid antigen testing to enable face-to-face learning in Australian schools, an ecological study.

OBJECTIVE: The objective of this study was to describe the use of SARS-CoV-2 rapid antigen testing of COVID-19 contacts in New South Wales schools to determine return to in-person school attendance instead of home quarantine, between 6 November and 21 December 2021. METHODS: COVID-19 school contacts were required to quarantine for two weeks postexposure to the case. Students who opted into daily rapid antigen testing logged their results in a database, prior to school attendance, and obtained SARS-CoV-2 nucleic amplification acid testing on day 12-16. Secondary attack rates (SARs) in schools utilising rapid antigen testing (Test-to-Stay schools) and those not utilising rapid antigen testing (non-Test-to-Stay school) were calculated. RESULTS: We identified 9,887 people in 293 schools who reported performing at least one rapid antigen test (RAT). The SAR in RAT schools was 3.4% (95% confidence interval: 2.7-4.1) and non-RAT schools was 2.8% (95% confidence interval: 2.4-3.3). A total of 30,535 school days were preserved through this program. CONCLUSIONS: The use of RATs preserved in-person learning without a significant increase to SAR. IMPLICATION FOR PUBLIC HEALTH: Disruptions in face-to-face learning have long-term detrimental impacts on children and adolescents. Rapid antigen testing has been shown to be beneficial to maintain face-to-face learning in Australian schools and may be a useful method to safeguard from school disruptions in future pandemics.

In the Murine and Bovine Maternal Mammary Gland Signal Transducer and Activator of Transcription 3 is Activated in Clusters of Epithelial Cells around the Day of Birth.

Signal transducers and activators of transcription (STAT) proteins regulate mammary development. Here we investigate the expression of phosphorylated STAT3 (pSTAT3) in the mouse and cow around the day of birth. We present localised colocation analysis, applicable to other mammary studies requiring identification of spatially congregated events. We demonstrate that pSTAT3-positive events are multifocally clustered in a non-random and statistically significant fashion. Arginase-1 expressing cells, consistent with macrophages, exhibit distinct clustering within the periparturient mammary gland. These findings represent a new facet of mammary STAT3 biology, and point to the presence of mammary sub-microenvironments.

Comparative Lipidomics of Oral Commensal and Opportunistic Bacteria.

The oral cavity contains a vast array of microbes that contribute to the balance between oral health and disease. In addition, oral bacteria can gain access to the circulation and contribute to other diseases and chronic conditions. There are a limited number of publications available regarding the comparative lipidomics of oral bacteria and fungi involved in the construction of oral biofilms, hence our decision to study the lipidomics of representative oral bacteria and a fungus. We performed high-resolution mass spectrometric analyses (<2.0 ppm mass error) of the lipidomes from five Gram-positive commensal bacteria: Streptococcus oralis, Streptococcus intermedius, Streptococcus mitis, Streptococcus sanguinis, and Streptococcus gordonii; five Gram-positive opportunistic bacteria: Streptococcus mutans, Staphylococcus epidermis, Streptococcus acidominimus, Actinomyces viscosus, and Nanosynbacter lyticus; seven Gram-negative opportunistic bacteria: Porphyromonas gingivalis. Prevotella brevis, Proteus vulgaris, Fusobacterium nucleatum, Veillonella parvula, Treponema denticola, and Alkermansia muciniphila; and one fungus: Candida albicans. Our mass spectrometric analytical platform allowed for a detailed evaluation of the many structural modifications made by microbes for the three major lipid scaffolds: glycerol, sphingosine and fatty acyls of hydroxy fatty acids (FAHFAs).

Freshwater invertebrate responses to fine sediment stress: A multi-continent perspective.

Excessive fine sediment (particles <2 mm) deposition in freshwater systems is a pervasive stressor worldwide. However, understanding of ecological response to excess fine sediment in river systems at the global scale is limited. Here, we aim to address whether there is a consistent response to increasing levels of deposited fine sediment by freshwater invertebrates across multiple geographic regions (Australia, Brazil, New Zealand and the UK). Results indicate ecological responses are not globally consistent and are instead dependent on both the region and the facet of invertebrate diversity considered, that is, taxonomic or functional trait structure. Invertebrate communities of Australia were most sensitive to deposited fine sediment, with the greatest rate of change in communities occurring when fine sediment cover was low (below 25% of the reach). Communities in the UK displayed a greater tolerance with most compositional change occurring between 30% and 60% cover. In both New Zealand and Brazil, which included the most heavily sedimented sampled streams, the communities were more tolerant or demonstrated ambiguous responses, likely due to historic environmental filtering of invertebrate communities. We conclude that ecological responses to fine sediment are not generalisable globally and are dependent on landscape filters with regional context and historic land management playing important roles.

Recent history of Veterinary Immunology in Australia.

This Commentary article reviews the history of veterinary immunology in Australia from the 1980s and discusses the key people and areas of research during this period.

Pilot Lipidomics Study of Copepods: Investigation of Potential Lipid-Based Biomarkers for the Early Detection and Quantification of the Biological Effects of Climate Change on the Oceanic Food Chain.

Maintenance of the health of our oceans is critical for the survival of the oceanic food chain upon which humanity is dependent. Zooplanktonic copepods are among the most numerous multicellular organisms on earth. As the base of the primary consumer food web, they constitute a major biomass in oceans, being an important food source for fish and functioning in the carbon cycle. The potential impact of climate change on copepod populations is an area of intense study. Omics technologies offer the potential to detect early metabolic alterations induced by the stresses of climate change. One such omics approach is lipidomics, which can accurately quantify changes in lipid pools serving structural, signal transduction, and energy roles. We utilized high-resolution mass spectrometry (≤2 ppm mass error) to characterize the lipidome of three different species of copepods in an effort to identify lipid-based biomarkers of copepod health and viability which are more sensitive than observational tools. With the establishment of such a lipid database, we will have an analytical platform useful for prospectively monitoring the lipidome of copepods in a planned long-term five-year ecological study of climate change on this oceanic sentinel species. The copepods examined in this pilot study included a North Atlantic species (Calanus finmarchicus) and two species from the Gulf of Mexico, one a filter feeder (Acartia tonsa) and one a hunter (Labidocerca aestiva). Our findings clearly indicate that the lipidomes of copepod species can vary greatly, supporting the need to obtain a broad snapshot of each unique lipidome in a long-term multigeneration prospective study of climate change. This is critical, since there may well be species-specific responses to the stressors of climate change and co-stressors such as pollution. While lipid nomenclature and biochemistry are extremely complex, it is not essential for all readers interested in climate change to understand all of the various lipid classes presented in this study. The clear message from this research is that we can monitor key copepod lipid families with high accuracy, and therefore potentially monitor lipid families that respond to environmental perturbations evoked by climate change.

Seasonal variability of lotic macroinvertebrate communities at the habitat scale demonstrates the value of discriminating fine sediment fractions in ecological assessments.

Despite lotic systems demonstrating high levels of seasonal and spatial variability, most research and biomonitoring practices do not consider seasonality when interpreting results and are typically focused at the meso-scale (combined pool/riffle samples) rather than considering habitat patch dynamics. We therefore sought to determine if the sampling season (spring, summer and autumn) influenced observed macroinvertebrate biodiversity, structure and function at the habitat unit scale (determined by substrate composition), and if this in turn influenced the assessment of fine sediment (sand and silt) pressures. We found that biodiversity supported at the habitat level was not seasonally consistent with the contribution of nestedness and turnover in structuring communities varying seasonally. Habitat differences in community composition were evident for taxonomic communities regardless of the season but were not seasonally consistent for functional communities, and, notably, season explained a greater amount of variance in functional community composition than the habitat unit. Macroinvertebrate biodiversity supported by silt habitats demonstrated strong seasonal differences and communities were functionally comparable to sand habitats in spring and to gravel habitats in autumn. Sand communities were impoverished compared to other habitats regardless of the season. Silt habitats demonstrated a strong increase in Ephemeroptera, Plecoptera and Trichoptera (EPT) taxa and functional richness from spring into autumn, while vegetation habitats displayed a peak in EPT abundance in summer. Only silt and sand habitats demonstrated temporal variability in functional evenness suggesting that these habitats are different in terms of their resource partitioning and productivity over time compared to other habitats. Gravel and vegetation habitats appeared to be more stable over time with functional richness and evenness remaining consistent. To accurately evaluate the influence of fine sediment on lotic ecosystems, it is imperative that routine biomonitoring and scientific research discriminate between sand and silt fractions, given they support different biodiversity, particularly during summer and autumn months.

Design and manufacture of one-size-fits-all healthcare face shields for the NHS during the COVID-19 pandemic.

During the COVID-19 pandemic, there was a shortage of personal protective equipment, PPE, which resulted in non-certified PPE being used by healthcare staffs. These would not provide the appropriate protection against the SARS-CoV-2 virus. Together with the local NHS Trust (University Hospitals of Derby and Burton (UHDB) NHS Foundation Trust) and a local small and medium enterprise (SME), Riverside Medical Packaging Ltd, the University of Derby (UoD) developed test protocols for PPE with a one-size-fits-all concept. Building on best practice in reviewing the literature and current design requirements, key design parameters were identified such as a minimum strap width and comfort level for healthcare related Face Shield. Two strap headbands made from fabric and elastomer with linear stiffness of 44.1 ± 0.3 N/m and 149.1 ± 3.1 N/m respectively were tested with respect to fit and comfort on small and large arc-shaped models. There was an exponential change in pressure from the side to the middle of the strap headbands. The high stiffness of the elastomer in a radial set-up influenced the pressure exerted on a wearer's head when the elastomer strap was used. Meanwhile the coefficient of friction between the fabric strap and arc-shaped model influenced the pressure exerted when a fabric strap was used. The ergonomics of the designed Face Shields supported the one-size-fits-all concept, whereby various gender and head circumferences were considered. The findings in this paper will promote new standards in the design of PPE with a one-size-fits-all target.

Construction of a Bacterial Lipidomics Analytical Platform: Pilot Validation with Bovine Paratuberculosis Serum.

Lipidomics analyses of bacteria offer the potential to detect and monitor infections in a host since many bacterial lipids are not present in mammals. To evaluate this omics approach, we first built a database of bacterial lipids for representative Gram-positive and Gram-negative bacteria. Our lipidomics analysis of the reference bacteria involved high-resolution mass spectrometry and electrospray ionization with less than a 1.0 ppm mass error. The lipidomics profiles of bacterial cultures clearly distinguished between Gram-positive and Gram-negative bacteria. In the case of bovine paratuberculosis (PTB) serum, we monitored two unique bacterial lipids that we also monitored in Mycobacterium avian subspecies PTB. These were PDIM-B C82, a phthiodiolone dimycocerosate, and the trehalose monomycolate hTMM 28:1, constituents of the bacterial cell envelope in mycolic-containing bacteria. The next step will be to determine if lipidomics can detect subclinical PTB infections which can last 2-to-4 years in bovine PTB. Our data further suggest that it will be worthwhile to continue building our bacterial lipidomics database and investigate the further utility of this approach in other infections of veterinary and human clinical interest.

Implementation of DNA Methylation Array Profiling in Pediatric Central Nervous System Tumors: The AIM BRAIN Project: An Australian and New Zealand Children's Haematology/Oncology Group Study.

DNA methylation array profiling for classifying pediatric central nervous system (CNS) tumors is a valuable adjunct to histopathology. However, unbiased prospective and interlaboratory validation studies have been lacking. The AIM BRAIN diagnostic trial involving 11 pediatric cancer centers in Australia and New Zealand was designed to test the feasibility of routine clinical testing and ran in parallel with the Molecular Neuropathology 2.0 (MNP2.0) study at Deutsches Krebsforschungszentrum (German Cancer Research Center). CNS tumors from 269 pediatric patients were prospectively tested on Illumina EPIC arrays, including 104 cases co-enrolled on MNP2.0. Using MNP classifier versions 11b4 and 12.5, we report classifications with a probability score ≥0.90 in 176 of 265 (66.4%) and 213 of 269 (79.2%) cases, respectively. Significant diagnostic information was obtained in 130 of 176 (74%) for 11b4, and 12 of 174 (7%) classifications were discordant with histopathology. Cases prospectively co-enrolled on MNP2.0 gave concordant classifications (99%) and score thresholds (93%), demonstrating excellent test reproducibility and sensitivity. Overall, DNA methylation profiling is a robust single workflow technique with an acceptable diagnostic yield that is considerably enhanced by the extensive subgroup and copy number profile information generated by the platform. The platform has excellent test reproducibility and sensitivity and contributes significantly to CNS tumor diagnosis.

BRAF-mediated brain tumors in adults and children: A review and the Australian and New Zealand experience.

The mitogen-activated protein kinase (MAPK) pathway signaling pathway is one of the most commonly mutated pathways in human cancers. In particular, BRAF alterations result in constitutive activation of the rapidly accelerating fibrosarcoma-extracellular signal-regulated kinase-MAPK significant pathway, leading to cellular proliferation, survival, and dedifferentiation. The role of BRAF mutations in oncogenesis and tumorigenesis has spurred the development of targeted agents, which have been successful in treating many adult cancers. Despite advances in other cancer types, the morbidity and survival outcomes of patients with glioma have remained relatively stagnant. Recently, there has been recognition that MAPK dysregulation is almost universally present in paediatric and adult gliomas. These findings, accompanying broad molecular characterization of gliomas, has aided prognostication and offered opportunities for clinical trials testing targeted agents. The use of targeted therapies in this disease represents a paradigm shift, although the biochemical complexities has resulted in unexpected challenges in the development of effective BRAF inhibitors. Despite these challenges, there are promising data to support the use of BRAF inhibitors alone and in combination with MEK inhibitors for patients with both low-grade and high-grade glioma across age groups. Safety and efficacy data demonstrate that many of the toxicities of these targeted agents are tolerable while offering objective responses. Newer clinical trials will examine the use of these therapies in the upfront setting. Appropriate duration of therapy and durability of response remains unclear in the glioma patient cohort. Longitudinal efficacy and toxicity data are needed. Furthermore, access to these medications remains challenging outside of clinical trials in Australia and New Zealand. Compassionate access is limited, and advocacy for mechanism of action-based drug approval is ongoing.

A novel transcriptional signature identifies T-cell infiltration in high-risk paediatric cancer.

BACKGROUND: Molecular profiling of the tumour immune microenvironment (TIME) has enabled the rational choice of immunotherapies in some adult cancers. In contrast, the TIME of paediatric cancers is relatively unexplored. We speculated that a more refined appreciation of the TIME in childhood cancers, rather than a reliance on commonly used biomarkers such as tumour mutation burden (TMB), neoantigen load and PD-L1 expression, is an essential prerequisite for improved immunotherapies in childhood solid cancers. METHODS: We combined immunohistochemistry (IHC) with RNA sequencing and whole-genome sequencing across a diverse spectrum of high-risk paediatric cancers to develop an alternative, expression-based signature associated with CD8+ T-cell infiltration of the TIME. Furthermore, we explored transcriptional features of immune archetypes and T-cell receptor sequencing diversity, assessed the relationship between CD8+ and CD4+ abundance by IHC and deconvolution predictions and assessed the common adult biomarkers such as neoantigen load and TMB. RESULTS: A novel 15-gene immune signature, Immune Paediatric Signature Score (IPASS), was identified. Using this signature, we estimate up to 31% of high-risk cancers harbour infiltrating T-cells. In addition, we showed that PD-L1 protein expression is poorly correlated with PD-L1 RNA expression and TMB and neoantigen load are not predictive of T-cell infiltration in paediatrics. Furthermore, deconvolution algorithms are only weakly correlated with IHC measurements of T-cells. CONCLUSIONS: Our data provides new insights into the variable immune-suppressive mechanisms dampening responses in paediatric solid cancers. Effective immune-based interventions in high-risk paediatric cancer will require individualised analysis of the TIME.

Histone H3-wild type diffuse midline gliomas with H3K27me3 loss are a distinct entity with exclusive EGFR or ACVR1 mutation and differential methylation of homeobox genes.

Diffuse midline gliomas (DMG) harbouring H3K27M mutation are paediatric tumours with a dismal outcome. Recently, a new subtype of midline gliomas has been described with similar features to DMG, including loss of H3K27 trimethylation, but lacking the canonical H3K27M mutation (H3-WT). Here, we report a cohort of five H3-WT tumours profiled by whole-genome sequencing, RNA sequencing and DNA methylation profiling and combine their analysis with previously published cases. We show that these tumours have recurrent and mutually exclusive mutations in either ACVR1 or EGFR and are characterised by high expression of EZHIP associated to its promoter hypomethylation. Affected patients share a similar poor prognosis as patients with H3K27M DMG. Global molecular analysis of H3-WT and H3K27M DMG reveal distinct transcriptome and methylome profiles including differential methylation of homeobox genes involved in development and cellular differentiation. Patients have distinct clinical features, with a trend demonstrating ACVR1 mutations occurring in H3-WT tumours at an older age. This in-depth exploration of H3-WT tumours further characterises this novel DMG, H3K27-altered sub-group, characterised by a specific immunohistochemistry profile with H3K27me3 loss, wild-type H3K27M and positive EZHIP. It also gives new insights into the possible mechanism and pathway regulation in these tumours, potentially opening new therapeutic avenues for these tumours which have no known effective treatment. This study has been retrospectively registered on clinicaltrial.gov on 8 November 2017 under the registration number NCT03336931 ( https://clinicaltrials.gov/ct2/show/NCT03336931 ).

Effect of Powder Bed Fusion Laser Sintering on Dimensional Accuracy and Tensile Properties of Reused Polyamide 11.

Polyamide 11 (PA11) is a plant-based nylon made from castor beans. Powder bed fusion laser sintering (PBF-LS) is an additive manufacturing process used for PA11 which allows for the reuse of the unsintered powder. The unsintered powder is mixed with virgin powders at different refresh rates, a process which has been studied extensively for most semi-crystalline polyamides. However, there is lack of information on the effect of using 100% reused PA11 powder and the effect of the number of times it is reused on its own, during powder bed fusion laser sintering. This paper investigates the effect of reusing PA11 powder in PBF-LS and the effect of the number of times it is reused on the dimensional accuracy, density and thermal and tensile properties. From the 100% virgin powder to the third reuse of the powder, there is a decrease in powder wastage, crystallinity and tensile strength. These are associated with the polymerisation and cross-linking process of polymer chains, upon exposure to high temperatures. This results in a higher molecular weight and, hence, a higher density. From the fourth reuse to the tenth reuse, the opposite is observed, which is associated with an increase in high-viscosity unmolten particles, resulting in defects in the PBF-LS parts.

Prey capture by the non-native carnivorous pitcher plant Sarracenia purpurea across sites in Britain and Ireland.

The carnivorous pitcher plant Sarracenia purpurea is native to North America, but has been introduced into Europe, where it is now widespread. Understanding of how this species functions in its non-native range is limited. We measured pitcher morphology and prey capture by S. purpurea in its non-native range in Britain and Ireland. Pitchers were removed from different plants at each of six bogs covering the species range in Britain and Ireland (n = 10 pitchers per site). For each pitcher we counted and identified every prey item and took measurements of morphology. We also compiled prey capture data for existing studies in Europe and North America. Prey capture characteristics varied between sites in Britain and Ireland. The amount of prey captured varied 20-fold between sites and was partially explained by differences in pitcher size; larger pitchers caught more prey. The primary prey was Formicidae, Diptera and Coleoptera. At the rank of order, prey composition varied between bogs, some contained mainly Formicidae, some mainly Diptera and some a mix. Prey capture was less evenly distributed at some bogs compared to others, suggesting more specialization. There was no overall difference in prey capture (composition or evenness) at the rank of order between plants in Europe compared to those in North America. At the rank of species, prey capture varied between populations even within the same order. This study demonstrates a large amount of variability between sites in prey capture characteristics. This may reflect different site characteristics and/or plant strategies, which will likely impact plant function, and may impact the inquiline community. In terms of prey capture at the rank of order, S. purpurea functions identically in its non-native range. This supports its use as a model system in a natural experiment for understanding food webs.

Sphingolipidomics of Bovine Pink Eye: A Pilot Study.

Sphingolipids are essential structural components of tear film that protect the surface of the eye from dehydration. A detailed analysis of the effects of pink eye infections on the sphingolipidome in cattle has not previously been undertaken. We recently published a new assay utilizing high-resolution mass spectrometric monitoring of the chloride adducts of sphingolipids that provides enhanced sensitivity and specificity. Utilizing this assay, we monitored decreases in the levels of tear film ceramides with short-chain fatty acids, hydroxy-ceramides, phytoceramides, and hydroxy-phytoceramides. Dihydroceramide levels were unaltered and increased levels of ceramides with long-chain fatty acids (24:0 and 24:1) were monitored in cattle with pink eye. The data from this pilot study (n = 8 controls and 8 pink eye) demonstrate a major disruption of the lipid tear film layer in pink eye disease, that can result in severe eye irritation and damage.

Serine ether glycerophospholipids: Decrements in the frontal cortex associated with mild cognitive impairment and Alzheimer's disease.

Ether glycerophospholipids (GPL) are involved in membrane fluidity and fusion. Vinyl-ether GPL are also conjectured to provide antioxidant capacity in the brain. The roles of these lipids in the processes involved in the development of dementia are not understood but choline and ethanolamine vinyl-ether GPL (i.e., plasmalogens) are decreased in the brains of subjects with dementia. In contrast, serine ether and vinyl-ether GPL have not been investigated in human brain. We therefore undertook an evaluation of these lipids, utilizing high-resolution mass spectrometry (HR-MS), in tissues from control and dementia subjects that we had previously characterized in-depth. We can report for the first time that a number of serine ether GPL and a more limited number of serine plasmalogens are present in human frontal cortex. In addition, we found that some of these frontal cortex lipids are decreased in Mild Cognitive Impairment (MCI), early-onset Alzheimer's disease (EOAD), and late-onset AD (LOAD). In contrast no alterations in serine ether GPL were monitored in the frontal cortex of donors with schizophrenia, demonstrating disease specificity. These data suggest that further studies of the roles of ether GPL, including serine ether GPL, in brain function are worthy of undertaking.