P07.04 Rapid-CNS2: Rapid comprehensive adaptive nanopore-sequencing of CNS tumors, a proof of concept study

BACKGROUND

The WHO classification 2021 includes multiple molecular markers for routine diagnostics in addition to histology. Sequencing setup for complete molecular profiling requires considerable investment, while batching samples for sequencing and methylation profiling can delay turnaround time. We introduce RAPID-CNS2, a nanopore adaptive sequencing pipeline that enables comprehensive mutational, methylation and copy number profiling of CNS tumours with a single third generation sequencing assay. It can be run for single samples and offers highly flexible target selection requiring no additional library preparation.

MATERIAL AND METHODS

Utilising ReadFish, a toolkit enabling targeted nanopore sequencing, we sequenced DNA from 22 diffuse glioma patient samples on a MinION device. Target regions comprised our Heidelberg brain tumour NGS panel and pre-selected CpG sites for methylation classification by an adapted random forest classifier. Pathognomonic alterations, copy number profiles, and methylation classes were called using a custom bioinformatics pipeline. Results were compared to their corresponding NGS panel-seq and EPIC array outputs.

RESULTS

Complete concordance with the EPIC array was found for copy number profiles from RAPID-CNS2. 94% pathognomonic mutations were congruent with NGS panel-seq. MGMT promoter status was correctly identified in all samples. Methylation families were detected with 96% congruence. Among the alterations decisive for rendering a classification-compatible integrated diagnosis, 97% of the alterations were consistent over the entire cohort (completely congruent in 19/22 cases and sufficient for unequivocal diagnosis in all).

CONCLUSION

RAPID-CNS2 provides a swift and highly flexible alternative to conventional NGS and array-based methods for SNV/Indel analysis, detection of copy number alterations and methylation classification. The turnaround time of ~4 days can be further shortened to <12h by altering target sizes. It offers a low-capital approach that would be cost-efficient for low throughput settings and invaluable in cases requiring immediate diagnoses.

Environmental impacts of an advanced oxidation process as tertiary treatment in a wastewater treatment plant

Due to global water scarcity, the use of reclaimed wastewater for crop irrigation is required; however, if the wastewater treatment is inadequate, it can be a source of environmental pollution. In order to improve wastewater reclamation, advanced oxidation processes (AOPs) have been tested. At full scale, ozonation is one such process that effectively removes micropollutants, despite its high-energy consumption. At pilot scale, other technologies such as the solar photo-Fenton process are being developed. This process is under consideration as a sustainable technology because it uses sunlight as a source of radiation. However, there is little information available on its environmental performance. In this work, we perform a comparative analysis between the ozonation and the photo-Fenton process as tertiary wastewater treatment processes used to reclaim wastewater for agricultural irrigation. We apply the Life Cycle Assessment (LCA) methodology for quantifying environmental impacts with ReCiPe and USEtox as life cycle impact assessment (LCIA) methods. The results show that both tertiary treatment options reduce water stress locally. Ozonation has a better overall environmental performance compared to the photo-Fenton process because the environmental impact of the required ozone is smaller than of the reactants involved in the solar photo-Fenton. Moreover, the first can be operated both day and night, and therefore needs no additional storage for collecting the nightly secondary effluent, and thus has lower infrastructure related impacts. Additionally, when the solar photo-Fenton process operates at an acidic pH, there are environmental drawbacks related to the pH adjustment, which consumes a large amount of acid thus liberating CO₂. Finally, the environmental impacts associated with the discharge of micropollutants to soil through the use of reclaimed water are very small compared to the other impacts generated by the treatment. However, due to the current LCIA method limitations of micropollutant impact assessment, these are subject to major uncertainty.

Bevacizumab plus hypofractionated radiotherapy versus radiotherapy alone in elderly patients with glioblastoma: the randomized, open-label, phase II ARTE trial

Background

The addition of bevacizumab to temozolomide-based chemoradiotherapy (TMZ/RT → TMZ) did not prolong overall survival (OS) in patients with newly diagnosed glioblastoma in phase III trials. Elderly and frail patients are underrepresented in clinical trials, but early reports suggested preferential benefit in this population.

Patients and methods

ARTE was a 2 : 1 randomized, multi-center, open-label, non-comparative phase II trial of hypofractionated RT (40 Gy in 15 fractions) with bevacizumab (10 mg/kg×14 days) (arm A, N = 50) or without bevacizumab (arm B, N = 25) in patients with newly diagnosed glioblastoma aged ≥65 years. The primary objective was to obtain evidence for prolongation of median OS by the addition of bevacizumab to RT. Response was assessed by RANO criteria. Quality of life (QoL) was monitored by the EORTC QLQ-C30/BN20 modules. Exploratory studies included molecular subtyping by 450k whole methylome and gene expression analyses.

Results

Median PFS was longer in arm A than in arm B (7.6 and 4.8 months, P = 0.003), but OS was similar (12.1 and 12.2 months, P = 0.77). Clinical deterioration was delayed and more patients came off steroids in arm A. Prolonged PFS in arm A was confined to tumors with the receptor tyrosine kinase (RTK) I methylation subtype (HR 0.25, P = 0.014) and proneural gene expression (HR 0.29, P = 0.025). In a Cox model of OS controlling for established prognostic factors, associations with more favorable outcome were identified for age <70 years (HR 0.52, P = 0.018) and Karnofsky performance score 90%-100% (HR 0.51, P = 0.026). Including molecular subtypes into that model identified an association of the RTK II gene methylation subtype with inferior OS (HR 1.73, P = 0.076).

Conclusion

Efficacy outcomes and exploratory analyses of ARTE do not support the hypothesis that the addition of bevacizumab to RT generally prolongs survival in elderly glioblastoma patients. Molecular biomarkers may identify patients with preferential benefit from bevacizumab.

Clinical trial registration number

NCT01443676.

Cerebrospinal fluid CXCL13 as a diagnostic marker of neuroborreliosis in children: a retrospective case-control study

Background

Lyme neuroborreliosis (LNB) is a frequent manifestation of Lyme disease in children and its current diagnosis has limitations. The elevation of the chemokine CXCL13 in the cerebrospinal fluid (CSF) of adult patients with LNB has been demonstrated and suggested as a new diagnostic marker. Our aim was to evaluate this marker in the CSF of children with suspected LNB and to determine a CXCL13 cut-off concentration that would discriminate between LNB and other central nervous system (CNS) infections.

Methods

For this single-center retrospective case-control study we used a diagnostic-approved ELISA to measure CXCL13 concentrations in the CSF of 185 children with LNB suspicion at presentation. Patients were classified into definite LNB (cases), non-LNB (controls with other CNS affections), and possible LNB. A receiver-operating characteristic curve was generated by comparison of cases and controls.

Results

CXCL13 was significantly elevated in the CSF of 53 children with definite LNB (median 774.7 pg/ml) compared to 91 control patients (median 4.5 pg/ml, p < 0.001). A cut-off of 55 pg/ml resulted in a sensitivity of 96.7% and a specificity of 98.1% for the diagnosis of definite LNB and the test exhibited a diagnostic odds ratio of 1525.3. Elevated CSF CXCL13 levels were also detected in three controls with viral meningitis (enterovirus n = 1, varicella-zoster virus n = 2) while other CNS affections such as idiopathic facial palsy did not lead to CXCL13 elevation. Of the 41 patients with possible LNB, 27% had CXCL13 values above the cut-off of 55 pg/ml (median 16.7 pg/ml).

Conclusions

CSF CXCL13 is highly elevated in children during early LNB as previously shown in adults. CXCL13 is a highly sensitive and specific marker that helps to differentiate LNB from other CNS affections in children.

BOARD-INVITED REVIEW: Quantifying water use in ruminant production

The depletion of water resources, in terms of both quantity and quality, has become a major concern both locally and globally. Ruminants, in particular, are under increased public scrutiny due to their relatively high water use per unit of meat or milk produced. Estimating the water footprint of livestock production is a relatively new field of research for which methods are still evolving. This review describes the approaches used to quantify water use in ruminant production systems as well as the methodological and conceptual issues associated with each approach. Water use estimates for the main products from ruminant production systems are also presented, along with possible management strategies to reduce water use. In the past, quantifying water withdrawal in ruminant production focused on the water demand for drinking or operational purposes. Recently, the recognition of water as a scarce resource has led to the development of several methodologies including water footprint assessment, life cycle assessment, and livestock water productivity to assess water use and its environmental impacts. These methods differ with respect to their target outcome (efficiency or environmental impacts), geographic focus (local or global), description of water sources (green, blue, and gray), handling of water quality concerns, the interpretation of environmental impacts, and the metric by which results are communicated (volumetric units or impact equivalents). Ruminant production is a complex activity where animals are often reared at different sites using a range of resources over their lifetime. Additional water use occurs during slaughter, product processing, and packaging. Estimating water use at the various stages of meat and milk production and communicating those estimates will help producers and other stakeholders identify hotspots and implement strategies to improve water use efficiency. Improvements in ruminant productivity (i.e., BW and milk production) and reproductive efficiency can also reduce the water footprint per unit product. However, given that feed production makes up the majority of water use by ruminants, research and development efforts should focus on this area. More research and clarity are needed to examine the validity of assumptions and possible trade-offs between ruminants' water use and other sustainability indicators.

Analysis of the 148Gd and 154Dy Content in Proton-Irradiated Lead Targets

This work presents the determination of the ¹⁴⁸Gd and ¹⁵⁴Dy content in Pb targets irradiated by 220-2600 MeV protons. It includes the chemical separation of lanthanides, followed by the preparation of proper samples, by molecular plating technique, for α-spectrometry measurements. The experimental cross section results were compared with theoretical predictions, calculated with the INCL++-ABLA07 code. The comparisons showed a satisfactory agreement for ¹⁴⁸Gd (less than within a factor two), while measured ¹⁵⁴Dy cross sections are higher than the theoretical values.

No Significant Cytotoxic Effect of the EZH2 Inhibitor Tazemetostat (EPZ-6438) on Pediatric Glioma Cells with Wildtype Histone 3 or Mutated Histone 3.3

BACKGROUND

Glioblastoma multiforme (GBM) and diffuse intrinsic pontine glioma (DIPG) belong to the most aggressive cancers in children with poor prognosis and limited therapeutic options. Therapeutic targeting of epigenetic proteins may offer new treatment options. Preclinical studies identified Enhancer of Zeste Homolog 2 (EZH2) within polycomb repressor complex 2 (PRC2) as a potential epigenetic anti-tumor target in adult GBM cells but similar inhibition studies in pediatric GBM/DIPG were still missing. Moreover, approximately 30% of pediatric high grade gliomas (pedHGG) including GBM and DIPG harbor a lysine 27 mutation (K27M) in histone 3.3 (H3.3) which is correlated with poor outcome and was shown to influence EZH2 function.

PATIENTS, MATERIALS AND METHODS

The present study investigated the correlation of expression of EZH2 and other PRC2 genes (EZH1, SUZ12, EED) with overall survival of pediatric GBM patients and the cytotoxic impact of EZH2 inhibition by the novel agent Tazemetostat in pediatric GBM/DIPG cells harboring either a H3.3 mutation or a H3 wildtype.

RESULTS

EZH2 gene expression does not correlate with survival of pedHGG patients, and EZH2 inhibition does not induce significant cytotoxicity in pedHGG cells independently of H3.3 mutations.

DISCUSSION AND CONCLUSION

We suggest that EZH2 inhibition might not offer an effective single agent treatment option for paedHGG patients. However, the therapeutic efficacy in combination with cytotoxic and/or other epigenetically active agents still has to be elucidated.

Peri-conceptional obesogenic exposure induces sex-specific programming of disease susceptibilities in adult mouse offspring

Vulnerability of the fetus upon maternal obesity can potentially occur during all developmental phases. We aimed at elaborating longer-term health outcomes of fetal overnutrition during the earliest stages of development. We utilized Naval Medical Research Institute (NMRI) mice to induce pre-conceptional and gestational obesity and followed offspring outcomes in the absence of any postnatal obesogenic influences. Male adult offspring developed overweight, insulin resistance, hyperleptinemia, hyperuricemia and hepatic steatosis; all these features were not observed in females. Instead, they showed impaired fasting glucose and a reduced fat mass and adipocyte size. Influences of the interaction of maternal diet∗sex concerned offspring genes involved in fatty liver disease, lipid droplet size regulation and fat mass expansion. These data suggest that a peri-conceptional obesogenic exposure is sufficient to shape offspring gene expression patterns and health outcomes in a sex- and organ-specific manner, indicating varying developmental vulnerabilities between sexes towards metabolic disease in response to maternal overnutrition.

Peri-conceptional obesogenic exposure induces sex-specific programming of disease susceptibilities in adult mouse offspring

Vulnerability of the fetus upon maternal obesity can potentially occur during all developmental phases. We aimed at elaborating longer-term health outcomes of fetal overnutrition during the earliest stages of development. We utilized Naval Medical Research Institute (NMRI) mice to induce pre-conceptional and gestational obesity and followed offspring outcomes in the absence of any postnatal obesogenic influences. Male adult offspring developed overweight, insulin resistance, hyperleptinemia, hyperuricemia and hepatic steatosis; all these features were not observed in females. Instead, they showed impaired fasting glucose and a reduced fat mass and adipocyte size. Influences of the interaction of maternal diet∗sex concerned offspring genes involved in fatty liver disease, lipid droplet size regulation and fat mass expansion. These data suggest that a peri-conceptional obesogenic exposure is sufficient to shape offspring gene expression patterns and health outcomes in a sex- and organ-specific manner, indicating varying developmental vulnerabilities between sexes towards metabolic disease in response to maternal overnutrition.