High Concordance of Different Assays in the Determination of Homologous Recombination Deficiency-Associated Genomic Instability in Ovarian Cancer.

PURPOSE: Poly(ADP-ribose) polymerase inhibitors (PARPi) have shown promising clinical results in the treatment of ovarian cancer. Analysis of biomarker subgroups consistently revealed higher benefits for patients with homologous recombination deficiency (HRD). The test that is most often used for the detection of HRD in clinical studies is the Myriad myChoice assay. However, other assays can also be used to assess biomarkers, which are indicative of HRD, genomic instability (GI), and BRCA1/2 mutation status. Many of these assays have high potential to be broadly applied in clinical routine diagnostics in a time-effective decentralized manner. Here, we compare the performance of a multitude of alternative assays in comparison with Myriad myChoice in high-grade serous ovarian cancer (HGSOC). METHODS: DNA from HGSOC samples was extracted from formalin-fixed paraffin-embedded tissue blocks of cases previously run with the Myriad myChoice assay, and GI was measured by multiple molecular assays (CytoSNP, AmoyDx, Illumina TSO500 HRD, OncoScan, NOGGO GISv1, QIAseq HRD Panel and whole genome sequencing), applying different bioinformatics algorithms. RESULTS: Application of different assays to assess GI, including Myriad myChoice, revealed high concordance of the generated scores ranging from very substantial to nearly perfect fit, depending on the assay and bioinformatics pipelines applied. Interlaboratory comparison of assays also showed high concordance of GI scores. CONCLUSION: Assays for GI assessment not only show a high concordance with each other but also in correlation with Myriad myChoice. Thus, almost all of the assays included here can be used effectively to assess HRD-associated GI in the clinical setting. This is important as PARPi treatment on the basis of these tests is compliant with European Medicines Agency approvals, which are methodologically not test-bound.

CVOT Summit Report 2023: new cardiovascular, kidney, and metabolic outcomes.

The 9th Cardiovascular Outcome Trial (CVOT) Summit: Congress on Cardiovascular, Kidney, and Metabolic Outcomes was held virtually on November 30-December 1, 2023. This reference congress served as a platform for in-depth discussions and exchange on recently completed outcomes trials including dapagliflozin (DAPA-MI), semaglutide (SELECT and STEP-HFpEF) and bempedoic acid (CLEAR Outcomes), and the advances they represent in reducing the risk of major adverse cardiovascular events (MACE), improving metabolic outcomes, and treating obesity-related heart failure with preserved ejection fraction (HFpEF). A broad audience of endocrinologists, diabetologists, cardiologists, nephrologists and primary care physicians participated in online discussions on guideline updates for the management of cardiovascular disease (CVD) in diabetes, heart failure (HF) and chronic kidney disease (CKD); advances in the management of type 1 diabetes (T1D) and its comorbidities; advances in the management of CKD with SGLT2 inhibitors and non-steroidal mineralocorticoid receptor antagonists (nsMRAs); and advances in the treatment of obesity with GLP-1 and dual GIP/GLP-1 receptor agonists. The association of diabetes and obesity with nonalcoholic steatohepatitis (NASH; metabolic dysfunction-associated steatohepatitis, MASH) and cancer and possible treatments for these complications were also explored. It is generally assumed that treatment of chronic diseases is equally effective for all patients. However, as discussed at the Summit, this assumption may not be true. Therefore, it is important to enroll patients from diverse racial and ethnic groups in clinical trials and to analyze patient-reported outcomes to assess treatment efficacy, and to develop innovative approaches to tailor medications to those who benefit most with minimal side effects. Other keys to a successful management of diabetes and comorbidities, including dementia, entail the use of continuous glucose monitoring (CGM) technology and the implementation of appropriate patient-physician communication strategies. The 10th Cardiovascular Outcome Trial Summit will be held virtually on December 5-6, 2024 ( http://www.cvot.org ).

Concomitant inhibition of PI3K/mTOR signaling pathways boosts antiproliferative effects of lanreotide in bronchopulmonary neuroendocrine tumor cells.

Introduction: Somatostatin analogues (SSAs) are commonly used in the treatment of hormone hypersecretion in neuroendocrine tumors (NETs), however the extent to which they inhibit proliferation is much discussed. Objective: We studied the antiproliferative effects of novel SSA lanreotide in bronchopulmonary NETs (BP-NETs). We focused on assessing whether pretreating cells with inhibitors for phosphatidylinositol 3-kinase (PI3K) and mammalian target for rapamycin (mTOR) could enhance the antiproliferative effects of lanreotide. Methods: BP-NET cell lines NCI-H720 and NCI-H727 were treated with PI3K inhibitor BYL719 (alpelisib), mTOR inhibitor everolimus and SSA lanreotide to determine the effect on NET differentiation markers, cell survival, proliferation and alterations in cancer-associated pathways. NT-3 cells, previously reported to express somatostatin receptors (SSTRs) natively, were used as control for SSTR expression. Results: SSTR2 was upregulated in NCI-H720 and NT-3 cells upon treatment with BYL719. Additionally, combination treatment consisting of BYL719 and everolimus plus lanreotide tested in NCI-H720 and NCI-H727 led to diminished cell proliferation in a dose-dependent manner. Production of proteins activating cell death mechanisms was also induced. Notably, a multiplexed gene expression analysis performed on NCI-H720 revealed that BYL719 plus lanreotide had a stronger effect on the downregulation of mitogens than lanreotide alone. Discussion/Conclusion: We report a widespread analysis of changes in BP-NET cell lines at the genetic/protein expression level in response to combination of lanreotide with pretreatment consisting of BYL719 and everolimus. Interestingly, SSTR expression reinduction could be exploited in therapeutic and diagnostic applications. The overall results of this study support the evaluation of combination-based therapies using lanreotide in preclinical studies to further increase its antiproliferative effect and ultimately facilitate its use in high-grade tumors.

Sweet Side Streams: Sugar Beet Pulp as Source for High-Performance Supercapacitor Electrodes.

Valorization of the lignocellulosic side and waste streams is key to making industrial processes more efficient from both an economic and ecological perspective. Currently, the production of sugars from beets results in pulps in large quantities. However, there is a lack of promising opportunities for upcycling these materials despite their promising properties. Here, we investigate beet pulps from two different stages of the sugar manufacturing process as raw materials for supercapacitor electrodes. We demonstrate that these materials can be efficiently converted to activated, highly porous carbons. The carbons exhibit pore dimensions approaching the size of the desolvated K+ and SO42- ions with surface areas up to 2600 m2 g-1. These carbons were subsequently manufactured into electrodes, assembled in supercapacitors, and tested with environmentally friendly aqueous electrolytes (6 M KOH and 1 M H2SO4). Further analysis demonstrated the presence of capacitance-enhancing functionalities, and up to 193 and 177 F g-1 in H2SO4 and KOH, respectively, were achieved, which outperformed supercapacitors prepared from commercial YP80 F. Overall, our study suggests that side streams from sugar manufacturing offer a hidden potential for use in high-performance energy storage devices.

High-Quality Cellulosic Fibers Engineered from Cotton-Elastane Textile Waste.

Even small amounts of elastane in cotton-elastane blended textiles can prevent fiber-to-fiber recycling strategies in textile recycling. Herein, the selective separation of elastane from cotton blends was addressed by the aminolytic degradation of the synthetic component. Polar aprotic solvents were tested as elastane solvents, but side reactions impeded aminolysis with some of them. Aminolysis of elastane succeeded under mild conditions using dimethyl sulfoxide in combination with diethylenetriamine and 1,5-diazabicyclo[4.3.0]non-5-ene as a cleaving agent and catalyst, respectively. The analysis of the nitrogen content in the recovered cellulose fraction demonstrated that 2 h of reaction at 80 °C reduced the elastane content to values lower than 0.08%. The characterization of the recovered cellulose showed that the applied conditions did not affect the macromolecular properties of cellulose and maintained a cellulose I crystal structure. Degraded elastane products were recovered through precipitation with water. Finally, the cellulosic component was turned into new fibers by dry-jet wet spinning with excellent tensile properties.

Mosaic chromosomal alterations in peripheral blood leukocytes of children in sub-Saharan Africa.

In high-income countries, mosaic chromosomal alterations in peripheral blood leukocytes are associated with an elevated risk of adverse health outcomes, including hematologic malignancies. We investigate mosaic chromosomal alterations in sub-Saharan Africa among 931 children with Burkitt lymphoma, an aggressive lymphoma commonly characterized by immunoglobulin-MYC chromosomal rearrangements, 3822 Burkitt lymphoma-free children, and 674 cancer-free men from Ghana. We find autosomal and X chromosome mosaic chromosomal alterations in 3.4% and 1.7% of Burkitt lymphoma-free children, and 8.4% and 3.7% of children with Burkitt lymphoma (P-values = 5.7×10-11 and 3.74×10-2, respectively). Autosomal mosaic chromosomal alterations are detected in 14.0% of Ghanaian men and increase with age. Mosaic chromosomal alterations in Burkitt lymphoma cases include gains on chromosomes 1q and 8, the latter spanning MYC, while mosaic chromosomal alterations in Burkitt lymphoma-free children include copy-neutral loss of heterozygosity on chromosomes 10, 14, and 16. Our results highlight mosaic chromosomal alterations in sub-Saharan African populations as a promising area of research.

Area deprivation and demographic factors associated with diabetes technology use in adults with type 1 diabetes in Germany.

Introduction: Diabetes technology improves glycemic control and quality of life for many people with type 1 diabetes (T1D). However, inequalities in access to diabetes technology exist in many countries. In Germany, disparities in technology use have been described in pediatric T1D, but no data for adults are available so far. We therefore aimed to analyze whether demographic factors and area deprivation are associated with technology use in a representative population of adults with T1D. Materials and methods: In adults with T1D from the German prospective diabetes follow-up registry (DPV), we analyzed the use of continuous subcutaneous insulin infusion (CSII), continuous glucose monitoring (CGM), and sensor augmented pump therapy (SAP, with and without automated insulin delivery) in 2019-2021 by age group, gender, migration background, and area deprivation using multiple adjusted regression models. Area deprivation, defined as a relative lack of area-based resources, was measured by quintiles of the German index of Multiple Deprivation (GIMD 2015, from Q1, least deprived, to Q5, most deprived districts). Results: Among 13,351 adults with T1D, the use of technology decreased significantly with older age: CSII use fell from 56.1% in the 18-<25-year age group to 3.1% in the ≥80-year age group, CGM use from 75.3% to 28.2%, and SAP use from 45.1% to 1.5% (all p for trend <0.001). The use of technology was also significantly higher in women than in men (CSII: 39.2% vs. 27.6%; CGM: 61.9% vs. 58.0%; SAP: 28.7% vs. 19.6%, all p <0.001), and in individuals without migration background than in those with migration background (CSII: 38.8% vs. 27.6%; CGM: 71.1% vs. 61.4%; SAP: 30.5% vs. 21.3%, all p <0.001). Associations with area deprivation were not linear: the use of each technology decreased only from Q2 to Q4. Discussion: Our real-world data provide evidence that higher age, male gender, and migration background are currently associated with lower use of diabetes technology in adults with T1D in Germany. Associations with area deprivation are more complex, probably due to correlations with other factors, like the higher proportion of migrants in less deprived areas or the federal structure of the German health care system.

Frequent ZNF217 mutations lead to transcriptional deregulation of interferon signal transduction via altered chromatin accessibility in B cell lymphoma.

Recent exome-wide studies discovered frequent somatic mutations in the epigenetic modifier ZNF217 in primary mediastinal B cell lymphoma (PMBCL) and related disorders. As functional consequences of ZNF217 alterations remain unknown, we comprehensively evaluated their impact in PMBCL. Targeted sequencing identified genetic lesions affecting ZNF217 in 33% of 157 PMBCL patients. Subsequent gene expression profiling (n = 120) revealed changes in cytokine and interferon signal transduction in ZNF217-aberrant PMBCL cases. In vitro, knockout of ZNF217 led to changes in chromatin accessibility interfering with binding motifs for crucial lymphoma-associated transcription factors. This led to disturbed expression of interferon-responsive and inflammation-associated genes, altered cell behavior, and aberrant differentiation. Mass spectrometry demonstrates that ZNF217 acts within a histone modifier complex containing LSD1, CoREST and HDAC and interferes with H3K4 methylation and H3K27 acetylation. Concluding, our data suggest non-catalytic activity of ZNF217, which directs histone modifier complex function and controls B cell differentiation-associated patterns of chromatin structure.

Development of the NOGGO GIS v1 Assay, a Comprehensive Hybrid-Capture-Based NGS Assay for Therapeutic Stratification of Homologous Repair Deficiency Driven Tumors and Clinical Validation.

The worldwide approval of the combination maintenance therapy of olaparib and bevacizumab in advanced high-grade serous ovarian cancer requires complex molecular diagnostic assays that are sufficiently robust for the routine detection of driver mutations in homologous recombination repair (HRR) genes and genomic instability (GI), employing formalin-fixed (FFPE) paraffin-embedded tumor samples without matched normal tissue. We therefore established a DNA-based hybrid capture NGS assay and an associated bioinformatic pipeline that fulfils our institution's specific needs. The assay´s target regions cover the full exonic territory of relevant cancer-related genes and HRR genes and more than 20,000 evenly distributed single nucleotide polymorphism (SNP) loci to allow for the detection of genome-wide allele specific copy number alterations (CNA). To determine GI status, we implemented an %CNA score that is robust across a broad range of tumor cell content (25-85%) often found in routine FFPE samples. The assay was established using high-grade serous ovarian cancer samples for which BRCA1 and BRCA2 mutation status as well as Myriad MyChoice homologous repair deficiency (HRD) status was known. The NOGGO (Northeastern German Society for Gynecologic Oncology) GIS (GI-Score) v1 assay was clinically validated on more than 400 samples of the ENGOT PAOLA-1 clinical trial as part of the European Network for Gynaecological Oncological Trial groups (ENGOT) HRD European Initiative. The "NOGGO GIS v1 assay" performed using highly robust hazard ratios for progression-free survival (PFS) and overall survival (OS), as well a significantly lower dropout rate than the Myriad MyChoice clinical trial assay supporting the clinical utility of the assay. We also provide proof of a modular and scalable routine diagnostic method, that can be flexibly adapted and adjusted to meet future clinical needs, emerging biomarkers, and further tumor entities.

Stable glycosylamines at the reducing ends of cellulose nanocrystals.

The reaction of reducing end groups in cellulose nanocrystals with dodecylamine was examined. Using a direct-dissolution solution-state NMR protocol, the regioselective formation of glucosylamines was shown. This provides an elegant approach to sustainably functionalize these bio-based nanomaterials, that may not require further reduction to more stable secondary amines.

EuroClonality-NGS Recommendations for Evaluation of B-Cell Clonality Analysis by Next-Generation Sequencing: A Structured Approach with the DEPART Algorithm.

Next-generation sequencing (NGS)-based clonality analysis allows in-depth assessment of the clonal composition of a sample with high sensitivity for detecting small clones. Within the EuroClonality-NGS Working Group, a protocol for NGS Ig clonality analysis was developed and validated previously. This NGS-based approach was designed to generate small amplicons, making it suitable for samples with suboptimal DNA quality, especially material derived from formalin-fixed, paraffin-embedded tissue. Using expert assessment of NGS Ig clonality results as a reference, a structured algorithmic approach to the assessment of NGS-amplicon-based B-cell clonality analysis was developed. A structured approach with the Detection of clonality through Evaluation of sample quality and assessment of Pattern, Abundance and RaTio (DEPART) algorithm was proposed, which consecutively evaluates sample quality, the pattern of the clonotypes present, the abundance of the most dominant clonotypes, and the ratio between the dominant clonotypes and the background to evaluate the different Ig gene targets. Specific issues with respect to evaluation of the various Ig targets as well as the integration of results of individual targets into a molecular clonality conclusion are discussed and illustrated with case examples. Finally, the importance of interpretation of NGS-based clonality results in clinical and histopathologic contexts is discussed. It is expected that these recommendations will have clinical utility to facilitate proper evaluation of clonality assessment.

Solution-state nuclear magnetic resonance spectroscopy of crystalline cellulosic materials using a direct dissolution ionic liquid electrolyte.

Owing to its high sustainable production capacity, cellulose represents a valuable feedstock for the development of more sustainable alternatives to currently used fossil fuel-based materials. Chemical analysis of cellulose remains challenging, and analytical techniques have not advanced as fast as the development of the proposed materials science applications. Crystalline cellulosic materials are insoluble in most solvents, which restricts direct analytical techniques to lower-resolution solid-state spectroscopy, destructive indirect procedures or to 'old-school' derivatization protocols. While investigating their use for biomass valorization, tetralkylphosphonium ionic liquids (ILs) exhibited advantageous properties for direct solution-state nuclear magnetic resonance (NMR) analysis of crystalline cellulose. After screening and optimization, the IL tetra-n-butylphosphonium acetate [P4444][OAc], diluted with dimethyl sulfoxide-d6, was found to be the most promising partly deuterated solvent system for high-resolution solution-state NMR. The solvent system has been used for the measurement of both 1D and 2D experiments for a wide substrate scope, with excellent spectral quality and signal-to-noise, all with modest collection times. The procedure initially describes the scalable syntheses of an IL, in 24-72 h, of sufficient purity, yielding a stock electrolyte solution. The dissolution of cellulosic materials and preparation of NMR samples is presented, with pretreatment, concentration and dissolution time recommendations for different sample types. Also included is a set of recommended 1D and 2D NMR experiments with parameters optimized for an in-depth structural characterization of cellulosic materials. The time required for full characterization varies between a few hours and several days.

Selected Kraft lignin fractions as precursor for carbon foam: Structure-performance correlation and electrochemical applications.

The rapid exhaustion of fossil fuels brings to the fore the need to search for energy efficient strategies. The conversion of lignin into advanced functional carbon-based materials is considered one of the most promising solutions for environmental protection and the use of renewable resources. This study analyzed the structure-performance correlation of carbon foams (CF) when lignin-phenol-formaldehyde (LPF) resins produced with different fractions of kraft lignin (KL) were employed as carbon source, and polyurethane foam (PU) as sacrificial mold. The lignin fractions employed were KL, fraction of KL insoluble in ethyl acetate (LFIns) and fraction of KL soluble in ethyl acetate (LFSol). The produced CFs were characterized by thermogravimetric analysis (TGA), X-ray diffractometry (XRD), Raman spectroscopy, 2D HSQC Nuclear magnetic resonance (NMR) analysis, scanning electron microscopy (SEM), Brunauer-Emmett-Teller (BET), and electrochemical measurements. The results showed that when LFSol was employed as a partial substitute for phenol in LPF resin synthesis, the final performance of the produced CF was infinitely higher. The improved solubility parameters of LFSol along with the higher S/G ratio and ß-O-4/α-OH content after fractionation were the key to produce CF with better carbon yields (54 %). The electrochemical measurements showed that LFSol presented the highest current density (2.11 × 10-4 mA.cm-2) and the lowest value of resistance to charge transfer (0.26 KΩ) in relation to the other samples, indicating that the process of electron transfer was faster in the sensor produced with LFSol. LFSol's potential for application as an electrochemical sensor was tested as a proof of concept and demonstrated excellent selectivity for the detection of hydroquinone in water.

Profile of the multicenter cohort of the German Cancer Consortium's Clinical Communication Platform.

Treatment concepts in oncology are becoming increasingly personalized and diverse. Successively, changes in standards of care mandate continuous monitoring of patient pathways and clinical outcomes based on large, representative real-world data. The German Cancer Consortium's (DKTK) Clinical Communication Platform (CCP) provides such opportunity. Connecting fourteen university hospital-based cancer centers, the CCP relies on a federated IT-infrastructure sourcing data from facility-based cancer registry units and biobanks. Federated analyses resulted in a cohort of 600,915 patients, out of which 232,991 were incident since 2013 and for which a comprehensive documentation is available. Next to demographic data (i.e., age at diagnosis: 2.0% 0-20 years, 8.3% 21-40 years, 30.9% 41-60 years, 50.1% 61-80 years, 8.8% 81+ years; and gender: 45.2% female, 54.7% male, 0.1% other) and diagnoses (five most frequent tumor origins: 22,523 prostate, 18,409 breast, 15,575 lung, 13,964 skin/malignant melanoma, 9005 brain), the cohort dataset contains information about therapeutic interventions and response assessments and is connected to 287,883 liquid and tissue biosamples. Focusing on diagnoses and therapy-sequences, showcase analyses of diagnosis-specific sub-cohorts (pancreas, larynx, kidney, thyroid gland) demonstrate the analytical opportunities offered by the cohort's data. Due to its data granularity and size, the cohort is a potential catalyst for translational cancer research. It provides rapid access to comprehensive patient groups and may improve the understanding of the clinical course of various (even rare) malignancies. Therefore, the cohort may serve as a decisions-making tool for clinical trial design and contributes to the evaluation of scientific findings under real-world conditions.

Design of experiments as a tool to guide the preparation of tailor-made activated carbons.

Activated carbon produced from biomass exhibits a high specific surface area due to the natural hierarchical porous structure of the precursor material. To reduce production costs of activated carbon, bio-waste materials receive more and more attention, which has led to a steep increase in the number of publications over the past decade. However, the characteristics of activated carbon are highly dependent on the properties of the precursor material used, making it difficult to draw assumptions about activation conditions for new precursor materials based on published work. Here, we introduce a Design of Experiment methodology with a Central Composite Design to better predict the properties of activated carbons from biomass. As a model precursor, we employ well-defined regenerated cellulose-based fibers which contain 25 wt.% chitosan as intrinsic dehydration catalyst and nitrogen donor. The use of the DoE methodology opens up the possibility to better identify the crucial dependencies between activation temperature and impregnation ratio on the yield, surface morphology, porosity and chemical composition of the activated carbon, independent of the used biomass. The use of DoE yields contour plots, which allows for more facile analysis on correlations between activation conditions and activated carbon properties, thus enabling its tailor-made manufacturing.

Debugging periodate oxidation of cellulose: Why following the common protocol of quenching excess periodate with glycol is a bad idea.

Periodate oxidation of cellulose to produce "dialdehyde cellulose" (DAC) has lately received increasing attention in sustainable materials development. Despite the longstanding research interest and numerous reported studies, there is still an enormous variation in the proposed preparation and work-up protocols. This apparently reduces comparability and causes reproducibility problems in DAC research. Two simple but prevalent work-up protocols, namely glycol quenching and filtration/washing, were critically examined and compared, resulting in this cautionary note. Various analytical techniques were applied to quantify residual iodine species and organic contaminations from quenching side reactions. The commonly practiced glycol addition cannot remove all oxidising iodine compounds. Both glycol and the formed formaldehyde are incorporated into DAC's polymeric structure. Quenching of excess periodate with glycol can thus clearly be discouraged. Instead, simple washing protocols are recommended which do not bear the risk of side reactions with organic contaminants. While simple washing was sufficient for mildly oxidised celluloses, higher oxidised samples were more likely to trap residual (per)iodate, as determined by thiosulfate titration. For work-up, simple washing with water is proposed while determining potential iodine contaminations after washing with a simple colorimetric test and, if needed, removal of residual periodate by washing with an aqueous sodium thiosulfate solution.

FACILITATE: A real-world, multicenter, prospective study investigating the utility of a rapid, fully automated real-time PCR assay versus local reference methods for detecting epidermal growth factor receptor variants in NSCLC.

Accurate testing for epidermal growth factor receptor (EGFR) variants is essential for informing treatment decisions in non-small cell lung cancer (NSCLC). Automated diagnostic workflows may allow more streamlined initiation of targeted treatments, where appropriate, while comprehensive variant analysis is ongoing. FACILITATE, a real-world, prospective, multicenter, European study, evaluated performance and analytical turnaround time of the Idylla™ EGFR Mutation Test compared with local reference methods. Sixteen sites obtained formalin-fixed paraffin-embedded biopsy samples with ≥ 10% neoplastic cells from patients with NSCLC. Consecutive 5 µm sections from patient samples were tested for clinically relevant NSCLC-associated EGFR variants using the Idylla™ EGFR Mutation Test and local reference methods; performance (concordance) and analytical turnaround time were compared. Between January 2019 and November 2020, 1,474 parallel analyses were conducted. Overall percentage agreement was 97.7% [n = 1,418; 95% confidence interval (CI): 96.8-98.3], positive agreement, 87.4% (n = 182; 95% CI: 81.8-91.4) and negative agreement, 99.2% (n = 1,236; 95% CI: 98.5-99.6). There were 38 (2.6%) discordant cases. Ninety percent of results were returned with an analytical turnaround time of within 1 week using the Idylla™ EGFR Mutation Test versus ∼22 days using reference methods. The Idylla™ EGFR Mutation Test performed well versus local methods and had shorter analytical turnaround time. The Idylla™ EGFR Mutation Test can thus support application of personalized medicine in NSCLC.