Design and characterization of a micro RNA-200c detecting Broccoli fluorescent light-up aptamer.

In the last decade the important role of small non-coding RNAs such as micro RNAs (miRs) in gene regulation in healthy and disease states became more and more evident. The miR-200-family of miRs has been shown to play a critical role in many diseases such as cancer and neurodegenerative disorders and could be potentially important for diagnosis and treatment. However, the size of miRs of about ~21-23nt provide challenges for their investigation.

Effects of hyperglycemia on neuronal network function in an in vitro model of the ischemic penumbra.

Introduction: Hyperglycemia is common in acute ischemic stroke, and associated with unfavorable outcome. However, the optimal glucose level is not known and cellular effects of hyperglycemia under hypoxia are largely unclear. We assessed how the extracellular glucose concentration affects cultured neuronal networks under experimental in vitro conditions, to provide a starting point for assessment of mechanisms at the neuronal network and cellular levels.

Evolution of glucose levels in patients with anterior circulation acute ischemic stroke treated with endovascular therapy using continuous glucose monitoring.

Introduction: Hyperglycemia is common in acute ischemic stroke, and associated with larger infarct volume and unfavorable functional outcome. To identify a subgroup that may benefit from glucose lowering in future studies, we assessed the evolution of glucose levels in the first 24 hrs after admission using continuous glucose monitoring in patients with anterior circulation large vessel occlusion ischemic stroke who underwent endovascular therapy (EVT).

Methods: In a prospective two center cohort study, consecutive patients with anterior circulation ischemic stroke, who were eligible for EVT within 24 hrs of symptom onset, were enrolled.

Rhodesain inhibitors on the edge of reversibility-irreversibility.

A comparative study of Michael acceptor and keto-Michael acceptor inhibitors of the cysteine protease rhodesain has been performed. Five new inhibitors have been prepared bearing the peptide structure of the known cysteine protease inhibitor K11777 and differing on the warhead. For the preparation of the Michael acceptor warhead, a Horner-Wadsworth-Emmons reaction was used.

Postnatal chest X-ray in children with asymptomatic congenital lung malformations.

Objective: The clinical implications of a postnatal chest X-ray (CXR) in asymptomatic children with a prenatally diagnosed congenital lung malformation (CLM) are uncertain. We assessed the justification for the postnatal use of CXR in these children.

Methods: We included patients with CLM confirmed through chest computed tomography angiography or histopathological analysis who were asymptomatic at birth, underwent routine postnatal CXR, and participated in our standard of care prospective structured longitudinal follow-up program.

Regulation of the DLC3 tumor suppressor by a novel phosphoswitch.

Deleted in liver cancer 3 (DLC3) is a Rho GTPase-activating protein (RhoGAP) that plays a crucial role in maintaining adherens junction integrity and coordinating polarized vesicle transport by modulating Rho activity at the plasma membrane and endomembranes. By employing bioinformatical sequence analysis, experiments, and assays we here identified a polybasic region (PBR) in DLC3 that facilitates the association of the protein with cellular membranes. Within the PBR, we mapped two serines whose phosphorylation can alter the electrostatic character of the region.

Complete response of metastatic microsatellite-stable V600E colorectal cancer to first-line oxaliplatin-based chemotherapy and immune checkpoint blockade.

The randomized METIMMOX trial (NCT03388190) examined if patients with previously untreated, unresectable abdominal metastases from microsatellite-stable (MSS) colorectal cancer (CRC) might benefit from potentially immunogenic, short-course oxaliplatin-based chemotherapy alternating with immune checkpoint blockade (ICB). Three of 38 patients assigned to this experimental treatment had metastases from -mutant MSS-CRC, in general a poor-prognostic subgroup explored here. The ≥70-year-old females presented with ascending colon adenocarcinomas with intermediate tumor mutational burden (6.

Amine-containing donepezil analogues as potent acetylcholinesterase inhibitors with increased polarity.

Functional dyspepsia (FD) is a gastrointestinal disorder characterized by postprandial fullness, upper abdominal bloating, and early satiation. Peripheral acetylcholinesterase (AChE) inhibitors such as acotiamide have shown efficacy in FD treatment, but their limited affinity towards the enzyme has hindered their effectiveness. Conversely, AChE inhibitors developed for Alzheimer's disease have high potency but exhibit strong central activity, making them unsuitable for FD treatment.

Treatment outcome according to genetic tumour alterations and clinical characteristics in digestive high-grade neuroendocrine neoplasms.

Background: Chemotherapy has limited efficacy in advanced digestive high-grade neuroendocrine neoplasms (HG-NEN) and prognosis is dismal. Predictive markers for palliative chemotherapy are lacking, and prognostic markers are limited.

Methods: Digestive HG-NEN patients (n = 229) were prospectively included 2013-2017.

Structure-based virtual screening of unbiased and RNA-focused libraries to identify new ligands for the HCV IRES model system.

Targeting RNA including viral RNAs with small molecules is an emerging field. The hepatitis C virus internal ribosome entry site (HCV IRES) is a potential target for translation inhibitor development to raise drug resistance mutation preparedness. Using RNA-focused and unbiased molecule libraries, a structure-based virtual screening (VS) by molecular docking and pharmacophore analysis was performed against the HCV IRES subdomain IIa.

Lower respiratory tract infections in children with congenital lung abnormalities.

Objective: We aimed to determine if the incidence of lower respiratory tract infections (LRTI) among children with asymptomatic, observationally managed congenital lung abnormalities (CLA) differed from that of symptomatic patients who underwent surgery. Second, we sought to compare the pre- and post-resection incidence of LRTI in patients who underwent surgery.

Methods: This retrospective cohort study included patients born between 1999 and 2021 with CLA confirmed by CT scan who were enrolled in a prospective longitudinal follow-up program.

Assessment of Nucleobase Protomeric and Tautomeric States in Nucleic Acid Structures for Interaction Analysis and Structure-Based Ligand Design.

With increasing interest in RNA as a therapeutic and a potential target, the role of RNA structures has become more important. Even slight changes in nucleobases, such as modifications or protomeric and tautomeric states, can have a large impact on RNA structure and function, while local environments in turn affect protonation and tautomerization. In this work, the application of empirical tools for p and tautomer prediction for RNA modifications was elucidated and compared with ab initio quantum mechanics (QM) methods and expanded toward macromolecular RNA structures, where QM is no longer feasible.

The Diagnostics and Management of Bronchopulmonary Sequestration: An International Survey among Specialized Caregivers.

Background:  Our objective was to explore the treatment preferences for bronchopulmonary sequestration (BPS) among an international group of specialized caregivers.

Methods:  Sixty-three participants from 17 countries completed an online survey concerning the diagnostics, treatment, and follow-up. Recruitment took place among members of the Collaborative Neonatal Network for the first European Congenital Pulmonary Airway Malformation Trial Consortium and through the Association for European Pediatric and Congenital Cardiology working group database.

Protease detection in the biosensor era: A review.

Proteases have been proposed as potential biomarkers for several pathological conditions including cancers, multiple sclerosis and cardiovascular diseases, due to their ability to break down the components of extracellular matrix and basement membrane. The development of protease biosensors opened up the possibility to investigate the proteolytic activity of dysregulated proteases with higher efficiency over the traditional detection assays due to their quick detection capability, high sensitivity and selectivity, simple instrumentation and cost-effective fabrication processes. In contrast to the recently published review papers that primarily focused on one specific class of proteases or one specific detection method, this review article presents different optical and electrochemical detection methods that can be used to design biosensors for all major protease families.

Non-covalent dyes in microscale thermophoresis for studying RNA ligand interactions and modifications.

Microscale Thermophoresis (MST) is a powerful biophysical technique that measures the mobility of biomolecules in response to a temperature gradient, making it useful for investigating the interactions between biological molecules. This study presents a novel methodology for studying RNA-containing samples using non-covalent nucleic acid-sensitive dyes in MST. This "mix-and-measure" protocol uses non-covalent dyes, such as those from the Syto or Sybr series, which lead to the statistical binding of one fluorophore per RNA oligo showing key advantages over traditional covalent labelling approaches.

Next-generation sequencing reveals mitogenome diversity in plasma extracellular vesicles from colorectal cancer patients.

Background: Recent reports have demonstrated that the entire mitochondrial genome can be secreted in extracellular vesicles (EVs), but the biological attributes of this cell-free mitochondrial DNA (mtDNA) remain insufficiently understood. We used next-generation sequencing to compare plasma EV-derived mtDNA to that of whole blood (WB), peripheral blood mononuclear cells (PBMCs), and formalin-fixed paraffin-embedded (FFPE) tumor tissue from eight rectal cancer patients and WB and fresh-frozen (FF) tumor tissue from eight colon cancer patients.

Methods: Total DNA was isolated before the mtDNA was enriched by PCR with either two primer sets generating two long products or multiple primer sets (for the FFPE tumors), prior to the sequencing.

Germline pathogenic variants in patients with high-grade gastroenteropancreatic neuroendocrine neoplasms.

High-grade gastroenteropancreatic (HG-GEP) neuroendocrine neoplasms (NENs) are highly aggressive cancers. The molecular etiology of these tumors remains unclear, and the prevalence of pathogenic germline variants in patients with HG-GEP NENs is unknown. We assessed sequencing data of 360 cancer genes in normal tissue from 240 patients with HG-GEP NENs; 198 patients with neuroendocrine carcinomas (NECs) and 42 with grade 3 neuroendocrine tumors (NET G3).

Sublobar Pulmonary Resection in Children With Congenital Lung Abnormalities: A Systematic Review.

Background: Lobectomy is currently the advised resection for symptomatic congenital lung abnormalities (CLA). Sublobar surgery is suggested as an alternative that enables to conserve healthy lung parenchyma. This systematic review aims to explore the outcomes of sublobar surgery in CLA patients as well as the corresponding surgical terminology and techniques.

Long-term neurodevelopment in children with resected congenital lung abnormalities.

To determine whether children who underwent resection of a congenital lung abnormality (CLA) are at higher risk for neurodevelopmental impairments than peers in the general population. The study population consisted of children born between 1999-2018 who underwent resection of a symptomatic CLA. Neurocognitive development (intelligence, memory, attention, visuospatial processing, executive functioning) and motor function of this population are monitored through our structured, prospective longitudinal follow-up program at the ages of 30 months, 5, 8, and 12 years.

Covalent -Adenosylhomocysteine-Based DNA Methyltransferase 2 Inhibitors with a New Type of Aryl Warhead.

The DNA methyltransferase 2 (DNMT2) is an RNA modifying enzyme associated with pathophysiological processes, such as mental and metabolic disorders or cancer. Although the development of methyltransferase inhibitors remains challenging, DNMT2 is not only a promising target for drug discovery, but also for the development of activity-based probes. Here, we present covalent SAH-based DNMT2 inhibitors decorated with a new type of aryl warhead.

β-Catenin Drives Butyrophilin-like Molecule Loss and γδ T-cell Exclusion in Colon Cancer.

Intraepithelial lymphocytes (IEL) expressing γδ T-cell receptors (γδTCR) play key roles in elimination of colon cancer. However, the precise mechanisms by which progressing cancer cells evade immunosurveillance by these innate T cells are unknown. Here, we investigated how loss of the Apc tumor suppressor in gut tissue could enable nascent cancer cells to escape immunosurveillance by cytotoxic γδIELs.

Improving binding entropy by higher ligand symmetry? - A case study with human matriptase.

Understanding different contributions to the binding entropy of ligands is of utmost interest to better predict affinity and the thermodynamic binding profiles of protein-ligand interactions and to develop new strategies for ligand optimization. To these means, the largely neglected effects of introducing higher ligand symmetry, thereby reducing the number of energetically distinguishable binding modes on binding entropy using the human matriptase as a model system, were investigated. A set of new trivalent phloroglucinol-based inhibitors that address the roughly symmetric binding site of the enzyme was designed, synthesized, and subjected to isothermal titration calorimetry.

Investigation of the Compatibility between Warheads and Peptidomimetic Sequences of Protease Inhibitors-A Comprehensive Reactivity and Selectivity Study.

Covalent peptidomimetic protease inhibitors have gained a lot of attention in drug development in recent years. They are designed to covalently bind the catalytically active amino acids through electrophilic groups called warheads. Covalent inhibition has an advantage in terms of pharmacodynamic properties but can also bear toxicity risks due to non-selective off-target protein binding.

Chemical Space Virtual Screening against Hard-to-Drug RNA Methyltransferases DNMT2 and NSUN6.

Targeting RNA methyltransferases with small molecules as inhibitors or tool compounds is an emerging field of interest in epitranscriptomics and medicinal chemistry. For two challenging RNA methyltransferases that introduce the 5-methylcytosine (mC) modification in different tRNAs, namely DNMT2 and NSUN6, an ultra-large commercially available chemical space was virtually screened by physicochemical property filtering, molecular docking, and clustering to identify new ligands for those enzymes. Novel chemotypes binding to DNMT2 and NSUN6 with affinities down to K = 37 µM and K = 12 µM, respectively, were identified using a microscale thermophoresis (MST) binding assay.