Rare Oncogenic Fusions in Pediatric Central Nervous System Tumors: A Case Series and Literature Review.

Central Nervous System (CNS) pediatric tumors represent the most common solid tumors in children with a wide variability in terms of survival and therapeutic response. By contrast to their adult counterpart, the mutational landscape of pediatric CNS tumors is characterized by oncogenic fusions rather than multiple mutated genes. CNS pediatric tumors associated with oncogenic fusions represent a complex landscape of tumors with wide radiological, morphological and clinical heterogeneity.

Validation of a targeted next-generation sequencing panel for pancreatic ductal adenocarcinomas.

Pancreatic ductal adenocarcinoma (PDAC) is reported to be amongst the cancers with the lowest survival rate at 5 years. In the present study we aimed to validate a targeted next-generation sequencing (tNGS) panel to use in clinical routine, investigating genes important for PDAC diagnostic, prognostic and potential theragnostic aspect. In this NGS panel we also designed target regions to inquire about loss of heterozygosity (LOH) of chromosome 18 that has been described to be possibly linked to a worse disease progression.

Designing Complex Tapestries with Photography-Inspired Manipulation of Self-Organized Thin-Films.

Thin-films patterned with complex motifs are of fundamental interest because of their advanced optical, mechanical and electronic properties, but fabrication of these materials remains challenging. Self-organization strategies, such as immersion controlled reaction-diffusion patterning, have shown great potential for production of patterned thin-films. However, the autonomous nature of such processes limits controllable pattern customizability and complexity.

Identification of "Structural Pin" Interactions and their Significance for the Conformational Control of Macrocyclic Scaffolds.

While peptide macrocycles with rigidified conformations have proven to be useful in the design of chemical probes of protein targets, conformational flexibility and rapid interconversion can be equally vital for biological activity and favorable physicochemical properties. This study introduces the concept of "structural pin", which describes a hydrogen bond that is largely responsible for stabilizing the entire macrocycle backbone conformation. Structural analysis of macrocycles using nuclear magnetic resonance (NMR), molecular modelling and X-ray diffraction indicates that disruption of the structural pin can drastically influence the conformation of the entire ring, resulting in novel states with increased flexibility.

Direct Environmental Lead Detection by Photoluminescent Perovskite Formation with Nanogram Sensitivity.

Although the global ban on leaded gasoline has markedly reduced lead poisoning, many other environmental sources of lead exposure, such as paint, pipes, mines, and recycling sites remain. Existing methods to identify these sources are either costly or unreliable. We report here a new, sensitive, and inexpensive lead detection method that relies on the formation of a perovskite semiconductor.

Patterning Complex Line Motifs in Thin Films Using Immersion-Controlled Reaction-Diffusion.

The discovery of self-organization principles that enable scalable routes toward complex functional materials has proven to be a persistent challenge. Here, reaction-diffusion driven, immersion-controlled patterning (R-DIP) is introduced, a self-organization strategy using immersion-controlled reaction-diffusion for targeted line patterning in thin films. By modulating immersion speeds, the movement of a reaction-diffusion front over gel films is controlled, which induces precipitation of highly uniform lines at the reaction front.

A Two-Step Diagnostic Approach for NTRK Gene Fusion Detection in Biliary Tract and Pancreatic Adenocarcinomas.

Background: It is of interest to determine the incidence and molecular characteristics of NTRK gene fusions in patients with bilio-pancreatic cancers, because of possible treatment with TRK inhibitors for advanced tumors. The aim of the present study was to apply the guidelines for NTRK testing algorithm to a series of patients with bilio-pancreatic cancers.

Methods: Immunohistochemistry screening was applied on formalin-fixed paraffin-embedded archival blocks from surgical resections, biopsies, or cytological samples of biliary tract and pancreatic adenocarcinomas.

Clinicopathological and molecular characterization of a case classified by DNA‑methylation profiling as "CNS embryonal tumor with BRD4-LEUTX fusion".

Central Nervous System (CNS) embryonal tumors represent a heterogeneous group of highly aggressive tumors occurring preferentially in children but also described in adolescents and adults. In 2021, the CNS World Health Organization (WHO) classification drastically changed the diagnosis of the other CNS embryonal tumors including new histo-molecular tumor types. Here, we report a pediatric case of a novel tumor type among the other CNS embryonal tumors classified within the methylation class "CNS Embryonal Tumor with BRD4-LEUTX Fusion".

Rapid formation of uniformly layered materials by coupling reaction-diffusion processes with mechanical responsiveness.

Straightforward manufacturing pathways toward large-scale, uniformly layered composites may enable the next generation of materials with advanced optical, thermal, and mechanical properties. Reaction-diffusion systems are attractive candidates to this aim, but while layered composites theoretically could spontaneously arise from reaction-diffusion, in practice randomly oriented patches separated by defects form, yielding nonuniformly patterned materials. A propagating reaction front can prevent such nonuniform patterning, as is the case for Liesegang processes, in which diffusion drives a reaction front to produce layered precipitation patterns.

Molecular pathology testing for non-small cell lung cancer: an observational study of elements currently present in request forms and result reports and the opinion of different stakeholders.

Background: For patients with non-small cell lung cancer (NSCLC), targeted therapies are becoming part of the standard treatment. It is of question which information the clinicians provide on test requests and how the laboratories adapt test conclusions to this knowledge and regulations.

Methods: This study consisted of two components; 1) checking the presence of pre-defined elements (administrative and key for therapy-choice) on completed requests and corresponding reports in Belgian laboratories, both for tissue- and liquid biopsy (LB)-testing and b) opinion analysis from Belgian pathologists/molecular biologists and clinicians during national pathology/oncology meetings.

The Role of Inactivation in Epithelial-Mesenchymal Plasticity of Pancreatic Ductal Adenocarcinoma: The Missing Link?

Pancreatic ductal adenocarcinoma (PDAC) presents a five-year survival rate of 10% and its incidence increases over the years. It is, therefore, essential to improve our understanding of the molecular mechanisms that promote metastasis and chemoresistance in PDAC, which are the main causes of death in these patients. is inactivated in 50% of PDACs and its loss has been associated with worse overall survival and metastasis, although some controversy still exists.

Immunohistochemistry as an accurate tool for the assessment of and mutations in primary and metastatic melanoma.

Metastatic melanoma is a fatal disease with poor prognosis. Ever since targeted therapy against oncogenic was approved, molecular profiling has become an integral part of the management of such patients. While molecular testing is not available in all pathology laboratories, immunohistochemistry (IHC) is a reliable screening option.

Analyses of DNA Methylation Profiling in the Diagnosis of Intramedullary Astrocytomas.

Intramedullary astrocytomas (IMAs) consist of a heterogeneous group of rare central nervous system (CNS) tumors associated with variable outcomes. A DNA methylation-based classification approach has recently emerged as a powerful tool to further classify CNS tumors. However, no DNA methylation-related studies specifically addressing to IMAs have been performed yet.

Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Genome Sequencing from Post-Mortem Formalin-Fixed, Paraffin-Embedded Lung Tissues.

Implementation of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) testing in the daily practice of pathology laboratories requires procedure adaptation to formalin-fixed, paraffin-embedded (FFPE) samples. So far, one study reported the feasibility of SARS-CoV-2 genome sequencing on FFPE tissues with only one contributory case of two. This study optimized SARS-CoV-2 genome sequencing using the Ion AmpliSeq SARS-CoV-2 Panel on 22 FFPE lung tissues from 16 deceased coronavirus disease 2019 (COVID-19) patients.

Clinical, radiological and molecular characterization of intramedullary astrocytomas.

Intramedullary astrocytomas (IMAs) are rare tumors, and few studies specific to the molecular alterations of IMAs have been performed. Recently, KIAA1549-BRAF fusions and the H3F3A p.K27M mutation have been described in low-grade (LG) and high-grade (HG) IMAs, respectively.

Design and Validation of a Gene-Targeted, Next-Generation Sequencing Panel for Routine Diagnosis in Gliomas.

The updated 2016 World Health Organization (WHO) classification system for gliomas integrates molecular alterations and histology to provide a greater diagnostic and prognostic utility than the previous, histology-based classification. The increasing number of markers that are tested in a correct diagnostic procedure makes gene-targeted, next-generation sequencing (NGS) a powerful tool in routine pathology practice. We designed a 14-gene NGS panel specifically aimed at the diagnosis of glioma, which allows simultaneous detection of mutations and copy number variations, including the 1p/19q-codeletion and Epidermal Growth Factor Receptor () amplification.

Guidelines for optimized gene knockout using CRISPR/Cas9.

CRISPR/Cas9 technology has evolved as the most powerful approach to generate genetic models both for fundamental and preclinical research. Despite its apparent simplicity, the outcome of a genome-editing experiment can be substantially impacted by technical parameters and biological considerations. Here, we present guidelines and tools to optimize CRISPR/Cas9 genome-targeting efficiency and specificity.

Prdm12 Directs Nociceptive Sensory Neuron Development by Regulating the Expression of the NGF Receptor TrkA.

In humans, many cases of congenital insensitivity to pain (CIP) are caused by mutations of components of the NGF/TrkA signaling pathway, which is required for survival and specification of nociceptors and plays a major role in pain processing. Mutations in PRDM12 have been identified in CIP patients that indicate a putative role for this transcriptional regulator in pain sensing. Here, we show that Prdm12 expression is restricted to developing and adult nociceptors and that its genetic ablation compromises their viability and maturation.

Methods of measurement for tumor mutational burden in tumor tissue.

Immunotherapies based on immune checkpoint inhibitors are emerging as an innovative treatment for different types of advanced cancers. While the utility of immune checkpoint inhibitors has been clearly demonstrated, the response rate is highly variable across individuals. Due to the cost and toxicity of these immunotherapies, a critical challenge in this field is the identification of predictive biomarkers to discriminate which patients may respond to immunotherapy.

Verification of chemistry reference ranges using a simple method in sub-Saharan Africa.

Background: Chemistry safety assessments are interpreted by using chemistry reference ranges (CRRs). Verification of CRRs is time consuming and often requires a statistical background.

Objectives: We report on an easy and cost-saving method to verify CRRs.

HbA1c: EQA in Germany, Belgium and the Netherlands using fresh whole blood samples with target values assigned with the IFCC reference system.

Background: External quality assessment/proficiency test (EQA/PT) organizers play an important role in monitoring the performance of HbA1c measurements. With increasing quality of the assays, HbA1c is increasingly used for diagnosis of diabetes and the demands on EQA/PT organizers themselves are rising constantly. EQA organizers in Germany (INSTAND), Belgium (WIV/IPV), and the Netherlands (SKML) organized a program with commutable samples and target values assigned with the International Federation of Clinical Chemistry and Laboratory Medicine (IFCC) reference system.

Prdm12 specifies V1 interneurons through cross-repressive interactions with Dbx1 and Nkx6 genes in Xenopus.

V1 interneurons are inhibitory neurons that play an essential role in vertebrate locomotion. The molecular mechanisms underlying their genesis remain, however, largely undefined. Here, we show that the transcription factor Prdm12 is selectively expressed in p1 progenitors of the hindbrain and spinal cord in the frog embryo, and that a similar restricted expression profile is observed in the nerve cord of other vertebrates as well as of the cephalochordate amphioxus.

The evolutionarily conserved transcription factor PRDM12 controls sensory neuron development and pain perception.

PR homology domain-containing member 12 (PRDM12) belongs to a family of conserved transcription factors implicated in cell fate decisions. Here we show that PRDM12 is a key regulator of sensory neuronal specification in Xenopus. Modeling of human PRDM12 mutations that cause hereditary sensory and autonomic neuropathy (HSAN) revealed remarkable conservation of the mutated residues in evolution.