Explore the vast range of titles available.

Oncogene amplification on extrachromosomal DNA (ecDNA) is a common event, driving aggressive tumor growth, drug resistance and shorter survival. Currently, the impact of nonchromosomal oncogene inheritance—random identity by descent—is poorly understood. Also unclear is the impact of ecDNA on somatic variation and selection. Here integrating theoretical models of random segregation, unbiased image analysis, CRISPR-based ecDNA tagging with live-cell imaging and CRISPR-C, we demonstrate that random ecDNA inheritance results in extensive intratumoral ecDNA copy number heterogeneity and rapid adaptation to metabolic stress and targeted treatment. Observed ecDNAs benefit host cell survival or growth and can change within a single cell cycle. ecDNA inheritance can predict, a priori, some of the aggressive features of ecDNA-containing cancers. These properties are facilitated by the ability of ecDNA to rapidly adapt genomes in a way that is not possible through chromosomal oncogene amplification. These results show how the nonchromosomal random inheritance pattern of ecDNA contributes to poor outcomes for patients with cancer. Random segregation of extrachromosomal DNA contributes to intratumoral heterogeneity and facilitates the rapid adaptation of human tumor cells to anticancer drugs.

Intratumour heterogeneity is a major cause of treatment failure in cancer. We present in-depth analyses combining transcriptomic and genomic profiling with ultra-deep targeted sequencing of multiregional biopsies in 10 patients with neuroblastoma, a devastating childhood tumour. We observe high spatial and temporal heterogeneity in somatic mutations and somatic copy-number alterations which are reflected on the transcriptomic level. Mutations in some druggable target genes including ALK and FGFR1 are heterogeneous at diagnosis and/or relapse, raising the issue whether current target prioritization and molecular risk stratification procedures in single biopsies are sufficiently reliable for therapy decisions. The genetic heterogeneity in gene mutations and chromosome aberrations observed in deep analyses from patient courses suggest clonal evolution before treatment and under treatment pressure, and support early emergence of metastatic clones and ongoing chromosomal instability during disease evolution. We report continuous clonal evolution on mutational and copy number levels in neuroblastoma, and detail its implications for therapy selection, risk stratification and therapy resistance. Neuroblastoma is a devastating tumour in children. Here, the authors analyse multi-region patient samples using genomics and transcriptomics, revealing temporal and spatial heterogeneity and questioning the reliability of single-biopsy based diagnostics.

Background Recently there have been numerous attempts to improve the genome of the pig. Despite these efforts, there is a substantial amount of work remaining to obtain a “finished version” of the genome; analysis of incomplete versions can lead to incorrect biological interpretations. To that end, we manually assembled and annotated a non-redundant, 16,146 RNA and 15,613 pig protein sequence libraries. We used it to assess the assembly and annotation status of the 3 latest builds of the genome and to the mouse and human genomes. Results Our analysis of 6,135 protein-coding genes reveals that the percentage of error-free assembled and annotated genes in NCBI and Ensembl builds 11.1 and MARC build 1.0 are 58.9, 51.7, and 47.1%, respectively. An examination of these errors revealed nine predominant sources that are detailed in the Results. Using our protein library, we determined 1:1 orthology to 16,496 mouse and 15,770 human proteins. 73.8% of these proteins were conserved among the 3 species; however, when a gene was missing from one of the three genomes, pigs were 5.0X more likely to have the human gene than mice. REACTOME, GO BP Direct, and Ingenuity Pathway Analysis functional enrichment analyses of pig-human orthologous genes revealed 8, 13, and 35 conserved pathways, and 0, 0, and 47 for human-mouse pathways, respectively. Last, we conducted an analysis of functional domain preservation for 3,465 proteins and discovered when a functional domain is missing from a protein in 1 of the 3 species, pigs are 2X more likely to have the human domain than mice. Conclusions These data strongly indicate that, overall, swine are a scientifically important intermediate species (rodent-human) for conducting scientific research on human health.

Background: Alpha-1 antitrypsin deficiency (AATD) is a genetic condition resulting from mutations in the alpha-1 antitrypsin (AAT) protein, a major systemic antiproteinase, resulting in reduced/no release of AAT, disrupting the proteinase/antiproteinase balance. A sustained imbalance can cause structural changes to the lung parenchyma, leading to emphysema. Predicting and assessing human responses to potential therapeutic candidates from preclinical animal studies have been challenging. Our aims were to develop a more physiologically relevant in vitro model of the proteinase/antiproteinase balance and assess whether the data generated could better predict the efficacy of pharmacological candidates to inform decisions on clinical trials, together with expected biomarker responses. Methods: We developed an in vitro model assessing the proteinase/antiproteinase balance by the changes in the fibrinogen cleavage products of neutrophil elastase (NE) and proteinase 3 (PR3). This allowed the assessment of physiological and pharmaceutical neutrophil serine proteinase (NSP) inhibitors to determine the putative threshold at which the maximal effect is achieved. Results: AAT significantly reduced NE and PR3 activity footprints, with the maximal reduction achieved at concentrations above 10 μM. The inhibitor MPH966 alone also significantly reduced NE footprint generation in a concentration-dependent manner, leveling out above 100 nM but had no effect on the PR3 footprint. At levels of AAT consistent with AATD, MPH966 had an additive effect, reducing the NE activity footprint more than either inhibitor alone. Conclusion: Our results support an inhibitor threshold above which the activity footprint generation appears resistant to increasing dosage. Our model can support the testing of inhibitors, confirming activity biomarkers as indicators of likely pharmaceutical efficacy, the assessment of NSP activity in the pathophysiology of emphysema, and the likely function of biological or pharmacological inhibitors in disease management.

We previously demonstrated that IL4, IL13, CLCA1, and CCL26 mRNA were significantly upregulated in the lungs of pigs given a low dose of all trans-retinoic acid (ATRA) and infected with Ascaris suum. We also demonstrated that ATRA induced a state of partial alternative activation in porcine macrophages (Mφs) and amplified certain aspects of M2a activation induced by IL-4. Given these results, we tested the effect of ATRA on IL-4 responses in two porcine intestinal epithelial cell lines, IPEC1 and IPEC-J2 and observed that ATRA increased mRNA for the IL-4 receptor alpha chain. ATRA also increased IL-4 induced phosphorylation of signal transducer and activator of transcription 6 (STAT6) and mRNA expression of the chloride channel, calcium activated, family member 1 (CLCA1), important for mucus formation, and chemokine (C-C motif) ligand 26 (CCL26), a potent eosinophil chemoattractant. We extended these findings to human Mφ THP-1 cells and showed that ATRA synergistically increased IL-4-induced CCL2, CCL13, and CCL26 mRNA and protein levels. Transglutaminase 2 mRNA, protein, and enzyme activity were synergistically induced in THP-1 cells pretreated with ATRA and then treated with IL-4, thus, ATRA increased signaling in response to IL-4 in porcine epithelial cells and porcine and human Mφs. Given the prevalence of allergic and parasitic diseases worldwide and the close similarities in the porcine and human immune responses, these findings have important implications for the nutritional regulation of allergic inflammation at mucosal surfaces.

Background The use of swine in biomedical research has increased dramatically in the last decade. Diverse genomic- and proteomic databases have been developed to facilitate research using human and rodent models. Current porcine gene databases, however, lack the robust annotation to study pig models that are relevant to human studies and for comparative evaluation with rodent models. Furthermore, they contain a significant number of errors due to their primary reliance on machine-based annotation. To address these deficiencies, a comprehensive literature-based survey was conducted to identify certain selected genes that have demonstrated function in humans, mice or pigs. Results The process identified 13,054 candidate human, bovine, mouse or rat genes/proteins used to select potential porcine homologs by searching multiple online sources of porcine gene information. The data in the Porcine Translational Research Database (( http://www.ars.usda.gov/Services/docs.htm?docid=6065 ) is supported by >5800 references, and contains 65 data fields for each entry, including >9700 full length (5′ and 3′) unambiguous pig sequences, >2400 real time PCR assays and reactivity information on >1700 antibodies. It also contains gene and/or protein expression data for >2200 genes and identifies and corrects 8187 errors (gene duplications artifacts, mis-assemblies, mis-annotations, and incorrect species assignments) for 5337 porcine genes. Conclusions This database is the largest manually curated database for any single veterinary species and is unique among porcine gene databases in regard to linking gene expression to gene function, identifying related gene pathways, and connecting data with other porcine gene databases. This database provides the first comprehensive description of three major Super-families or functionally related groups of proteins (Cluster of Differentiation (CD) Marker genes, Solute Carrier Superfamily, ATP binding Cassette Superfamily), and a comparative description of porcine microRNAs.

As an emerging technology, polymer electrolyte fuel cells (PEFCs) powered by clean hydrogen can be a great source of renewable power generation with flexible utilization because of high gravimetric energy density of hydrogen. To be used in real‐life applications, PEFCs need to maintain their performance for long‐term use under a wide range of conditions. Therefore, it's important to understand the degradation of the PEFC under protocols that are closely related to the catalyst lifetime. Alloying Pt with transitional metal improves catalyst activity. It is also crucial to understand Pt alloys degradation mechanisms to improve their durability. To study durability of Pt alloys, accelerated stress tests (ASTs) are performed on Pt−Co catalyst supported on two types of carbon. Two different AST protocols were being studied: Membrane Electrolyte Assembly (MEA) AST based on the protocol introduced by the Million Mile Fuel Cell Truck consortium in 2023 and Catalyst AST, adopted from the U.S. Department of Energy (DoE). Higher degradation of catalyst observed for PtCo supported on high surface area carbon when subjected to two accelerated stress tests (ASTs) for polymer electrolyte fuel cells.

MYCN amplification drives one in six cases of neuroblastoma. The supernumerary gene copies are commonly found on highly rearranged, extrachromosomal circular DNA (ecDNA). The exact amplicon structure has not been described thus far and the functional relevance of its rearrangements is unknown. Here, we analyze the MYCN amplicon structure using short-read and Nanopore sequencing and its chromatin landscape using ChIP-seq, ATAC-seq and Hi-C. This reveals two distinct classes of amplicons which explain the regulatory requirements for MYCN overexpression. The first class always co-amplifies a proximal enhancer driven by the noradrenergic core regulatory circuit (CRC). The second class of MYCN amplicons is characterized by high structural complexity, lacks key local enhancers, and instead contains distal chromosomal fragments harboring CRC-driven enhancers. Thus, ectopic enhancer hijacking can compensate for the loss of local gene regulatory elements and explains a large component of the structural diversity observed in MYCN amplification. MYCN amplification is common in neuroblastomas. Here the authors analyse the MYCN amplicon structure and its epigenetic regulation by integrating short- and longread genomic and epigenomic data and find two classes of MYCN amplicons in neuroblastomas, one driven by local enhancers and the other by hijacking of distal regulatory elements.

Dysregulated gene expression contributes to most prevalent features in human cancers. Here, we show that most subtypes of acute myeloid leukemia (AML) depend on the aberrant assembly of MYB transcriptional co-activator complex. By rapid and selective peptidomimetic interference with the binding of CBP/P300 to MYB, but not CREB or MLL1, we find that the leukemic functions of MYB are mediated by CBP/P300 co-activation of a distinct set of transcription factor complexes. These MYB complexes assemble aberrantly with LYL1, E2A, C/EBP family members, LMO2, and SATB1. They are organized convergently in genetically diverse subtypes of AML and are at least in part associated with inappropriate transcription factor co-expression. Peptidomimetic remodeling of oncogenic MYB complexes is accompanied by specific proteolysis and dynamic redistribution of CBP/P300 with alternative transcription factors such as RUNX1 to induce myeloid differentiation and apoptosis. Thus, aberrant assembly and sequestration of MYB:CBP/P300 complexes provide a unifying mechanism of oncogenic gene expression in AML. This work establishes a compelling strategy for their pharmacologic reprogramming and therapeutic targeting for diverse leukemias and possibly other human cancers caused by dysregulated gene control.

IntroductionType 1 diabetes is a chronic autoimmune disease that often presents with diabetic ketoacidosis at diagnosis. Since detection of type 1 diabetes risk is possible using genetic risk scores and autoantibody assays, prevention of diabetic ketoacidosis or delayed onset of type 1 diabetes may be possible and may improve outcomes. Several pilot screening programmes for type 1 diabetes risk have emerged worldwide but outcomes measured in these screening programmes are heterogeneous, making it difficult to compare and synthesise findings across studies. To improve the standardisation of outcome reporting and measurement, we aim to develop a patient-oriented core outcome set for studies of type 1 diabetes risk screening.Methods and analysisThis five-step protocol was developed in alignment with the COS-STAndardised Protocol Statement and the Core Outcome Measures in Effectiveness Trials framework. The five steps will include: (1a) conducting a rapid literature review, (1b) gathering input on candidate outcomes from members of the public, (2) combining literature and public input to prepare a preliminary list of outcomes, (3) conducting Delphi surveys with a range of stakeholders to begin to establish consensus on outcomes, (4) holding a final consensus meeting to establish consensus on outcomes and (5) establishing the outcome measurement instruments for the core outcome set.Ethics and disseminationEthics approval has been provided by The Hospital for Sick Children Research Ethics Board. The core outcome set will be distributed to researchers and clinicians involved in diabetes screening and clinical care, patient and family networks, research funders, journal editors, public health experts, and policymakers. Disseminated materials will be tailored to the various end users in the form of publication through academic journals, policy briefs, conferences, educational webinars, websites and social media.