bluuebunny/crossref_metadata_2025_split huggingface dataset:
Protein network analysis links the NSL complex to Parkinson’s disease and mitochondrial biology
Authors: Kelly Katie , Lewis Patrick A. , Plun-Favreau Helene , Manzoni Claudia 
Published: January 2023

AbstractWhilst the majority of PD cases are sporadic, much of our understanding of the pathophysiological basis of disease can be traced back to the study of rare, monogenic forms of disease. In the past decade, the availability of Genome-Wide Association Studies (GWAS) has facilitated a shift in focus, toward identifying common risk variants conferring increased risk of developing PD across the population. A recent mitophagy screening assay of GWAS candidates has functionally implicated the non-specific lethal (NSL) complex in the regulation of PINK1-mitophagy. Here, a bioinformatics approach has been taken to investigate the proteome of the NSL complex, to unpick its relevance to PD progression. The mitochondrial NSL interactome has been built, mining 3 separate repositories: PINOT, HIPPIE and MIST, for curated, literature-derived protein-protein interaction (PPI) data. We built; i) the ‘mitochondrial’ interactome, applying gene-set enrichment analysis (GSEA) to explore the relevance of the NSL mitochondrial interactome to PD and, ii) the PD-oriented interactome to uncover biological pathways underpinning the NSL /PD association. In this study, we find the mitochondrial NSL interactome to be significantly enriched for the protein products of PD associated genes, including the Mendelian PD genesLRRK2andVPS35. Additionally, the PD associated interactome is enriched for mitochondrial processes;“mitochondrial cell death”,“mitochondrial protein localisation”, “membrane protein localisation”and“mitochondrial transport”. Our data points to NSL complex members OGT and WDR5 as key drivers of this increased PD association. These findings strengthen a role for mitochondrial quality control in both familial and sporadic disease.
A defined clathrin-mediated trafficking pathway regulates sFLT1/VEGFR1 secretion from endothelial cells
Authors: Kinghorn Karina , Gill Amy , Marvin Allison , Li Renee , Quigley Kaitlyn , le Noble Ferdinand , Mac Gabhann Feilim , Bautch Victoria L 
Published: January 2023

ABSTRACTFLT1/VEGFR1 negatively regulates VEGF-A signaling and is required for proper vessel morphogenesis during vascular development and vessel homeostasis. Although a soluble isoform, sFLT1, is often mis-regulated in disease and aging, how sFLT1 is trafficked and secreted from endothelial cells is not well understood. Here we define requirements for constitutive sFLT1 trafficking and secretion in endothelial cells from the Golgi to the plasma membrane, and we show that sFLT1 secretion requires clathrin at or near the Golgi. Perturbations that affect sFLT1 trafficking blunted endothelial cell secretion and promoted intracellular mis-localization in cells and zebrafish embryos. siRNA-mediated depletion of specific trafficking components revealed requirements for RAB27A, VAMP3, and STX3 for post-Golgi vesicle trafficking and sFLT1 secretion, while STX6, ARF1, and AP1 were required at the Golgi. Depletion of STX6 altered vessel sprouting in a 3D angiogenesis model, indicating that endothelial cell sFLT1 secretion is important for proper vessel sprouting. Thus, specific trafficking components provide a secretory path from the Golgi to the plasma membrane for sFLT1 in endothelial cells that utilizes a specialized clathrin-dependent intermediate, suggesting novel therapeutic targets.
The MIR-NATMAPT-AS1does not regulate Tau expression in human neurons
Authors: Policarpo Rafaela , Wolfs Leen , Martínez-Montero Saul , Vandermeulen Lina , Royaux Ines , Van Peer Gert , Mestdagh Pieter , Sierksma Annerieke , De Strooper Bart , d’Ydewalle Constantin 
Published: January 2023

AbstractTheMAPTgene encodes Tau protein, a member of the large family of microtubule-associated proteins. Tau forms large insoluble aggregates that are toxic to neurons in several neurological disorders and neurofibrillary Tau tangles represent a key pathological hallmark of Alzheimer’s disease (AD) and other ‘tauopathies’1,2. Several Tau-lowering strategies are being investigated as a potential treatment for AD but the mechanisms that regulate Tau expression at the transcriptional or translational level are not well understood3,4. Recently, Simone etal.5reported the discovery of a new type of natural antisense transcripts called ‘MIR-NATs’ (referring to Mammalian-wide Interspersed Repeats – Natural Antisense Transcripts). Simone and colleagues usedMAPT-AS1, a MIR-NAT associated to theMAPTgene as an archetype of this new class of long non-coding RNAs. According to Simone etal.,MAPT-AS1represses Tau translation by competing for ribosomal RNA. We investigated the potential functions ofMAPT-AS1in neurons using the same gain- and loss-of-function experiments as described in the original report and expanded our analysis with complementary approaches. Our data do not support a role forMAPT-AS1in regulating Tau expression in human neurons and urge to cautiously interpret the data provided by Simone etal.5.
Targeted volume Correlative Light and Electron Microscopy of an environmental marine microorganism
Authors: Mocaer Karel , Mizzon Giulia , Gunkel Manuel , Halavatyi Aliaksandr , Steyer Anna , Oorschot Viola , Schorb Martin , Kieffre Charlotte Le , Yee Daniel P. , Chevalier Fabien , Gallet Benoit , Decelle Johan , Schwab Yannick , Ronchi Paolo 
Published: January 2023

AbstractPhotosynthetic microalgae are responsible for an important fraction of CO2fixation and O2production on Earth. Three-dimensional ultrastructural characterization of these organisms in their natural environment can contribute to a deeper understanding of their cell biology. However, the low throughput of volume electron microscopy (vEM) methods, along with the complexity and heterogeneity of environmental samples, pose great technical challenges. In the present study, we used a workflow based on a specific EM sample preparation, compatible with both light and vEM imaging in order to target one cell among a complex natural community. This method revealed the 3D subcellular landscape of a photosynthetic dinoflagellate with quantitative characterization of multiple organelles. We could show that this cell contains a single convoluted chloroplast and the arrangement of the flagellar apparatus with its associated photosensitive elements. Moreover, we observed chromatin features that could shed light on how transcriptional activity takes place in organisms where chromosomes are permanently condensed. Together with providing insights in dinoflagellates biology, this proof-of-principle study illustrates an efficient tool for the targeted ultrastructural analysis of environmental microorganisms in heterogeneous mixes.
Efficiently Quantifying DNA Methylation for Bulk- and Single-cell Bisulfite Data
Authors: Fischer Jonas , Schulz Marcel H. 
Published: January 2023

AbstractMotivationDNA CpG methylation (CpGm) has proven to be a crucial epigenetic factor in the gene regulatory system. Assessment of DNA CpG methylation values via whole-genome bisulfite sequencing (WGBS) is, however, computationally extremely demanding.ResultsWe present FAst MEthylation calling (FAME), the first approach to quantify CpGm values directly from bulk or single-cell WGBS reads without intermediate output files. FAME is very fast but as accurate as standard methods, which first produce BS alignment files before computing CpGm values. We present experiments on bulk and single-cell bisulfite datasets in which we show that data analysis can be significantly sped-up and help addressing the current WGBS analysis bottleneck for large-scale datasets without compromising accuracy.AvailabilityAn implementation of FAME is open source and licensed under GPL-3.0 athttps://github.com/FischerJo/FAME.
Environmental and molecular regulation of asexual reproduction in the sea anemone Nematostella vectensis
Authors: Al-Shaer Layla , Leach Whitney , Baban Noor , Yagodich Mia , Gibson Mathew C. , Layden Michael J. 
Published: January 2023

AbstractCnidarians exhibit incredible reproductive diversity, with most capable of sexual and asexual reproduction. Here we investigate factors that influence asexual reproduction in the burrowing sea anemoneNematostella vectensis, which can propagate asexually by transverse fission of the body column. By altering culture conditions, we demonstrate that the presence of a burrowing substrate strongly promotes transverse fission. In addition, we show that animal size does not affect fission rates, and that the plane of fission is fixed along the oral-aboral axis of the polyp. Homeobox transcription factors and components of the TGFβ, Notch, and FGF signaling pathways are differentially expressed in polyps undergoing physal pinching suggesting they are important regulators of transverse fission. Gene ontology analyses further suggest that during transverse fission the cell cycle is suppressed and that cell adhesion and patterning mechanisms are downregulated to promote separation of the body column. Finally, we demonstrate that the rate of asexual reproduction is sensitive to population density. Collectively, these experiments provide a foundation for mechanistic studies of asexual reproduction inNematostella, with implications for understanding the reproductive and regenerative biology of other cnidarian species.
Human aneuploid cells depend on the RAF/MEK/ERK pathway for overcoming increased DNA damage
Authors: Zerbib Johanna , Ippolito Marica Rosaria , Eliezer Yonatan , De Feudis Giuseppina , Reuveni Eli , Kadmon Anouk Savir , Martin Sara , Viganò Sonia , Leor Gil , Berstler James , Laue Kathrin , Cohen-Sharir Yael , Scorzoni Simone , Vazquez Francisca , Ben-David Uri , Santaguida Stefano 
Published: January 2023

AbstractAneuploidy is a hallmark of human cancer, yet the cellular mechanisms that allow cells to cope with aneuploidy-induced cellular stresses remain largely unknown. Such coping mechanisms may present cellular vulnerabilities that can be harnessed for targeting cancer cells. Here, we induced aneuploidy in non-transformed RPE1-hTERT cells and derived multiple stable clones with various degrees of chromosome imbalances. We performed an unbiased genomic profiling of 6 isogenic clones, using whole-exome and RNA sequencing. We then functionally interrogated their cellular dependency landscapes, using genome-wide CRISPR/Cas9 screens and large-scale drug screens. We found that aneuploid clones activated the DNA damage response (DDR), and were consequently more resistant to further DNA damage induction. Interestingly, aneuploid cells also exhibited elevated RAF/MEK/ERK pathway activity, and were more sensitive to several clinically-relevant drugs targeting this pathway, and in particular to genetic and chemical CRAF inhibition. CRAF activity was functionally linked to the resistance to DNA damage induction, as CRAF inhibition sensitized aneuploid cells to DNA damage-inducing chemotherapies. The association between aneuploidy, RAF/MEK/ERK signaling, and DDR was independent of p53. The increased activity and dependency of aneuploid cells on the RAF/MEK/ERK pathway was validated in another isogenic aneuploid system, and across hundreds of human cancer cell lines, confirming their relevance to human cancer. Overall, our study provides a comprehensive resource for genetically-matched karyotypically-stable cells of various aneuploidy states, and reveals a novel therapeutically-relevant cellular dependency of aneuploid cells.
Increased RNA and protein degradation is required for counteracting transcriptional burden and proteotoxic stress in human aneuploid cells
Authors: Ippolito Marica Rosaria , Zerbib Johanna , Eliezer Yonatan , Reuveni Eli , Viganò Sonia , De Feudis Giuseppina , Kadmon Anouk Savir , Vigorito Ilaria , Martin Sara , Laue Kathrin , Cohen-Sharir Yael , Scorzoni Simone , Vazquez Francisca , Santaguida Stefano , Ben-David Uri 
Published: January 2023

AbstractAneuploidy, an abnormal chromosome composition, results in a stoichiometric imbalance of protein complexes, which jeopardizes the fitness of aneuploid cells. Aneuploid cells thus need to compensate for the imbalanced DNA levels by regulating their RNA and protein levels, a phenomenon known as dosage compensation. However, the molecular mechanisms involved in dosage compensation in human cells – and whether they can be targeted to selectively kill aneuploid cancer cells – remain unknown. Here, we addressed this question via molecular dissection of multiple diploid vs. aneuploid cell models. Using genomic and functional profiling of a novel isogenic system of RPE1-hTERT cells with various degrees of aneuploidy, we found that aneuploid cells cope with both transcriptional burden and proteotoxic stress. At the mRNA level, aneuploid cells increased RNA synthesis, but concomitantly elevated several RNA degradation pathways, in particular the nonsense-mediated decay (NMD) and the microRNA-mediated mRNA silencing pathways. Consequently, aneuploid cells were more sensitive to the genetic or chemical perturbation of several key components of these RNA degradation pathways. At the protein level, aneuploid cells experienced proteotoxic stress, resulting in reduced translation and increased protein degradation, rendering them more sensitive to proteasome inhibition. These findings were recapitulated across hundreds of human cancer cell lines and primary tumors, confirming that both non-transformed and transformed cells alter their RNA and protein metabolism in order to adapt to the aneuploid state. Our results reveal that aneuploid cells are dependent on the over- or under-activation of several nodes along the gene expression process, identifying these pathways as clinically-actionable vulnerabilities of aneuploid cells.
EomesrestrictsBrachyuryfunctions at the onset of mammalian gastrulation
Authors: Schüle Katrin M. , Weckerle Jelena , Probst Simone , Wehmeyer Alexandra E. , Zissel Lea , Schröder Chiara M. , Tekman Mehmet , Kim Gwang-Jin , Schlägl Inga-Marie , Sagar  , Arnold Sebastian J. 
Published: January 2023

AbstractMammalian specification of mesoderm and definitive endoderm (DE) is instructed by the two related Tbx transcription factors (TFs)Eomesodermin(Eomes) andBrachyurysharing partially redundant functions. Gross differences of mutant embryonic phenotypes suggest specific functions of each TF. To date, the molecular details of separated lineage-specific gene-regulation byEomesandBrachyuryremain poorly understood. Here, we combine embryonic and stem cell-based analyses to delineate the non-overlapping, lineage-specific transcriptional activities. On a genome-wide scale binding of both TFs overlaps at promoters of target genes, but shows specificity for distal enhancer regions, that is conferred by differences in Tbx DNA-binding motifs. The unique binding to enhancer sites instructs the specification of anterior mesoderm (AM) and DE byEomesand caudal mesoderm byBrachyury. Remarkably, EOMES antagonizes BRACHYURY gene-regulatory functions in co-expressing cells during early gastrulation to ensure the proper sequence of early AM and DE lineage specification followed by posterior mesoderm derivatives.HighlightsDetailed comparative analysis of the two critical developmental regulatorsEomesandBrachyuryin mouse embryos and differentiating embryonic stem cellsTbx factors EOMES and BRACHYURY control distinct gene programs to specify different mesoderm and endoderm subsetsProgram specificity is conferred by binding to non-overlapping enhancers with distinct binding motifsEOMES restricts the activities of BRACHYURY thus ensuring the proper sequence of mesoderm and endoderm lineage specification
Newly born mesenchymal cells disperse through a rapid mechanosensitive migration
Authors: Riddell Jon , Noureen Shahzeb Raja , Sedda Luigi , Glover James D. , Ho William K. W. , Bain Connor A. , Berbeglia Arianna , Brown Helen , Anderson Calum , Chen Yuhang , Crichton Michael L. , Yates Christian A. , Mort Richard L. , Headon Denis J. 
Published: January 2023

SummaryEmbryonic mesenchymal cells are dispersed within an extracellular matrix but can coalesce to form condensates with key developmental roles. Cells within condensates undergo fate and morphological changes, and induce cell fate changes in nearby epithelia to produce structures including hair follicles, feathers or intestinal villi. Here, by imaging of mouse and chicken embryonic skin, we find that mesenchymal cells undergo much of their dispersal in early interphase, in a stereotyped process of displacement driven by three hours of rapid and persistent migration, followed by a long period of low motility. The cell division plane and the elevated migration speed and persistence of newly born mesenchymal cells are mechanosensitive, aligning with tension in the tissue. This early G1 migratory behaviour disperses mesenchymal cells and allows the daughters of recent divisions to travel long distances to enter dermal condensates, demonstrating an unanticipated effect of a cell cycle sub-phase on core mesenchymal behaviour.HighlightsAfter mesenchymal cell division the speed and persistence of daughter cell migration is elevated for 180 minutesMesenchymal cell division and migration are directed by tissue tensionNewly born mesenchymal cells are uniquely responsive to tissue strainNewly born mesenchymal cells are preferentially recruited to dermal condensatesIncreased dispersal of newly born cells enables long distance travel to dermal condensatesGraphical abstract
Backup transcription factor binding sites protect human genes from mutations in the promoter
Authors: Brown Jay C. 
Published: January 2023

AbstractThis study was designed to test the idea that human gene promoters have evolved to be resistant to the effects of mutations in their primary function, the control of gene expression. It is proposed that the transcription factor/transcription factor binding site (TF/TFBS) pair having the greatest effect on control of a gene is the one with the highest abundance in the promoter. Other pairs would have the same effect on gene expression and would predominate in the event of a mutation in the most abundant pair. It is expected that the overall promoter architecture proposed here will be highly resistant to mutagenic change that would otherwise affect expression of the gene. The idea was tested beginning with a database of 42 human genes highly specific for expression in brain. For each gene, information was accumulated about its expression level and about the TFBS occupancy of the five most abundant TF/TFBS pairs. Expression level was then plotted against TFBS occupancy separately for each of the five pairs, and the plots were compared with each other. The plots were found to be similar, and the results were interpreted to indicate that the TFBS occupancy ranks evolved to yield the same effect on gene expression level with multiple ranks able to function in the event of mutation in another. A similar analysis was conducted with a database of 31 human liver specific genes, and the overall result was found to be the same. Backup TFBS occupancy ranks were interpreted to be present in both brain and liver specific genes. Finally, the TFBSs in the brain specific and liver specific gene populations were compared with each other with the goal of identifying any brain selective or liver selective TFBSs. Of the 89 TFBSs in the pooled population, 58 were found only in brain specific but not liver specific genes, 8 only in liver specific but not brain specific genes and 23 were found in both brain and liver specific genes. The results were interpreted to emphasize the large number of TFBS in brain specific but not liver specific genes.
Extracellular vesicles and co-isolated endogenous retroviruses differently affect dendritic cells
Authors: Cocozza Federico , Martin-Jaular Lorena , Lippens Lien , Di Cicco Aurelie , Arribas Yago A , Dingli Florent , Richard Michael , Merle Louise , Poullet Patrick , Loew Damarys , Lévy Daniel , Hendrix An , Kassiotis George , Joliot Alain , Tkach Mercedes , Théry Clotilde 
Published: January 2023

ABSTRACTCells secrete membrane-enclosed extracellular vesicles (EVs) and non-vesicular nanoparticles (ENPs) that may play a role in intercellular communication. Tumor-derived EVs have been proposed either to induce immune priming of antigen presenting cells, or, to be immuno-suppressive agents promoting tumor immune escape. We suspect that such disparate functions are due to variable composition in EV subtypes and ENPs of the analyzed EV preparations. We aimed to exhaustively characterize the array of secreted EVs and ENPs of murine tumor cell lines. Unexpectedly, we identified virus-like particles (VLPs) from endogenous murine leukemia virus in preparations of EVs produced by tumor cells. We established a robust protocol to separate small (s)EVs from VLPs and ENPs. We compared their protein composition and analyzed their functional interaction with target dendritic cells (DCs). ENPs were poorly captured and did not affect DCs. sEVs specifically induced DC death. A mixed EV/VLP preparation was the most efficient to induce DC maturation and antigen presentation. Our results call for systematic re-evaluation of the respective proportions and functions of non-viral EVs and VLPs produced by tumors and their contribution to anti-tumor immune responses and to tumor progression.
Nanopore-based direct RNA sequencing of theTrypanosoma bruceitranscriptome identifies novel lncRNAs
Authors: Kruse Elisabeth , Göringer H. Ulrich 
Published: January 2023

AbstractTrypanosomatids are single-cell eukaryotic parasites. Unlike higher eukaryotes, they control gene expression posttranscriptionally and not at the level of transcription initiation. This involves all known cellular RNA circuits, from mRNA processing to mRNA decay to translation, in addition to a large panel of RNA-interacting proteins that modulate mRNA abundance. However, other forms of gene regulation, for example, by lncRNAs, cannot be excluded. LncRNAs are poorly studied in trypanosomatids, with only a single lncRNA characterized today. Furthermore, it is not clear whether the complete inventory of trypanosomatid lncRNAs is known because of the inherent cDNA recoding and DNA amplification limitations of short-read RNA sequencing. Here we overcome these limitations by using long-read direct RNA sequencing (DRS) on nanopore arrays. We analyze the native RNA pool of the two main lifecycle stages of the African trypanosomeT. bruceiwith a special emphasis on the inventory of lncRNAs. We identify 207 previously unknown lncRNAs, 109 of which are stage-specifically expressed. We also present insights into the complexity of theT. bruceitranscriptome, including alternative transcriptional start and stop sites and potential transcript isoforms to provide a bias-free understanding of the intricate RNA landscape inT. brucei.