bluuebunny/crossref_metadata_2025_split huggingface dataset:
Creation of a novel trigeminal tractography atlas for automated trigeminal nerve identification
Authors: Zhang Fan , Xie Guoqiang , Leung Laura , Mooney Michael A. , Epprecht Lorenz , Norton Isaiah , Rathi Yogesh , Kikinis Ron , Al-Mefty Ossama , Makris Nikos , Golby Alexandra J. , O’Donnell Lauren J. 
Published: January 2020

AbstractDiffusion MRI (dMRI) tractography has been successfully used to study the trigeminal nerves (TGNs) in many clinical and research applications. Currently, identification of the TGN in tractography data requires expert nerve selection using manually drawn regions of interest (ROIs), which is prone to inter-observer variability, time-consuming and carries high clinical and labor costs. To overcome these issues, we propose to create a novel anatomically curated TGN tractography atlas that enables automated identification of the TGN from dMRI tractography. In this paper, we first illustrate the creation of a trigeminal tractography atlas. Leveraging a well-established computational pipeline and expert neuroanatomical knowledge, we generate a data-driven TGN fiber clustering atlas using tractography data from 50 subjects from the Human Connectome Project. Then, we demonstrate the application of the proposed atlas for automated TGN identification in new subjects, without relying on expert ROI placement. Quantitative and visual experiments are performed with comparison to expert TGN identification using dMRI data from two different acquisition sites. We show highly comparable results between the automatically and manually identified TGNs in terms of spatial overlap and visualization, while our proposed method has several advantages. First, our method performs automated TGN identification, and thus it provides an efficient tool to reduce expert labor costs and inter-operator bias relative to expert manual selection. Second, our method is robust to potential imaging artifacts and/or noise that can prevent successful manual ROI placement for TGN selection and hence yields a higher successful TGN identification rate.
ATF4 mediates fetal globin upregulation in response to reduced β-globin
Authors: Boontanrart Mandy , Stehli Gautier , Banovic Marija , Schröder Markus S. , Wyman Stacia , Lew Rachel , Bordi Matteo , Gowen Benjamin , DeWitt Mark , Corn Jacob E. 
Published: January 2020

AbstractFetal development and anemias such as β-hemoglobinopathies trigger rapid production of red blood cells in a process known as stress erythropoiesis. Cellular stress prompts differentiating erythroid precursors to express high levels of fetal γ-globin, which has suggested strategies to treat hemoglobinopathies such as thalassemia and sickle cell disease. However, the mechanisms underlying γ-globin production during cellular stress are still poorly defined. Here we use CRISPR-Cas genome editing and CRISPRi transcriptional repression to model the stress caused by reduced levels of adult β-globin. We find that loss of β-globin is sufficient to induce widespread globin compensation, including robust re-expression of γ-globin. Time-course RNA-seq of differentiating isogenic erythroid precursors identified the ATF4 transcription factor as a causal regulator of this response. ChIP-seq of multiple erythroid precursor genotypes and differentiation states revealed that β-globin knockout leads to reduced engagement of ATF4 targets involved in the unfolded protein response. This ATF4 program indirectly regulates the levels of BCL11A, a key repressor of γ-globin. Identification of ATF4 as a key regulator of globin compensation adds mechanistic insight to the poorly understood phenomenon of stress-induced globin compensation and could be relevant for proposed gene editing strategies to treat hemoglobinopathies.
Individual yeast cells signal at different levels but each with good precision
Authors: Andrews Steven S. , Brent Roger 
Published: January 2020

AbstractDifferent isogenic cells have been shown to exhibit widely varying responses to the same extracellular signal. Based on the assumption that this variation arises from noise in the signaling pathways that cells use to transmit information from surface to nucleus, recent publications asserted that single cells cannot detect their surroundings accurately. Here, we analyze existing data on gene expression induced by theSaccharomyces cerevisiaepheromone response system, finding that individual cells signal consistently over time, implying that response variation arises primarily from stable cell-to-cell differences rather than signaling noise. Individual cells transmit at least 2.7 bits of information through the pheromone response system, enabling each cell to distinguish between at least 6 pheromone concentrations. In principle, cells can gain further precision by internally referencing these responses with measurements of constitutively expressed genes. Combination with prior results shows that only about 6% of total response variation arises from signaling pathway noise.One-sentence summarySingle yeast cells signal consistently over time, indicating that their signaling pathways transmit information precisely.
Negative linkage disequilibrium between amino acid changing variants reveals interference among deleterious mutations in the human genome
Authors: Garcia Jesse A. , Lohmueller Kirk E. 
Published: January 2020

AbstractWhile there has been extensive work on patterns of linkage disequilibrium (LD) for neutral loci, the extent to which negative selection impacts LD is less clear. Forces like Hill-Robertson interference and negative epistasis are expected to lead to deleterious mutations being found on distinct haplotypes. However, the extent to which these forces depend on the selection and dominance coefficients of deleterious mutations and shape genome-wide patterns of LD in natural populations with complex demographic histories has not been tested. In this study, we first used forward-in-time simulations to generate predictions as to how selection impacts LD. Under models where deleterious mutations have additive effects on fitness, deleterious variants less than 10 kb apart tend to be carried on different haplotypes, generating an excess of negative LD relative to pairs of synonymous SNPs. In contrast, for recessive mutations, there is no consistent ordering of how selection coefficients affect r2decay. We then examined empirical data of modern humans from the 1000 Genomes Project. LD between derived nonsynonymous SNPs is more negative compared to pairs of derived synonymous variants. This result holds when matching SNPs for frequency in the sample (allele count), physical distance, magnitude of background selection, and genetic distance between pairs of variants, suggesting that this result is not due to these potential confounding factors. Lastly, we introduce a new statisticHR(j)which allows us to detect interference using unphased genotypes. Application of this approach to high-coverage human genome sequences confirms our finding that deleterious alleles tend to be located on different haplotypes more often than are neutral alleles. Our findings suggest that either interference or negative epistasis plays a pervasive role in shaping patterns of LD between deleterious variants in the human genome, and consequently influencing genome-wide patterns of LD.
Bayesian non-parametric clustering of single-cell mutation profiles
Authors: Borgsmüller Nico , Bonet Jose , Marass Francesco , Gonzalez-Perez Abel , Lopez-Bigas Nuria , Beerenwinkel Niko 
Published: January 2020

AbstractThe high resolution of single-cell DNA sequencing (scDNA-seq) offers great potential to resolve intra-tumor heterogeneity by distinguishing clonal populations based on their mutation profiles. However, the increasing size of scDNA-seq data sets and technical limitations, such as high error rates and a large proportion of missing values, complicate this task and limit the applicability of existing methods. Here we introduce BnpC, a novel non-parametric method to cluster individual cells into clones and infer their genotypes based on their noisy mutation profiles. BnpC employs a Dirichlet process mixture model coupled with a Markov chain Monte Carlo sampling scheme, including a modified split-merge move and a novel posterior estimator to predict clones and genotypes. We benchmarked our method comprehensively against state-of-the-art methods on simulated data using various data sizes, and applied it to three cancer scDNA-seq data sets. On simulated data, BnpC compared favorably against current methods in terms of accuracy, runtime, and scalability. Its inferred genotypes were the most accurate, and it was the only method able to run and produce results on data sets with 10,000 cells. On tumor scDNA-seq data, BnpC was able to identify clonal populations missed by the original cluster analysis but supported by supplementary experimental data. With ever growing scDNA-seq data sets, scalable and accurate methods such as BnpC will become increasingly relevant, not only to resolve intra-tumor heterogeneity but also as a pre-processing step to reduce data size. BnpC is freely available under MIT license athttps://github.com/cbg-ethz/BnpC.
An ancient satellite repeat controls gene expression and embryonic development inAedes aegyptithrough a highly conserved piRNA
Authors: Halbach Rebecca , Miesen Pascal , Joosten Joep , Taşköprü Ezgi , Pennings Bas , Vogels Chantal B.F. , Merkling Sarah H. , Koenraadt Constantianus J. , Lambrechts Louis , van Rij Ronald P. 
Published: January 2020

AbstractTandem repeat elements such as the highly diverse class of satellite repeats occupy large parts of eukaryotic chromosomes. Most occur at (peri)centromeric and (sub)telomeric regions and have been implicated in chromosome organization, stabilization, and segregation1. Others are located more dispersed throughout the genome, but their functions remained largely enigmatic. Satellite repeats in euchromatic regions were hypothesized to regulate gene expressionin cisby modulation of the local heterochromatin, orin transvia repeat-derived transcripts2,3. Yet, due to a lack of experimental models, gene regulatory potential of satellite repeats remains largely unexplored. Here we show that, in the vector mosquitoAedes aegypti, a satellite repeat promotes sequence-specific gene silencing via the expression of two abundant PIWI-interacting RNAs (piRNAs). Strikingly, whereas satellite repeats and piRNA sequences generally evolve extremely fast4-6, this locus was conserved for approximately 200 million years, suggesting a central function in mosquito biology. Tandem repeat-derived piRNA production commenced shortly after egg-laying and inactivation of the most abundant of the two piRNAs in early embryos resulted in an arrest of embryonic development. Transcriptional profiling in these embryos revealed the failure to degrade maternally provided transcripts that are normally cleared during maternal-to-zygotic transition. Our results reveal a novel mechanism in which satellite repeats regulate global gene expressionin transvia piRNA-mediated gene silencing, which is fundamental to embryonic development. These findings highlight the regulatory potential of this enigmatic class of repeats.
Protrudin functions as a scaffold in the endoplasmic reticulum to support axon regeneration in the adult central nervous system
Authors: Petrova Veselina , Pearson Craig S. , Tribble James R. , Solano Andrea G. , Reid Evan , Williams Pete A. , Geller Herbert M. , Eva Richard , Fawcett James W. 
Published: January 2020

SummaryAdult mammalian central nervous system axons have intrinsically poor regenerative capacity, so axonal injury has permanent consequences. One approach to enhancing regeneration is to increase the axonal supply of growth molecules and organelles. We achieved this by expressing the adaptor molecule Protrudin which is normally found at low levels in non-regenerative neurons. Elevated Protrudin expression enabled robust central nervous system regeneration bothin vitroin primary cortical neurons andin vivoin the injured adult optic nerve. Protrudin overexpression facilitated the accumulation of endoplasmic reticulum, integrins and Rab11 endosomes in the distal axon, whilst removing Protrudin’s endoplasmic reticulum localization, kinesin-binding or phosphoinositide-binding properties abrogated the regenerative effects. These results demonstrate that Protrudin promotes regeneration by functioning as a scaffold to link axonal organelles, motors and membranes, establishing important roles for these cellular components in mediating regeneration in the adult central nervous system.
Downregulation of both mismatch repair and non-homologous end-joining pathways in hypoxic brain tumour cell lines
Authors: Cowman Sophie , Pizer Barry , Sée Violaine 
Published: January 2020

AbstractGlioblastoma, a grade IV astrocytoma, has a poor survival rate in part due to ineffective treatment options available. These tumours are heterogeneous with areas of low oxygen levels, termed hypoxic regions. Many intra-cellular signalling pathways, including DNA repair, can be altered by hypoxia. Since DNA damage induction and subsequent activation of DNA repair mechanisms is the cornerstone of glioblastoma treatment, alterations to DNA repair mechanisms could have a direct influence on treatment success. Our aim was to elucidate the impact of chronic hypoxia on DNA repair gene expression in a range of glioblastoma cell lines. We adopted a NanoString transcriptomic approach to examine the expression of 180 DNA repair related genes in four classical glioblastoma cell lines (U87-MG, U251-MG, D566-MG, T98G) exposed to 5 days of normoxia (21% O2), moderate (1% O2) or severe (0.1% O2) hypoxia. We observed altered gene expression in several DNA repair pathways including homologous recombination repair, non-homologous end-joining and mismatch repair, with hypoxia primarily resulting in downregulation of gene expression. The extend of gene expression changes was function of the hypoxic severity. Some, but not all, of these downregulations were directly under the control of HIF activity. For example, the downregulation ofLIG4, a key component of non-homologous end-joining, was reversed upon inhibition of the hypoxia inducible factor (HIF). In contrast, the downregulation of the mismatch repair gene,PMS2, was not affected by HIF inhibition. This suggests that numerous molecular mechanisms lead to hypoxia-induced reprogramming of the transcriptional landscape of DNA repair. Whilst the global impact of hypoxia on DNA repair gene expression is likely to lead to genomic instability, tumorigenesis and reduced sensitivity to anti-cancer treatment, treatment re-sensitizing might require additional approaches to a simple HIF inhibition.
scTPA: A web tool for single-cell transcriptome analysis of pathway activation signatures
Authors: Zhang Yan , Zhang Yaru , Hu Jun , Zhang Ji , Guo Fangjie , Zhou Meng , Zhang Guijun , Yu Fulong , Su Jianzhong 
Published: January 2020

ABSTRACTThe most fundamental challenge in current single-cell RNA-seq data analysis is functional interpretation and annotation of cell clusters. The biological pathways in distinct cell types have different activation patterns, which facilitates understanding cell functions in single-cell transcriptomics. However, no effective web tool has been implemented for single-cell transcriptomic data analysis based on prior biological pathway knowledge. Here, we introduce scTPA (http://sctpa.bio-data.cn/sctpa), which is a web-based platform providing pathway-based analysis of single-cell RNA-seq data in human and mouse. scTPA incorporates four widely-used gene set enrichment methods to estimate the pathway activation scores of single cells based on a collection of available biological pathways with different functional and taxonomic classifications. The clustering analysis and cell-type-specific activation pathway identification were provided for the functional interpretation of cell types from pathway-oriented perspective. An intuitive interface allows users to conveniently visualize and download single-cell pathway signatures. Together, scTPA is a comprehensive tool to identify pathway activation signatures for dissecting single cell heterogeneity.
Human Telomerase Expression is under Direct Transcriptional Control of the Telomere-binding-factor TRF2
Authors: Sharma Shalu , Mukherjee Ananda Kishore , Roy Shuvra Shekhar , Bagri Sulochana , Lier Silje , Verma Meenakshi , Sengupta Antara , Kumar Manish , Nesse Gaute , Pandey Deo Prakash , Chowdhury Shantanu 
Published: January 2020

AbstractTight regulatory mechanisms to maintain repression of human Telomerase (hTERT), the sole protein that synthesizes telomeres, is crucial for normal adult somatic cells. In contrast, enhanced telomerase activity and resulting pathological maintenance of telomeres, is widely understood as causal in >90% of human cancers. These implicate underlying mechanisms connectinghTERTregulation and telomeres, possibly through telomeric proteins, that remain unclear. In light of of recent work by us and others showing non-telomeric function of the telomere-binding protein TRF2, here we examined whether and how TRF2 affectedhTERTregulation. Direct binding of TRF2 – spanning ∼450 bp of thehTERTpromoter from the Transcriptional Start Site (TSS) – led to TRF2-dependent recruitment of the polycomb repressor complex PRC2 in both normal and cancer cells. This induced repressor histone modifications resulting in TRF2-dependenthTERTrepression. Mutations in thehTERTpromoter, found frequently in aggressive glioblastoma and reported to destabilize the G-quadruplex structure, resulted in loss of TRF2 binding and consequenthTERTover-expression. Conversely, using G-quadruplex-stabilizing ligands we regained TRF2 binding,hTERTre-suppression, in highly proliferating glioblastoma cells with telomerase hyperactivation due tohTERTpromoter mutations. Together, results herein demonstrate direct control ofhTERTthrough TRF2 in a G-quadruplex-dependent manner – implicating mechanisms of how telomerase regulation might be linked to telomeres in normal and cancer cells.
Fast and efficient generation of knock-in human organoids using homology-independent CRISPR/Cas9 precision genome editing
Authors: Artegiani Benedetta , Hendriks Delilah , Beumer Joep , Kok Rutger , Zheng Xuan , Joore Indi , de Sousa Lopes Susana Chuva , van Zon Jeroen , Tans Sander , Clevers Hans 
Published: January 2020

AbstractCRISPR/Cas9 technology has revolutionized genome editing and is applicable to the organoid field. However, precise integration of exogenous DNA sequences in human organoids awaits robust knock-in approaches. Here, we describeCRISPR/Cas9-mediatedHomology-independentOrganoidTransgenesis (CRISPR-HOT), which allows efficient generation of knock-in human organoids representing different tissues. CRISPR-HOT avoids extensive cloning and outperforms homology directed repair (HDR) in achieving precise integration of exogenous DNA sequences at desired loci, without the necessity to inactivate TP53 in untransformed cells, previously used to increase HDR-mediated knock-in. CRISPR-HOT was employed to fluorescently tag and visualize subcellular structural molecules and to generate reporter lines for rare intestinal cell types. A double reporter labelling the mitotic spindle by tagged tubulin and the cell membrane by tagged E-cadherin uncovered modes of human hepatocyte division. Combining tubulin tagging with TP53 knock-out revealed TP53 involvement in controlling hepatocyte ploidy and mitotic spindle fidelity. CRISPR-HOT simplifies genome editing in human organoids.
The Flemmingsome reveals an ESCRT-to-membrane coupling required for completion of cytokinesis
Authors: Addi Cyril , Presle Adrien , Frémont Stéphane , Cuvelier Frédérique , Rocancourt Murielle , Milin Florine , Schmutz Sandrine , Chamot-Rooke Julia , Douché Thibaut , Duchateau Magalie , Gianetto Quentin Giai , Ménager Hervé , Matondo Mariette , Zimmermann Pascale , Gupta-Rossi Neetu , Echard Arnaud 
Published: January 2020

ABSTRACTCytokinesis requires the constriction of ESCRT-III filaments on the side of the midbody, where abscission occurs. After ESCRT recruitment at the midbody, it is not known how the ESCRT-III machinery localizes to the abscission site. To reveal novel actors involved in abscission, we obtained the proteome of intact, post-abscission midbodies (Flemmingsome) and identified 489 proteins enriched in this organelle. Among those proteins, we further characterized a plasma membrane-to-ESCRT module composed of the transmembrane proteoglycan syndecan-4, ALIX and syntenin, a protein that bridges ESCRT-III/ALIX to syndecans. The three proteins were highly recruited first at the midbody then at the abscission site, and their depletion delayed abscission. Mechanistically, direct interactions between ALIX, syntenin and syndecan-4 were essential for proper enrichment of the ESCRT-III machinery at the abscission site, but not at the midbody. We propose that the ESCRT-III machinery must be physically coupled to a membrane protein at the cytokinetic abscission site for efficient scission, revealing novel common requirements in cytokinesis, exosome formation and HIV budding.
The WD and linker domains of ATG16L1 required for non-canonical autophagy limit lethal respiratory infection by influenza A virus at epithelial surfaces
Authors: Wang Yingxue , Zhang Weijiao , Jefferson Matthew , Sharma Parul , Bone Ben , Kipar Anja , Coombes Janine L. , Pearson Timothy , Man Angela , Zhekova Alex , Bao Yongping , Tripp Ralph A , Yamauchi Yohei , Carding Simon R. , Mayer Ulrike , Powell Penny P. , Stewart James P. , Wileman Thomas 
Published: January 2020

SummaryRespiratory viruses such as influenza A virus (IAV) and SARS-CoV-2 (Covid-19) cause pandemic infections where cytokine storm syndrome, lung inflammation and pneumonia lead to high mortality. Given the high social and economic cost of these viruses, there is an urgent need for a comprehensive understanding of how the airways defend against virus infection. Viruses entering cells by endocytosis are killed when delivered to lysosomes for degradation. Lysosome delivery is facilitated by non-canonical autophagy pathways that conjugate LC3 to endo-lysosome compartments to enhance lysosome fusion. Here we use mice lacking the WD and linker domains of ATG16L1 to demonstrate that non-canonical autophagy protects mice from lethal IAV infection of the airways. Mice with systemic loss of non-canonical autophagy are exquisitely sensitive to low-pathogenicity murine-adapted IAV where extensive viral replication throughout the lungs, coupled with cytokine amplification mediated by plasmacytoid dendritic cells, leads to fulminant pneumonia, lung inflammation and high mortality. IAV infection was controlled within epithelial barriers where non-canonical autophagy slowed fusion of IAV with endosomes and reduced activation of interferon signalling. This was consistent with conditional mouse models andex vivoanalysis showing that protection against IAV infection of lung was independent of phagocytes and other leukocytes. This establishes non-canonical autophagy pathways in airway epithelial cells as a novel innate defence mechanism that can restrict IAV infection and lethal inflammation at respiratory surfaces.