bluuebunny/crossref_metadata_2025 huggingface dataset:
ORIGINS: a protein network-based approach to quantify cell pluripotency from scRNA-seq data
Authors: Senra Daniela , Guisoni Nara , Diambra Luis
Published: May 2022

Trajectory inference is a common application of scRNA-seq data. However, it is often necessary to previously determine the origin of the trajectories, the stem or progenitor cells. In this work, we propose a computational tool to quantify pluripotency from single cell transcriptomics data. This approach uses the protein-protein interaction (PPI) network associated with the differentiation process as a scaffold and the gene expression matrix to calculate a score that we call differentiation activity. This score reflects how active the differentiation network is for each cell. We benchmark the performance of our algorithm with two previously published tools, LandSCENT [1] and CytoTRACE [2], for four data sets: breast, colon, hematopoietic and lung. We show that our algorithm is more efficient than LandSCENT and requires less RAM memory than the other programs. We also illustrate a complete workflow from the count matrix to trajectory inference using the breast data set.

Graphical abstract
Retinoic acid signaling in mouse retina endothelial cells is required for early angiogenic growth
Authors: Como Christina N. , Cervantes Cesar , Pawlikowski Brad , Siegenthaler Julie
Published: May 2022

The development of the retinal vasculature is essential to maintain health of the tissue, but the developmental mechanisms are not completely understood. The aim of this study was to investigate the cell-autonomous role of retinoic acid signaling in endothelial cells during retina vascular development. Using a temporal and cell-specific mouse model to disrupt retinoic acid signaling in endothelial cells in the postnatal retina (Pdgfbicre/+ dnRAR403fl/fl mutants), we discovered that angiogenesis in the retina is significantly decreased with a reduction in retina vascularization, endothelial tip cell number and filipodia, and endothelial ‘crowding’ of stalk cells. Interestingly, by P15, the vasculature can overcome the early angiogenic defect and fully vascularized the retina. At P60, the vasculature is intact with no evidence of retina cell death or altered blood retinal barrier integrity. Further, we identified that the angiogenic defect seen in mutants at P6 correlates with decreased Vegfr3 expression in endothelial cells. Collectively, our work identified a previously unappreciated function for endothelial retinoic acid signaling in early retinal angiogenesis.
MorphoGNN: Morphological Embedding for Single Neuron with Graph Neural Networks
Authors: Zhu Tianfang , Yao Gang , Hu Dongli , Xie Chuangchuang , Gong Hui , Li Anan
Published: May 2022

With the development of optical imaging systems, neuroscientists can now obtain large datasets of morphological structure at a single neuron scale positioned across the whole mouse brain. However, the enormous amount of morphological data challenges the classic approach of neuron classification, indexing and other analysis tasks. In this paper, we propose MorphoGNN, a single neuron morphological embedding based on the graph neural networks (GNN). This method learns the spatial structure information between the nodes of reconstructed neuron fibers by its nearest neighbors on each layer and captures the lower-dimensional representation of a single neuron through an end-to-end model. This model is composed of densely connected edge convolution (EdgeConv) layers and a double pooling operator, regularized with joint cross-entropy loss and triplet loss. An increasing population of the neighbor nodes meets the need of learning more information with features expanding at the deep layer. We tested the proposed embeddings on the neuron classification and retrieval tasks. Our method achieves competitive performance both on the general point cloud dataset and the neuron morphology dataset.
A role for gene expression and mRNA stability in nutritional compensation of the circadian clock
Authors: Kelliher Christina M. , Stevenson Elizabeth-Lauren , Loros Jennifer J. , Dunlap Jay C.
Published: May 2022

Compensation is a defining principle of a true circadian clock, where its approximately 24-hour period length is relatively unchanged across environmental conditions. Known compensation effectors directly regulate core clock factors to buffer the oscillator’s period length from variables in the environment. Temperature Compensation mechanisms have been experimentally addressed across circadian model systems, but much less is known about the related process of Nutritional Compensation, where circadian period length is maintained across physiologically relevant nutrient levels. Using the filamentous fungus Neurospora crassa, we performed a genetic screen under glucose and amino acid starvation conditions to identify new regulators of Nutritional Compensation. Our screen uncovered 16 novel mutants, and together with 4 mutants characterized in prior work, a model emerges where Nutritional Compensation of the fungal clock is achieved at the levels of transcription, chromatin regulation, and mRNA stability. However, eukaryotic circadian Nutritional Compensation is completely unstudied outside of Neurospora. To test for conservation in cultured mammalian cells, we selected the top two hits from our fungal genetic screen, performed siRNA knockdown experiments of the mammalian homologs, and characterized the cell lines with respect to compensation. We find that the wild-type mammalian clock is also compensated across a large range of external glucose concentrations, as observed in Neurospora, and that knocking down CPSF6 or SETD2 in human cells also results in nutrient-dependent period length changes. We conclude that, like Temperature Compensation, Nutritional Compensation is a conserved circadian process in fungal and mammalian clocks and that it may share common molecular determinants.
Functional connectivity dynamics reflect disability and multi-domain clinical impairment in patients with relapsing-remitting multiple sclerosis
Authors: Romanello Amy , Krohn Stephan , Schwanenflug Nina von , Chien Claudia , Bellmann-Strobl Judith , Ruprecht Klemens , Paul Friedemann , Finke Carsten
Published: May 2022

Background

Functional neuroimaging studies have revealed complex and heterogeneous patterns of aberrant functional connectivity (FC) in multiple sclerosis (MS), yet it remains unclear how time-resolved FC relates to variance in clinical disease severity.

Objectives

To characterize brain activity in MS patients with time-resolved FC analysis and explore the relationship between disease severity, multi-domain impairments, and altered network dynamics.

Methods

Resting-state functional MRI data were acquired from 101 MS patients and 101 age- and sex-matched healthy controls (HC). Dynamic FC analysis identified five connectivity states that were compared between HC and patients with high vs. low disability.

Results

Patients with higher disease severity exhibited a more widespread spatiotemporal pattern of altered FC and spent more time in a high-connectivity, low-occurrence state compared to patients with lower disease severity and HC. Depressive symptom severity was positively related to functional dynamics on global and network scales in patients, while fatigue and motor impairment were inversely related to frontoparietal network connectivity with the basal ganglia.

Conclusions

Time-resolved FC analysis uncovered alterations in network dynamics and clinical correlations that remained undetected with a static account of brain activity. Such time-varying approaches are thus crucial for disentangling the relationship between brain dynamics, disease severity, and symptoms in MS.
HIV rapidly targets a diverse pool of CD4+ T cells to establish productive and latent infections
Authors: Gantner Pierre , Buranapraditkun Supranee , Pagliuzza Amélie , Dufour Caroline , Pardons Marion , Mitchell Julie L. , Kroon Eugène , Sacdalan Carlo , Tulmethakaan Nicha , Pinyakorn Suteeraporn , Robb Merlin L. , Phanuphak Nittaya , Ananworanich Jintanat , Hsu Denise , Vasan Sandhya , Trautmann Lydie , Fromentin Rémi , Chomont Nicolas
Published: May 2022

Upon infection, HIV disseminates throughout the human body within 1-2 weeks. However, its early cellular targets remain poorly characterized. We analyzed productively and latently infected cells in blood and lymphoid tissue from individuals in acute infection. The phenotype of productively infected cells rapidly evolved with time and differed between blood and lymph nodes. The TCR repertoire of productively infected cells was heavily biased, with preferential infection of previously expanded/disseminated cells, but composed almost exclusively of unique clonotypes, indicating that they were the product of independent infection events. Latent genetically intact proviruses were already archived early in infection. Hence, productive infection is initially established in a pool of phenotypically and clonotypically distinct T cells in blood and lymph nodes and latently infected cells are generated simultaneously.

One-Sentence Summary

HIV initially infects phenotypically and clonotypically distinct T cells and establishes a latent reservoir concomitantly.
The recruitment of indirect-waves within primary motor cortex during motor imagery: A directional Transcranial Magnetic Stimulation study
Authors: Neige Cécilia , Ciechelski Valentin , Lebon Florent
Published: May 2022

Motor imagery (MI) refers to the mental simulation of an action without any overt movement. While numerous transcranial magnetic stimulation (TMS) studies provided evidence for a modulation of corticospinal excitability and intracortical inhibition during MI, the neural signature within the primary motor cortex is not clearly established. In the current study, we used directional TMS to probe the modulation of the excitability of early and late indirect-waves (I-waves) generating pathways during MI. Corticospinal responses evoked by TMS with posterior-anterior (PA) and anterior-posterior (AP) current flow within primary motor cortex evoke preferentially early and late I-waves, respectively. Seventeen participants were instructed to stay at rest or to imagine isometric maximal contractions of the right flexor carpi radialis. We demonstrated that the increase of corticospinal excitability during MI is greater with PA than AP orientation. By using paired-pulse stimulations, we confirmed that short-interval intracortical inhibition (SICI) increased during MI in comparison to rest with PA orientation whereas we found that it decreased with AP orientation. Overall, these results indicate that the specific early I-waves generating pathway activated by PA orientation is probably more sensitive to the corticospinal excitability and intracortical inhibition modulations induced by MI.
Continuous sensing of IFNα by hepatic endothelial cells shapes a vascular antimetastatic barrier
Authors: Tran Ngoc Lan , Ferreira Lorena Maria , Alvarez-Moya Blanca , Buttiglione Valentina , Ferrini Barbara , Zordan Paola , Monestiroli Andrea , Fagioli Claudio , Bezzecchi Eugenia , Scotti Giulia Maria , Esposito Antonio , Leone Riccardo , Gnasso Chiara , Brendolan Andrea , Guidotti Luca G. , Sitia Giovanni
Published: May 2022

Hepatic metastases are a poor prognostic factor of colorectal carcinoma (CRC) and new strategies to reduce the risk of liver CRC colonization are highly needed. Herein, we used mouse models of hepatic metastatization to demonstrate that the continuous infusion of therapeutic doses of interferon-alpha (IFNα) controls CRC invasion by acting onhepatic endothelial cells (HECs). Mechanistically, IFNα promoted the development of a vascular antimetastatic niche characterized by liver sinusoidal endothelial cells (LSECs) defenestration extracellular matrix and glycocalyx deposition, thus strengthening the liver vascular barrier impairing CRC trans-sinusoidal migration, without requiring a direct action on tumor cells, hepatic stellate cells, hepatocytes, or liver dendritic cells (DCs), Kupffer cells (KCs) and liver capsular macrophages (LCMs). Moreover, IFNα endowed LSECs with efficient cross-priming potential that, along with the early intravascular tumor burden reduction, supported the generation of antitumor CD8+T cells and ultimately led to the establishment of a protective long-term memory T cell response. These findings provide a rationale for the use of continuous IFNα therapy in perioperative settings to reduce CRC metastatic spreading to the liver.
Novel mechanism of hypoxic neuronal injury mediated by non-excitatory amino acids and astroglial swelling
Authors: Álvarez-Merz Iris , Fomitcheva Ioulia V. , Sword Jeremy , Hernández-Guijo Jesús M. , Solís José M. , Kirov Sergei A.
Published: May 2022

Bleeding into cerebral parenchyma during hemorrhagic stroke or head trauma leads to ischemia and release of plasmatic content, including amino acids (AA). Although excitotoxic AA have been extensively studied, little is known about non-excitatory AA during hypoxic injury. Hypoxia-induced synaptic depression becomes irreversible after adding non-excitatory AA to hippocampal slices, alongside their intracellular accumulation and increased tissue electrical resistance. A combination of four non-excitatory AA (L-alanine, glycine, L-glutamine, L-serine: AGQS) at plasmatic concentrations was applied to brain slices from transgenic mice expressing EGFP in pyramidal neurons or astrocytes during normoxia or hypoxia. Two-photon imaging, changes in light transmittance (LT), and electrophysiological field recordings followed by electron microscopy in hippocampal CA1st. radiatumwere used to monitor synaptic function concurrently with cellular swelling and injury. During normoxia, AGQS-induced increase in LT was due to astroglial but not neuronal swelling. Fast LT raise during hypoxia and AGQS manifested neuronal and astroglial swelling accompanied by a permanent loss of synaptic transmission and irreversible dendritic beading, signifying acute tissue damage. Neuronal injury was not triggered by spreading depolarization which did not occur in our experiments. Hypoxia without AGQS did not cause cell swelling, leaving dendrites intact. Inhibition of NMDA receptors prevented neuronal damage and irreversible loss of synaptic function. Deleterious effects of AGQS during hypoxia were prevented by alanine-serine-cysteine transporters (ASCT2) and volume-regulated anion channels (VRAC) blockers. Our findings suggest that swelling induced by intracellular accumulation of non-excitatory AA and release of excitotoxins through antiporters and VRAC may exacerbate the hypoxia-induced neuronal injury.

Significance Statement

Little is known if non-excitatory amino acids (AA) contribute to cellular injury when released during bleeding, as in hemorrhagic stroke and head trauma. Alanine, glycine, glutamine, and serine are one of the most abundant in plasma. Remarkably, during hypoxia, these non-excitatory AA caused severe neuronal and astroglial swelling and irreversible dendritic injury alongside a permanent loss of synaptic function. Activation of NMDA receptors was implicated in the onset of damage. Experimental evidence pointed to the involvement of alanine-serine-cysteine transporter 2 (ASCT2) and volume-regulated anion channels (VRAC) as molecular mechanisms underlying AA-induced damage during hypoxia. A detailed understanding of how brain injury evolves with non-excitatory AA during hypoxia will help design brain recovery treatments in neurological conditions involving bleeding.
Mechanism of Curaxin-dependent Nucleosome Unfolding by FACT
Authors: Volokh Olesya I. , Sivkina Anastasia L. , Moiseenko Andrey V. , Popinako Anna V. , Karlova Maria G. , Valieva Maria , Kotova Elena Y. , Kirpichnikov Mikhail P. , Formosa Timothy , Studitsky Vasily M. , Sokolova Olga S.
Published: May 2022

Human FACT (FACT) is a multifunctional histone chaperone involved in transcription, replication and DNA repair. Curaxins are anticancer compounds that induce FACT- dependent nucleosome unfolding and trapping of FACT in the chromatin of cancer cells (c-trapping) through an unknown molecular mechanism. Here, we analyzed the effects of curaxin CBL0137 on nucleosome unfolding by FACT using spFRET and electron microscopy. By itself, FACT adopted multiple conformations, including a novel, compact, four-domain state in which the previously unresolved NTD of the SPT16 subunit of FACT was localized, apparently stabilizing a compact configuration. Multiple, primarily open conformations of FACT-nucleosome complexes were observed during curaxin-supported nucleosome unfolding. The structures of intermediates suggest “decision points” in the unfolding/folding pathway where FACT can either promote disassembly or assembly of nucleosomes, with the outcome possibly being influenced by additional factors. The data suggest novel mechanisms of nucleosome unfolding by FACT and c-trapping by curaxins.
Identification of a novel deFADding activity in 5’ to 3’ exoribonucleases
Authors: Sharma Sunny , Yang Jun , Doamekpor Selom K. , Grudizen-Nogalska Ewa , Tong Liang , Kiledjian Megerditch
Published: May 2022

Identification of metabolite caps including FAD on the 5’ end of RNA has uncovered a previously unforeseen intersection between cellular metabolism and gene expression. To understand the function of FAD caps in cellular physiology, we characterised the proteins interacting with FAD caps in budding yeast. Here we demonstrate that highly conserved 5’-3’ exoribonucleases, Xrn1 and Rat1, physically interact with the RNA 5’ FAD cap and both possess FAD cap decapping (deFADding) activity and subsequently degrade the resulting RNA. Xrn1 deFADding activity was also evident in human cells indicating its evolutionary conservation. Furthermore, we report that the recently identified bacterial 5’-3’ exoribonuclease RNase AM also possesses deFADding activity that can degrade FAD-capped RNAs in vitro and in E. coli cells. To gain a molecular understanding of the deFADding reaction, an RNase AM crystal structure with three manganese ions coordinated by a sulfate molecule and the active site amino acids was generated that provided details underlying hydrolysis of the FAD cap. Our findings reveal a general propensity for 5’-3’ exoribonucleases to hydrolyse and degrade RNAs with 5’ end noncanonical caps in addition to their well characterized 5’ monophosphate RNA substrates indicating an evolutionarily conserved intrinsic property of 5’-3’ exoribonucleases.
Small-angle x-ray microdiffraction from fibrils embedded in tissue thin sections
Authors: Nepal Prakash , Bashit Abdullah Al , Yang Lin , Makowski Lee
Published: May 2022

Small-angle x-ray scattering (SAXS) from fibrils embedded in a fixed, thin section of tissue includes contributions from the fibrils; the polymeric matrix surrounding the fibrils; other constituents of the tissue; and cross-terms due to the spatial correlation between fibrils and neighbouring molecules. This complex mixture severely limits the amount of information that can be extracted from scattering studies. However, availability of micro- and nano-beams has made possible measurement of scattering from very small volumes which, in some cases, may be dominated by a single fibrillar constituent. In those cases, information about the predominant species may be accessible. Nevertheless, even in these cases, the correlations between the positions of fibrils and other constituents have significant impact on the observed scattering. Here, we propose strategies to extract partial information about fibril structure and tissue organization on the basis of SAXS from samples of this type. We show that the spatial correlation function of the fibril in the direction perpendicular to the fibril axis can be computed and contains information about the predominant fibril structure and the organization of the surrounding tissue matrix. It has significant advantages over approaches based on techniques developed for x-ray solution scattering. We present examples of the calculation of correlation in different types of samples to demonstrate the kinds of information that can be obtained from these measurements.

Synopsis

The availability of micro- and nano- x-ray beams is making possible measurement of scattering from very small volumes, opening possibilities for derivingin situstructural information on fibrillar constituents in complex materials and tissues. This work outlines a set of strategies for confronting the formidable technical obstacles to extracting useful structural information from scattering derived from these materials.
A Commercial ARHGEF17/TEM4 antibody cross-reacts with Nuclear Mitotic Apparatus protein 1 (NuMA)
Authors: Prifti Diogjena Katerina , Lauzier Annie , Elowe Sabine
Published: May 2022

The Rho family Guanine nucleotide exchange factor (GEF) ARHGEF17 (also known as TEM4) is a large protein with only 3 annotated regions: an N-terminal actin-binding domain, a Rho-specific dbl homology (DH)- pleckstrin homology (PH) type GEF domain and a seven bladed β propeller fold at the C-terminus with unknown function. TEM4 has been implicated in numerous activities that rely on regulation of the cytoskeleton including cell migration, cell-cell junction formation and the spindle assembly checkpoint during mitosis. Here we have assessed the specificity of a TEM4 polyclonal antibody that has been commonly used as a Western blotting and immunocytochemistry probe for TEM4 in mammalian cells. We find that this antibody, in addition to its intended target, cross-reacts with the Nuclear Mitotic Apparatus Protein 1 (NuMA) in Western blotting and immunoprecipitation, and detects NuMA preferentially in immunocytochemistry. This cross-reactivity, with an abundant chromatin- and mitotic spindle-associated factor, is likely to affect the interpretation of experiments that make use of this antibody probe, in particular by immunocytochemistry and immunoprecipitation.
Phylogenetic trees of closely related bacterial species and subspecies based on frequencies of short nucleotide sequences
Authors: Nakano Yoshio , Domon Yusaku , Yamagishi Kenji
Published: May 2022

Bacterial phylogenetic analyses are commonly performed to explore relationships among various bacterial species and genera based on their 16S rRNA gene sequences; however, the results are limited by mosaicism, intragenomic heterogeneity, and difficulty in distinguishing between related species. In this study, we aimed to perform genome-wide comparisons of different bacterial species, namely Escherichia coli and Shigella and Yersinia, Klebsiella, and Neisseria spp. or serotypes of Listeria monocytogenes, based on their K-mer profiles to construct phylogenetic trees. Pentanucleotide frequency analysis (512 patterns of 5 nucleotides each) was performed to distinguish highly similar species from each other, such as Yersinia species, along with Shigella spp. and E. coli. Moreover, Escherichia albertii strains were clearly distinguished from E. coli and Shigella, despite being closely related to enterohemorrhagic E. coli in the phylogenetic tree. In addition, the phylogenetic tree of Ipomoea species based on pentamer frequency in chloroplast genomes correlated with previously reported morphological similarities. Furthermore, a support vector machine clearly classified E. coli and Shigella genomes based on pentanucleotide profiles. These results suggest that phylogenetic analysis based on penta- or hexamer profiles is a useful alternative for microbial phylogenetic studies. In addition, we introduced an R application, Phy5, which generates a phylogenetic tree based on genome-wide comparisons of pentamer profiles. The online version of Phy5 can be accessed at https://phy5.shinyapps.io/Phy5R/.
Fast and Accurate Bayesian Polygenic Risk Modeling with Variational Inference
Authors: Zabad Shadi , Gravel Simon , Li Yue
Published: May 2022

The recent proliferation of large scale genome-wide association studies (GWASs) has motivated the development of statistical methods for phenotype prediction using single nucleotide polymorphism (SNP) array data. These polygenic risk score (PRS) methods formulate the task of polygenic prediction in terms of a multiple linear regression framework, where the goal is to infer the joint effect sizes of all genetic variants on the trait. Among the subset of PRS methods that operate on GWAS summary statistics, sparse Bayesian methods have shown competitive predictive ability. However, most existing Bayesian approaches employ Markov Chain Monte Carlo (MCMC) algorithms for posterior inference, which are computationally inefficient and do not scale favorably with the number of SNPs included in the analysis. Here, we introduce Variational Inference of Polygenic Risk Scores (VIPRS), a Bayesian summary statistics-based PRS method that utilizes Variational Inference (VI) techniques to efficiently approximate the posterior distribution for the effect sizes. Our experiments with genome-wide simulations and real phenotypes from the UK Biobank (UKB) dataset demonstrated that variational approximations to the posterior are competitively accurate and highly efficient. When compared to state-of-the-art PRS methods, VIPRS consistently achieves the best or second best predictive accuracy in our analyses of 36 simulation configurations as well as 12 real phenotypes measured among the UKB participants of “White British” background. This performance advantage was higher among individuals from other ethnic groups, with an increase in R2 of up to 1.7-fold among participants of Nigerian ancestry for Low-Density Lipoprotein (LDL) cholesterol. Furthermore, given its computational efficiency, we applied VIPRS to a dataset of up to 10 million genetic markers, an order of magnitude greater than the standard HapMap3 subset used to train existing PRS methods. Modeling this expanded set of variants conferred significant improvements in prediction accuracy for a number of highly polygenic traits, such as standing height.
Extracellular Vesicle exchange is favored by cell proximity
Authors: Colombo Federico , Norton Erienne Grace , Cocucci Emanuele
Published: May 2022

Extracellular vesicles (EVs) are biological nanovectors that retain information of the cell of origin and convey signals to recipient cells. Therefore, EVs are ideal platforms for the development of diagnostic tools and of bio-inspired drug delivery technologies. However, the dynamics of EV distribution in physiological conditions are still underexplored. Using an elegant series of experiments, including quantitative assays to define EV transfer and five dimension live cell imaging, we observe the release and internalization of EVs in real time and we demonstrate that EVs are mainly exchanged at the cell-cell interface. These observations prompt paradigm shifting consequences: first, EVs are mostly short-range intercellular vectors that influence adjacent cells; second, our data explain why increases in the internal pressure and permeability of the parenchyma, two hallmarks of inflammation and cancer, can facilitate EV escape from the damaged tissue. In conclusion, we provide experimental evidence supporting why EVs have great potential for the implementation of specific and sensitive liquid biopsy tests.
A molecular phenology scale of fruit development
Authors: Tornielli Giovanni Battista , Sandri Marco , Fasoli Marianna , Amato Alessandra , Pezzotti Mario , Zuccolotto Paola , Zenoni Sara
Published: May 2022

Fruit growth and development consists of a continuous succession of physical, biochemical, and physiological changes driven by a genetic program that dynamically responds to environmental cues. Establishing recognizable stages over the whole fruit lifetime represents a fundamental requirement for research and fruit crop cultivation. This is especially relevant in perennial crops like the grapevine to scale the development of its fruit across genotypes and growing conditions.

In this work, molecular-based information from several grape berry transcriptomic datasets was exploited to build a molecular phenology scale (MPhS) and to map the ontogenic development of the fruit. The proposed statistical pipeline consisted in an unsupervised learning procedure yielding an innovative combination of semiparametric, smoothing and dimensionality reduction tools. The transcriptomic distance between fruit samples was precisely quantified by means of the MPhS that also enabled to highlight the winding dynamics of the transcriptional program over berry development through the calculation of the rate of variation of MPhS stages by time.

The MPhS allowed the alignment of time-series fruit samples proving to be a step forward in mapping the progression of grape berry development with higher precision compared to classic time- or phenotype-based approaches and inspiring the use of the transcriptional information to scale the developmental progression of any organ in any plant species.
Sex differences in islet stress responses support female beta cell resilience
Authors: Brownrigg George P. , Xia Yi Han , Chu Chieh Min Jamie , Wang Su , Chao Charlotte , Zhang Jiashuo Aaron , Skovsø Søs , Panzhinskiy Evgeniy , Hu Xiaoke , Johnson James D. , Rideout Elizabeth J.
Published: May 2022

Objective

Pancreatic β cells play a key role in glucose homeostasis; dysfunction of this critical cell type causes type 2 diabetes (T2D). Emerging evidence points to sex differences in β cells, but few studies have examined male-female differences in β cell stress responses and resilience across multiple contexts, including diabetes. Here, we address the need for high-quality information on sex differences in β cell/islet gene expression and function using both human and rodent samples.

Methods

We compared β cell gene expression and insulin secretion in donors living with T2D to non-diabetic donors in both males and females. In mice, we generated a well-powered islet RNAseq dataset from 20-week-old male and female siblings with equivalent insulin sensitivity. Because on our unbiased analysis of gene expression pointed to sex differences in endoplasmic reticulum (ER) stress response, we subjected islets isolated from age-matched male and female mice to thapsigargin treatment and monitored protein synthesis, cell death, and β cell insulin production and secretion. Transcriptomic and proteomic analyses were used to characterize sex differences in islet responses to ER stress.

Results

Our single-cell analysis of human β cells revealed sex-specific changes to gene expression and function in T2D, correlating with more robust insulin secretion in islets isolated from female donors living with T2D compared to male T2D donors. In mice, RNA sequencing revealed differential enrichment of unfolded protein response pathway-associated genes, where female islets showed higher expression of genes linked with protein synthesis, folding, and processing. This differential expression was biologically significant, as female islets were more resilient to ER stress induction with thapsigargin. Specifically, female islets maintained better insulin secretion and showed a distinct transcriptional response under ER stress compared with males.

Conclusions

Our data demonstrate that physiologically significant sex differences in β cell gene expression exist in both humans and mice, and that female β cells maintain better insulin production and secretion across multiple physiological and pathological contexts.
Proteomic Analysis of Huntington’s Disease Medium Spiny Neurons Identifies Alterations in Lipid Droplets
Authors: Tshilenge Kizito-Tshitoko , Aguirre Carlos Galicia , Bons Joanna , Basisty Nathan , Song Sicheng , Rose Jacob , Lopez-Ramirez Alejandro , Gerencser Akos , Naphade Swati , Loureiro Ashley , Wehrfritz Cameron , Holtz Anja , Mooney Sean , Schilling Birgit , Ellerby Lisa M.
Published: May 2022

Huntington’s disease (HD) is a neurodegenerative disease caused by a CAG repeat expansion in the Huntingtin (HTT) gene. The resulting polyglutamine (polyQ) tract alters the function of the HTT protein. Although HTT is expressed in different tissues, the medium spiny projection neurons (MSNs) in the striatum are particularly vulnerable in HD. Thus, we sought to define the proteome of human HD patient-derived MSNs. We differentiated HD72 induced pluripotent stem cells and isogenic controls into MSNs and carried out quantitative proteomic analysis by two approaches. First, using data-dependent acquisitions with FAIMS (FAIMS-DDA) for label-free quantification on the Orbitrap Lumos mass spectrometer, we identified 6,323 proteins with at least two unique peptides (FDR ≤ 0.01). Of these, 901 proteins were significantly altered in the HD72-MSNs, compared to isogenic controls. Second, we quantitatively validated protein candidates by comprehensive data-independent acquisitions on a TripleTOF 6600 mass spectrometer quantifying 3,106 proteins with at least two unique peptides. Functional enrichment analysis identified pathways related to the extracellular matrix, including TGF-ý regulation of extracellular matrix, epithelial-mesenchymal transition, DNA replication, senescence, cardiovascular system, organism development, regulation of cell migration and locomotion, aminoglycan glycosaminoglycan proteoglycan, growth factor stimulus and fatty acid processes. Conversely, processes associated with the downregulated proteins included neurogenesis-axogenesis, the brain-derived neurotrophic factor-signaling pathway, Ephrin-A: EphA pathway, regulation of synaptic plasticity, triglyceride homeostasis cholesterol, plasmid lipoprotein particle immune response, interferon-γ signaling, immune system major histocompatibility complex, lipid metabolism and cellular response to stimulus. Moreover, proteins involved in the formation and maintenance of axons, dendrites, and synapses (e.g., Septin protein members) are dysregulated in HD72-MSNs. Importantly, lipid metabolism pathways were altered, and we found that lipid droplets accumulated in the HD72-MSNs, suggesting a deficit in lipophagy. Our proteomics analysis of HD72-MSNs identified relevant pathways that are altered in MSNs and confirm current and new therapeutic targets for HD.
Characterization and visualization of global metabolomic responses ofBrachypodium distachyonto environmental changes
Authors: Mahood Elizabeth H. , Bennett Alexandra A. , Komatsu Karyn , Kruse Lars H. , Lau Vincent , Ishka Maryam Rahmati , Jiang Yulin , Bravo Armando , Bowen Benjamin P. , Louie Katherine , Harrison Maria J. , Provart Nicholas J. , Vatamaniuk Olena K. , Moghe Gaurav D.
Published: May 2022

Plant responses to environmental change are mediated via changes in cellular metabolomes. However, <5% of signals obtained from tandem liquid chromatography mass spectrometry (LC-MS/MS) can be identified, limiting our understanding of how different metabolite classes change under biotic/abiotic stress. To address this challenge, we performed untargeted LC-MS/MS of leaves, roots and other organs ofBrachypodium distachyon, a model Poaceae species, under 17 different organ-condition combinations, including copper deficiency, heat stress, low phosphate and arbuscular mycorrhizal symbiosis (AMS). We used a combination of information theory-based metrics and machine learning-based identification of metabolite structural classes to assess metabolomic changes. Both leaf and root metabolomes were significantly affected by the growth medium. Leaf metabolomes were more diverse than root metabolomes, but the latter were more specialized and more responsive to environmental change. We also found that one week of copper deficiency shielded the root metabolome, but not the leaf metabolome, from perturbation due to heat stress. Using a recently published deep learning based method for metabolite class predictions, we analyzed the responsiveness of each metabolite class to environmental change, which revealed significant perturbations of various lipid classes and phenylpropanoids such as cinnamic acids and flavonoids. Co-accumulation analysis further identified condition-specific metabolic biomarkers. Finally, to make these results publicly accessible, we developed a novel visualization platform on the Bioanalytical Resource website, where significantly perturbed metabolic classes can be readily visualized. Overall, our study illustrates how emerging chemoinformatic methods can be applied to reveal novel insights into the dynamic plant metabolome and plant stress adaptation.
Direct specification of lymphatic endothelium from non-venous angioblasts
Authors: Lupu Irina-Elena , Kirschnick Nils , Weischer Sarah , Martinez-Corral Ines , Forrow Aden , Lahmann Ines , Riley Paul R. , Zobel Thomas , Makinen Taija , Kiefer Friedemann , Stone Oliver A.
Published: May 2022

The lymphatic vasculature is essential for tissue fluid homeostasis, immune cell surveillance and dietary lipid absorption, and has emerged as a key regulator of organ growth and repair1. Despite significant advances in our understanding of lymphatic function, the precise developmental origin of lymphatic endothelial cells (LECs) has remained a point of debate for over a century2-5. It is currently widely accepted that most LECs are derived from venous endothelium4,6, although other sources have been described, including mesenchymal cells3, hemogenic endothelium7 and musculoendothelial progenitors8,9. Here we show that the initial expansion of mammalian LECs is driven primarily by the in situ differentiation of specialized angioblasts and not migration from venous endothelium. Single-cell RNA sequencing and genetic lineage tracing experiments in mouse revealed a population of Etv2+Prox1+ lymphangioblasts that arise directly from paraxial mesoderm-derived progenitors. Conditional lineage labelling and morphological analyses showed that these specialized angioblasts emerge within a tight spatiotemporal window, and give rise to LECs in numerous tissues. Analysis of early LEC proliferation and migration supported these findings, suggesting that emergence of LECs from venous endothelium is limited. Collectively, our data reconcile discrepancies between previous studies and indicate that LECs form through both de novo specification from lymphangioblasts and transdifferentiation from venous endothelium.
Baseline control of optimal performance in recurrent neural networks
Authors: Ogawa Shun , Fumarola Francesco , Mazzucato Luca
Published: May 2022

Changes in behavioral state, such as arousal and movements, strongly affect neural activity in sensory areas. Recent evidence suggests that they may be mediated by top-down projections regulating the statistics of baseline input currents to sensory areas, inducing qualitatively different effects across sensory modalities. What are the computational benefits of these baseline modulations? We investigate this question within a brain-inspired framework for reservoir computing, where we vary the quenched baseline inputs to a random neural network. We found that baseline modulations control the dynamical phase of the reservoir network, unlocking a vast repertoire of network phases. We uncover a new zoo of bistable phases exhibiting the simultaneous coexistence of fixed points and chaos, of two fixed points, and of weak and strong chaos. Crucially, we discovered a host of novel phenomena, including noise-driven enhancement of chaos and ergodicity breaking; neural hysteresis, whereby transitions across phase boundary retain the memory of the initial phase. Strikingly, we found that baseline control can achieve optimal performance without any fine tuning of recurrent couplings. In summary, baseline control of network dynamics opens new directions for brain-inspired artificial intelligence and provides a new interpretation for the ubiquitously observed behavioral modulations of cortical activity.
Single cell transcriptomics identifies conserved regulators of neurosecretory lineages
Authors: Steger Julia , Cole Alison G. , Denner Andreas , Lebedeva Tatiana , Genikhovich Grigory , Ries Alexander , Reischl Robert , Taudes Elisabeth , Lassnig Mark , Technau Ulrich
Published: May 2022

Communication in bilaterian nervous systems is mediated by electrical and secreted signals, however, the evolutionary origin and relation of neurons to other secretory cell types has not been elucidated. Here we use developmental single cell RNA-sequencing in the cnidarian Nematostella vectensis, representing an early evolutionary lineage with a simple nervous system. Validated by transgenics, we demonstrate that neurons, stinging cells, and gland cells arise from a common multipotent progenitor population. We identify the conserved transcription factor gene SoxC as a key upstream regulator of all neurosecretory lineages and demonstrate that SoxC knockdown eliminates both neuronal and secretory cell types. While in vertebrates and many other bilaterians neurogenesis is largely restricted to early developmental stages, we show that in the sea anemone differentiation of neurosecretory cells is maintained throughout all life stages, and follows the same molecular trajectories from embryo to adulthood, ensuring lifelong homeostasis of neurosecretory cell lineages.
Loss of transcriptional heterogeneity in aged human muscle stem cells
Authors: Barruet Emilie , Striedinger Katharine , Marangoni Pauline , Pomerantz Jason H.
Published: May 2022

Age-related loss of muscle mass and function negatively impacts healthspan and lifespan. Satellite cells function as muscle stem cells in muscle maintenance and regeneration by self-renewal, activation, proliferation and differentiation. These processes are perturbed in aging at the stem cell population level, contributing to muscle loss. However, how representation of subpopulations within the human satellite cell pool change during aging remains poorly understood. We previously reported a comprehensive baseline of human satellite cell (Hu-MuSCs) transcriptional activity in muscle homeostasis describing functional heterogenous human satellite cell subpopulations such as CAV1+ Hu-MUSCs (Barruet et al., 2020). Here, we sequenced additional satellite cells from new healthy donors and performed extended transcriptomic analyses with regard to aging. We found an age-related loss of global transcriptomic heterogeneity and identified new markers (CAV1, CXCL14, GPX3) along with previously described ones (FN1, ITGB1, SPRY1) that are altered during aging in human satellite cells. These findings describe new transcriptomic changes that occur during aging in human satellite cells and provide a foundation for understanding functional impact.
Strategic exploration in the macaque’s prefrontal cortex
Authors: Jahn Caroline I. , Grohn Jan , Cuell Steven , Emberton Andrew , Bouret Sebastien , Walton Mark E. , Kolling Nils , Sallet Jérôme
Published: May 2022

Humans have been shown to strategically explore. They can identify situations in which gathering information about distant and uncertain options is beneficial for the future. Because primates rely on scare resources when they forage, they are also thought to strategically explore, but whether they use the same strategies as humans and the neural bases of strategic exploration in monkeys are largely unknown. We designed a sequential choice task to investigate whether monkeys mobilize strategic exploration based on whether that information can improve subsequent choice, but also to ask the novel question about whether monkeys adjust their exploratory choices based on the contingency between choice and information, by sometimes providing the counterfactual feedback, about the option not chosen. We show that monkeys decreased their reliance on expected value when exploration could be beneficial, but this was not mediated by changes in the effect of uncertainty on choices. We found strategic exploratory signals in anterior and mid-cingulate cortex (ACC/MCC) and dorsolateral prefrontal cortex (dlPFC). This network was most active when a low value option was chosen which suggests a role in counteracting expected value signals, when exploration away from value should to be considered. Such strategic exploration was abolished when the counterfactual feedback was available. Learning from counterfactual outcome was associated with the recruitment of a different circuit centered on the medial orbitofrontal cortex (OFC), where we showed that monkeys represent chosen and unchosen reward prediction errors. Overall, our study shows how ACC/MCC-dlPFC and OFC circuits together could support exploitation of available information to the fullest and drive behavior towards finding more information through exploration when it is beneficial.
siRNAs targeting a chromatin-associated RNA induce its transcriptional silencing in human cells
Authors: Ouvrard Julien , Muniz Lisa , Nicolas Estelle , Trouche Didier
Published: May 2022

Transcriptional gene silencing by small interfering RNAs (siRNAs) has been widely described in various species, such as plants or fission yeasts. In mammals, its extent remained somewhat debated. Previous studies showed that siRNAs targeting gene promoters can induce the silencing of the targeted promoter, although the involvement of off-target mechanisms was also suggested. Here, by nascent RNA capture and RNA Pol II ChIP, we show that siRNAs targeting a chromatin-associated non-coding RNA induce its transcriptional silencing. Deletion of the sequence targeted by one of these siRNAs on the two alleles by genome editing further show that this silencing is due to base pairing of the siRNA to the target. Moreover, by using cells with heterozygous deletion of the target sequence, we show that only the wild type allele, but not the deleted allele, is silenced by the siRNA, indicating that transcriptional silencing occurs only in cis. Finally, we demonstrate that both Ago1 and Ago2 are involved in this transcriptional silencing. Altogether, our data demonstrate that siRNAs targeting a chromatin-associated RNA at distance from its promoter induce its transcriptional silencing. Our results thus extend the possible repertoire of endogenous or exogenous interfering RNAs.
Integrating and formatting biomedical data as pre-calculated knowledge graph embeddings in the Bioteque
Authors: Fernández-Torras Adrià , Duran-Frigola Miquel , Bertoni Martino , Locatelli Martina , Aloy Patrick
Published: May 2022

Biomedical data is accumulating at a fast pace and integrating it into a unified framework is a major challenge, so that multiple views of a given biological event can be considered simultaneously. Here we present the Bioteque, a resource of unprecedented size and scope that contains pre-calculated biomedical descriptors derived from a gigantic knowledge graph, displaying more than 450 thousand biological entities and 30 million relationships between them. The Bioteque integrates, harmonizes, and formats data collected from over 150 data sources, including 12 biological entities (e.g., genes, diseases, drugs) linked by 67 types of associations (e.g., ‘drug treats disease’, ‘gene interacts with gene’). We show how Bioteque descriptors facilitate the assessment of high-throughput protein-protein interactome data, the prediction of drug response and new repurposing opportunities, and demonstrate that they can be used off-the-shelf in downstream machine learning tasks without loss of performance with respect to using original data. The Bioteque thus offers a thoroughly processed, tractable, and highly optimized assembly of the biomedical knowledge available in the public domain.