bluuebunny/crossref_metadata_2025_split huggingface dataset:
Language model-based B cell receptor sequence embeddings can effectively encode receptor specificity
Authors: Wang Meng , Patsenker Jonathan , Li Henry , Kluger Yuval , Kleinstein Steven H. 
Published: June 2023

ABSTRACTHigh throughput sequencing of B cell receptors (BCRs) is increasingly applied to study the immense diversity of antibodies. Learning biologically meaningful embeddings of BCR sequences is beneficial for predictive modeling and interpretability. Several embedding methods have been developed for BCRs, but no direct performance benchmarking exists. Moreover, the impact of the input sequence length and paired-chain information on the prediction remains to be explored. We evaluated the performance of multiple embedding models to predict BCR sequence properties and receptor specificity. Despite the differences in model architectures, most embeddings effectively capture BCR sequence properties and specificity. BCR-specific embeddings slightly outperform general protein language models in predicting specificity. In addition, incorporating full-length heavy chains and paired light chain sequences improve the prediction performance of all embeddings. This study provides insights into the properties of BCR embeddings to improve downstream prediction applications for antibody analysis and discovery.
DNA methylation governs the sensitivity of repeats to restriction by the HUSH-MORC2 corepressor
Authors: Pandiloski Ninoslav , Horvath Vivien , Karlsson Ofelia E. , Christoforidou Georgia , Dorazehi Fereshteh , Koutounidou Symela , Matas Jon , Gerdes Patricia , Garza Raquel , Jönsson Marie E. , Adami Anita , Atacho Diahann , Johansson Jenny G. , Englund Elisabet , Kokaia Zaal , Jakobsson Johan , Douse Christopher H. 
Published: June 2023

ABSTRACTThe human silencing hub (HUSH) complex binds to transcripts of LINE-1 retrotransposons (L1s) and other genomic repeats, recruiting MORC2 and other effectors to remodel chromatin. However, how HUSH and MORC2 operate alongside DNA methylation, a central epigenetic regulator of repeat transcription, remains poorly understood. Here we interrogate this relationship in human neural progenitor cells (hNPCs), a somatic model of brain development that tolerates removal of DNA methyltransferase DNMT1. Upon loss of MORC2 or HUSH subunit TASOR in hNPCs, L1s remain silenced by robust promoter methylation. However, genome demethylation and activation of evolutionarily-young L1s attracts MORC2 binding. Simultaneous depletion of DNMT1 and MORC2 causes massive accumulation of L1 transcripts. We identify the same mechanistic hierarchy at pericentromeric α-satellites and clustered protocadherin genes, repetitive elements important for chromosome structure and neurodevelopment respectively. Our data delineate the independent epigenetic control of repeats in somatic cells, with implications for understanding the vital functions of HUSH-MORC2 in hypomethylated contexts throughout human development.
Microbiome remodeling through bacterial competition and host behavior enables rapid adaptation to environmental toxins
Authors: Kim Dan , Pérez-Carrascal Olga Maria , DeSousa Catherin , Jung Da Kyung , Bohley Seneca , Wijaya Lila , Trang Kenneth , Khoury Sarah , Shapira Michael 
Published: June 2023

AbstractHuman activity is altering the environment in a rapid pace, challenging the adaptive capacities of genetic variation within animal populations. Animals also harbor extensive gut microbiomes, which play diverse roles in host health and fitness and may help expanding host capabilities. The unprecedented scale of human usage of xenobiotics and contamination with environmental toxins describes one challenge against which bacteria with their immense biochemical diversity would be useful, by increasing detoxification capacities. To explore the potential of bacteria-assisted rapid adaptation, we usedCaenorhabditis elegansworms harboring a defined microbiome, and neomycin as a model toxin, harmful for the worm host and neutralized to different extents by some microbiome members. Worms raised in the presence of neomycin showed delayed development and decreased survival but were protected when colonized by neomycin-resistant members of the microbiome. Two distinct mechanisms facilitated this protection: gut enrichment driven by altered bacterial competition for the strain best capable of modifying neomycin; and host avoidance behavior, which depended on the conserved JNK homolog KGB-1, enabling preference and acquisition of neomycin-protective bacteria. We further tested the consequences of adaptation, considering that enrichment for protective strains may represent dysbiosis. We found that neomycin-adapted gut microbiomes caused increased susceptibility to infection as well as an increase in gut lipid storage, suggesting metabolic remodeling. Our proof-of-concept experiments support the feasibility of bacteria-assisted host adaptation and suggest that it may be prevalent. The results also highlight trade-offs between toxin adaptation and other traits of fitness.
SR-BI regulates the synergistic mast cell response by modulating the plasma membrane-associated cholesterol pool
Authors: Capellmann Sandro , Kauffmann Marlies , Arock Michel , Huber Michael 
Published: June 2023

AbstractThe high-affinity IgE receptor FcεRI is the fundamental mast cell (MC) receptor responsible for the involvement of MCs in IgE-associated allergic disorders. Activation of the FcεRI is achieved via crosslinking by multivalent antigen (Ag) recognized by IgE, which results in degranulation and pro-inflammatory cytokine production. In comparison to the T and B cell receptor complexes, for which several co-receptors that orchestrate the initial signaling have been described, information is scarce about FcεRI-associated proteins. Additionally, it is not completely clear how FcεRI signaling synergizes with input from other receptors and how potential regulators affect this synergistic response. We aimed at identifying new regulators of FcεRI and found that the HDL receptor SR-BI (gene name:Scarb1/SCARB1) is expressed in MCs, functionally associates with FcεRI and regulates the local plasma membrane cholesterol content in cholesterol-rich plasma membrane nanodomains as shown by using the cholesterol-sensitive probe GFP-D4. This impacted on the activation of murine MCs upon co-stimulation of the FcεRI with different receptors known to synergize with FcεRI-signaling pathways. Amongst them we investigated the co-activation of the FcεRI with the receptor tyrosine kinase KIT, the IL-33 receptor and GPCRs activated by adenosine or PGE2.Scarb1-deficient bone marrow-derived MCs (BMMCs) showed reduced cytokine secretion in response to these co-stimulation conditions suggesting a role for plasma membrane-associated cholesterol regulating MC-driven inflammation. MimickingScarb1deficiency by membrane cholesterol depletion employing MβCD, we identified PKB and PLCγ1 as cholesterol-sensitive signaling molecules activated downstream of FcεRI in BMMCs. Specifically, when murine MCs were stimulated with SCF and Ag in combination, PLCγ1 activation appeared to be drastically boosted and this could be mitigated by cholesterol depletion. Inhibiting SR-BI in BMMCs phenocopied this effect. Similarly, SR-BI inhibition also attenuated the synergistic response to PGE2and anti-IgE in the human ROSAKITWTmast cell line suggesting that SR-BI is a crucial regulator of synergistic MC activation by regulating the local plasma membrane cholesterol concentration.
Exact Sketch-Based Read Mapping
Authors: Schulz Tizian , Medvedev Paul 
Published: June 2023

AbstractGiven a sequencing read, the broad goal of read mapping is to find the location(s) in the reference genome that have a “similar sequence”. Traditionally, “similar sequence” was defined as having a high alignment score and read mappers were viewed as heuristic solutions to this well-defined problem. For sketch-based mappers, however, there has not been a problem formulation to capture what problem an exact sketch-based mapping algorithm should solve. Moreover, there is no sketch-based method that can find all possible mapping positions for a read above a certain score threshold.In this paper, we formulate the problem of read mapping at the level of sequence sketches. We give an exact dynamic programming algorithm that finds all hits above a given similarity threshold. It runs in 𝒪 (|t| + |p| +ℓ2) time and Θ(ℓ2) space, where |t| is the number ofk-mers inside the sketch of the reference, |p| is the number ofk-mers inside the read’s sketch andℓis the number of times thatk-mers from the pattern sketch occur in the sketch of the text. We evaluate our algorithm’s performance in mapping long reads to the T2T assembly of human chromosome Y, where ampliconic regions make it desirable to find all good mapping positions. For an equivalent level of precision as minimap2, the recall of our algorithm is 0.88, compared to only 0.76 of minimap2.2012 ACM Subject ClassificationApplied computing → Computational biology
The essential inter-domain interaction between NUDT9H and channel domain of human TRPM2 is also accomplished in trans
Authors: Ehrlich Wiebke , Kühn Frank J.P. 
Published: June 2023

AbstractChannel function of human transient receptor potential melastatin type 2 (hsTRPM2) essentially depends on its C-terminal domain NUDT9H, which is homologous to the human Nudix hydrolase NUDT9. This cytosolic enzyme specifically binds and cleaves adenosine 5′-diphosphate ribose (ADPR), which in turn represents the principal agonist of TRPM2. For hsTRPM2 the experimental data strongly suggest, that binding of ADPR to NUDT9H as well as to a separate N-terminal binding pocket induces channel gating. Recent cryogenic electron microscopy (cryo-EM) analyses have provided the first concrete clues as to how NUDT9H interacts with the channel domain. In the present study we take an alternative approach by testing co-expression of NUDT9H together with a C-terminally truncated non-functional variant of hsTRPM2. Our data obtained from co-immunoprecipitation and proximity ligation assays reveal that NUDT9H and channel domain also specifically interact when co-expressed as independent proteins. Most importantly, calcium imaging as well as whole-cell patch-clamp recordings demonstrate that this in-trans interaction restores channel function, after stimulation either with intracellular ADPR or with extracellular hydrogen peroxide. Moreover, point mutation N1326D within the NUDT9H domain previously shown to be essential for TRPM2 function significantly reduces co-immunoprecipitation of NUDT9H as well as ADPR-dependent channel activity. These findings open up new possibilities to identify the molecular determinants of this crucial inter-domain interaction.
Entropy predicts early MEG, EEG and fMRI responses to natural images
Authors: Muukkonen I. , Salmela V.R. 
Published: June 2023

AbstractTo reduce the redundancy in the input, the human visual system employs efficient coding. Therefore, images with varying entropy (amount of information) should elicit distinct brain responses. Here, we show that a simple entropy model outperforms all current models, including many deep neural networks, in predicting early MEG/EEG and fMRI responses to visual objects. This suggests that the neural populations in the early visual cortex adapt to the information in natural images.
Investigating apparent differences between standard DKI and axisymmetric DKI and its consequences for biophysical parameter estimates
Authors: Oeschger Jan Malte , Tabelow Karsten , Mohammadi Siawoosh 
Published: June 2023

AbstractPurposeIdentify differences between the acquisition-time efficient axisymmetric diffusion kurtosis imaging (DKI) model and standard DKI and their consequences on biophysical parameter estimates using standard DKI parameters as the ground truth.MethodsNoise-free, synthetic diffusion MRI (dMRI) human brain data are generated using standard DKI and fitted with axisymmetric DKI and standard DKI. Then, the five axisymmetric DKI tensor metrics (AxTM), the parallel and perpendicular diffusivity and kurtosis and mean of the kurtosis tensor, attainable with both DKI models are computed. Next, the five biophysical parameters axon water fraction and dispersion, extra axonal parallel and perpendicular diffusivity and intra axonal parallel diffusivity are estimated from the AxTM using the WMTI-Watson model. Finally, the number of substantially differing voxels (SDV), defined as voxels where estimation results of both DKI models differ more than 5%, is calculated for the AxTM and the biophysical parameters.ResultsFor the AxTM, the number of SDV was biggest for the parallel (26%) and perpendicular (51%) kurtosis while the other three AxTM had very few SDV (less than 5%). The biophysical parameters had much more SDV than the AxTM from which they were computed, ranging from 29% to 50%.ConclusionAxisymmetric DKI is a viable alternative to standard DKI in studies focusing on effects based on the parallel and perpendicular diffusion and mean of the kurtosis tensor. However, our findings urge caution when using axisymmetric DKI to investigate effects based on the parallel and perpendicular kurtosis or use it to estimate the biophysical parameters.
Utilizing a dual endogenous reporter system to identify functional regulators of aberrant stem cell and differentiation activity in colorectal cancer
Authors: Spisak Sandor , Chen David , Likasitwatanakul Pornlada , Doan Paul , Li Zhixin , Bala Pratyusha , Vizkeleti Laura , Tisza Viktoria , De Silva Pushpamail , Giannakis Marios , Wolpin Brian , Qi Jun , Sethi Nilay S. 
Published: June 2023

AbstractAberrant stem cell-like activity and impaired differentiation are central to the development of colorectal cancer (CRC). To identify functional mediators that regulate these key cellular programs in CRC, we developed an endogenous reporter system by genome-editing human CRC cell lines with knock-in fluorescent reporters at the SOX9 and KRT20 locus to report aberrant stem cell-like activity and differentiation, respectively, and then performed pooled genetic perturbation screens. Constructing a dual reporter system that simultaneously monitored aberrant stem cell-like and differentiation activity in the same CRC cell line improved our signal to noise discrimination. Using a focused-library CRISPR screen targeting 78 epigenetic regulators with 542 sgRNAs, we identified factors that contribute to stem cell-like activity and differentiation in CRC. Perturbation single cell RNA sequencing (Perturb-seq) of validated hits nominated SMARCB1 of the BAF complex (also known as SWI/SNF) as a negative regulator of differentiation across an array of neoplastic colon models. SMARCB1 is a dependency in CRC and required forin vivogrowth of human CRC models. These studies highlight the utility of a biologically designed endogenous reporter system to uncover novel therapeutic targets for drug development.
Single cell compendium of the muscle microenvironment in peripheral artery disease reveals capillary endothelial heterogeneity and activation of resident macrophages
Authors: Turiel Guillermo , Desgeorges Thibaut , Masschelein Evi , Birrer Manuela , Zhang Jing , Engelberger Stephan , De Bock Katrien 
Published: June 2023

AbstractBackgroundPeripheral artery disease (PAD) is caused by atherosclerosis and chronic narrowing of lower limb arteries leading to decreased muscle perfusion and oxygenation. Current guidelines for treating PAD include endovascular strategies or bypass surgery but long-term outcomes have been suboptimal. This is likely due to our limited understanding of the contribution of the microvasculature as well as other cell types, in particular macrophages, to PAD skeletal muscle pathophysiology. We used single cell sequencing to investigate cellular and transcriptional heterogeneity of the skeletal muscle microenvironment in PAD.MethodsSamples from the medial head of thegastrocnemiusmuscle of individuals undergoing either lower limb aneurysm surgery (controls) or PAD bypass surgery (PAD) were collected. Samples were either frozen for histological evaluation (control: n=4; PAD: n=6) or were immediately processed for single cell RNA sequencing of mononuclear cells (control: n=4; PAD: n= 4). Bioinformatic tools were used to annotate cell types and their subpopulations, to study transcriptional changes and to analyze cellular interactions.ResultsWe generated a dataset comprised of 106,566 high-quality, deep-sequenced cells that compose the muscle microenvironment. Focusing on endothelial cells (ECs) and macrophages, we confirmed the presence of ATF3/4+ECs with angiogenic and immune regulatory capacities in human muscle and found that their transcriptional profile profoundly alters during PAD. Also, capillary ECs display features of endothelial to mesenchymal transition. Furthermore, we identifiedLYVE1hiMHCIIlowresident macrophages as the dominant macrophage population in human muscle, even under a chronic inflammatory condition such as PAD. During PAD,LYVE1hiMHCIIlowmacrophages get activated and acquire a more pro-inflammatory profile. Finally, we map strong intercellular communication in the muscle microenvironment, which is significantly altered in PAD.ConclusionsThe dataset we present here provides a highly valuable resource for gaining deeper insights into the critical roles that cells in the muscle microenvironment may play in PAD skeletal muscle pathology. We propose that targeting the crosstalk between ECs and macrophages could provide novel insights for developing effective treatments against this disease.
Kinetic and functional analysis of abundant microRNAs in extracellular vesicles from normal and stressed cultures of Chinese Hamster Ovary (CHO) cells
Authors: Belliveau Jessica , Thompson Will , Papoutsakis Eleftherios Terry 
Published: June 2023

AbstractChinese hamster ovary (CHO) cells release and exchange large quantities of extracellular vesicles (EVs). EVs are highly enriched in microRNAs (miRs, or miRNAs), which are responsible for most of their biological effects. We have recently shown that the miR content of CHO EVs varies significantly under culture stress conditions. Here, we provide a novel stoichiometric (“per-EV”) quantification of miR and protein levels in large CHO EVs produced under ammonia, lactate, osmotic, and age-related stress. Each stress resulted in distinct EV miR levels, with selective miR loading by parent cells. Our data provide a proof of concept for the use of CHO EV cargo as a diagnostic tool for identifying culture stress. We also tested the impact of three select miRs (let-7a, miR-21, and miR-92a) on CHO cell growth and viability. Let-7a—abundant in CHO EVs from stressed cultures—reduced CHO cell viability, while miR-92a—abundant in CHO EVs from unstressed cultures—promoted cell survival. Overexpression of miR-21 had a slight detrimental impact on CHO cell growth and viability during late exponential-phase culture, an unexpected result based on the reported anti-apoptotic role of miR-21 in other mammalian cell lines. These findings provide novel relationships between CHO EV cargo and cell phenotype, suggesting that CHO EVs may exert both pro- and anti-apoptotic effects on target cells, depending on the conditions under which they were produced.Graphical Abstract
Genome-wide kinetic profiling of pre-mRNA 3’ end cleavage
Authors: Ulloa Leslie Torres , Calvo-Roitberg Ezequiel , Pai Athma A. 
Published: June 2023

ABSTRACTCleavage and polyadenylation is necessary for the formation of mature mRNA molecules. The rate at which this process occurs can determine the temporal availability of mRNA for subsequent function throughout the cell and is likely tightly regulated. Despite advances in high-throughput approaches for global kinetic profiling of RNA maturation, genome-wide 3’ end cleavage rates have never been measured. Here, we describe a novel approach to estimate the rates of cleavage, using metabolic labeling of nascent RNA, high-throughput sequencing, and mathematical modeling. Using in-silico simulations of nascent RNA-seq data, we show that our approach can accurately and precisely estimate cleavage half-lives for both constitutive and alternative sites. We find that 3’ end cleavage is fast on average, with half-lives under a minute, but highly variable across individual sites. Rapid cleavage is promoted by the presence of canonical sequence elements and an increased density of polyadenylation signals near a cleavage site. Finally, we find that cleavage rates are associated with the localization of RNA Polymerase II at the end of a gene and faster cleavage leads to quicker degradation of downstream read-through RNA. Our findings shed light on the features important for efficient 3’ end cleavage and the regulation of transcription termination.
A pathogenic missense mutation in kainate receptors elevates dendritic excitability and synaptic integration through dysregulation of SK channels
Authors: Nomura Toshihiro , Taniguchi Sakiko , Wang Yi-Zhi , Yeh Nai-Hsing , Wilen Anika P , Castillon Charlotte C.M. , Foote Kendall M. , Xu Jian , Armstrong John N. , Savas Jeffrey N. , Swanson Geoffrey T. , Contractor Anis 
Published: June 2023

AbstractNumerous rarede novovariants that cause neurodevelopmental disorders (NDDs) occur within genes encoding synaptic proteins, including ionotropic glutamate receptors (iGluRs). However, in many cases it remains unclear how damaging missense variants affect brain function. Here we determined the physiological consequences of an NDD causing missense mutation in theGRIK2kainate receptor (KAR) gene, that results in a single amino acid change p.Ala657Thr in the GluK2 receptor subunit. We engineered the equivalent mutation in the mouseGrik2gene, yielding a GluK2(A657T) mouse, to better understand the human disorder and determine how hippocampal neuronal function is disrupted. Synaptic KAR currents in hippocampal CA3 pyramidal neurons from heterozygous A657T mice exhibited slow decay kinetics, consistent with incorporation of the mutant subunit into functional receptors. Unexpectedly, CA3 neurons demonstrated elevated action potential spiking due to down-regulation of the small conductance Ca2+activated K+channel (SK), which mediates the post-spike afterhyperpolarization (AHP). The reduction in SK activity resulted in increased CA3 dendritic excitability, increased EPSP-spike coupling and lowered the threshold for the induction of LTP of the associational commissural (AC) synapses in the distal dendrites of CA3 neurons. Pharmacological inhibition of SK channels in wild-type (WT) mice increased dendritic excitability and EPSP-spike coupling, mimicking the phenotype in A657T mice and suggesting a causative role for attenuated SK activity in aberrant excitability observed in the mutant mice. These findings demonstrate that a disease-associated missense mutation inGRIK2leads to altered signaling through neuronal KARs, pleiotropic effects on neuronal and dendritic excitability, and implicate these processes in neuropathology in patients with genetic NDDs.