bluuebunny/crossref_metadata_2025_split huggingface dataset:
Neddylation regulates the development and function of excitatory neurons
Authors: Torres Josefa , Vural Zehra , Fiosins Maksims , Benseler Fritz , Bonn Stefan , Rizzoli Silvio O. , Rhee JeongSeop , Brose Nils , Tirard Marilyn 
Published: December 2024

SummaryThe development and function of neurons is orchestrated by a plethora of regulatory mechanisms that control the abundance, localization, interactions, and function of proteins. A key role in this regard is assumed by post-translational protein modifications (PTMs). While some PTM types, such as phosphorylation or ubiquitination, have been explored comprehensively, PTMs involving ubiquitin-like modifiers (Ubls) have remained comparably enigmatic (Ubls). This is particularly true for the Ubl Nedd8 and its conjugation to proteins, i.e. neddylation, in nerve cells. In the present study, we generated a conditional Nedd8 knock-out mouse line and examined the consequences of Nedd8-deletion in cultured postmitotic glutamatergic neurons. Our findings reveal that Nedd8-ablation in young glutamatergic neurons causes alterations in the expression of developmental transcription factors that control neuronal differentiation, ultimately leading to defects in the development of a mature glutamatergic neuronal phenotype. Apparent manifestations of these defects include increased vGlut2 expression levels, reduced vGlut1 and endophilin 1 expression levels, reduced dendrite complexity, and increased transmitter release probability. Collectively, our results highlight a pivotal role for neddylation in controlling the fate of glutamatergic neurons and excitatory synaptic transmission.HighlightsReduced dendrite complexity in Nedd8-deficient neuronsIncreased synaptic vesicle fusion probability in Nedd8-deficient neuronsAltered synaptic vesicle cycling in Nedd8-deficient neuronsNeddylation controls the maturation of glutamatergic neuronsGraphical AbstractResearch Topic
Single Cell RNAseq to identify subpopulations of glial progenitors in iPSC-derived oligodendroglial lineage cultures
Authors: Blaszczyk Gabriela J , Piscopo Valerio E C , Goldsmith Taylor M , Chapleau Alexandra , Sirois Julien , Bernard Geneviève , Antel Jack P , Durcan Thomas M 
Published: December 2024

SummaryCellular heterogeneity is a common issue in differentiation protocols of oligodendrocytes (OLs) from human induced pluripotent stem cells. Our previous work described a novel method to generate OLs and highlighted the presence of glial progenitors. Here, we unravel the glial heterogeneity and characterize the response of isolated subpopulations to differentiation. This study provides a novel tool for studying the dynamics of glial development invitroand on a transcriptomic level.
Coordinated alternative splicing decisions via stepwise exon definition
Authors: Kristofori Panajot , Braun Simon , Busch Anke , Zarnack Kathi , König Julian , Legewie Stefan , Li Congxin 
Published: December 2024

AbstractAlternative splicing of pre-mRNA is a fundamental step in human gene regulation and aberrant slic-ing is tightly linked to diseases including cancer. Various splicing events, such as alternative exon (AE) choice and intron retention (IR), are controlled by a common molecular machinery, the spliceo-some. However, it remains elusive how the regulation of spliceosome activity coordinately affects these splicing decisions. Here, we analyze a large-scale mutagenesis screen and genome-wide RNA sequencing data to show that IR and AE choice are tightly coupled, as IR products primarily accu-mulate in alternative exons showing intermediate inclusion levels. Using data-driven mathematical modeling, we reveal that multistep exon recognition by the spliceosome explains the observed AE-IR dependency for cis-acting sequence mutations and upon knockdown of trans-acting RNA-binding proteins. Furthermore, we show that multistep exon definition is frequently perturbed in cancer cells, which leads to the coordinated deregulation of intron retention and AE choice. In conclusion, we showed that the spliceosome coordinates complex splicing decisions via stepwise exon definition, which potentially facilitates the search for common molecular mechanisms for mis-splicing in cancer.
Widespread Distribution of α-Synuclein Oligomers inLRRK2-related Parkinson’s Disease
Authors: Sekiya Hiroaki , Franke Lukas , Hashimoto Yuki , Takata Mariko , Nishida Katsuya , Futamura Naonobu , Hasegawa Kazuko , Kowa Hisatomo , Ross Owen A. , McLean Pamela J. , Toda Tatsushi , Wszolek Zbigniew K. , Dickson Dennis W. 
Published: December 2024

AbstractMutations in leucine-rich repeat kinase 2 (LRRK2) are the most common cause of familial and sporadic Parkinson’s disease (PD). While the clinical features ofLRRK2-PD patients resemble those of typical PD, there are significant differences in the pathological findings. The pathological hallmark of definite PD is the presence of α-synuclein (αSYN)-positive Lewy-related pathology; however, approximately half ofLRRK2-PD cases do not have Lewy-related pathology. Lewy-related pathology is a late-stage αSYN aggregation that can be visualized with hematoxylin and eosin stains or conventional immunohistochemistry (IHC). Increasing evidence has indicated that αSYN oligomers, which represent the early-stage of αSYN aggregation, may have neurotoxicity. Visualization of αSYN oligomers requires specialized staining techniques, such as αSYN-proximity ligation assay (PLA). The distribution and severity of αSYN oligomers in the human brain ofLRRK2-PD patients remain unknown. In this study, we performed phosphorylated αSYN-IHC and αSYN-PLA staining on postmortem brain sections of patients with three pathogenic LRRK2 mutants: p.G2019S (n=5), p.I2020T (n=5), and p.R1441C (n=4). The severity of Lewy-related pathology and αSYN oligomers were assessed semi-quantitatively in the brainstem, limbic lobe, basal ganglia, and cerebral cortex. αSYN oligomers were detected inLRRK2-PD cases even in cases without Lewy-related pathology; a negative correlation was observed between Lewy-related pathology and αSYN oligomers (r=-0.26 [-0.39, -0.12]; P<0.0001). Our findings suggest that αSYN oligomers may represent a common pathological feature ofLRRK2-PD. Notably, patients harboring p.G2019S and p.I2020T had significantly higher levels of αSYN oligomers in those without Lewy-related pathology compared to those with Lewy-related pathology. These cases also had a trend toward shorter disease duration. These results imply that inLRRK2-PD, αSYN oligomers may initially accumulate in the brain but do not progress to form Lewy-related pathology. The present study suggests that targeting αSYN oligomers may be a therapeutic strategy forLRRK2-PD even if there is no Lewy-related pathology.
Applying computational protein design to engineer affibodies for affinity-controlled delivery of vascular endothelial growth factor and platelet-derived growth factor
Authors: Svendsen Justin E. , Ford Madeleine R. , Asnes Chandler L. , Oh Simon C. , Dorogin Jonathan , Fear Karly M. , O’Hara-Smith Johnathan R. , Harms Michael J. , Hosseinzadeh Parisa , Hettiaratchi Marian H. 
Published: December 2024

AbstractEffective angiogenesis requires the coordinated presentation of vascular endothelial growth factor (VEGF) and platelet-derived growth factor (PDGF), which play competing roles in stimulating vascular outgrowth and stabilization. Dysregulation in VEGF and PDGF secretion are implicated in abnormal vascular structures, poor vessel stability, and inadequate tissue repair. Current biomaterial delivery vehicles for these proteins have a limited ability to precisely control the kinetics of protein release, preventing systematic exploration of their temporal effects. Here, we combined yeast surface display and computational protein design to engineer eight VEGF-specific and PDGF-specific protein binders called affibodies with a broad range of affinities (dissociation constants = 2.23-9260 nM) for affinity-controlled protein release. Starting from one VEGF- and one PDGF-specific affibody discovered from yeast surface display, computational modeling was used to select disruptive mutations to create VEGF-specific affibodies with lower affinities for VEGF and expand the affinity range of PDGF-specific affibodies. In both cases, the specificity of the affibodies for their target protein was either maintained or enhanced. Soluble protein-specific affibodies modulated protein bioactivity as evidenced by changes in VEGF-induced endothelial cell proliferation and luminescent output of a PDGF-responsive fibroblast cell line. Affibody-conjugated polyethylene glycol maleimide (PEG-mal) hydrogels sustained VEGF and PDGF release compared to hydrogels without affibodies, enabling tunability of protein release over 7 days. VEGF and PDGF released from affibody-conjugated hydrogels exhibited higher bioactivity compared to proteins released from hydrogels without affibodies, highlighting the potential of these engineered affinity interactions to prolong protein bioactivity. This work underscores the power of computational protein design to enhance biomaterial functionality, creating a platform for tunable protein delivery to support angiogenesis and tissue repair.
Change in Resting-State functional MRI Connectivity to Measure Individual Response to Epilepsy Surgery
Authors: Cediel Emilio G. , Duran Erika A. , Laux Jeffrey , Leggio Olivia , Reuther William , Robinson Belfin , Wabulya Angela , Boerwinkle Varina L. 
Published: December 2024

ABSTRACTObjectiveThis study evaluates fractional power spectrum contribution (fPSC), a biomarker derived from resting-state functional MRI (rs-fMRI), as an indicator of epileptogenic network activity in drug-resistant epilepsy (DRE) patients undergoing surgery. We aimed to assess pre-to post-operative changes in fPSC and their correlation with seizure outcomes.MethodsA retrospective cohort of 56 pediatric DRE patients with pre- and post-operative rs-fMRI were evaluated. Independent component analysis (ICA) was applied to identify resting-state networks (RSNs). Each ICA RSN’s power spectrum within the range of 0.06–0.25 Hz was quantified by fPSC. The change in this fPSC was compared pre- and post-operatively using paired t-tests. Multivariate analyses including correlations with clinical outcomes were evaluated by linear mixed effects models and ANOVA.ResultsAmong the 56 patients, 80.4% demonstrated greater than 50% seizure reduction post-surgery, with 64.3% achieving seizure freedom. fPSC significantly decreased after surgery (t=3.0, p=0.005), indicating a reduction in epileptogenic network activity. The mixed effects model, controlling for covariates, also showed a significant effect of post-surgical scan on fPSC reduction (χ²=8.4, df=1, p=0.004). However, there was insufficient evidence to establish an association between changes in fPSC and clinical improvement score (p=0.16) or seizure frequency (p=0.49).ConclusionThe observed reduction in fPSC post-surgery highlights its potential as a biomarker of atypical network activity in epilepsy, offering a network-specific, whole-brain approach independent of anatomical coordinates. However, its lack of correlation with clinical outcomes underscores the need for further refinement and validation to establish fPSC as a reliable measure of epileptogenic burden.HIGHLIGHTSfPSC analysis using rs-fMRI detects a moderate treatment effect of epilepsy surgery, independent of relative network volume changes.fPSC analysis provides a method to quantify whole-brain network dysfunction in epilepsy without the need for a seizure onset zone identification-hypothesis.A trend towards direct correlation is observed between fPSC post-operative change and seizure outcomes in epilepsy surgery.
Whole-exome sequencing in children with dyslexia identifies rare variants inCLDN3and ion channel genes
Authors: Marianski Krzysztof , Talcott Joel B. , Stein John , Monaco Anthony P. , Fisher Simon E. , Bishop Dorothy V.M. , Newbury Dianne F. , Paracchini Silvia 
Published: December 2024

AbstractDyslexia is a specific difficulty in learning to read that affects 5-10% of school-aged children and is strongly influenced by genetic factors. While previous studies have identified common genetic variants associated with dyslexia, the role of rare variants has only recently begun to emerge from pedigree studies and has yet to be systematically tested in larger cohorts. Here, we present a whole-exome sequencing (WES) study of 53 individuals with dyslexia, followed by replication analysis in 38 cases with reading difficulties and 82 controls assessed with reading measures. Our stringent bioinformatics filtering strategy highlighted five brain-expressed genes carrying rare variants:CACNA1D,CACNA1G,CLDN3,CNGB1,andCP. Notably, a specific variant (7-73769649-G-A) in theCLDN3gene was identified in six independent cases, showing a four-fold higher frequency compared to population reference datasets.CACNA1DandCACNA1Gencode subunits of voltage-gated calcium channels (VGCC) expressed in neurons, and variants in both genes have been implicated in neurodevelopmental disorders such as autism spectrum disorder (ASD) and epilepsy. Segregation analysis in available family members were consistent with patterns of dominant inheritance with variable expressivity. In total, high-impact variants in the five genes of interest were found in 26% (N = 14) of individuals of the discovery cohort. Overall, our findings support the involvement of rare variants in developmental dyslexia and indicate that larger WES studies may uncover additional associated genes.
Actively Protective Combinatorial Analysis: a Scalable Novel Method for Detecting Variants that Contribute to Reduced Disease Prevalence in High-Risk Individuals
Authors: Sardell J , Das S , Taylor K , Stubberfield C , Malinowski A , Strivens M , Gardner S 
Published: December 2024

AbstractWe present a novel method for routinely identifying disease resilience associations that offers powerful insights for the discovery of a new class of disease protective targets. We show how this can be used to identify mechanisms in the background of normal cellular biology that work to slow or stop progression of complex, chronic diseases.Actively protective combinatorial analysis identifies combinations of features that contribute to reducing risk of disease in individuals who remain healthy even though their genomic profile suggests that they have high risk of developing disease. These protective signatures can potentially be used to identify novel drug targets, pharmacogenomic and/or therapeutic mRNA opportunities and to better stratify patients by overall disease risk and mechanistic subtype.We describe the method and illustrate how it offers increased power for detecting disease-associated genetic variants relative to traditional methods. We exemplify this by identifying individuals who remain healthy despite possessing several disease signatures associated with increased risk of myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) or amyotrophic lateral sclerosis (ALS). We then identify combinations of SNP-genotypes significantly associated with reduced disease prevalence in these high-risk protected cohorts.We discuss how actively protective combinatorial analysis generates novel insights into the genetic drivers of established disease biology and detects gene-disease associations missed by standard statistical approaches such as meta-GWAS. The results support the mechanism of action hypotheses identified in our original causative disease analyses. They also illustrate the potential for development of precision medicine approaches that can increase healthspan by reducing the progression of disease.
Silicon-rhodamine-enabled Identification (SeeID) for Near-Infrared Light Controlled Proximity Labeling In Vitro and In Vivo
Authors: Wang Wenjing , Guo Hongyang , Yan Xiaosa , Pan Xuanzhen , Wang Xiaofei , Rong Yiming , Bai Zexiao , Zhang Liwan , Wu Zhaofa , Zhao Xinyu , Huang Weiren , Qin Wei , Chu Ling 
Published: December 2024

AbstractAdvancement in fluorescence imaging techniques enables the study of protein dynamics and localization with unprecedented spatiotemporal resolution. However, current imaging tools are unable to elucidate dynamic protein interactomes underlying imaging observations. In contrast, proteomics tools such as proximity labeling enable the analysis of protein interactomes at a single time point but lack information about protein dynamics. We herein developed Silicon-rhodamine-enabled Identification (SeeID) for near-infrared light controlled proximity labeling that could bridge the gap between imaging and proximity labeling. SeeID was benchmarked through characterization of various organelle-specific proteomes and the KRAS protein interactome. The fluorogenic nature of SiR allows for intracellular proximity labeling with high subcellular specificity. Leveraging SiR as both a fluorophore and a photocatalyst, we developed a protocol that allows the study of dynamic protein interactomes of Parkin during mitophagy. We discovered the association of the proteasome complex with Parkin at early time points, indicating the involvement of the ubiquitin-proteasome system for protein degradation in the early phase of mitophagy. In addition, by virtue of the deep tissue penetration of near-infrared light, we achieved spatiotemporally controlled proximity labeling in vivo across the mouse brain cortex with a labeling depth of ∼2 mm using an off-the-shelf 660 nm LED light set-up.
Stress Induced Signaling Pathways in Burkitt’s Lymphoma Play Novel Mechanisms in Fate Determination and Pathogenesis of Germinal Center-Derived B-Lymphomas
Authors: Gothwal Santosh K , Barlow Jacqueline H 
Published: December 2024

AbstractB cell receptor signaling, NF-κB signaling, BCL6 and p53 regulation are essential for germinal center (GC) B cell fate. Dysregulation of these pathways drives the pathogenesis and treatment resistance of GC-derived B-lymphomas (GCDBL). To explore how these pathways affect GCDBL fate and pathogenesis, we treated Raji cells (a GCDBL and Burkitt’s lymphoma) with mild hydroxyurea (HU) to simulate genotoxic stress encountered by GC B cells. Genome-wide mapping of histone H3K4me3 and p53 target analysis in HU-treated Raji cells combined with transcriptome analysis of human tonsil GC B cells identifiedATAD2B(a p53 target) as differentially expressed. We found that p53 suppressesATAD2BandATAD2, whileATAD2andBCL6transcripts positively correlate in DLBCLs, suggesting that p53 regulates BCL6 in GC B cells via ATAD2 suppression. We propose that p53 regulation ofBCL6quality assures GC B cells before GC exit. Unlike BCL6 suppression of IFN-γ and NF-κB signaling in GC B cells, we identifiedIFNGR1as a loosely bound BCL6 target and observed loss of BCL6 regulation on genes encoding inhibitory subunits of NF-κB signaling in B-lymphoma treated with a Bruton tyrosine kinase (BTK) inhibitor. These adaptations, alongside with prevalent genetic inactivation of NF-κB inhibitory genes in DLBLCs, likely contribute to DLBCL pathogenesis and therapy resistance. Our findings highlight the pivotal role of the p53-BCL6 axis in GC B cell fate and its dysregulation in DLBCL pathogenesis and chemoresistance.Key HighlightsGenes induced in human Burkitt’s lymphoma under genotoxic stress are largely independent of histone H3K4me3 marks at transcriptional start sites (TSS).Loss of BCL6 regulation on genes encoding components of IFN-γ signaling is associated with reduced survival and the pathogenesis of DLBCL.Inactivating mutations in genes encoding components of the NF-κB inhibitory subunit serve as an adaptation for DLBCL pathogenesis.BCL6expression is correlated withATAD2overexpression in DLBCL and solid tumors.
Pangenomic structural variant patterns reflect evolutionary diversification inBrassica napus
Authors: Afsharyan Nazanin P. , Golicz Agnieszka A. , Snowdon Rod J. 
Published: December 2024

AbstractBackgroundUnderstanding genetic diversity is crucial for enhancing crop productivity. This study explores species-wide genome structural variation and its role in intraspecific and ecogeographical diversification ofBrassica napus, a recently evolved, globally important allopolyploid crop.ResultsWe performed whole-genome long-read DNA-sequencing and constructed reference-guided genome assemblies for 94 diverse, homozygous accessions, including winter-type, spring-type, and East Asian oilseed, along with kale forms and swedes/rutabagas. We investigated pangenomic patterns of genomic structural variants (SV) and determined pangenome-wide distributions and frequencies of inversions, gene presence-absence variants, and collective SV including insertions and deletions. Results revealed pangenome-wide patterns for insertions, deletions, inversions, and large chromosomal deletions/duplications, reflecting evolutionary diversification across morphotypes and ecotypes. Collective SV were unevenly distributed and biased toward subgenome A, with asymmetrical selection pattern favoring subgenome C. Selection signatures for inversions exhibited no subgenome asymmetry; however, selection signal strength and frequency increased in paracentric chromosome regions, highlighting their evolutionary significance. Selective sweep analysis identified regions for collective SV and inversions, harboring genes for organ formation, cell division and expansion in swede, and stress responses in East Asian oilseed rape. Large chromosomal duplications and deletions distinguished swede from oilseed rape, particularly in subgenome C, including copy-number variation in flowering-time genesBnFLC.C09andBnATX2.C08, and cell wall development geneBnCEL2.C08.ConclusionsThese findings underscore functional and evolutionary significance of pangenomic SV formation duringB. napusdiversification. Information on SV patterns with putative functional relevance, provides breeding insights, particularly for developing molecular markers to optimize performance ofB. napusand otherBrassicacrops.
Possible involvement of ghost introgressions in the striking diversity of Vomeronasal type 1 receptor genes in East African cichlids
Authors: Taki Shunsuke , Zhang Zicong , Aibara Mitsuto , Nagasawa Tatsuki , Nikaido Masato 
Published: December 2024

AbstractCichlids that have undergone adaptive radiation are genetically close but exhibit extreme ecological and morphological diversity, making them useful for understanding speciation mechanisms. Vomeronasal type 1 receptors (V1R) are highly conserved among teleost fish at the amino acid sequence level and believed to play a fundamental role in reproduction. We previously reported the surprisingly high sequence diversity of V1Rs among certain cichlid species, suggesting a possible role for V1Rs in their speciation. In this study, we investigated the process of evolutionary diversification of all 6 V1Rs (V1R1-6) by using the genome data of 528 cichlid species, encompassing nearly all lineages. In the case of V1R2, two highly divergent alleles (1.17%: variant sites/CDS length) without recombination were preserved and shared among cichlids found in all of the East African Great Lakes. In the case of V1R6, numerous highly variable alleles that could be derived from multiple recombination events between two highly divergent alleles (1.39%: variant sites/CDS length) were found among the Lake Victoria cichlids. Additionally, we identified highly divergent alleles of V1R1 within the tribe Tropheini, and of both V1R3 and V1R6 within Trematocarini and Ectodini. Because one of the two divergent alleles of these V1Rs emerged rapidly during cichlid evolution, they are likely to have been derived from introgression. However, despite extensive investigations, we could not identify the source lineages for these introgressions, implying that they may have become extinct. This study revealed the potential role of introgression in explaining the remarkable diversity of V1Rs in East African cichlids.