bluuebunny/crossref_metadata_2025 huggingface dataset:
Identification of PTGR2 inhibitors as a new therapy for diabetes and obesity
Authors: Chang Yi-Cheng , Hsieh Meng-Lun , Lee Hsiao-Lin , Hee Siow-Wey , Chang Chi-Fon , Yen Hsin-Yung , Chen Yi-An , Chen Yet-Ran , Chou Ya-Wen , Li Fu-An , Ke Yi-Yu , Chen Shih-Yi , Hung Ming-Shiu , Hung Alfur Fu-Hsin , Huang Jing-Yong , Chiu Chu-Hsuan , Lin Shih-Yao , Shih Sheue-Fang , Hsu Chih-Neng , Hwang Juey-Jen , Yeh Teng-Kuang , Rachel Cheng Ting-Jen , Liao Karen Chia-Wen , Laio Daniel , Lin Shu-Wha , Chen Tzu-Yu , Hu Chun-Mei , Vogel Ulla , Saar Daniel , Kragelund Birthe B. , Tsou Lun Kelvin , Tseng Yu-Hua , Chuang Lee-Ming
Published: December 2024

Peroxisome proliferator-activated receptor γ (PPARγ) is a master transcriptional regulator of systemic insulin sensitivity and energy balance. The anti-diabetic drug thiazolidinediones (TZDs) are potent synthetic PPARγ ligands with undesirable side effects, including obesity, fluid retention, and osteoporosis. 15-keto prostaglandin E2 (15-keto-PGE2) is an endogenous PPARγ ligand metabolized by prostaglandin reductase 2 (PTGR2). Here, we confirmed that 15-keto-PGE2 binds and activates PPARγ via covalent binding. In patients with type 2 diabetes and obese mice, serum 15-keto-PGE2 levels were decreased. Administration of 15-keto-PGE2 improves glucose homeostasis and prevented diet-induced obesity in mice. Either genetic inhibition of PTGR2 or PTGR2 inhibitor BPRPT0245 protected mice from diet-induced obesity, insulin resistance, and hepatic steatosis without fluid retention and osteoporosis. In conclusion, inhibition of PTGR2 is a new therapeutic approach to treat diabetes and obesity through increasing endogenous PPARγ ligands without side effects of synthetic PPARγ ligands TZDs.
Transmissibility of a newPlasmodium falciparum3D7 bank for use in malaria volunteer infection studies evaluating transmission blocking interventions
Authors: Lynch Sean A. , Abd-Rahman Azrin N. , Peters Jenny M. , Heunis Juanita M. , Gower Jeremy , Potter Adam J. , Webster Rebecca , Jennings Helen , Mathison Susan , Sahai Nischal , Amante Fiona H. , Barber Bridget E.
Published: December 2024

Transmission blocking activity is an important characteristic of antimalarial drugs, and can be evaluated in malaria volunteer infection studies (VIS). We undertook a pilot VIS to evaluate the suitability of a recently manufacturedP. falciparum3D7 bank (3D7-MBE-008) for evaluating transmission blocking interventions. Four adults were inoculated withP. falciparum3D7-MBE-008 infected erythrocytes and administered piperaquine on days 8 and 10 to clear asexual parasitemia while allowing gametocyte development. On day 25, participants were randomised (1:1) to receive either 0.25 mg/kg primaquine (primaquine group) or no intervention (control group). Transmissibility was assessed by enriched membrane feeding assays on days 25, 29, 32, and 39, with transmission intensity (proportion of mosquitoes infected) determined by 18S qPCR. All participants were infective on day 25, with a median 94% (range, 12%–100%) of mosquitoes positive for oocysts, and 76% (range, 8%–94%) positive for sporozoites. In the primaquine group, mosquito infectivity decreased substantially between days 25 and 29. In the control group, mosquito infectivity remained high up to day 32, and persisted to day 39 in one participant. TheP. falciparum3D7-MBE-008 parasite bank induced blood-stage infections that were highly transmissible to mosquitoes and is therefore suitable for evaluating transmission blocking interventions.

Trial registrationanzctr.org.au (registration number: ACTRN12622001097730), registered 08/08/2022.
Cluefish: mining the dark matter of transcriptional data series with over-representation analysis enhanced by aggregated biological prior knowledge
Authors: Franklin Ellis , Billoir Elise , Veber Philippe , Ohanessian Jérémie , Delignette-Muller Marie Laure , Prud’homme Sophie Martine
Published: December 2024

Interpreting transcriptomic data presents significant challenges, particularly in non-targeted approaches. While modern functional enrichment methods are well-suited for experimental designs involving two conditions, they are less applicable to data series. In this context, we developed Cluefish, a free and open-source, semi-automated R workflow designed for untargeted, comprehensive biological interpretation of transcriptomic data series. Cluefish applies over-representation analysis on pre-clustered protein-protein interaction networks, using clusters as anchors to identify smaller, more specific biological functions. Innovative features, including cluster merging and recovery of isolated genes through shared biological contexts, enable a more complete exploration of the data. In our case study with zebrafish embryos exposed to a dose-gradient of dibutyl phthalate, Cluefish—combined with DRomics, a tool for dose-response analysis—identified gene clusters deregulated at low doses and linked to biological functions overlooked by the standard approach. Notably, it revealed that retinoid signalling disruption may be the most sensitive pathway affected by dibutyl phthalate during zebrafish development, potentially leading to morphological changes. The Cluefish workflow aims to provide valuable clues for biological hypothesis generation and experimental validation. It is freely available athttps://github.com/ellfran-7/cluefish.

GRAPHICAL ABSTRACT

A graphical abstract will be provided at revision.
The impact of human agents on spatial navigation and knowledge acquisition in a Virtual Environment
Authors: Sánchez-Pacheco T. , Sarría-Mosquera M. , Gärtner K. , Schmidt V. , Nolte D. , König S.U. , Pipa G. , König P.
Published: December 2024

Concepts of spatial navigation rest on the idea of landmarks, which are immobile features or objects in the environment. However, behaviorally relevant objects or fellow humans are often mobile. This raises the question of how the presence of human agents influences spatial exploration and knowledge acquisition. Here, we investigate exploration and performance in subsequent spatial tasks within a virtual environment containing numerous human avatars. In the exploration phase, agents had a locally limited effect on navigation. They prompted participants to revisit locations with agents during their initial exploration without significantly altering overall exploration patterns or the extent of the area covered. However, agents and buildings competed for visual attention. When spatial recall was tested, pointing accuracy toward buildings improved when participants directed their attention to the buildings and nearby agents. In contrast, pointing accuracy for agents showed weaker performance and did not benefit from visual attention directed toward the adjacent building. Active agents and incongruent agent-environment pairings further enhanced pointing accuracy, revealing that violations of expectations by agents can significantly shape navigational knowledge acquisition. Overall, agents influenced spatial exploration by directing attention locally, with the interaction between agent salience and environmental features playing a key role in shaping navigational knowledge acquisition.
Cleavage of the TrkB-FL Receptor During Epileptogenesis: Insights from a Kainic Acid-Induced Model of Epilepsy and Human Samples
Authors: Ribeiro-Rodrigues Leonor , Fonseca-Gomes João , Paulo Sara L. , Viais Ricardo , Ribeiro Filipa F. , Miranda-Lourenço Catarina , Mouro Francisco M. , Belo Rita F. , Ferreira Catarina B. , Tanqueiro Sara R. , Ferreira-Manso Mafalda , Umemori Juzoh , Castrén Eero , Paiva Vítor H. , Sebastião Ana M. , Aronica Eleonora , Rainha Campos Alexandre , Bentes Carla , Xapelli Sara , Diógenes Maria José
Published: December 2024

Abstract

Brain-derived neurotrophic factor (BDNF) is essential for neuronal survival, differentiation, and plasticity. In epilepsy, BDNF exhibits a dual role, exerting both antiepileptic and pro-epileptic effects. The cleavage of its main receptor, full-length tropomyosin-related kinase B (TrkB-FL), was suggested to occur in status epilepticus (SE) in vitro. Moreover, under excitotoxic conditions, TrkB-FL was found to be cleaved, resulting in the formation of a new intracellular fragment, TrkB-ICD. Thus, we hypothesized that TrkB-FL cleavage and TrkB-ICD formation could represent an uncovered mechanism in epilepsy.

We used a rat model of mesial temporal lobe epilepsy (mTLE) induced by kainic acid (KA) to investigate TrkB-FL cleavage and TrkB-ICD formation during SE and established epilepsy (EE). Animals treated with 10 mg/kg of KA exhibited TrkB-FL cleavage during SE, with hippocampal levels of TrkB-FL and TrkB-ICD correlating with seizure severity. Notably, TrkB-FL cleavage and TrkB-ICD formation were also detected in animals with EE, which exhibited spontaneous recurrent convulsive seizures, neuronal death, mossy fiber sprouting, and long-term memory impairment. Importantly, hippocampal samples from patients with refractory epilepsy also showed TrkB-FL cleavage with increased TrkB-ICD levels. Additionally, overexpression of TrkB-ICD in the hippocampus of healthy rodents resulted in long-term memory impairment.

Our findings suggest that TrkB-FL cleavage and the subsequent TrkB-ICD production occur throughout epileptogenesis, with the extent of cleavage correlating positively with seizure occurrence. Moreover, we found that TrkB-ICD impairs memory. This work uncovers a novel mechanism in epileptogenesis that could serve as a potential therapeutic target in mTLE, with implications for preserving cognitive function.
A haplotype-based evolutionary history of barley domestication
Authors: Guo Yu , Jayakodi Murukarthick , Himmelbach Axel , Ben-Yosef Erez , Davidovich Uri , David Michal , Hartmann-Shenkman Anat , Kislev Mordechai , Fahima Tzion , Schuenemann Verena J. , Reiter Ella , Krause Johannes , Steffenson Brian J. , Stein Nils , Weiss Ehud , Mascher Martin
Published: December 2024

Barley is an old crop with a complex history. Its evolution and the molecular basis of domestication have been intensely studied. This research has ruled out a single origin of the crop and motivated a model of mosaic genomics ancestry. As more and better genome sequences have become available, this concept can be refined: where do the building blocks of the mosaic, that is, the haplotypes come from? Were all cultivated barleys created equal or did some wild barley populations contribute more to some domesticated lineages? To answer these and other questions, we pursue a haplotype-based approach to connect diversity and population structure in wild and domesticated barley. We sequence the genomes of 628 genebank accessions and 23 archaeological specimens. Using these data, we infer the spatiotemporal origins of haplotypes and map the contributions of different wild barley populations either during the initial phase of domestication or through later gene flow. Ancient DNA sequences corroborate our genome-wide analysis in present-day samples. Our results indicate that an early domesticated founder population formed in the Fertile Crescent during an extended period of pre-domestication cultivation. A practical implication of our findings is that the high haplotype differentiation between barley populations, which arose possibly without, and most likely on top of, selective forces, complicates the mapping of adaptive loci.
GRN_modeler: An Intuitive Tool for Constructing and Evaluating Gene Regulatory Networks and its Applications to Oscillators and a Light Biosensor
Authors: Holló Gábor , Park Jung Hun , Boni Emanuele , Schaerli Yolanda
Published: December 2024

Modeling and simulating gene regulatory networks (GRNs) is crucial for understanding biological processes, predicting system behavior, guiding the design of synthetic biological systems, and interpreting experimental data. In synthetic biology, GRNs play a pivotal role in enabling the design and control of complex systems for a wide range of applications. However, GRN simulations can be time-consuming and often require specialized expertise. To make this process more accessible, we developed a user-friendly application with a graphical user interface (GUI), allowing users to create simple phenomenological models without requiring prior programming experience. We demonstrate the versatility of our tool through several examples, including the design of novel oscillator families capable of robust oscillation with an even number of nodes. These complement the well-known repressilator family, which only oscillates with odd-numbered nodes. Furthermore, we showcase how GRN modeler allowed us to develop a light-detecting biosensor inEscherichia colithat can track light intensity over several days, leaving a record in the form of ring patterns in bacterial colonies. In summary, our work empowers biologists to model their systems of interest even without programming expertise.
Spatial-DC: a robust deep learning-based method for deconvolution of spatial proteomics
Authors: Li Yuan , Kong Qian , Wu Zihan , Xu Yanfen , Mao Yiheng , Gu Yunjie , Wang Xi , Gao Weina , Tian Ruijun , Yao Jianhua
Published: December 2024

Spatial proteomics studies the spatial distribution of proteins within cells or tissues, providing a new perspective for comprehending cellular processes and disease mechanisms. One important challenge of current spatial proteomics technologies is low resolution, resulting in multiple cells in each spatial proteomics spot. While methods have been proposed to infer the composition of potential cell types in such spots for spatial transcriptomics, the depressed correlation and divergent quantification between transcriptome and proteome limits their capability in spatial proteomics.

To enhance the utility of spatial proteomics data, we propose Spatial-DC (Spatial Digital Cytometry), a deep learning-based framework that infers cell-type composition in each spot and reconstructs spatially and cell-type resolved proteomic profiles. We achieve this by utilizing transfer learning and self-supervised learning with graph convolutional networks (GCN), which enables the incorporation of target spatial proteomics with reference single-cell or single-cell-type proteomics data.

Through extensive simulations of spatial proteomics data, we demonstrate that Spatial-DC outperforms eight state-of-the-art methods in estimating cell-type composition and provides meaningful reconstructions of proteomic profiles for individual cell types. We apply Spatial-DC to different tissues measured using both multiplexed antibody-based and mass spectrometry (MS)-based spatial proteomics technologies. The results showcase Spatial-DC’s superior sensitivity in providing more refined cell-type distribution maps compared to cell-type-specific marker-based distributions and its feasibility in reconstructing spatially and cell-type resolved proteomic profiles from real-world spatial proteomics data. Moreover, we validate Spatial-DC with a newly self-collected pancreatic cancer spatial proteomics data characterized by complex tumor microenvironment (TME) and identify the signaling direction and strength at both spatial and cell-type levels within the TME, suggesting cell-type-specific and spatially-resolved interactions linked to tumor outcomes.

Our results highlight Spatial-DC as a versatile tool for the deconvolution of spatial proteomics data across various tissue slices, providing a reliable foundation for downstream analysis.
The effect of an increasing elephant population on the allometry of trees
Authors: Thel Lucie , Stols Dietre , Orth Sarah , Lagendijk D.D. Georgette , Slotow Rob , Venter Jan A. , Fritz Herve
Published: December 2024

African savannas, which support a diverse range of plant species, from evergreen trees to deciduous shrubs, are regulated by complex interactions between climatic, fire, soil and herbivory processes. African elephants (Loxodonta africana) exert substantial top-down control over vegetation dynamics by utilising large amounts of plant biomass, as well as through various forms of non-consumptive effects. However, how much elephants affect the pattern of proportional growth between different tree components such as roots, stems or branches (known as allometry), remains understudied. Using vegetation data collected in 2000-2001 and 2019 for more than 3500 individual trees inside and outside Madikwe Game Reserve, South Africa, we determined the long-term effects of an increasing elephant population on allometric relationships in 13 tree species. The presence of elephants reduced logged canopy volume, and increasing elephant population in Madikwe reduced logged tree height and logged initial growth rate of the allometric relationship between tree height and tree diameter, without modifying asymptotic change in growth rate. Although not significantly, elephants seemed to increase asymptotic change in growth rate of canopy volume according to tree diameter, suggesting that compensatory mechanisms for the loss of height might happen in the longer-term. Although the species-specific elephant use index increased over the 20 years of the study, no consistent effect on allometric coefficients was detectable. Our study emphasises the necessity of long-term, species-specific studies to improve our understanding of how elephants affect allometric relationships in trees, which will ultimately guide management of savanna systems with increasing elephant numbers.
A High-Throughput Platform for Assessing Single Fly Learning and Memory: IndividualDrosophilaOlfactory Conditioner (iDOC)
Authors: Ortega Antonio , Tedre Erik , Baz El-Sayed , Tsao Chang-Hui , Chen Chien-Chun , Liu Sha
Published: December 2024

Olfactory conditioning inDrosophila melanogasteris a widely used behavioral paradigm for uncovering the neural basis of learning and memory. The traditional T-maze assay, however, relies on group-level assessments and cannot examine individual flies’ learning and memory abilities. To address this limitation, we developed the IndividualDrosophilaOlfactory Conditioner (iDOC), an apparatus for single-fly conditioning and memory assessment. Using iDOC, we demonstrated aversive olfactory learning, short-term memory (STM), anesthesia-resistant memory (ARM), and protein synthesis-dependent long-term memory (LTM) in individual flies, consistent with previous experiments conducted using the T-maze. As an individual memory assessment method, iDOC can be integrated with other behavioral assays at the single animal level, such as sleep monitoring. Notably, we found that spaced training, which induces LTM, also promotes post-learning sleep, while massed training, which induces ARM, did not. iDOC thus provides a powerful platform for investigating learning and memory and its interplay with other behavioral processes at the individual animal level.

Highlights

Developed iDOC for high-throughput, single-fly aversive olfactory training and memory assessment

Demonstrated aversive learning, STM, ARM, and LTM in individual flies using iDOC

Spaced conditioning, and not massed conditioning, promotes sleep
Syn-tasiR-VIGS: Virus-Based Targeted RNAi in Plants By Synthetic Trans Acting Small Interfering RNAs Derived from Minimal Precursors
Authors: Cisneros Adriana E. , Alarcia Ana , Llorens-Gámez Juan José , Puertes Ana , Juárez-Molina María , Primc Anamarija , Carbonell Alberto
Published: December 2024

Synthetic trans-acting small interfering RNAs (syn-tasiRNAs) are 21-nucleotide (nt) small RNAs designed to silence plant transcripts with high specificity. Their use as biotechnological tools for functional genomics and crop improvement is limited by the need to transgenically express longTASprecursors to produce syn-tasiRNAsin vivo. Here, we show that authentic and highly effective syn-tasiRNAs can be produced from minimal, non-TASprecursors consisting of a 22-nt endogenous microRNA target site, an 11-nt spacer and the 21 nt syn-tasiRNA sequence(s). These minimal precursors, when transgenically expressed inArabidopsis thalianaandNicotiana benthamiana, generated highly phased syn-tasiRNAs that silenced one or multiple plant genes with high efficacy. Remarkably, minimal but not full-lengthTASprecursors produced authentic syn-tasiRNAs and induced widespread gene silencing inN. benthamianawhen expressed from an RNA virus, which can be applied by spraying infectious crude extracts onto leaves in a GMO-free manner. This strategy, named syn-tasiRNA-based virus-induced gene silencing (syn-tasiR-VIGS), was further used to vaccinate plants against a pathogenic virus, resulting in complete plant immunization. Our results reveal that syn-tasiRNA precursors can be significantly shortened without compromising silencing efficacy, and that syn-tasiR-VIGS represents a versatile, scalable and non-transgenic platform for precision RNAi and antiviral vaccination in plants.

Graphical abstract
GeneSetCluster 2.0: a comprehensive toolset for summarizing and integrating gene-sets analysis
Authors: Ortega-Legarreta Asier , Maillo Alberto , Mouzo Daniel , López-Pérez Ana Rosa , Kular Lara , Kakhki Majid Pahlevan , Jagodic Maja , Tegner Jesper , Lagani Vincenzo , Ewing Ewoud , Gomez-Cabrero David
Published: December 2024

Background

Gene-Set Analysis (GSA) is commonly used to analyze high-throughput experiments. However, GSA cannot readily disentangle clusters or pathways due to redundancies in upstream knowledge bases, which hinders comprehensive exploration and interpretation of biological findings. To address this challenge, we developed GeneSetCluster, an R package designed to summarize and integrate GSA results. Over time, we and users as well identified limitations in the original version, such as difficulties in managing redundancies across multiple gene-sets, large computational times, and its lack of accessibility for users without programming expertise.

Results

We present GeneSetCluster 2.0, a comprehensive upgrade that delivers methodological, computational, interpretative, and user-experience enhancements. Methodologically, GeneSetCluster 2.0 introduces a novel approach to address duplicated gene-sets and implements a seriation-based clustering algorithm that reorders results, aiding pattern identification. Computationally, the package is optimized for parallel processing, significantly reducing execution time. GeneSetCluster 2.0 enhances cluster annotations by associating clusters with relevant tissues and biological processes to improve biological interpretation, particularly for human and mouse data. To broaden accessibility, we have developed a user-friendly web application enabling non-programmers to use it. This version also ensures seamless integration between the R package, catering to users with programming expertise, and the web application for broader audiences. We evaluated the updates in a single-cell RNA public dataset.

Conclusion

GeneSetCluster 2.0 offers substantial improvements over its predecessor. Furthermore, by bridging the gap between bioinformaticians and clinicians in multidisciplinary teams, GeneSetCluster 2.0 facilitates collaborative research. The R package and web application, along with detailed installation and usage guides, are available on GitHub (https://github.com/TranslationalBioinformaticsUnit/GeneSetCluster2.0), and the web application can be accessed athttps://translationalbio.shinyapps.io/genesetcluster/.
Bacteria-powered living materials enable coral larval settlement
Authors: Levy Natalie , Kundu Samapti , Freckelton Marnie , Dinasquet Julie , Flores Isabel , Galindo-Martínez Claudia T. , Tresguerres Martin , La Garza Vanessa De , Sun Yazhi , Karimi Zahra , Drury Crawford , Jury Christopher P. , Hancock Josh , Chen Shaochen , Hadfield Michael , Wangpraseurt Daniel
Published: December 2024

The global decline of coral reefs calls for new strategies to rapidly restock coral populations and maintain ecosystem functions and services. Low recruitment success on degraded reefs hampers coral sexual propagation and contributes to limited genetic diversity and reef resilience. Here, we introduce a living bacteria-powered reef ink (Brink) for assisted coral recruitment. Brink can be rapidly applied to restoration substrates via photopolymerization, and it has been formulated to cultivate two settlement-inducing bacterial strains (Cellulophaga lyticaandThalassotalea euphylliae). Settlement assays performed with broadcast spawning (Montipora capitata) and brooding (Pocillopora acuta) Indo-Pacific corals showed that Brink-coated substrates increased settlement >5-fold compared to uncoated control substrates. Brink can be applied as a coating or 3D bioprinted, leading to various potential applications for integration with reef engineering. Our approach underscores the potential of using functional living materials for augmented ecosystem engineering and reef rehabilitation.

Synopsis

This study introduces a functional and sustainable bacteria-powered living material that enhances coral settlement, promoting coral reef rehabilitation and ecosystem resilience.
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

The 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.

Highlights

Reduced dendrite complexity in Nedd8-deficient neurons

Increased synaptic vesicle fusion probability in Nedd8-deficient neurons

Altered synaptic vesicle cycling in Nedd8-deficient neurons

Neddylation controls the maturation of glutamatergic neurons

Graphical Abstract

Research 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

Cellular 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

Alternative 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

Mutations 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

Effective 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

Objective

This 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.

Methods

A 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.

Results

Among 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).

Conclusion

The 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.

HIGHLIGHTS

fPSC 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

Dyslexia 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

We 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

Advancement 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

B 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 Highlights

Genes 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

Background

Understanding 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.

Results

We 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.

Conclusions

These 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.