bluuebunny/crossref_metadata_2025 huggingface dataset:
ABCA1 activity is associated with reduced Alzheimer’s Disease risk in APOE ε4 non-carriers
Authors: Peña-Tauber Andrés , Hernández Arriaza Ricardo , Le Guen Yann , Park Junyoung , Greicius Michael D.
Published: January 2025

Background and Objectives

ABCA1has been associated with Alzheimer’s Disease (AD) via large-scale genetic studies, but the mechanisms by which it impacts disease risk are unknown. ABCA1 catalyzes apolipoprotein lipidation in the central nervous system and is known to interact molecularly with ApoE. We explored whether variants altering ABCA1 activity depend on the presence of differentAPOEisoforms to modify AD risk.

Methods

We meta-analyzed European- and African-ancestry whole-genome and whole-exome sequencing datasets from the Alzheimer’s Disease Sequencing Project and UK Biobank. We used Cox hazards regression to assess the impact of rare (MAF < 1%) predicted damaging (loss-of-function, or missense with a REVEL score > 0.75) variants inABCA1on AD risk inAPOEsubgroups and performedAPOEinteraction analyses considering allAPOEgenotypes. We then leveraged plasma HDL levels, a phenotype known to be impacted byABCA1variants, as a measure of ABCA1 activity and examined whether cumulative effects on HDL levels byABCA1missense variants predict AD risk.

Results

Rare damaging (LOF + REVEL ≥ 75) variants onABCA1increased AD risk inAPOEε2/ε3 and ε3/ε3 but not ε3/ε4 or ε4/ε4 cohorts. Interaction analyses indicated that damagingABCA1variants increase AD risk considering allAPOEisoforms (hazard ratio [HR] = 1.48; 95% confidence interval [CI] = 1.22, 1.79; p = 5.80E-05) and interact with bothAPOEε2 (HR = 1.99; 95% CI = 1.30, 3.05; p = 0.002) and ε4 (HR = 0.76; 95% CI = 0.61, 0.95; p = 0.014). Predicted ABCA1 activity based on a weighted sum of HDL-associatedABCA1missense variants was protective against AD (HR = 0.10; 95% CI = 0.04, 0.27; p = 2.83E-06) and interacted withAPOEε4 to counteract this protective effect (HR = 11.66; 95% CI = 3.81, 35.66; p = 1.67E-05), while there was no significant interaction with ε2.

Conclusions

ABCA1 activity is protective against AD risk inAPOEε4 non-carriers. Distinct interactions betweenABCA1and the mainAPOEisoforms suggest the proteins may work together to affect AD risk and motivates the development and testing ofABCA1therapeutics in specificAPOEsubpopulations.
The evolution of robustness and fragility during long-term bacterial adaptation
Authors: Chihoub Doha , Pintard Coralie , Lenski Richard E. , Tenaillon Olivier , Couce Alejandro
Published: January 2025

Most mutations affecting fitness are harmful, and their inevitable occurrence reduces mean population fitness. Theory predicts that well-adapted populations may evolve mechanisms to minimize this deleterious load. Direct selection to increase mutational robustness can be achieved in the laboratory. However, its spontaneous evolution during general adaptation remains uncertain, with mixed evidence across model systems. Here, we studied the effects of highly pleiotropic point mutations inEscherichia coliover a 15,000-generation adaptive trajectory. The fitness effects of both beneficial and deleterious mutations were attenuated with increased adaptation over time. In contrast, pleiotropic effects in new environments became more severe and widespread with greater adaptation. These results show that trade-offs between robustness and fragility can rapidly evolve in regulatory networks, regardless of whether driven by adaptive or non-adaptive processes. More broadly, these results show that adaptation can generate a hidden potential for phenotypic diversity, unpredictably shaping evolutionary prospects in new environments.
Emergence of high-connectivity states before epileptic seizures: Multi-patient validation, physiological correlates, and network modeling
Authors: Medina Nicolas , Vila-Vidal Manel , Tost Ana , Khawaja Mariam , Carreño Mar , Roldán Pedro , Rumià Jordi , Centeno María , Conde Estefanía , Donaire Antonio , Tauste Campo Adrià
Published: January 2025

Epilepsy affects approximately 50 million people worldwide, making it one of the most prevalent neurological disorders. Predicting seizures through reliable pre-seizure biomarkers could greatly enhance neuromodulation therapies for drug-resistant patients. Recent research using stereo-electroencephalography (sEEG) has revealed specific changes in network dynamics during pre-seizure periods. In particular, our previous work demonstrated that day-time dependent alterations preceding seizures are largely driven by an increased occurrence of recurrent, short-lasting (0.6s) high-connectivity network configurations, termed High-Connectivity States (HCS). In this study, we replicated these findings using long-term sEEG recordings from a publicly available database and another patient undergoing presurgical evaluation with depth electrodes. For the latter patient, we leveraged all available monitoring information to validate the robustness of HCS alterations across different recording configurations. Additionally, we compared HCS dynamics with other sEEG measurements (e.g., power activity) and electrocardiogram-derived variables (e.g., heart rate) and developed a low-dimensional statistical network model to capture key network features of the pre-seizure period. Our results confirmed the specific emergence of HCS hours before seizure onset, consistent across monopolar, bipolar, and common average referential recordings. Notably, preictal HCS probability alterations were distributed across the frequency power spectrum and exhibited stronger correlations with heart rate fluctuations than with grand-average functional connectivity. The statistical model indicated that preictal HCS probability changes arise from shifts in network topology rather than changes in mean connectivity, highlighting the role of complex interactions between epileptogenic and non-epileptogenic brain regions. These findings suggest that integrating HCS probability with both invasive and non-invasive monitoring variables could establish it as a promising biomarker for an early detection of upcoming epileptic seizures.
Mutation hot spots for clinical pathogenicity across the SLC6 transporter family
Authors: Huang Jiahui , Digles Daniela , Ecker Gerhard F.
Published: January 2025

Genetic mutations of the Solute Carrier 6 (SLC6) family can lead to a diversity of clinal syndromes, such as creatine deficiency. Studying the impact of genetic mutations at the SLC6 family level is valuable not only for their medical significance but also for their conserved sequence and structural features. Within this work, we aim to link the disease-related mutations to their clinical significance from protein-protein interactions (PPIs) perspective, addressing how particular mutations may affect these critical interaction hotspots.

In this study, we integrated both curated mutation data from previous work and predictive output from AlphaMissense to examine the entire SLC6 family. The mutations were mapped both onto the sequences and structures of SLC6 transporters. Thereby, a clustering of pathogenic mutations appeared on the surface regions that are likely involved in PPIs. After modeling complexes of SLC6s with potential shared interactors, we assessed these models overall and interface quality. By analyzing the complex interfaces together with the pathogenic mutations, we identified specific hotspots in the interfaces enriched with pathogenic mutations. In-depth examinations of selected PPIs offered insights into how particular mutations may affect these critical interaction hotspots.

The hotspots were identified on the ECL3 and ECL4. For instance, Thr394Lys in SLC6A8 was found in the model interfaces, supported by experimental data showing the significant enrichment of the mutated proteins in the ER. Understanding these mutation hotspots can shed light on the broader structure-function relationships of SLC6 transporters and encourage therapeutic interventions targeting protein-protein interactions affected by pathogenic mutations.
LGBTQ+ realities in the biological sciences
Authors: Cooper Katelyn M. , Busch Carly A. , Accorsi Alice , Applewhite Derek A. , Bhanderi Parth B. , da Rocha-Azevedo Bruno , Roy Abhijit Deb , Campanale Joseph P. , Chang Fred , Chipuk Jerry E. , Ligon Lee A. , Luxton G.W. Gant , Graham Austin J. , Hochman-Mendez Camila , Ozugergin Imge , Park Zachory M. , Thomas Claire M. , Valm Alex M. , Zhu Hongxian , Alvania Rebecca S.
Published: January 2025

While scientific environments have been described as unwelcoming to the LGBTQ+ community, and fields like physics have systematically documented these challenges, the climate in biology workplaces has not been assessed. We conducted the largest survey to date of LGBTQ+ experiences in biology, including 1419 biologists across five professional societies, with 486 identifying as LGBTQ+. Trans and gender non-conforming (TGNC) biologists reported lower belonging and morale within the workplace, professional societies, and the biology community compared to cis, straight biologists. They also reported being less comfortable with the climate of various professional biology environments. While LGBTQ+ biologists report that their workplaces are moderately inclusive, over 20% of all LGBTQ+ biologists and nearly 40% of TGNC biologists experience exclusionary behavior at work. This landmark survey provides the first comprehensive analysis of the LGBTQ+ climate in biology, revealing specific challenges faced by TGNC scientists and identifying interventions to enhance inclusivity for scientists.

Teaser

Climate study for LGBTQ+ biologists highlights exclusion of trans and gender nonconforming scientists.
Isolation of a novel plant growth-promotingDyellasp. from a Danish natural soil
Authors: Dethier Laura , Jespersen J. Rasmus P. , Lloyd Jemma , Pupi Elena , Zhou Wanru , Liu Fang , Bai Yang , Halkier Barbara Ann , Xu Deyang
Published: January 2025

Environmental soils are natural reservoirs of unexplored microbes, including potentially beneficial microbes to improve plant performance. Here, we isolated 75 bacterial strains from surface-sterilized roots ofArabidopsis thaliana(Arabidopsis) grown in a natural soil derived from an alder swamp. Culture-dependent isolation of individual strains from the roots followed by monoassociation-based screening identified seven bacteria that promoted Arabidopsis seedling weight. Of those, we identified a new species from theDyellagenus which increased biomass of tomato and Arabidopsis seedlings in agar as well as the shoot biomass of Arabidopsis grown in both the alder swamp soil and potting soil.Dyella sp. A4 specifically promoted the elongation of lateral roots without affecting lateral root number and primary root elongation. The newDyella sp. A4 expands the toolbox of biostimulants for plant growth promotion via modulating root architecture.
Met-ID: An Open-Source Software for Comprehensive Annotation of Multiple On-Tissue Chemical Modifications in MALDI-MSI
Authors: Bjärterot Patrik , Nilsson Anna , Shariatgorji Reza , Vallianatou Theodosia , Kaya Ibrahim , Svenningsson Per , Käll Lukas , Andrén Per E.
Published: January 2025

Here, we introduce Met-ID, a graphical interface software designed to efficiently identify metabolites from MALDI-MSI datasets. Met-ID enables annotation ofm/zfeatures from any type of MALDI-MSI experiment, involving either derivatizing or conventional matrices. It utilizes structural information for derivatizing matrices to generate a subset of targets that contain only functional groups specific to the derivatization agent. The software is able to identify multiple derivatization sites on the same molecule, facilitating identification of the derivatized compound. This ability is exemplified by FMP-10, a reactive matrix that assists the covalent charge-tagging of molecules containing phenolic hydroxyl and/or primary or secondary amine groups. Met-ID also permits users to recalibrate data with knownm/zratios, boosting confidence in mass match results. Furthermore, Met-ID includes a database featuring MS2 spectra of numerous chemical standards, consisting of neurotransmitters and metabolites derivatized with FMP-10, alongside peaks for FMP-10 itself, all accessible directly through the software. The MS2 spectral database supports user-uploaded spectra and enables comparison of these spectra with user-provided tissue MS2 spectra for similarity assessment. Although initially installed with basic data, Met-ID is designed to be customizable, encouraging users to tailor the software to their specific needs. While several MSI-oriented software solutions exist, Met-ID stands out as a pioneer in seamlessly combining both MS1 and MS2 functionalities. Developed in alignment with the FAIR Guiding Principles for scientific software, Met-ID is freely available as an open-source tool on GitHub, ensuring wide accessibility and collaboration.
Bcl-2 Oligomerizes Bax on the Mitochondrial Membrane Surface Preventing the Initial Stages of Apoptosis
Authors: Ayscough Sophie E. , Clifton Luke A. , Ådén Jörgen , Köhler Sebastian , Paracini Nicolò , Doutch James , Bragginton Éilís C , Leung Anna. E. , Bogojevic Oliver , Poon Jia-Fei , Nagy Tamás Milán , Wacklin-Knecht Hanna P. , Gröbner Gerhard
Published: January 2025

The Bcl-2 family of proteins control mitochondrial outer membrane (MOM) pore formation, crucial to cellular clearanceviaapoptosis. However, the molecular principles by which opposing family members inhibit, mediate or promote MOM perforation remain elusive. Here, we demonstrate that cell-protecting Bcl-2 directly sequesters cell-killing Bax into a protein-protein complex at the membrane interface preventing Bax forming apoptotic pores. Neutron reflectometry showed Bax association with Bcl-2 occurs through the formation of Bax protein oligomers on the membrane surface. Bax binding to the membrane surface was proportional to the membrane-embedded Bcl-2 suggestive of protein-protein complex formation through both Bcl-2/Bax and Bax/Bax interactions. Bcl-2/Bax sequestration to prevent perforation was observed in membrane models with and without pro-apoptotic cardiolipin present. Our findings shed fundamental new light on the communication of Bcl-2 with its cell-killing relatives at the mitochondriás membraneous exterior to prevent cells from undergoing apoptosis.

Teaser

Membrane-embedded Bcl-2 sequesters Bax, to prevent the perforation of mitochondrial membranes by Bax which would initiate apoptosis.
Impact of natural transformation on the acquisition of novel genes in bacteria
Authors: Mazzamurro Fanny , Touchon Marie , Charpentier Xavier , Rocha Eduardo P. C.
Published: January 2025

Natural transformation is the only process of gene exchange under the exclusive control of the recipient bacteria. It has often been considered as a source of novel genes but quantitative assessments of this claim are lacking. To investigate the potential role of natural transformation in gene acquisition, we analysed a large collection of genomes of Acinetobacter baumannii (Ab) and Legionella pneumophila (Lp) for which transformation rates were experimentally determined. Natural transformation rates are weakly correlated with genome size. But they are negatively associated with gene flow in both species. This might result from a negative balance between transformation's ability to cure the chromosome from mobile genetic elements (MGEs), resulting in gene loss, and its facilitation of gene acquisition. By focusing on the latter, we found that transformation was significantly associated with small gene acquisition events while MGEs-driven gene acquisition tend to be associated with larger ones. Events of gene gain by transformation were spread more evenly in the chromosome than MGEs encoding the ability to integrate autonomously. We estimated the contribution of natural transformation to gene gains by comparing recombination-driven gene acquisition rates between transformable and non-transformable strains. Natural transformation may have caused the acquisition of up to 6.4% (Ab) and 1.1% (Lp) of the novel genes. This low contribution of natural transformation to the acquisition of novel genes implies that most novel genes must have been acquired by other means. Interestingly, the ones potentially acquired by transformation include almost 15% of the recently acquired antibiotic resistance genes in A. baumannii. Hence, natural transformation may drive the acquisition of relatively few novel genes but these may have high fitness impact.
Survival Reinforced Transfer Learning for Multicentric Proteomic Subtyping and Biomarker Discovery
Authors: Xie Linhai , Jiang Pei , Chang Cheng
Published: January 2025

Omics-based molecular subtyping in large-scale and multicentric cohort studies is a prerequisite for proteomics-driven precision medicine (PDPM). However, keeping the subtypes with robust molecular features and significant associations with prognosis among different cohorts is challenging due to the biological heterogeneity and technical inconsistency. Herein, we propose a subtyping algorithm, named Survival Reinforced Patient Stratification (SRPS), to adapt the known subtypes from the discovery cohort to another by simultaneously preserving the distinct prognosis and molecular characteristics of each subtype. SRPS has been benchmarked on simulated and real-world datasets, where it shows a 12% increase in classification accuracy and possesses the best prognostic discriminations. Moreover, based on the calculated subtype significance score, an ‘unpopular’ protein, Peptidylprolyl Isomerase C (PPIC), was identified as the top-1 remarkable protein for subtyping the hepatocellular carcinoma (HCC) patients with the worst prognosis. Eventually, PPIC was experimentally proved to be a pro-cancer protein in HCC, confirming our work as a practice of interpretable machine learning guided biological discovery in PDPM research.
Alpha-Synuclein co-pathology in Alzheimer’s Disease drives tau accumulation
Authors: Struebing Felix L. , De Vecchi Teodoro , Widmann Jeannine , Song Xiaoxuan , Fierli Federico , Ruf Viktoria , Tang Qilin , Arzberger Thomas , Roeber Sigrun , Koeglsperger Thomas , Windl Otto , Haass Christian , Winkelmann Juliane , Herms Jochen
Published: January 2025

The molecular basis for accelerated cognitive decline seen in Alzheimer’s Disease (AD) cases presenting with cortical alpha-Synuclein (α-Syn) co-pathology is not well understood. We show that such co-pathology brains express higher levels of microtubule-associated protein tau and that increasing α-Syn expression is sufficient to drive tau accumulation. Our results reveal a hitherto unknown link between the pathogenesis of AD and Parkinson’s Disease whereby tau and α-Syn synergistically drive dementia-related pathology.
Cryptocercusgenomes expand knowledge of adaptations to xylophagy and termite sociality
Authors: Jones Alun R. C. , Mikhailova Alina A. , Aumont Cédric , Berger Juliette , Bornberg-Bauer Erich , Liu Cong , He Shulin , Wang Zongqing , Winkler Sylke , Legendre Frédéric , McMahon Dino P. , Harrison Mark C.
Published: January 2025

Subsociality and wood-eating or xylophagy are understood as key drivers in the evolution of eusociality in Blattodea (cockroaches and termites), two features observed in the cockroach genusCryptocercus, the sister group of all termites. We present and analyse two new high-quality genomes from this genus,C. punctulatusfrom North America andC. meridianusfrom Southeast Asia, to explore the evolutionary transitions to xylophagy and subsociality within Blattodea. Our analyses reveal evidence of relaxed selection in bothCryptocercusand termites, indicating that a reduction in effective population size may have occurred in their subsocial ancestors. These findings challenge the expected positive correlation between dN/dS ratios and social complexity, asCryptocercusexhibits elevated dN/dS values that may exceed those of eusocial termites. Additionally, we identify positive selection on mitochondrial ribosomal proteins and components of the NADH dehydrogenase complex, suggesting significant evolutionary changes in energy production. Future studies incorporating additional genomic data from diverse blattodean species are essential to elucidate the molecular mechanisms driving transitions to xylophagy and eusociality.
A novel mouse model of voluntary stretching and its application in breast cancer research
Authors: He Yi , Berrueta Lisbeth , Wang Yan , Badger Gary J. , Langevin Helene M.
Published: January 2025

Background

Stretching exercises such as yoga are recommended for cancer survivors to manage symptoms and promote wellbeing in clinical settings. Although other types of exercise (e.g. running) can reduce the growth of tumors in animal models, the role of stretching on tumor growth remains unclear, and the lack of a preclinical self-stretching model has impeded mechanistic studies on health benefits of stretching. We sought to develop a voluntary stretching animal model to address this research gap and apply it to breast cancer research.

Methods

Using food, water, and enrichment in the home cage as motivators for stretching, a two-week 24/7 behavior monitoring was conducted in a video-based customizable home-cage behavior tracking system, Noldus PhenoTyper, to promote self-stretching in FVB mice. Subsequently, this model was utilized in a comparative study of voluntary stretching and voluntary running on tumor growth and plasma protein profiles in the MET-1 orthotopic mammary tumor FVB mouse model.

Results

The new voluntary stretching model effectively elicited mouse self-stretching in the custom cage setting in the long-term observation and significantly inhibited tumor growth as effectively as voluntary wheel running. Moreover, plasma proteomic analysis demonstrated that voluntary stretch versus voluntary running distinctly impacted systemic protein profiles, possibly linking to different cellular and molecular mechanisms underlying anti-cancer effects and, potentially, exercise-induced benefits in other health conditions.

Conclusion

Our work provides the first preclinical voluntary stretching model, which may be well suited to breast cancer research and a valuable research tool to facilitate investigations of stretching health benefits across various research fields.
Single Cell Spatial Transcriptomics Reveals Immunotherapy-Driven Bone Marrow Niche Remodeling in AML
Authors: Gui Gege , Bingham Molly A. , Herzog Julius R. , Wong-Rolle Abigail , Dillon Laura W. , Goswami Meghali , Martin Eddie , Reeves Jason , Kim Sean , Bahrami Arya , Degenhardt Hermann , Zaki George , Divakar Prajan , Schrom Edward C , Calvo Katherine , Hourigan Christopher S. , Hansen Kasper , Zhao Chen
Published: January 2025

Given the successful graft-versus-leukemia cell treatment effect observed with allogeneic hematopoietic stem cell transplant for patients with refractory or relapsed acute myeloid leukemia, immunotherapies have also been investigated in the nontransplant setting. Here, we use a multi-omic approach to investigate spatiotemporal interactions in the bone marrow niche between leukemia cells and immune cells in patients with refractory or relapsed acute myeloid leukemia treated with a combination of the immune checkpoint inhibitor pembrolizumab and hypomethylating agent decitabine. We derived precise segmentation data by extensively training nuclear and membrane cell segmentation models, which enabled accurate transcript assignment and deep learning-feature-based image analysis. To overcome read-depth limitations, we integrated the single-cell RNA sequencing data with single-cell-resolution spatial transcriptomic data from the same sample. Quantifying cell-cell distances between cell edges rather than cell centroids allowed us to conduct a more accurate downstream analysis of the tumor microenvironment, revealing that multiple cell types of interest had global enrichment or local enrichment proximal to leukemia cells after pembrolizumab treatment, which could be associated with their clinical responses. Furthermore, ligand-receptor analysis indicated a potential increase inTWEAKsignaling between leukemia cells and immune cells after pembrolizumab treatment.

Highlights

Spatial transcriptomic analysis of R-AML bone marrow niches provides detailed information about intercellular interactions in the tumor microenvironment.

Immunotherapy shifts the cell composition of the leukemia neighborhood.

Graphical abstract
SpaIM: Single-cell Spatial Transcriptomics Imputation via Style Transfer
Authors: Li Bo , Tang Ziyang , Budhkar Aishwarya , Liu Xiang , Zhang Tonglin , Yang Baijian , Su Jing , Song Qianqian
Published: January 2025

Spatial transcriptomics (ST) technologies have revolutionized our understanding of cellular ecosystems. However, these technologies face challenges such as sparse gene signals and limited gene detection capacities, which hinder their ability to fully capture comprehensive spatial gene expression profiles. To address these limitations, we propose leveraging single-cell RNA sequencing (scRNA-seq), which provides comprehensive gene expression data but lacks spatial context, to enrich ST profiles. Herein, we introduce SpaIM, an innovative style transfer learning model that utilizes scRNA-seq information to predict unmeasured gene expressions in ST data, thereby improving gene coverage and expressions. SpaIM segregates scRNA-seq and ST data into data-agnostic contents and data-specific styles, with the contents capture the commonalities between the two data types, while the styles highlight their unique differences. By integrating the strengths of scRNA-seq and ST, SpaIM overcomes data sparsity and limited gene coverage issues, making significant advancements over 12 existing methods. This improvement is demonstrated across 53 diverse ST datasets, spanning sequencing- and imaging-based spatial technologies in various tissue types. Additionally, SpaIM enhances downstream analyses, including the detection of ligand-receptor interactions, spatial domain characterization, and identification of differentially expressed genes. Released as open-source software, SpaIM increases accessibility for spatial transcriptomics analysis. In summary, SpaIM represents a pioneering approach to enrich spatial transcriptomics using scRNA-seq data, enabling precise gene expression imputation and advancing the field of spatial transcriptomics research.
scGraphETM: Graph-Based Deep Learning Approach for Unraveling Cell Type-Specific Gene Regulatory Networks from Single-Cell Multi-Omics Data
Authors: Dong Wenqi , Zhou Manqi , Han Boyu , Wang Fei , Li Yue
Published: January 2025

In the forefront of single-cell multi-omics research, the challenge of elucidating intricate gene regulatory networks (GRNs) at a cellular level is paramount. This study introduces the Single Cell Graph Network Embedded Topic Model (scGraphETM), a novel computational approach aimed at unraveling the complexities of cell-specific GRNs from multiomics single-cell sequencing data. Central to our investigation is the integration of single-cell RNA sequencing and single-cell ATAC sequencing data, leveraging the strengths of both to uncover the underpinnings of cellular regulation. The scGraphETM model innovatively combines a variational autoencoder framework with a graph neural network. By conceptualizing transcription factors (TFs), genes, and regulatory elements (RE) as nodes, and their regulatory interactions as edges, the model adeptly captures the dynamic regulatory interplay within cells. It uniquely incorporates both universal and cell-specific features, enabling the model to generalize across cell populations while also identifying unique regulatory dynamics within individual cells. Our results reveal that scGraphETM surpasses existing methodologies in accurately modeling cell-type clustering, cross-modality imputation and cell-type specific TF-RE relationships.
Durable reconstitution of sinonasal epithelium by transplant of CFTR gene corrected airway stem cells
Authors: Bravo Dawn T , Vaidyanathan Sriram , Baker Jeanette , Sinha Vrishti , Tsai Esmond , Roozdar Pooya , Kong William W , Atkinson Patrick J , Patel Zara M , Hwang Peter H , Rao Vidya K , Negrin Robert S , Wine Jeffrey J , Milla Carlos , Sellers Zachary M , Desai Tushar J , Porteus Matthew , Nayak Jayakar V
Published: January 2025

Modulator agents that restore cystic fibrosis transmembrane conductance regulator (CFTR) function have revolutionized outcomes in cystic fibrosis, an incurable multisystem disease. Barriers exist to modulator use, making local CFTR gene and cell therapies attractive, especially in the respiratory tract. We used CRISPR to gene-correct CFTR in upper airway basal stem cells (UABCs) and show durable local engraftment into recipient murine respiratory epithelium. Interestingly, the human cells recapitulate the in vivo organization and differentiation of human sinus epithelium, with little expansion or contraction of the engrafted population over time, while retaining expression of the CFTR transgene. Our results indicate that human airway stem cell transplantation with locoregional restoration of CFTR function is a feasible approach for treating CF and potentially other diseases of the respiratory tract.
ECD functions as a novel RNA-binding protein to regulate mRNA splicing
Authors: Raza Mohsin , Rajan Asher Rajkumar , Kalluchi Achyuth , Saleem Irfana , Kennedy Benjamin B. , Bhakat Kishor K. , Band Hamid , Rowley M. Jordan , Band Vimla
Published: January 2025

The human ecdysoneless protein (ECD) plays an essential role in the regulation of cell cycle and cell survival. ECD has been implicated in RNA splicing through its association with the protein components of splicing complex. Here, using electrophoretic mobility shift assay and mutational analysis, we demonstrate that ECD directly binds to RNA through its N-terminal region, specifically using amino acids 135-148. Using enhanced CLIP-seq analyses in human cells, we identified a large repertoire of mRNAs bound to ECD. RNA-seq analyses revealed that ECD depletion in cells leads to widespread RNA splicing aberrations associated with alterations in gene expression. Significantly, we demonstrate that ECD mediates mRNA splicing by directly binding to RNA sequences located near splicing sites. Mechanistically, we demonstrate that ECD directly binds to U5 small nuclear RNA (snRNA), and this interaction is critical for maintaining the expression of key protein components of U5 small nuclear protein (snRNP) complex. Notably, RNA binding defective mutant of ECD fails to rescue downregulated levels of U5 snRNP components or cell proliferation block induced by ECD knockout. Collectively, we provide compelling evidence that ECD regulates RNA splicing by directly associating with RNAs, and the RNA binding activity of ECD is essential for its function.
Performance of an Electroencephalography-Measuring Headband or Actigraphy Compared with Polysomnography in Older Adults with Sleep Disturbances
Authors: Miner Brienne , Pan Yulu , Cho Gawon , Talarczyk Jarett , Chen Anne , Burzynski Chase , Polisetty Lakshmi , Doyle Margaret , Iannone Lynne , Mejnartowicz Slawomir , Breier Richard A. , Gill Thomas M. , Yaggi Henry K. , Knauert Melissa
Published: January 2025

Study Objectives

In older adults, self-reported sleep measures may be inaccurate, but polysomnography (PSG) is burdensome. We assessed the performance of an electroencephalography-measuring headband (HB) or actigraphy (ACT) compared with PSG in older adults with sleep disturbances.

Methods

Sixty-three adults aged ≥60 years who reported symptoms of insomnia and/or daytime sleepiness ≥once/week completed a week-long, home-based protocol during which they wore the HB for seven nights, an actigraph for seven days and nights, and completed a one-night level II unattended PSG. For the current analysis, we compared total sleep time (TST) and wake after sleep onset (WASO) from all three devices on the PSG night. We calculated absolute differences and intraclass correlation coefficients (ICCs) for TST and WASO between HB and ACT, respectively, vs. PSG. We also evaluated the performance of the HB among subgroups of the poorest sleepers according to the presence of sleep apnea, insomnia, poor sleep quality, and periodic limb movements of sleep. Feasibility of the HB was assessed by measures of adherence (i.e., ability to use the HB over seven nights) and usability (i.e., ratings of items from the WEarable Acceptability Range [WEAR] scale).

Results

The average age was 72.8 [standard deviation 6.6] years, 63.5% were female, and 63.5% identified as non-Hispanic White. On PSG, averages for TST and WASO were 370.1 [93] and 88.9 [63] minutes, respectively. For the HB vs. PSG, mean differences and ICCs were -11.9 minutes and 0.83 [0.74, 0.89] for TST; and -15.5 minutes and 0.65 [0.48, 0.77] for WASO. For ACT vs. PSG, mean differences for TST and WASO were larger, and ICCs showed lower levels of agreement. The HB performed well among the poorest sleepers, with ICCs >0.65 for TST and WASO. On average, participants wore the HB for 6.5 [0.8] nights, and usability was rated highly.

Conclusions

The HB demonstrated good agreement with PSG, outperforming ACT, including among the poorest sleepers. Devices like the HB might provide feasible measures of sleep that are more accurate than ACT and enhance the management of sleep health in older adults with sleep disturbances. Future research should focus on further validation of these devices in habitual sleep environments.
Reduced systemic autophagy by simultaneous loss of ATG4B, ATG4C and ATG4D leads to accelerated aging in mice
Authors: Martínez-García Gemma G. , Suárez María F. , Rodríguez-Santamaria Mª Del Mar , Roiz-Valle David , Bárcena Clea , Corrochano-Ruiz Andrés , Tamargo-Gómez Isaac , Mayoral Pablo , Astudillo Aurora , Sveen Christina , Engedal Nikolai , López-Otín Carlos , Fernández Álvaro F. , Mariño Guillermo
Published: January 2025

Autophagy is a housekeeping catabolic process crucial for maintaining cell, tissue and organism functions. Through the years, the study of animal models with tissue-specific inactivation of autophagy essential genes has allowed us to understand its protective roles in the context of multiple human diseases, including cancer and neurodegeneration. However, due to the essential nature of autophagy, the effects of its systemic inhibition in mammals have not been explored in detail. Here, we report the generation of ATG4A-only mice, simultaneously deficient for three of the four mammalian ATG4 proteases (ATG4B, ATG4C and ATG4D). Through extensive characterization of ATG4A-only cells, which show a severe (albeit not complete) deficiency in autophagic activity, we define the specific roles of ATG4A protease towards ATG8 proteins (its physiological substrates), shedding some light into the evolutionarily-acquired complexity of mammalian ATG4-ATG8 system. Moreover, we show that the profound whole-body autophagy deficiency of ATG4A-only mice not only impacts the function of multiple tissues, but also leads to the development of an accelerated aging phenotype, characterized by the accumulation of genetic damage, systemic senescence, and premature death. Thus, through the analysis of ATG4A-only mice and other murine models deficient for ATG4 proteases, we not only provide new insights on how autophagy maintains cell, tissue, and organismal homeostasis, but also show for the first time that the degree of autophagic competency ultimately emerges as a critical determinant of organismal longevity.
Aberrant Modular Dynamics of Functional Networks in Schizophrenia and Their Relationship with Neurotransmitter and Gene Expression Profiles
Authors: Zhen Yi , Yang Yaqian , Zheng Yi , Zheng Zhiming , Zheng Hongwei , Tang Shaoting
Published: January 2025

Introduction: Numerous studies have emphasized the time-varying modular architecture of functional brain networks and its relevance to cognitive functions in healthy participants. However, how brain modular dynamics change in schizophrenia and how these alterations relate to neurotransmitter and transcriptomic signatures have not been well elucidated. Methods: We harmonized resting-state fMRI data from a multi-site sample including 223 patients and 279 healthy controls and applied the multilayer network method to estimate the regional module switching rate (flexibility) of functional brain connectomes. We examined aberrant flexibility in patients relative to controls and explored its relations to neurotransmitter systems and postmortem gene expression. Results: Compared with controls, patients with schizophrenia had significantly higher flexibility in the somatomotor and right visual regions, and lower flexibility in the left parahippocampal gyrus, right supramarginal gyrus, right frontal-operculum-insula, bilateral precuneus posterior cingulate cortex, and bilateral inferior parietal gyrus. These alterations were associated with multiple neurotransmitter systems and weighted gene transcriptomic profiles. The most relevant genes were preferentially enriched for biological processes of transmembrane transport and brain development, specific cell types, and previously identified schizophrenia-related genes. Conclusions: This study reveals aberrant modular dynamics in schizophrenia and its relations to neurotransmitter systems and schizophrenia-related transcriptomic profiles, providing insights into the understanding of the pathophysiology underlying schizophrenia.
Stable lentiviral-mediated expression of Cytochrome P450 2D6 in HepaRG cells: New means forin vitroassessment of xenobiotic biotransformation and cytotoxicity
Authors: Coppens-Exandier Hugo , Mackanga Franz , Darde Thomas , Bonhomme Corentin , Ribault Catherine , Gicquel Thomas , Pelletier Romain , Roshchina Flyuza , Schaefer Estelle , Chesné Christophe , Jamin Agnès , Corlu Anne , Loyer Pascal
Published: January 2025

Primary cultures of Human Hepatocytes (PHH) are the gold standard to investigate drug-hepatotoxicityin vitro, however, large-scale studies using these primary liver cells are not possible because of the shortage in liver biopsies. HepaRG model is often considered as the closest surrogate to PHH for toxicity studiesin vitro. However, differentiated HepaRG cells express very low levels of the cytochrome P450 2D6 (CYP2D6) protein, which is essential for the biotransformation of nearly 25% of drugs on the market. To overcome this limitation, infection of progenitor HepaRG cells were performed using lentiviral particles containing a transgene encoding a single mRNA translated into a polypeptide undergoing proteolytic cleavage via the T2A peptide to produce both CYP2D6 and GFP. Differentiated HepaRG cells transduced with lentivirus stably expressed GFP and catalytically active human CYP2D6 enzyme at levels close to those found in high PHH metabolizers. As expected, CYP2D6 protein was found mostly located in the endoplasmic reticulum. Using the CYP2D6 transgenic HepaRG cells, we showed that tramadol was metabolized in both, N- and O-desmethyl tramadol as observed in human serum in contrast with the production of N-desmethyl tramadol only in parental HepaRG cells via the CYP3A4 catalytic activity. Similarly, after perhexiline (PHX) treatments, higher IC50were found in CYP2D6 expressing HepaRG cells associated to lower mitochondrial damages compared to those found in parental cells for the same PHX concentrations. Gene profiling between parental and transgenic cells demonstrated that the CYP2D6 expressing HepaRG cells had kept their ability to proliferate and differentiate with low impact on the expression of the hepatocyte specific functions. However, we identified a limited set of genes such as NXF3 and TRIM63, which were up-regulated by the mRNA encoded by the lentiviral transgene. Together, these data confirmed that the CYP2D6 transgenic HepaRG cells represent a suitable optimized transgenic model of HepaRG cells to evaluate biotransformation and toxicity of specific compounds metabolized by CYP2D6.
NCBP2-AS2 is a mitochondrial microprotein, regulates energy metabolism and neurogenesis, and is downregulated in Alzheimer’s disease
Authors: Popova Stanislava , Bhattarai Prabesh , Yilmaz Elanur , Lascu Daniela , Kuo Juo-Han , Erdem Gizem , Coban Basak , Michling Jitka , Cosacak Mehmet Ilyas , Tayran Huseyin , Kurth Thomas , Schambony Alexandra , Buchholz Frank , Gentzel Marc , Kizil Caghan
Published: January 2025

Microproteins, short functional peptides encoded by small genes, are emerging as critical regulators of cellular processes, yet their roles in mitochondrial function and neurodegeneration remain underexplored. In this study, we identify NCBP2-AS2 as an evolutionarily conserved mitochondrial microprotein with significant roles in energy metabolism and neurogenesis. Using a combination of cellular and molecular approaches, including CRISPR/Cas9 knockout models, stoichiometric co- immunoprecipitation, and advanced imaging techniques, we demonstrate that NCBP2-AS2 localizes to the inner mitochondrial space and interacts with translocase of the inner membrane (TIM) chaperones. These interactions suggest a role in ATPase subunit transport, supported by the observed reductions in ATPase subunit levels and impaired glucose metabolism in NCBP2-AS2-deficient cells. In zebrafish, NCBP2-AS2 knockout led to increased astroglial proliferation, microglial abundance, and enhanced neurogenesis, particularly under amyloid pathology. Notably, we show that NCBP2-AS2 expression is consistently downregulated in human Alzheimer’s disease brains and zebrafish amyloidosis models, suggesting a conserved role in neurodegenerative pathology. These findings reveal a novel link between mitochondrial protein transport, energy metabolism, and neural regeneration, positioning NCBP2-AS2 as a potential therapeutic target for mitigating mitochondrial dysfunction and promoting neurogenesis in neurodegenerative diseases such as Alzheimer’s disease.
Optimized vectors for genetic engineering ofAureobasidium pullulans
Authors: Colarusso Analeigha , Williams Audrey , Gladfelter Amy S. , Wirshing Alison C.E. , Lew Daniel J.
Published: January 2025

Aureobasidium pullulansis a polyextremotolerant black yeast that exhibits impressive morphological plasticity. Consequently, it shows promise as a model system for investigating mechanisms of cell adaptation to different environments and the regulation of cell shape. Here, we build upon the current toolkit for working withA. pullulansand design and test 25 vectors with seven different codon-optimized fluorophores and three selection cassettes. This includes vectors that allow for dual expression of GFP and mCherry tagged proteins at theURA3locus and vectors that enable homology-based deletion or C-terminal tagging of endogenous genes without the need for cloning. This versatile vector series for working withA. pullulanswill enable a broad range of experiments in this emerging model system.

An optimized plasmid toolkit for genetic engineering of the emerging model fungus,A. pullulans.
Basigin Links Altered Skeletal Stem Cell Lineage Dynamics with Glucocorticoid-induced Bone Loss and Impaired Angiogenesis
Authors: Ambrosi Thomas H. , Morales David , Chen Kun , Hunt Ethan , Weldon Kelly , Maifeld Amber N. , Chavez Fatima I.M. , Wang Yuting , Murphy Matthew P. , Cressman Amin , Wheeler Erika E. , Saiz Augustine , Leach J. Kent , Fierro Fernando , Chan Charles K.F. , Lane Nancy E.
Published: January 2025

Glucocorticoid (GC) induced osteoporosis (GIOP) and osteonecrosis remain a significant health issue with few approved therapies that can treat the bone loss and dysfunction of skeletal vasculature. Therefore, we aimed to investigate the cellular and molecular processes by which GCs affect osteogenesis and angiogenesis, as well as how treatment with parathyroid hormone (hPTH 1-34) modifies these effects in a mouse model of GIOP. GC treatment reduced bone mass through decreased bone formation by skeletal stem cells (SSCs) while also increasing osteoclast mediated resorption. Concomitantly, endothelial cells were increased in numbers but displayed distorted phenotypical features. However, hPTH treatment reversed GC induced changes in osteogenesis and angiogenesis to control levels. Transplantation studies of SSCs combined with molecular analysis by single cell RNA-sequencing and functional testing of primary human cells tied GC-induced skeletal changes to altered stem and progenitor cell differentiation dynamics. This in turn perpetuated reduced osteogenesis and vascular malformation through direct SSC-endothelial crosstalk mediated at least in part by Basigin. Intriguingly, antibody-mediated blockade of Basigin during GC treatment prevented detrimental bone loss. In addition, when administered to aged mice, anti-Basigin therapy reinstated bone remodeling to significantly improve bone mass independent of sex. These findings, while helping to explain the cellular and molecular basis of how hPTH treatment can mitigate GC induced bone loss, provide new therapeutic vantage points for GIOP and other conditions associated with bone loss.
Understanding health innovation adoption: A realist evaluation of pulse oximeter implementation in primary care for children under five in four West African countries
Authors: LOUART Sarah , BALDE Habibata , COULIBALY Abdourahmane , DAGOBI Abdoua Elhadji , KADIO Kadidiatou , HEDIBLE Gildas Boris , LEROY Valeriane , ROBERT Emilie , RIDDE Valery
Published: January 2025

Introduction Hypoxemia is an important contributor to child mortality, particularly in low-resource settings where diagnostic tools are scarce. The AIRE project introduced pulse oximeters (POs) into 202 primary healthcare centres (PHCs) in Burkina Faso, Guinea, Mali, and Niger, integrating them into the Integrated Management of Childhood Illness (IMCI) guidelines. This initiative aimed to strengthen diagnostic capacities for identifying hypoxemia and to improve care management for critically ill children under five. This study examined how healthcare workers (HCWs) adopted POs and explored the contexts and mechanisms influencing their adoption. Methods We conducted a realist evaluation to analyse adoption patterns, focusing on interactions between the Intervention, Contexts, Actors, Mechanisms, and Outcomes (ICAMO configurations). Data collection included 299 interviews with HCWs, patients' families, and institutional actors, conducted in 16 selected PHCs, at the institutional level, and in district hospitals, complemented by site observations. Analysis was performed using NVivo software, identifying ICAMO configurations as demi-regularities to explain variations in PO use and adoption. Results Training enabled HCWs to recognize the utility of POs, further motivating their use. Support-focused supervision fostering a sense of support, while control-focused approaches sometimes resulted in mechanical use driven by external pressure. In contexts of high workloads and children's agitation, difficulties in using POs were observed. In settings with limited diagnostic tools, POs increased HCWs' diagnostic confidence, encouraging adoption and improving decision-making. Observing or knowing the benefits of POs on children's health provided HCWs with a sense of relief and pride, further reinforcing PO adoption. However, structural barriers and challenges related to institutional adoption may threaten long-term use. Conclusion This study highlights the necessary conditions for adopting POs in PHCs. While widely used by healthcare workers, addressing challenges related to training, supply chain logistics, and referral systems to hospitals is essential to ensure long-term sustainability and improve child health outcomes.