bluuebunny/crossref_metadata_2025 huggingface dataset:
SLC4A1MUTATIONS THAT CAUSE DISTAL RENAL TUBULAR ACIDOSIS ALTER CYTOPLASMIC PH AND CELLULAR AUTOPHAGY
Authors: Essuman Grace , Rizvi Midhat , Almomani Ensaf , Ullah Shahid A. K M. , Hasib Sarder M. A. , Chelangarimiyandoab Forough , Mungara Priyanka , Schmitt Manfred J. , Hureaux Marguerite , Vargas-Poussou Rosa , Touret Nicolas , Cordat Emmanuelle
Published: October 2024

Distal renal tubular acidosis (dRTA) is a disorder characterized by the inability of the collecting duct system to secrete acids during metabolic acidosis. The pathophysiology of dominant or recessiveSLC4A1variant related dRTA has been linked with the mis trafficking defect of mutant kAE1 protein. However,in vivostudies in kAE1 R607H dRTA mice and humans have revealed a complex pathophysiology implicating a loss of kAE1-expressing intercalated cells and intracellular relocation of the H+-ATPase in the remaining type-A intercalated cells. These cells also displayed accumulation of ubiquitin and p62 autophagy markers. The highly active transport properties of collecting duct cells require the maintenance of cellular energy and homeostasis, a process dependent on intracellular pH. Therefore, we hypothesized that the expression of dRTA variants affect intracellular pH and autophagy pathways. In this study, we report the characterization of newly identified dRTA variants and provide evidence of abnormal autophagy and degradative pathways in mouse inner medullary collecting duct cells and kidneys from mice expressing kAE1 R607H dRTA mutant protein. We show that reduced transport activity of the kAE1 variants correlated with increased cytosolic pH, reduced ATP synthesis, attenuated downstream autophagic pathways pertaining to the fusion of autophagosomes and lysosomes and/or lysosomal degradative activity. Our study elucidated a close relationship between the expression of defective kAE1 proteins, reduced mitochondrial activity and decreased autophagy and protein degradative flux.
Mechanistic insights into structure-based design of a Lyme disease subunit vaccine
Authors: Brangulis Kalvis , Malfetano Jill , Marcinkiewicz Ashley L. , Wang Alan , Chen Yi-Lin , Lee Jungsoon , Liu Zhuyun , Yang Xiuli , Strych Ulrich , Bottazzi Maria-Elena , Pal Utpal , Hsieh Ching-Lin , Chen Wen-Hsiang , Lin Yi-Pin
Published: October 2024

The quality of protective immunity plays a critical role in modulating vaccine efficacy, with native antigens often not able to trigger sufficiently strong immune responses for pathogen killing. This warrants creation of structure-based vaccine design, leveraging high-resolution antigen structures for mutagenesis to improve protein stability and efficient immunization strategies. Here, we investigated the mechanisms underlying structure-based vaccine design using CspZ-YA, a vaccine antigen fromBorrelia burgdorferi, the bacteria causing Lyme disease (LD), the most common vector-borne disease in the Northern Hemisphere. Compared to wild-type CspZ-YA, we found CspZ-YAI183Yand CspZ-YAC187Srequired lower immunization frequency to protect mice from LD-associated manifestations and bacterial colonization. We observed indistinguishable human and mouse antigenicity between wild-type and mutant CspZ-YA proteins after native infection or active immunization. This supports our newly generated, high-resolution structures of CspZ-YAI183Yand CspZ-YAC187S, showing no altered surface epitopes after mutagenesis. However, CspZ-YAI183Yand CspZ-YAC187Sfavored the interactions between helices H and I, consistent with their elevated thermostability. Such findings are further strengthened by increasing ability of protective CspZ-YA monoclonal antibodies in binding to CspZ-YA at a physiological temperature (37°C). Overall, this study demonstrated enhanced intramolecular interactions improved long-term stability of antigens while maintaining protective epitopes, providing a mechanism for structure-based vaccine design. These findings can ultimately be extended to other vaccine antigens against newly emerging pathogens for the improvement of protective immunity.
Tuning Spatial Distributions of Selection Pressure to Suppress Emergence of Resistance
Authors: Tunstall Thomas , Madgwick Philip G. , Kanitz Ricardo , Möbius Wolfram
Published: October 2024

Control measures such as insecticides or antimicrobials are used to contain biological agents such as pathogenic bacteria and vectors of human and plant diseases, respectively. Following control measure application, a resistant subpopulation may eventually rise to such frequency that the control measure will be rendered ineffective: The timescale over which this occurs is the ‘effective lifetime’ of the control measure. Prolonging this timescale relaxes urgency at which novel control measure needs to be developed. Spatial heterogeneity in control measure application can influence the rate at which resistance to the control measure evolves; in the agricultural context, this fact is exploited by distributing insecticides in mosaics across cropping regions in order to slow the rate of resistance evolution.

Contemporary and historical modeling practices, which aim to inform agricultural practices, often employ assumptions which squeeze out the impact of the spatio-temporal heterogeneity endemic to nature. In this paper, we present a minimal model of continuous dispersal and spatio-temporal heterogeneity in selection pressure distribution which exhibits a novel dynamic: The spatial distribution of selection pressure may be tuned in order to minimize the initial rate at which resistance evolves, thus increasing the effective lifetime of a pesticide.

Author summary

There are many contexts in which humans apply control measures to biological agents: pesticides are applied in fields to kill the pests that damage crops, mosquito nests are distributed to prevent the spread of malaria, and cancer drugs are applied to kill off tumors in humans. These control measures are examples of ‘selection pressures’, which select against strains which are susceptible to them. If a mutation occurs which confers resistance, the control agent will select for the resistant strain, thus reducing the efficacy of the control agent as the frequency of resistance increases in the population. This necessitates more of the control agent to be applied, or for a novel control agent to be developed. The former may have unintended consequences on the local environment, and the latter is expensive and time-intensive. It is preferable to carefully tunehowthe control agent is applied - perhaps instead of one massive compact region of control measure application, it is better to apply the control measure over multiple smaller regions? Here, we use a toy model of motile organisms to demonstrate that an optimal distribution exists for a variety of scenarios.
Anti-PTHrP blockade limits CD8+ T-cell exhaustion in anti-cancer immunotherapy
Authors: Moës Bastien , Gao Yunfeng , Demina Ekaterina , Kremer Richard , Rudd Christopher E.
Published: October 2024

Cancer is a major global health concern, with immune suppression hindering treatment. Immunotherapy, specifically immune checkpoint blockage on T cells, has revolutionized cancer treatment. T-cell exhaustion is an abnormal activation state that develops when continuous exposure to antigens, like cancer. In this context, recent evidence suggests that parathyroid hormone-related protein (PTHrP) plays a previously underappreciated role in fostering an immunosuppressive tumor microenvironment. Further, blocking PTHrP activity reduces primary tumor growth, prevents metastasis, and prolongs survival in mice with various cancers. Here, we confirm that administration of anti-PTHrP monoclonal antibodies can reduce the growth of B16-PDL1 melanoma tumors and that although the therapy did not alter the presence of CD4+ and CD8+ TILs, we noted that all stages of T-cell exhaustion were reduced. Further, the expression of cytolytic proteins PERFORIN and GZMB also increased. By contrast, anti-PTHrP therapy increased the relative presence of pre-pro B cells with a decline in mature B cells in the bone marrow. Overall, our data indicates that anti-PTHrP therapy acts by reducing T-cell exhaustion and by affecting B-cell development. These provide further mechanistic evidence to support the application of anti-PTHrP blockade as an alternate therapeutic approach to boost anti-tumor immunity.
Single-Cell Proteomic and Transcriptomic Characterization of Drug-Resistant Prostate Cancer Cells Reveals Molecular Signatures Associated with Morphological Changes
Authors: Woo Jongmin , Loycano Michael , Amanullah Md , Qian Jiang , Amend Sarah , Pienta Kenneth , Zhang Hui
Published: October 2024

This study delves into the proteomic intricacies of drug-resistant cells (DRCs) within prostate cancer, which are known for their pivotal roles in therapeutic resistance, relapse, and metastasis. Utilizing single-cell proteomics (SCP) with an optimized high-throughput Data Independent Acquisition (DIA) approach with the throughput of 60 sample per day, we characterized the proteomic landscape of DRCs in comparison to parental PC3 cells. This optimized DIA method allowed for robust and reproducible protein quantification at the single-cell level, enabling the identification and quantification of over 1,300 proteins per cell on average. Distinct proteomic sub-clusters within the DRC population were identified, closely linked to variations in cell size. The study uncovered novel protein signatures, including the regulation of proteins critical for cell adhesion and metabolic processes, as well as the upregulation of surface proteins and transcription factors pivotal for cancer progression. Furthermore, by integrating SCP and single-cell RNA-seq (scRNA-seq) data, we identified six upregulated and ten downregulated genes consistently altered in drug-treated cells across both SCP and scRNA-seq platforms. These findings underscore the heterogeneity of DRCs and their unique molecular signatures, providing valuable insights into their biological behavior and potential therapeutic targets.
Focused learning by antibody language models using preferential masking of non-templated regions
Authors: Ng Karenna , Briney Bryan
Published: October 2024

Existing antibody language models (LMs) are pre-trained using a masked language modeling (MLM) objective with uniform masking probabilities. While these models excel at predicting germline residues, they often struggle with mutated and non-templated residues, which are crucial for antigen-binding specificity and concentrate in the complementarity-determining regions (CDRs). Here, we demonstrate that preferential masking of the non-templated CDR3 is a compute-efficient strategy to enhance model performance. We pre-trained two antibody LMs (AbLMs) using either uniform or preferential masking and observed that the latter improves residue prediction accuracy in the highly variable CDR3. Preferential masking also improves antibody classification by native chain pairing and binding specificity, suggesting improved CDR3 understanding and indicating that non-random, learnable patterns help govern antibody chain pairing. We further show that specificity classification is largely informed by residues in the CDRs, demonstrating that AbLMs learn meaningful patterns that align with immunological understanding.
Profiling of epithelial functional states and fibroblast phenotypes in hormone therapy-naïve localised prostate cancer
Authors: Apostolov Eva , Roden Daniel L , Holliday Holly , Cazet Aurélie , Harvey Kate , Zhang Hanyun , Wu Sunny Z , van der Leij Sophie , Selth Luke A , Bartonicek Nenad , Al-Eryani Ghamdan , He Mengxiao , Lundeberg Joakim , Reeves John , Kench James G , Potter Alison J , Stricker Phillip , Joshua Anthony M , Horvath Lisa , Swarbrick Alexander
Published: October 2024

Localised prostate cancers (PCa) are heterogeneous and multifocal, with diverse outcomes. Current prognostic methods are epithelium-centric, overlooking the complex cellular landscape within the tumour microenvironment (TME), which remains incompletely characterised. We performed a comprehensive analysis of cancerous and adjacent-benign cores from 24 patients with hormone therapy-naïve localised PCa using single-cell RNA-sequencing. By integrating copy number variation and transcriptional signatures, we classified epithelial cells across a malignant spectrum, revealing widespread molecular perturbation. We found an expansion of Club cell phenotypes, suggestive of Luminal dedifferentiation. We also performed a detailed annotation of stromal phenotypes, focusing on fibroblasts, and identified a novel peri-neural fibroblast population. Spatial transcriptomics elucidated the precise anatomical distribution of CAFs within the PCa TME. This study provides a valuable foundation for advancing our understanding of PCa pathobiology and developing a comprehensive cellular model of the disease.

Statement of Significance

Our study leverages single-cell RNA-sequencing and spatial transcriptomics to provide a comprehensive cellular annotation of hormone therapy-naïve localised PCa. We reveal widespread molecular perturbations in epithelial cells and map distinct fibroblast populations to specific anatomical niches. Notably, we identify a novel peri-neural phenotype associated with nerves, which merits further functional characterisation and exploration as a potential therapeutic target.
Limits to the inference of gene regulation from bulk tissue expression data
Authors: Chu C. Pan , Morin Alexander , Pavlidis Paul
Published: October 2024

Motivation

Thousands of studies have used co-expression analysis of bulk tissue samples to probe gene regulation. However, the extent that intracellular regulatory signals are present in these data is unclear. Specifically, we lack clarity of the factors that promote or impede the propagation of intracellular regulatory signals from the single cell level to the bulk tissue level. To bring these issues into focus, we developed a novel computational simulator, grounded in real data, to explore the theoretical relationship between events in single cells and bulk tissue expression profiles, and clarify the conditions required for the propagation of intracellular regulatory signals in complex tissues such as the brain.

Results

Our simulator first generates single cell expression profiles and subsequently samples and aggregates these single cells to produce bulk tissue expression profiles. Using this framework, we found that there are very specific and unlikely conditions under which intracellular dynamic regulatory signals can be propagated to the bulk tissue level. For the most part, such regulatory relationships, however strong at the single cell level, are unlikely to be detectable. Our results provide a quantitative explanation for why regulatory network inference from co-expression has proved challenging - even with the assistance of other data modalities - and gives the scientific community a set of tools to further explore these issues in both single-cell and bulk tissue data.

Availability and implementation

All relevant data are within the manuscript and supplementary files. The code for all data analyses and generation of figures are available on GitHub (https://github.com/PavlidisLab/coex-simulation). A copy of the data has been deposited in Borealis, the Canadian Dataverse Repository (https://borealisdata.ca/dataset.xhtml?persistentId=doi:10.5683/SP3/2CWXY6).
CCAFE: Estimating Case and Control Allele Frequencies from GWAS Summary Statistics
Authors: Stoneman Hayley R , Price Adelle , Gignoux Christopher R , Hendricks Audrey E
Published: October 2024

Methods involving summary statistics in genetics can be quite powerful but can be limited in utility. For instance, many post-hoc analyses of disease studies require case and control allele frequencies (AFs), which are not always published. We present two frameworks to derive case and control AFs from GWAS summary statistics using the odds ratio, case and control sample sizes, and either the total (case and control aggregated) AF or standard error (SE). In simulations and real data, derivations of case and controls AFs using total AF is highly accurate across all settings (e.g., minor AF, condition prevalence). Conversely, derivations using SE underestimate common variant AFs (e.g. minor allele frequency >0.3) in the presence of covariates. We develop an adjustment using gnomAD AFs as a proxy for true AFs, which reduces the bias when using SE. While estimating case and control AFs using the total AF is preferred due to its high accuracy, estimating from the SE can be used more broadly since SE can be derived from p-values and beta estimates, which are commonly provided. The methods provided here expand the utility of publicly available genetic summary statistics and promote the reusability of genomic data. The R packageCCAFE, with implementations of both methods, is freely available on Bioconductor and GitHub.
Pervasive and recurrent hybridisation prevents inbreeding depression in Europe’s most threatened seabird
Authors: Izquierdo-Arànega Guillem , Cuevas-Caballé Cristian , Giannelli Francesco , Paris Josephine Rosanna , Bourgeois Karen , Trucchi Emiliano , González-Solís Jacob , Riutort Marta , Obiol Joan Ferrer , Rozas Julio
Published: October 2024

Hybridisation is a double-edged sword: while it can erode distinct evolutionary lineages, it can also introduce genetic diversity and adaptive potential into dwindling populations. In the Critically Endangered Balearic shearwater (Puffinus mauretanicus), this dilemma is exacerbated by a limited understanding of the extent and consequences of hybridisation with the Yelkouan shearwater (P. yelkouan). This knowledge gap has limited the scope of science-based conservation strategies to avoid the Balearic shearwater’s imminent extinction. Here, we investigate shearwater hybridisation dynamics and their effect on genome-wide diversity in the Balearic shearwater. Divergence dating, demographic modelling and admixture analyses suggest that these two poorly-differentiated shearwater lineages experienced recurrent episodes of divergence and widespread hybridisation during glacial cycles. Selection scans reveal a 500 kb region hosting an adaptive haplotype that potentially underpins interspecific differences in migratory behaviour, and which has been repeatedly introgressed between taxa. Moreover, we show that interspecific gene flow has prevented increases in homozygosity and genetic load, and through forward simulations we illustrate how it can enhance the Balearic shearwater’s resilience to future population bottlenecks. Our findings illustrate how introgression can be crucial for maintaining genetic diversity in threatened taxa, and highlight the need for considering the protection of hybridisation in conservation plans.
IL-13/IL-13Rα2 axis promotes proliferation of angiosarcoma cells
Authors: Saito Hinako , Omori Issei , Iwasawa Okuto , Sugimori Ayaka , Nakajima Hibari , Ichimura Ryuzo , Sato Shinichi , Sumida Hayakazu
Published: October 2024

Angiosarcoma is a rare and aggressive soft tissue sarcoma with a poor prognosis and limited treatment options. The role of interleukin-13 (IL-13) and its receptors in angiosarcoma pathogenesis has been largely unknown. We detected high IL-13 receptor α2 (IL-13Rα2) expression in angiosarcoma cell lines and patient samples compared to other cell types and benign vascular tumors. Moreover, histological analysis showed the presence of IL-13 in the angiosarcoma microenvironment. Functional studies using angiosarcoma cell lines, MO-LAS-B cells, revealed the promoting effect of IL-13 on cell proliferation. The effect was inhibited by siRNA-mediated knockdown ofIL13RA2or neutralizing antibodies against IL-13, suggesting the direct impact of IL-13/IL-13Rα2 axis in the angiosarcoma proliferation. In addition, IL-13 stimulation increased mRNA levels ofIL13RA2andVEGFA, suggesting an underlying positive feedback mechanism, which was attenuated by a STAT6 inhibitor. These findings highlight the importance of the IL-13/IL-13Rα2 axis in angiosarcoma progression and its potential as a novel therapeutic target for this challenging malignancy.
Genomic, phenotypic and environmental correlates of speciation in the midwife toads (Alytes)
Authors: Ambu Johanna , Litvinchuk Spartak N , Caballero-Díaz Carlos , Nicieza Alfredo , Velo-Antón Guillermo , Gonçalves Helena , Martínez-Freiría Fernando , Martínez-Gil Helena , Beltrán Juan Francisco , Donaire-Barroso David , Hernandez Axel , Suchan Tomasz , Crochet Pierre-André , Martínez-Solano ĺñigo , Dufresnes Christophe
Published: October 2024

Speciation, i.e., the formation of new species, implies that diverging populations evolve genetic and phenotypic factors that promote reproductive isolation (RI), but the adaptive vs. neutral origin of these factors and their relative contributions across the speciation continuum remain elusive. Here we test which of genomic, bioacoustic, morphological and environmental differentiation best predicts RI across the midwife toads (genusAlytes), a diversification of Mediterranean amphibians. Hybrid zone analyses in theA. obstetricanscomplex support that without strong geographic barriers to dispersal, the extent of introgression (which should reflect the strength of RI) covaries with genomic divergence irrespective of other factors. Phenotypic divergence become important later along the continuum, namely between non-admixing species attributed to distinct subgenera. Our results suggest that by putatively causing intrinsic incompatibilities in hybrids, the genetic mutations accumulating randomly between allopatric populations act as the initial trigger of RI, while substantial ecological and behavioral differentiation is a long-term consequence of species divergence that ultimately promotes sympatry. Whereas speciation is usually claimed to be primarily adaptive, our study corroborates recent findings that new species may also be a neutral outcome of gradual phylogeographic divergence, which has practical implications for species delimitation.
Deciphering the RNA recognition by Musashi-1 to design protein and RNA mutants for in vitro and in vivo applications
Authors: Pérez-Ràfols Anna , Pérez-Ropero Guillermo , Cerofolini Linda , Sperotto Luca , Roca-Martínez Joel , Anahí Higuera-Rodríguez Rosa , Russomanno Pasquale , Kaiser Wolfgang , Vranken Wim , Danielson Helena , Provenzani Alessandro , Martelli Tommaso , Sattler Michael , Buijs Jos , Fragai Marco
Published: October 2024

RNA Recognition Motifs (RRMs) are essential post-transcriptional regulators of gene expression in eukaryotic cells. The Human Musashi-1 (MSI-1) is an RNA-binding protein that recognizes (G/A)U1-3AGU and UAG sequences in diverse RNAs through two RRMs and regulates the fate of target RNA.

Here, we combined structural biology and computational approaches to analyse the binding of the RRM domains of human MSI-1 with single-stranded and structured RNAs ligands. We used our recently developed computational tool RRMScorer to design a set of mutants of the MSI-1 protein to bind novel RNA sequences to alter the binding selectivity. Thein-silicopredictions of the designed protein-RNA interactions are assessed by NMR and SPR. These experiments also are used to study the competition of the two RRM domains of MSI-1 for the same binding site within linear and harpin RNA. Our experimental results confirm thein-silicodesigned interactions, thus opening the way for the development of new biomolecules for in vitro and in vivo studies and downstream applications.
Calcium homeostatic feedback control predicts atrial fibrillation initiation, remodeling, and progression
Authors: Moise Nicolae , Weinberg Seth H.
Published: October 2024

Atrial fibrillation (AF) is a progressive disorder, with arrhythmia episodes becoming increasingly longer and ultimately permanent. The chaotic electrical activity by itself is well-known to drive progression, a process classically summarized as “AF begets AF.” However, the mechanisms underlying this progression are not yet well defined. We hypothesize that calcium homeostatic feedback regulating ion channel expression is a critical mechanistic component of this pathological process. We propose a modeling framework that tracks both short-term beat-to-beat electrical and calcium activity and long-term tissue substrate remodeling as a single coupled dynamical system. Importantly, the full AF progression from healthy to pathological remodeled tissue is reproduced, in contrast with prior studies that consider “snapshots” of various AF stages. Simulations predict that single cells respond to fast pacing by maintaining intracellular calcium concentrations through dynamic ion channel expression and electrical phenotype changes. In two-dimensional (2D) homogeneous tissue, spontaneous spiral waves stabilize into permanent re-entry. In 2D heterogeneous tissue, we observe the initiation of re-entrant activity in response to fast pacing, followed by increasingly longer intermittent, and then permanent, arrhythmic activity. Simulations predict critical properties of re-entrant wave locations, leading to a novel hypothesis: spiral wave activity itself drives underlying substrate remodeling and the emergence of remodeled tissue “niches” that support the stabilization of fast re-entrant activity. Thus, the model joins multiple lines of inquiry (i.e., long-term calcium regulation, ion channel co-expression and remodeling, and tissue-scale arrhythmia spatiotemporal organization) into a single coherent framework, and for the first time, captures the dynamics of the long-term natural history of AF.
A new discrete-geometry approach for integrative docking of proteins using chemical crosslinks
Authors: Zhang Yichi , Jindal Muskaan , Viswanath Shruthi , Sitharam Meera
Published: October 2024

The structures of protein complexes allow us to understand and modulate the biological functions of the proteins. Integrative docking is a computational method to obtain the structures of a protein complex, given the atomic structures of the constituent proteins along with other experimental data on the complex, such as chemical crosslinks or SAXS profiles. Here, we develop a new discrete geometry-based method, wall-EASAL, for integrative rigid docking of protein pairs given the structures of the constituent proteins and chemical crosslinks. The method is an adaptation of EASAL (Efficient Atlasing and Search of Assembly Landscapes), a state-of-the-art discrete geometry method for efficient and exhaustive sampling of macromolecular configurations under pairwise inter-molecular distance constraints. We provide a mathematical proof that the method finds a structure satisfying the crosslink constraints under a natural condition satisfied by energy landscapes. We compare wall-EASAL with IMP (Integrative Modeling Platform), a commonly used integrative modeling method, on a benchmark, varying the numbers, types, and sources of input crosslinks, and sources of monomer structures. The wall-EASAL method performs better than IMP in terms of the average satisfaction of the configurations to the input crosslinks and the average similarity of the configurations to their corresponding native structures. The ensembles from IMP exhibit greater variability in these two measures. Further, wall-EASAL is more efficient than IMP. Although the current study uses crosslinks, the method is general and any source of distance constraints can be used for integrative docking with wall-EASAL. However, the current implementation only supports binary rigid protein docking,i.e., assumes that the monomer structures are known and remain rigid. Additionally, the current implementation is deterministic,i.e., it does not account for uncertainties in the crosslinking data beyond using distance bounds. Neither of these appears to be a theoretical or algorithmic limitation of the EASAL methodology. Structures from wall-EASAL can be incorporated in methods for modeling large macromolecular assemblies, for example by suggesting rigid bodies or restraints for use in these methods. This will facilitate the characterization of assemblies and cellular neighborhoods at increased efficiency, accuracy, and precision. The wall-EASAL method is available athttps://bitbucket.org/geoplexity/easal-dev/src/Crosslinkand the benchmark is available athttps://github.com/isblab/Integrative_docking_benchmark.
DeepRNA-Twist : Language Model guided RNA Torsion Angle Prediction with Attention-Inception Network
Authors: Abir Abrar Rahman , Tahmid Md Toki , Rayan Rafiqul Islam , Rahman M Saifur
Published: October 2024

RNA torsion and pseudo-torsion angles are critical in determining the three-dimensional conformation of RNA molecules, which in turn governs their biological functions. However, current methods are limited by RNA’s structural complexity and flexibility, as it can adopt multiple conformations, with experimental techniques being costly and computational approaches struggling to capture the intricate sequence dependencies needed for accurate predictions. To address these challenges, we introduce DeepRNA-Twist, a novel deep learning framework designed to predict RNA torsion and pseudo-torsion angles directly from sequence. DeepRNA-Twist utilizes RNA language model embeddings, which provides rich, context-aware feature representations of RNA sequences. Additionally, it introduces 2A3IDC module (AttentionAugmentedInceptionInsideInception withDilatedCNN), combining inception networks with dilated convolutions and multi-head attention mechanism. The dilated convolutions capture long-range dependencies in the sequence without requiring a large number of parameters, while the multi-head attention mechanism enhances the model’s ability to focus on both local and global structural features simultaneously. DeepRNA-Twist was rigorously evaluated on benchmark datasets, including RNA-Puzzles, CASP-RNA, and SPOT-RNA-1D, and demonstrated significant improvements over existing methods, achieving state-of-the-art accuracy. Source code is available athttps://github.com/abrarrahmanabir/DeepRNA-Twist
Capturing single-molecule properties does not ensure accurate prediction of biomolecular phase diagrams
Authors: Feito Alejandro , Sanchez-Burgos Ignacio , Rey Antonio , Collepardo-Guevara Rosana , Espinosa Jorge R. , Tejedor Andres R.
Published: October 2024

Intracellular liquid-liquid phase separation of proteins and nucleic acids represents a fundamental mechanism by which cells organise their components into biomolecular condensates that perform multiple biological tasks. Computer simulations provide powerful tools to investigate biomolecular phase separation, offering microscopic insights into the physicochemical principles that regulate these systems. In this study, we investigate the phase behaviour of the low-complexity domain (LCD) of hnRNPA1 and several mutants via Molecular Dynamics simulations. We systematically compare the performance of five state-of-the-art residue-resolution coarse-grained protein models: HPS, HPS-cation-π, CALVADOS2, Mpipi, and Mpipi-Recharged. Our evaluation focuses on how well these models reproduce experimental coexistence densities and single-protein radii of gyration for the LCD-hnRNPA1 set of mutants. While most models yield similar intramolecular contact maps and reasonable estimates of the single-protein radius of gyration compared to in vitro measurements, only Mpipi-Recharged, Mpipi, and CALVADOS2 accurately predict phase diagrams that align with experimental data. This suggests that force field parameterizations optimized solely to reproduce single-protein properties may not always capture the phase behaviour of protein solutions. Additionally, our findings reveal that some residue-resolution coarse-grained models can lead to significant discrepancies in predicting the roles of individual intermolecular interactions, even for relatively simple intrinsically disordered proteins like the low-complexity domain of hnRNPA1. Our work highlights the importance of balancing both single-molecule and collective properties of proteins to accurately predict condensate formation and material properties.
V- and VL-Scores Uncover Viral Signatures and Origins of Protein Families
Authors: Zhou Kun , Kosmopoulos James C , Dieppa Colon Etan , Badciong Peter John , Anantharaman Karthik
Published: October 2024

Viruses are key drivers of microbial diversity, nutrient cycling, and co-evolution in ecosystems, yet their study is hindered due to challenges in culturing. Traditional gene-centric methods, which focus on a few hallmark genes like for capsids, miss much of the viral genome, leaving key viral proteins and functions undiscovered. Here, we introduce two powerful annotation-free metrics, V-score and VL-score, designed to quantify the virus-likeness of protein families and genomes and create an open-access searchable database, V-Score-Search. By applying V- and VL-scores to public databases (KEGG, Pfam, and eggNOG), we link 38−77% of protein families with viruses, a 9−16x increase over current estimates. These metrics outperform existing approaches, enabling precise detection of viral genomes, prophages, and host-derived auxiliary viral genes (AVGs) from fragmented sequences, and significantly improving genome binning. Remarkably, we identify up to 17x more AVGs, dominated by non-metabolic proteins of unknown function. This innovation unlocks new insights into virus signatures and host interactions, with wide-ranging implications from genomics to biotechnology.
Altered systemic bioenergetic reserve in chronic kidney disease predisposes hearts to worse functional outcomes
Authors: Young Megan , Aastrup Malene , Patel Nikayla , Cullen Fenn , Hansen Esben S.S. , Clark James E. , Eykyn Thomas R. , Vaeggemose Michael , Vujic Ana , Karatzia Loucia , Valkovič Ladislav , Miller Jack J.J.J. , Buus Niels H. , Laustsen Christoffer , Yaqoob Magdi M. , Aksentijevic Dunja
Published: October 2024

Chronic kidney disease (CKD) is the tenth biggest killer worldwide and is projected to be the fifth leading cause of mortality by 2040. CKD is an inherently systemic disease with progressive deterioration of kidney, muscle, and liver function creating a vicious cycle of comorbidity. However, whether systemic energetic deficiency in CKD contributes to cardiac dysfunction of the uraemic cardiomyopathy remains unknown. Using two pre-clinical renal failure models of different aetiology in rats (4-week 0.75% adenine diet and 12-week post-partial nephrectomy) we investigated both cardiac and systemic metabolic remodelling in CKD. In addition to significant uraemia, anaemia and alterations in exogenous plasma substrate homeostasis, non-targeted1H NMR spectroscopy metabolomic profiling of peripheral tissues (skeletal muscle, liver, kidneys) revealed extensive metabolic alterations and changes in bioenergetic reserve in both experimental CKD models. Similarly,31P magnetic resonance spectroscopy assessment of the exercising lower leg muscle of CKD human patients identified systemic bioenergetic deficiency. During exercise CKD patients were unable to utilise the energetic capacity to the same extent as healthy controls. Both experimental CKD models developed mild cardiac dysfunction, however metabolic remodelling was less severe than that of systemic organs. Upon challenge with 25-minute total global ischemia, CKD hearts from both experimental models had poorer functional outcome. Thus, in CKD perturbation of systemic metabolism precedes and exceeds severity of cardiac metabolic changes. Prevention of systemic metabolic derangement in CKD may be a new therapeutic approach to improve cardiac functional outcomes in CKD.

One Sentence Summary

Perturbations of systemic metabolism precede and exceed severity of cardiac metabolic changes in chronic kidney disease.
The metabolic costs of meiotic drive
Authors: Bradshaw Sasha L , Rodriguez Enrique , Wang Hanting , Yu Cyn Thea , De La Noue Cyril De Villiers , Hafezjee Aadil , Pomiankowski Andrew , Camus M. Florencia
Published: October 2024

Selfish genetic elements, such as meiotic drive genes, disrupt Mendel’s law of equal segregation by biasing their own transmission, often at a detriment to the rest of the genome. The Malaysian stalk-eyed fly (Teleopsis dalmanni)sex-ratio (SR) meiotic drive system is located within a series of large inversions on the X chromosome subject to low recombination and is associated with deleterious effects on fitness. Here we examine the metabolic effects of meiotic drive across male and female stalk-eyed flies. High-resolution O2k respirometry coupled with whole-organism respirometry were used to obtain mitochondrial function and metabolic rates. Complimentary assays on food consumption established downstream effects of metabolism on nutrient acquisition. The experiments demonstrate that individuals with SR meiotic drive elements have impaired mitochondrial function and reduced capacity for ATP synthesis, as shown by a lower respiratory control ratio and weaker contribution of Complex I to respiration. Drive individuals also exhibited an increased basal metabolic rate and consumed a greater amount of food than wild-type individuals. These findings show that the drive genotype imposes metabolic costs in both male and female hosts. The disruption in mitochondrial function likely leads to compensation via an increase in both basal metabolic rate and nutrient acquisition. A potential cause lies in the accumulation of deleterious mutations in the inversions on the X chromosome that house the meiotic drive, which are subject to weak natural selection. In females, the drive chromosome has a dominant effect, with a single copy causing substantial metabolic compromise. There was little evidence of male-specific metabolic costs, nor evidence of an accumulation of sexually antagonistic effects of drive chromosomes on female metabolism. These results suggest that direct metabolic costs from meiotic drive on spermatogenesis and from sexually antagonistic selection are relatively weak. This research provides new insight into the interplay between meiotic drive and metabolism, drawing attention to the broader physiological repercussions selfish genetic elements may have on their hosts.
RGS10 Attenuates Systemic Immune Dysregulation Induced by Chronic Inflammatory Stress
Authors: Jernigan Janna E. , Staley Hannah A. , Baty Zachary , Bolen MacKenzie L. , Gomes Beatriz Nuñes , Holt Jenny , Cole Cassandra L. , Neighbarger Noelle K. , Dheeravath Kruthika , Merchak Andrea R. , Menees Kelly B. , Coombes Stephen A. , Tansey Malú Gámez
Published: October 2024

Regulator of G-protein signaling 10 (RGS10), a key homeostatic regulator of immune cells, has been implicated in multiple diseases associated with aging and chronic inflammation including Parkinson’s Disease (PD). Interestingly, subjects with idiopathic PD display reduced levels of RGS10 in subsets of peripheral immune cells. Additionally, individuals with PD have been shown to have increased activated peripheral immune cells in cerebral spinal fluid (CSF) compared to age-matched healthy controls. However, it is unknown whether CSF-resident peripheral immune cells in individuals with PD also exhibit decreased levels of RGS10. Therefore, we performed an analysis of RGS10 levels in the proteomic database of the CSF from the Michael J. Fox Foundation Parkinson’s Progression Markers Initiative (PPMI) study. We found that RGS10 levels are decreased in the CSF of individuals with PD compared to healthy controls and prodromal individuals. Moreover, we find that RGS10 levels decrease with age but not PD progression and that males have less RGS10 than females in PD. Importantly, studies have established an association between chronic systemic inflammation (CSI) and neurodegenerative diseases, such as PD, and known sources of CSI have been identified as risk factors for developing PD; however, the role of peripheral immune cell dysregulation in this process has been underexplored. As RGS10 levels are decreased in the CSF and circulating peripheral immune cells of individuals with PD, we hypothesized that RGS10 regulates peripheral immune cell responses to CSI prior to the onset of neurodegeneration. To test this, we induced CSI for 6 weeks in C57BL6/J mice and RGS10 KO mice to assess circulating and CNS-associated peripheral immune cell responses. We found that RGS10 deficiency synergizes with CSI to induce a bias for inflammatory and cytotoxic cell populations, a reduction in antigen presentation in peripheral blood immune cells, as well as in and around the brain that is most notable in males. These results highlight RGS10 as an important regulator of the systemic immune response to CSI and implicate RGS10 as a potential contributor to the development of immune dysregulation in PD.
Reduced Liver Mitochondrial Energy Metabolism Impairs Food Intake Regulation Following Gastric Preloads and Fasting
Authors: Ponte Michael E. , Prom John C. , Newcomb Mallory A. , Jordan Annabelle B. , Comfort Lucas L. , Hu Jiayin , Puchalska Patrycja , Geisler Caroline E. , Hayes Matthew R. , Morris E. Matthew
Published: October 2024

Objective

The capacity of the liver to serve as a peripheral sensor in the regulation of food intake has been debated for over half a century. The anatomical position and physiological roles of the liver suggest it is a prime candidate to serve as an interoceptive sensor of peripheral tissue and systemic energy state. Importantly, maintenance of liver ATP levels and within-meal food intake inhibition is impaired in human subjects with obesity and obese pre-clinical models. Previously, we have shown decreased hepatic mitochondrial energy metabolism (i.e., oxidative metabolism & ADP-dependent respiration) in male liver-specific, heterozygous PGC1a mice results in increased short-term diet-induced weight gain with increased within meal food intake. Herein, we tested the hypothesis that decreased liver mitochondrial energy metabolism impairs meal termination following nutrient oral pre-loads.

Methods

Liver mitochondrial respiratory response to changes in ΔGATPand adenine nucleotide concentration following fasting were examined in male liver-specific, heterozygous PGC1a mice. Further, food intake and feeding behavior during basal conditions, following nutrient oral pre-loads, and following fasting were investigated.

Results

We observed male liver-specific, heterozygous PGC1a mice have reduced mitochondrial response to changes in ΔGATPand tissue ATP following fasting. These impairments in liver energy state are associated with larger and longer meals during chow feeding, impaired dose-dependent food intake inhibition in response to mixed and individual nutrient oral pre-loads, and greater acute fasting-induced food intake.

Conclusion

These data support previous work proposing liver-mediated food intake regulation through modulation of peripheral satiation signals.
Gene-Excessive Sleepiness Interactions Suggest Treatment Targets for Obstructive Sleep Apnea Subtype
Authors: Nagarajan Pavithra , Kurniansyah Nuzulul , Lee Jiwon , Gharib Sina A. , Xu Yushan , Zhang Yiyan , Spitzer Brian , Faquih Tariq , Zhou Hufeng , Boerwinkle Eric , Chen Han , Gottlieb Daniel J. , Guo Xiuqing , Heard-Costa Nancy L. , Hidalgo Bertha A. , Levy Daniel , Liu Peter Y. , Mei Hao , Montalvan Rebecca , Mukherjee Sutapa , North Kari E. , O’Conner George T. , Palmer Lyle J. , Patel Sanjay R. , Psaty Bruce M. , Purcell Shaun M. , Raffield Laura M. , Rich Stephen S. , Rotter Jerome I. , Saxena Richa , Smith Albert V , Stone Katie L. , Zhu Xiaofeng ,   TOPMed Sleep Trait WG, Cade Brian E. , Sofer Tamar , Redline Susan , Wang Heming
Published: October 2024

Obstructive sleep apnea (OSA) is a multifactorial sleep disorder characterized by a strong genetic basis. Excessive daytime sleepiness (EDS) is a symptom that is reported by a subset of OSA patients, persisting even after treatment with continuous positive airway pressure (CPAP). It is recognized as a clinical subtype underlying OSA carrying alarming heightened cardiovascular risk. Thus, conceptualizing EDS as an exposure variable, we sought to investigate EDS’s influence on genetic variation linked to apnea-hypopnea index (AHI), a diagnostic measure of OSA severity. This study serves as the first large-scale genome-wide gene x environment interaction analysis for AHI, investigating the interplay between its genetic markers and EDS across and within specific sex. Our work pools together whole genome sequencing data from seven cohorts, enabling a diverse dataset (four population backgrounds) of over 11,500 samples. Among the total 16 discovered genetic targets with interaction evidence with EDS, eight are previously unreported for OSA, includingCCDC3,MARCHF1, andMED31identified in all sexes;TMEM26,CPSF4L, andPI4K2Bidentified in males; andRAP1GAPandYY1identified in females. We discuss connections to insulin resistance, thiamine deficiency, and resveratrol use that may be worthy of therapeutic consideration for excessively sleepy OSA patients.
Sequence-based TCR-Peptide Representations Using Cross-Epitope Contrastive Fine-tuning of Protein Language Models
Authors: Im Chiho , Zhao Ryan , Boyd Scott D. , Kundaje Anshul
Published: October 2024

Understanding T-Cell receptor (TCR) and epitope interactions is critical for advancing our knowledge of the human immune system. Traditional approaches that use sequence similarity or structure data often struggle to scale and generalize across diverse TCR/epitope interactions. To address these limitations, we introduce ImmuneCLIP, a contrastive fine-tuning method that leverages pre-trained protein language models to align TCR and epitope embeddings in a shared latent space. ImmuneCLIP is evaluated on epitope ranking and binding prediction tasks, where it consistently outperforms sequence-similarity based methods and existing deep learning models. Furthermore, ImmuneCLIP shows strong generalization capabilities even with limited training data, highlighting its potential for studying diverse immune interactions and uncovering patterns that improve our understanding of human immune recognition systems.
Single-molecule analysis reveals the mechanism of chromatin ubiquitylation by variant PRC1 complexes
Authors: Teslenko Alexandra , Fierz Beat
Published: October 2024

Chromatin regulation relies on ‘writer’ enzymes that add post-translational modifications (PTMs) to histone proteins. Variant Polycomb repressive complex 1 (PRC1) exists as several subtypes, which are key ‘writers’ of ubiquitylation on histone H2A lysine 119 (H2AK119ub), crucial for transcriptional repression during development and cell identity determination. The mechanism by which dynamic chromatin exploration by varia nt PRC1 complexes is coupled to ubiquitin writing is unknown. Here, we developed a single-molecule approach to directly observe chromatin interactions and ubiquitylation by PRC1. We find that variant PRC1 transiently samples chromatin until reaching a catalytically competent nucleosome-bound state, resulting in E2 recruitment and ubiquitin transfer. Variant PRC1 is weakly processive in ubiquitylating neighboring nucleosomes. Moreover, activity differences between PRC1 subtypes, containing either a PCGF1 or PCGF4 subunit, result from distinct probabilities of achieving a catalytically competent state. Our results thus demonstrate that the dynamic formation of an active complex between variant PRC1, E2 and chromatin is the critical determinant of subtype-specific variant PRC1 activity.