bluuebunny/crossref_metadata_2025 huggingface dataset:
Cell-free DNA Fragmentomics Assay to Discriminate the Malignancy of Breast Nodules and Evaluate Treatment Response
Authors: Liu Jiaqi , Li Yalun , Tang Wanxiangfu , Dai Lijun , Jia Ziqi , Cao Heng , Li Chenghao , Liu Yuchen , Huang Yansong , Wu Jiang , Ma Dongxu , Qiao Guangdong , Bao Hua , Chang Shuang , Zhu Dongqin , Yang Shanshan , Wu Xuxiaochen , Wu Xue , Xu Hengyi , Chen Hongyan , Shao Yang , Wang Xiang , Liu Zhihua , Su Jianzhong
Published: October 2024

The fragmentomics-based cell-free DNA (cfDNA) assays have recently illustrated prominent abilities to identify various cancers from non-conditional healthy controls, while their accuracy for identifying early-stage cancers from benign lesions with inconclusive imaging results remains uncertain. Especially for breast cancer, current imaging-based screening methods suffer from high false-positive rates for women with breast nodules, leading to unnecessary biopsies, which add to discomfort and healthcare burden. Here, we enroll 560 female participants in this multi-center study and demonstrate that cfDNA fragmentomics is a robust non-invasive biomarker for breast cancer using whole-genome sequencing. Among the multimodal cfDNA fragmentomics profiles, the fragment size ratio (FSR), fragment size distribution (FSD), and copy number variation (CNV) show more distinguishing ability than Griffin, motif breakpoint (MBP), and neomer. The cfDNA fragmentomics (cfFrag) model using the optimal three fragmentomics features discriminated early-stage breast cancers from benign nodules, even at a low sequencing depth (3×). Notably, it demonstrated a specificity of 94.1% in asymptomatic healthy women at a 90% sensitivity for breast cancers. Moreover, we comprehensively showcase the clinical utilities of the cfFrag model in predicting patient responses to neoadjuvant chemotherapy (NAC) and in combining with multimodal features, including radiological results and cfDNA methylation features (with AUC values of 0.93 – 0.94 and 0.96, respectively).
Safety and implementation of a phase 1 randomized GLA-SE-adjuvanted CH505TF gp120 HIV vaccine trial in newborns
Authors: Violari Avy , Otwombe Kennedy , Hahn William , Chen Shiyu , Josipovic Deirdre , Baba Vuyelwa , Angelidou Asimenia , Smolen Kinga K. , Levy Ofer , Mkhize Nonhlanhla N , Woodward Amanda S , Martin Troy M. , Haynes Bart , Williams Wilton B. , Sagawa Zachary K. , Kublin James , Polakowski Laura , Brewinski Isaacs Margaret , Yen Catherine , Tomaras Georgia , Corey Lawrence , Janes Holly , Gray Glenda
Published: October 2024

Background

The neonatal immune system is uniquely poised to generate broadly neutralizing antibodies (bnAbs) and thus infants are ideal for evaluating HIV vaccine candidates. We present the design and safety of a novel glucopyranosyl lipid A (GLA)-stable emulsion (SE) adjuvant admixed with a first-in-infant CH505 transmitter-founder (CH505TF) gp120 immunogen designed to induce precursors for bnAbs against HIV.

Methods

HVTN 135 is a phase I randomized, placebo-controlled trial of CH505TF+GLA-SE or placebo. Healthy infants in South Africa aged ≤5 days, born to mothers living with HIV but HIV nucleic acid negative at birth were randomized to five doses of CH505TF + GLA-SE or placebo at birth and 8, 16, 32, and 54 weeks.

Results

38 infants (median age = 4 days; interquartile range 4, 4.75 days) were enrolled November 2020 to January 2022. Among 28 (10) infants assigned to receive CH505TF + GLA-SE (placebo), most (32/38) completed the 5-dose immunization series and follow-up (35/38). Solicited local and systemic reactions were more frequent in vaccine (8, 28.6% local; 16, 57.1% systemic) vs. placebo recipients (1, 10% local, p = 0.25; 4, 40.0% systemic, p = 0.38). All events were Grade 1 except two Grade 2 events (pain, lethargy). Serious vaccine-related adverse events were not recorded.

Conclusions

This study illustrates the feasibility of conducting trials of novel adjuvanted HIV vaccines in HIV-exposed infants receiving standard infant vaccinations. The safety profile of the CH505TF + GLA-SE vaccine was reassuring.

Trial registration

ClinicalTrials.govNCT04607408

Funding

National Institute of Allergy and Infectious Diseases (NIAID) at the National Institutes of Health (NIH)

Brief summary

This paper summarizes the phase 1 trial design and safety profile of an experimental CH505TF immunogen + GLA-SE HIV vaccine in infants born to mothers living with HIV.
Suppressing PDGFRβ Signaling Enhances Myocyte Fusion to Promote Skeletal Muscle Regeneration
Authors: Xue Siwen , Benvie Abigail M. , Blum Jamie E. , Kolba Nikolai J , Cosgrove Benjamin D. , Thalacker-Mercer Anna , Berry Daniel C.
Published: October 2024

Muscle cell fusion is critical for forming and maintaining multinucleated myotubes during skeletal muscle development and regeneration. However, the molecular mechanisms directing cell-cell fusion are not fully understood. Here, we identify platelet-derived growth factor receptor beta (PDGFRβ) signaling as a key modulator of myocyte fusion in adult muscle cells. Our findings demonstrate that genetic deletion ofPdgfrβenhances muscle regeneration and increases myofiber size, whereas PDGFRβ activation impairs muscle repair. Inhibition of PDGFRβ activity promotes myonuclear accretion in both mouse and human myotubes, whereas PDGFRβ activation stalls myotube development by preventing cell spreading to limit fusion potential. Transcriptomics analysis show that PDGFRβ signaling cooperates with TGFβ signaling to direct myocyte size and fusion. Mechanistically, PDGFRβ signaling requires STAT1 activation, and blocking STAT1 phosphorylation enhances myofiber repair and size during regeneration. Collectively, PDGFRβ signaling acts as a regenerative checkpoint and represents a potential clinical target to rapidly boost skeletal muscle repair.
Differential reconfiguration of brain networks in children in response to standard versus rewarded go/no-go task demands
Authors: Mitchell Mackenzie E , Henry Teague R , Fogleman Nicholas D , Michael Cleanthis , Nugiel Tehila , Cohen Jessica R
Published: October 2024

Response inhibition and sustained attention are critical for higher-order cognition and rely upon specific patterns of functional brain network organization. This study investigated how functional brain networks reconfigure to execute these cognitive processes during a go/no-go task with and without the presence of rewards in 26 children between the ages of 8 and 12 years. First, we compared task performance between standard and rewarded versions of a go/no-go task. We found that the presence of rewards reduced commission error rate, a measure considered to indicate improved response inhibition. Tau, thought to index sustained attention, did not change across task conditions. Next, changes in functional brain network organization were assessed between the resting state, the standard go/no-go task, and the rewarded go/no-go task. Relative to the resting state, integration decreased and segregation increased during the standard go/no-go task. A further decrease in integration and increase in segregation was observed when rewards were introduced. These patterns of reconfiguration were present globally and across several key brain networks of interest, as well as in individual regions implicated in the processes of response inhibition, attention, and reward processing. These findings align with patterns of brain network organization found to support the cognitive strategy of sustained attention, rather than response inhibition, during go/no-go task performance and suggest that rewards enhance this organization. Overall, this study used large-scale brain network organization and a within-subjects multi-task design to examine different cognitive strategies and the influence of rewards on response inhibition and sustained attention in late childhood.
KinPFN: Bayesian Approximation of RNA Folding Kinetics using Prior-Data Fitted Networks
Authors: Scheuer Dominik , Runge Frederic , Franke Jörg K.H. , Wolfinger Michael T. , Flamm Christoph , Hutter Frank
Published: October 2024

RNA is a dynamic biomolecule crucial for cellular regulation, with its function largely determined by its folding into complex structures, while misfolding can lead to multifaceted biological sequelae. During the folding process, RNA traverses through a series of intermediate structural states, with each transition occurring at variable rates that collectively influence the time required to reach the functional form. Understanding these folding kinetics is vital for predicting RNA behavior and optimizing applications in synthetic biology and drug discovery. Whilein silicokinetic RNA folding simulators are often computationally intensive and time-consuming, accurate approximations of the folding times can already be very informative to assess the efficiency of the folding process. In this work, we presentKinPFN, a novel approach that leverages prior-data fitted networks to directly model the posterior predictive distribution of RNA folding times. By training on synthetic data representing arbitrary prior folding times,KinPFNefficiently approximates the cumulative distribution function of RNA folding times in a single forward pass, given only a few initial folding time examples. Our method offers a modular extension to existing RNA kinetics algorithms, promising significant computational speed-ups orders of magnitude faster, while achieving comparable results. We showcase the effectiveness ofKinPFNthrough extensive evaluations and real-world case studies, demonstrating its potential for RNA folding kinetics analysis, its practical relevance, and generalization to other biological data.
Automatic Detection and Extraction of Key Resources from Tables in Biomedical Papers
Authors: Ozyurt Ibrahim Burak , Bandrowski Anita
Published: October 2024

Tables are useful information artifacts that allow easy detection of data “missingness” by humans and have been deployed by several publishers to improve the amount of information present for key resources and reagents such as antibodies, cell lines, and other tools that constitute the inputs to a study. The STAR*Methods tables, specifically, have increased the “findability” of these key resources, but they have not been commonly available outside of the Cell Press journal family. To improve the availability of these tables in the broader biomedical literature, we have attempted to automatically process BioRxiv preprints to create tables from text or to recognize tables already created by authors and structure them for later use by publishers and search systems, to improve “findability” of resources in a larger amount of the scientific literature. The extraction of key resource tables in PDF files by the best in class tools resulted in Grid Table Similarity (GriTS) score of 0.12, so we have created several multimodal pipelines employing machine learning approaches for key resource table page identification, Table Transformer models for table detection and table structure recognition and a new table-specific language model for row over-segmentation to improve the extraction of text in tables created by biomedical authors and published on BioRxiv to around GriTS score of 0.90 enabling the deployment of automated research resource extraction tools onto BioRxiv.

Author summary

Tables are useful information artifacts that allow for easy detection of data “missingness” by humans and have been implemented by several publishers to improve the amount of information present for key resources and reagents such as antibodies, cell lines, and other tools that constitute the inputs to a study. To improve the availability of these tables in the broader biomedical literature, we introduced four pipelines for key resource table extraction from biomedical documents in PDF format. Our approach reconstructs key resource tables using image level table detection and structure detection generated table boundary, column (and row) bounding box information together with PDF text alignment. To remedy row over-segmentation resulting from overflowing table cell contents, we introduced a language modeling (LM) based row merging solution where a character-level generative pre-trained transformer (GPT) model was pre-trained on more than 11 million scientific table contents from PubMed Central Open Access Subset (PMC OAS). All introduced pipelines significantly outperformed GROBID baseline while our Table LM based row merging based pipeline, significantly outperformed all other pipelines including our OCR based pipeline.
Detecting single motor-unit activity in magnetomyography
Authors: Noury Nima , Marquetand Justus , Hartwig Stefan , Middelmann Thomas , Broser Philip , Siegel Markus
Published: October 2024

Studying the discharge patterns of motor units (MUs) is key to understanding the mechanisms underlying human motor behavior. Intramuscular electromyography (iEMG) allows direct study of MU activity, but is invasive. Surface electromyography (sEMG) offers a non-invasive alternative, but with lower spatial resolution. Recent advances in optically pumped magnetometers (OPMs) have sparked interest in the magnetic counterpart of EMG, magnetomyography (MMG), as an additional non-contact modality to study the neuromuscular system. However, it remains unclear whether MMG signals recorded with superconducting quantum interference devices (SQUIDs) or OPMs can be used to directly detect individual MUs. We addressed this question in a proof-of-principle study in which we recorded MMG signals from the abductor digiti minimi (ADM) muscle using SQUIDs and OPMs. Critically, we simultaneously recorded iEMG from the same muscle to validate the non-invasive measurements. First, we found that invasively recorded MUs can be detected in simultaneously recorded SQUID and OPM MMG signals. Second, we found that invasively validated MUs can be extracted directly from SQUID and OPM MMG. This provides converging evidence that individual MU activity is accessible using non-contact MMG. Our findings highlight the potential of MMG as a non-contact modality to measure and study muscle activity in health and disease.Studying the discharge patterns of motor units (MUs) is key to understanding the mechanisms underlying human motor behavior. Intramuscular electromyography (iEMG) allows direct study of MU activity, but is invasive. Surface electromyography (sEMG) offers a non-invasive alternative, but with lower spatial resolution. Recent advances in optically pumped magnetometers (OPMs) have sparked interest in the magnetic counterpart of EMG, magnetomyography (MMG), as an additional non-contact modality to study the neuromuscular system. However, it remains unclear whether MMG signals recorded with superconducting quantum interference devices (SQUIDs) or OPMs can be used to directly detect individual MUs. We addressed this question in a proof-of-principle study in which we recorded MMG signals from the abductor digiti minimi (ADM) muscle using SQUIDs and OPMs. Critically, we simultaneously recorded iEMG from the same muscle to validate the non-invasive measurements. First, we found that invasively recorded MUs can be detected in simultaneously recorded SQUID and OPM MMG signals. Second, we found that invasively validated MUs can be extracted directly from SQUID and OPM MMG. This provides converging evidence that individual MU activity is accessible using non-contact MMG. Our findings highlight the potential of MMG as a non-contact modality to measure and study muscle activity in health and disease.
Parameter Dependence in Identifiability Applied to FP-Fisher-KPP Reaction-Diffusion Equations Parameterized for Tauopathy Network Modeling
Authors: Rahimabadi Arsalan , Benali Habib
Published: October 2024

Parameterization and a priori identifiability analysis are two interconnected steps that should be carried out in advance of model calibration. In the first place, we propose a framework for parameterizing a recently introduced and analytically studied generalization of the celebrated Fisher-Kolmogorov-Petrovsky-Piskunov (Fisher-KPP) reaction-diffusion (Re-Di) equation with fractional polynomial (FP) terms to model heterogeneous nonlinear diffusion in the propagation of a given species through directed networks, exemplified by the tauopathy progression in Alzheimer's disease (AD). Next, we present our results on identifiability in a generic sense for the parameterized FP-Fisher-KPP Re-Di equations with regular multi-experimental designs, seamlessly applicable to meromorphic systems, encompassing analytic systems. In particular, the concept of generic local minimal dependence of unknown parameters and regularly parameterized initial conditions will be formalized through the use of one-parameter Lie groups of transformations, and a decomposition method to explore this new concept will be devised. Finally, the Allen Mouse Brain Connectivity Atlas (AMBCA) dataset is utilized to develop a model for tauopathy progression in the mouse brain, which will subsequently be employed to implement the proposed methodology for analyzing a priori identifiability.
Genealogies under purifying selection
Authors: Khudiakova Ksenia A. , Boenkost Florin , Tourniaire Julie
Published: October 2024

Selection against deleterious mutations, called purifying selection, plays a central role in evolution and acts in all populations. It is known that the genetic patterns observed in genomic regions undergoing purifying selection differ from those resulting from neutral evolution. However, a comprehensive understanding of the underlying mechanisms shaping those patterns is still lacking.

In the present work, we use simulations combined with a genealogical approach to identify the effect of purifying selection on the ancestry and thus on the genetic diversity. Our analysis relies on the postulate that the genealogy belongs to the universality class of Beta-coalescents. Under this assumption, we derive statistics measuring the distortion of the genealogy. This approach allows us to consider a wide range of regimes (i.e. arbitrary selection and mutation strengths) and uncover a rich phase diagram. We find that, for strong selection, the limiting genealogy is given by Kingman’s coalescent on a polynomial timescale. As selection gets weaker, Muller’s ratchet starts operating, setting off the emergence of multiple mergers in the genealogical structures. Our results show that while multiple-merger coalescents are often interpreted as the signature of selective sweeps in rapidly adapting populations, these structures can also appear in the context of Muller’s ratchet.
Temporary cerebral ischaemia impairs thromboxane A2 constriction and induces hypertrophic remodelling in peripheral mesenteric arteries of hypertensive rats: limited reversal despite long-term suberoylanilide hydroxamic acid cerebroprotection
Authors: Díaz-Pérez Andrea , Lope-Piedrafita Silvia , Pérez Belén , Vázquez-Sufuentes Paula , Rodriguez-Garcia Maria , Briones Ana M , Navarro Xavier , Penas Clara , Jiménez-Altayó Francesc
Published: October 2024

Stroke induces brain injury, especially severe in hypertensive patients, and elevates mortality rates through non-neurological complications. However, the potential effects of a transient ischaemic episode on the peripheral vasculature of hypertensive individuals remain unclear. Here, we investigated whether transient cerebral ischaemia (90 min)/reperfusion (1 or 8 days) induces alterations in mesenteric resistance artery (MRA) properties in adult male spontaneously hypertensive rats (SHR). In addition, we assessed whether the reported cerebroprotective effects of suberoylanilide hydroxamic acid (SAHA; 50 mg/kg; administered intraperitoneally at 1, 4, or 6 h after reperfusion onset) extend long-term and include beneficial effects on MRAs. Functional and structural properties of MRAs were examined at 1- and 8-days post-stroke. Nuclei distribution, collagen content, and oxidative stress were assessed. Ischaemic brain damage was evaluated longitudinally using magnetic resonance imaging. Following stroke, MRAs from SHR exhibited non-reversible impaired contractile responses to the thromboxane A2 receptor agonist U46619. Stroke increased the MRA cross-sectional area, wall thickness, and wall/lumen ratio due to augmented collagen deposition. These changes were partially sustained 8 days later. SAHA did not improve U46619-induced contractions but mitigated stroke-induced oxidative stress and collagen deposition, preventing MRA remodelling at 24 h of reperfusion. Furthermore, SAHA induced sustained cerebroprotective effects over 8 days, including reduced brain infarct and oedema, and improved neurological scores. However, SAHA had minimal impact on chronic MRA contractile impairments and remodelling. These findings suggest that stroke causes MRA changes in hypertensive subjects. While SAHA treatment offers long-term protection against brain damage, it cannot fully restore MRA alterations.
RAS/PI3K pathway mutations sensitise epithelial ovarian cancer cells to a PARP/NAMPT inhibitor combination
Authors: Gruet Michael , Xu Yitao , An Lyutong , Ma Yurui , Balcells Cristina , Tyson Katie , Spear Sarah , Xu Yuewei , McKinney Flora , Babuta Julia , Bray Chandler , Wickremesinghe Chiharu , Siskos Alexandros P. , Nijhuis Anke M. , Tate Edward W. , McNeish Iain A. , Benito Adrian , Keun Hector C.
Published: October 2024

The combination of PARP and NAMPT inhibitors (PARPi/NAMPTi) has been explored for the treatment of TNBC, Ewing Sarcoma and high grade serous carcinoma (HGSC). However, dose limiting toxicity has hampered NAMPTi in clinical trials. To maximise the therapeutic window, we set out to identify predictive genomic biomarkers. Bioinformatic analysis and screening of a panel of epithelial ovarian cancer (EOC) cell lines revealed that cells with RAS/PI3K pathway mutations were sensitive to the NAMPTi FK866. Activity of olaparib and FK866 was associated with a reduction in nicotinamide mononucleotide (NMN) and the PARP substrate nicotinamide adenine dinucleotide (NAD+), with coincident increases in ROS production, DNA damage and apoptosis induction. Caspase 3/7 activity was upregulated to a greater extent in RAS/PI3K mutant cell lines. Finally, the combination significantly reduced omental tumour weight and increased overall survival in mice injected with ID8Trp53-/-;Pten-/-cells. This study highlights the potential of the PARPi/NAMPTi combination in RAS/PI3K pathway mutant EOC.
Sensorimotor integration enhances temperature stimulus processing
Authors: Anderson Lindsay S , Costabile Jamie D , Schwinn Sina , Calderon Delia , Haesemeyer Martin
Published: October 2024

Animals optimize behavior by integrating sensory input with motor actions. We hypothe-sized that coupling thermosensory information with motor output enhances the brain’s capacity to process temperature changes, leading to more precise and adaptive behaviors. To test this, we developed a virtual “thermal plaid” environment where zebrafish either actively controlled temperature changes (sensorimotor feedback) or passively experienced the same thermal fluctuations. Our findings demonstrate that sensorimotor feedback amplifies the influence of thermal stimuli on swim initiation, resulting in more structured and organized motor output. We show that previously identified mixed-selectivity neurons that simultaneously encode thermal cues and motor activity enable the integration of sensory and motor feedback to optimize behavior. These results highlight the role of sensorimotor integration in refining thermosensory processing, revealing critical neural mechanisms underlying flexible thermoregulatory behavior. Our study offers new insights into how animals adaptively process environmental stimuli and adjust their actions, contributing to a deeper understanding of the neural circuits driving goal-directed behavior in dynamic environments.
Defense mechanisms inLupinus luteusagainstColletotrichum lupini, involving TIR-NBS-LRR protein, hypersensitive response and phenylpropanoid pathways
Authors: Armijo-Godoy Grace , Levicoy Daniela , Martínez-Hernández J. Eduardo , Rupayan Annally , Hernández Sebastián , Carrasco Makarena , Caligari Peter DS , Baroncelli Riccardo , Salvo-Garrido Haroldo
Published: October 2024

Lupins are key grain legumes for future crop production, providing highly sustainable protein, essential in the face of global warming, food security challenges, and the need for sustainable agriculture. Despite their potential, lupin crops are frequently devastated byColletotrichum lupini, a member of the world’s top ten fungal pathogenic genera. In our previous study, we identifiedLluR1, the firstC. lupiniresistance gene, in a wildLupinus luteusaccession. Further research was necessary to unravel the defense mechanisms involved. Histological analysis revealed a hypersensitive response againstC. lupini, while transcriptome analysis highlighted a complex network of differentially expressed genes, including TIR-NBS-LRR proteins, hypersensitive response, and phenylpropanoid pathways. SNPs were identified that distinguish the protein sequences underlying immunity. These findings, along with orthology in other lupin species, offer valuable insights for developing breeding strategies to enhanceC. lupiniresistance in lupins, with significant potential impacts on food, feed, and human nutrition.
A percolation-type criticality threshold controls immune protein coating of surfaces
Authors: Wang Zhicheng , Kulkarni Sahil , Nong Jia , Zamora Marco , Ebrahimimojarad Alireza , Hood Elizabeth , Shuvaeva Tea , Zaleski Michael , Gullipalli Damodar , Wolfe Emily , Espy Carolann , Arguiri Evguenia , Wang Yufei , Marcos-Contreras Oscar A , Song Wenchao , Muzykantov Vladimir R , Fu Jinglin , Radhakrishnan Ravi , Myerson Jacob W , Brenner Jacob S
Published: October 2024

When a material enters the body, it is immediately attacked by hundreds of proteins, organized into complex networks of binding interactions and reactions. How do such complex systems interact with a material, “deciding” whether to attack? We focus on the “complement” system of ∼40 blood proteins that bind microbes, nanoparticles, and medical devices, initiating inflammation. We show a sharp threshold for complement activation upon varying a fundamental material parameter, the surface density of potential complement attachment points. This sharp threshold manifests at scales spanning single nanoparticles to macroscale pathologies, shown here for diverse engineered and living materials. Computational models show these behaviors arise from a minimal subnetwork of complement, manifesting percolation-type critical transitions in the complement response. This criticality switch explains the “decision” of a complex signaling network to interact with a material, and elucidates the evolution and engineering of materials interacting with the body.
IOP-induced blood-retinal barrier compromise contributes to RGC death in glaucoma
Authors: Zhang Chi , Simón Marina , Lim Haeyn , Tolman Nicholas G. , Horbal Logan , Juarez Felicia A. , Bhandari Aakriti , Montgomery Christa , John Simon W.M.
Published: October 2024

The integrity of the blood-retinal barrier (BRB) has been largely unexplored in glaucoma. We reveal that elevated intraocular pressure (IOP) partially compromises the BRB in two human-relevant inherited mouse models of glaucoma (DBA/2J andLmx1bV265D). Experimentally increasing IOP in mouse eyes further confirms this. Notably, the compromise induces subtle leakage, happening without bleeding or detected endothelial cell junction disruption, and it precedes neurodegeneration. Leakage occurs from peripheral veins in the retinal ganglion cell layer with a concomitant loss of the transcytosis inhibitor MFSD2A. Importantly, stabilizing β-catenin in retinal endothelial cells prevents both vascular leakage and neurodegeneration in the DBA/2J model. The occurrence of leakage in all 3 high IOP models indicates that BRB compromise may be a common, yet overlooked, mechanism in glaucoma. These findings suggest that IOP-induced BRB compromise plays a critical role in glaucoma, offering a new therapeutic target.
Engineering mtDNA Deletions by Reconstituting End-Joining in Human Mitochondria
Authors: Fu Yi , Land Max , Cui Ruobing , Kavlashvili Tamar , Kim Minsoo , Lieber Toby , Ryu Keun Woo , DeBitetto Emily , Masilionis Ignas , Saha Rahul , Takizawa Meril , Baker Daphne , Tigano Marco , Reznik Ed , Sharma Roshan , Chaligne Ronan , Thompson Craig B. , Pe’er Dana , Sfeir Agnel
Published: October 2024

Recent breakthroughs in the genetic manipulation of mitochondrial DNA (mtDNA) have enabled the precise introduction of base substitutions and the effective removal of genomes carrying harmful mutations. However, the reconstitution of mtDNA deletions responsible for severe mitochondrial myopathies and age-related diseases has not yet been achieved in human cells. Here, we developed a method to engineer specific mtDNA deletions in human cells by co-expressing end-joining (EJ) machinery and targeted endonucleases. As a proof-of-concept, we used mito-EJ and mito-ScaI to generate a panel of clonal cell lines harboring a ∼3.5 kb mtDNA deletion with the full spectrum of heteroplasmy. Investigating these isogenic cells revealed a critical threshold of ∼75% deleted genomes, beyond which cells exhibited depletion of OXPHOS proteins, severe metabolic disruption, and impaired growth in galactose-containing media. Single-cell multiomic analysis revealed two distinct patterns of nuclear gene deregulation in response to mtDNA deletion accumulation; one triggered at the deletion threshold and another progressively responding to increasing heteroplasmy. In summary, the co-expression of mito-EJ and programable nucleases provides a powerful tool to model disease-associated mtDNA deletions in different cell types. Establishing a panel of cell lines with a large-scale deletion at varying levels of heteroplasmy is a valuable resource for understanding the impact of mtDNA deletions on diseases and guiding the development of potential therapeutic strategies.

Graphical Abstract

Highlights

Combining prokaryotic end-joining with targeted endonucleases generates specific mtDNA deletions in human cells

Engineering a panel of cell lines with a large-scale deletion that spans the full spectrum of heteroplasmy

75% heteroplasmy is the threshold that triggers mitochondrial and cellular dysfunction

Two distinct nuclear transcriptional programs in response to mtDNA deletions: threshold-triggered and heteroplasmy-sensing
Genes Underlying Adaptive Physiological Shifts Among Hibernating Mammals
Authors: Drabeck Danielle H. , Anderson Myana , Roback Emma Y. , Lusczek Elizabeth R. , Tri Andrew N. , Lassen Jens Flensted , Kowalczyk Amanda E , McGaugh Suzanne , Iles Tinen L
Published: October 2024

Hibernation has evolved several times in mammals to overcome harsh winter climates and food scarcity. During hibernation, animals undergo extreme shifts in metabolic rate, heart rate, respiration, and body temperature. These changes reduce energy consumption and allow animals to survive solely on their fat reserves. Understanding the mechanisms for these extreme shifts has long been recognized as a model for translational medicine as hibernators do not exhibit the same adverse effects of extended immobility that non-hibernating mammals suffer. Though work on individual species has illuminated important mechanisms of these functional changes, the genomic basis of this phenotype remains largely unknown, and few studies have drawn on comparative work to elucidate commonalities across diverse hibernating mammals. Synthesizing both single species and comparative approaches, we use metabolomic data from active and denning black bears (Ursus americanus) to guide bioinformatic analyses of genes using tests of selection and evolutionary rate convergence across independent lineages of hibernating mammals. We identify several genes with significant signatures of selection and evolutionary rate convergence in hibernators that represent both previously known and novel genetic mechanisms of the hibernation phenotype. These data provide novel insights into the genetic basis of this adaptation and serve to direct clinical research in hibernation-based therapies.
Exploring voltage-gated sodium channel conformations and protein-protein interactions using AlphaFold2
Authors: Lopez-Mateos Diego , Narang Kush , Yarov-Yarovoy Vladimir
Published: October 2024

Voltage-gated sodium (NaV) channels are vital regulators of electrical activity in excitable cells, playing critical roles in generating and propagating action potentials. Given their importance in physiology, NaVchannels are key therapeutic targets for treating numerous conditions, yet developing subtype-selective drugs remains challenging due to the high sequence and structural conservation among NaVfamily members. Recent advances in cryo-electron microscopy have resolved nearly all human NaVchannels, providing valuable insights into their structure and function. However, limitations persist in fully capturing the complex conformational states that underlie NaVchannel gating and modulation. This study explores the capability of AlphaFold2 to sample multiple NaVchannel conformations and assess AlphaFold Multimer’s accuracy in modeling interactions between the NaVα-subunit and its protein partners, including auxiliary β-subunits and calmodulin. We enhance conformational sampling to explore NaVchannel conformations using a subsampled multiple sequence alignment approach and varying the number of recycles. Our results demonstrate that AlphaFold2 models multiple NaVchannel conformations, including those from experimental structures, new states not yet experimentally identified, and potential intermediate states. Furthermore, AlphaFold Multimer models NaVcomplexes with auxiliary β-subunits and calmodulin with high accuracy, and the presence of protein partners significantly alters the conformational landscape of the NaVα-subunit. These findings highlight the potential of deep learning-based methods to expand our understanding of NaVchannel structure, gating, and modulation, with significant implications for future drug discovery efforts.
Transfer to different host grapevines causes rapid and widespread transcriptional plasticity in the specialist insectDaktulosphaira vitifoliae
Authors: Collison W. Nate , Zafar Syed Adeel , Groen Simon C. , Nabity Paul D.
Published: October 2024

Insect herbivores employ many adaptive mechanisms to successfully colonize host plants. Transcriptional plasticity is one important mechanism that enables host use in polyphagous insects that maintain a broad host range. However, whether specialist herbivores also rely on transcriptional plasticity to feed successfully on different hosts remains largely unexplored. Here, we measure genome-wide transcriptional plasticity of grape phylloxera,Daktulosphaira vitifoliae, a grapevine (Vitisspp.) specialist, after transfer onto different host grapevines for a single generation using RNA-seq. We show that the transcriptome ofD. vitifoliaeis highly plastic and responsive to host genotype – 4,820 genes (37% of the 12,876 expressed genes) are significantly differentially expressed in at least one contrast comparing host genotypes. Genes with functions related to host manipulation (predicted secretory effectors), cuticle and chitin, detoxification of xenobiotics, and development were enriched among host-responsive genes, with predicted secretory effectors being most strongly enriched (Fisher’s exact test odds ratio = 8.3, BH-adjusted p-value = 0). We further linked gene co-expression modules toD. vitifoliaefitness using weighted gene co-expression network analysis. The co-expression module most strongly correlated with fitness was enriched for predicted secretory effectors, including a novel group of proline-rich genes that exist as a tandem gene cluster. The only module negatively correlated with fitness was enriched for genes encoding glycoside hydrolase enzymes that function in carbohydrate metabolism. Overall, our results show that the phylloxerid transcriptome is highly plastic and rapidly reprogrammed when transferred onto distinct hosts, which may be an adaptive mechanism underlying host use in this clonally reproducing herbivore.
Integrated temporal profiling of iPSCs-derived motor neurons from ALS patients carrying C9orf72, FUS, TARDBP, and SOD1 mutations
Authors: Ma Guoming , Xia Congcong , Lyu Boyu , Liu Jie , Luo Fang , Guan Mingfeng , Wang Junying , Sun Li , Zhang Lin , Chen Yan , Mao Yingwei , Yu Guoqiang , Wang Wenyuan
Published: October 2024

Amyotrophic Lateral Sclerosis (ALS) is a lethal neurodegenerative disease that damages motor neurons in the central nervous system, causing progressive muscle weakness that ultimately leads to death. However, its underlying mechanisms still need to be fully understood, particularly the heterogeneity and similarity between various gene mutants during disease progression. In this study, we conducted temporal RNA-seq profiling in human induced pluripotent stem cells (hiPSCs) and iPSC-derived motor neurons (iMNs) carrying the C9orf72, FUS, TARDBP, and SOD1 mutations from both ALS patients and healthy individuals. We discovered dysregulated gene expression and alternative splicing (AS) throughout iMN development and maturation, and ALS iMNs display enrichment of cytoskeletal defects and synaptic alterations from premature stage to mature iMNs. Our findings indicate that synaptic gene dysfunction is the common molecular hallmark of fALS, which might result in neuronal susceptibility and progressive motor neuron degeneration. Analysis of upstream splicing factors revealed that differentially expressed RNA-binding proteins (RBPs) in ALS iMNs may cause abnormal AS events, suggesting the importance of studying RBP defects in ALS research. Overall, our research provides a comprehensive and valuable resource for gaining insights into the shared mechanisms of ALS pathogenesis during motor neuron development and maturation in iMN models.
Weekly inhaled salmeterol xinafoate, a selective β2 adrenergic receptor agonist drug, therapeutically inhibits cancer growth and prolongs survivalin vivo
Authors: She Xiaofei , Ma Junxian , Gao Hua
Published: October 2024

Humans have spent approximately 99.5% of the 2.5 million years of evolutionary history as hunter-gatherers, which helped to evolutionarily mold our minds and bodies to the hunting and gathering lifestyle. Physical activity associated with hunting animals, gathering plants, and evading predators is essential for human survival, evolution, and prosperity. Thus, physical activity (acute stress) is mostly beneficial to the body, whereas psycho-emotional stress (chronic stress) is usually detrimental at the psychological, physiological, and pathological levels. Although physical activity exerts anticancer effects and psycho-emotional stress exhibits cancer-promoting effects, both function through the same pathway involving activation of the sympathetic nervous system, release of catecholamines, and stimulation of β2 adrenergic receptor (β2AR) expressed on cancer cells. Here, salmeterol xinafoate was chosen to mimic physical activity. A once-weekly administration of salmeterol xinafoate by the intraperitoneal, inhalation, or transdermal route, dose-dependently extended latency, reduced cancer incidence and growth, and prolonged survivalin vivo. Remarkably, the best complete response rates were 75%, 30%, and 71.43% for the therapeutic treatment of lung cancer, breast cancer, and melanoma, respectively. Notably, the salmeterol xinafoate doses used in our experiments are comparable to those used in patients. Moreover, in endogenous β2AR knockout cancer cells, the exogenous β2AR mutant with impaired salmeterol xinafoate binding or downstream signaling prevented the anticancer effects of salmeterol xinafoatein vivo, demonstrating the on-target action of salmeterol xinafoate on cancer cells and the requirement of the downstream signaling pathway. Finally, we showed that treatment with salmeterol xinafoate dose-dependently decreased the self-renewal capacity of lung cancer stem cells, breast cancer stem cells, and melanoma stem cells. From the perspective of human evolution into cancer biology, our study reveals that β2AR represents an ideal anticancer drug target and that salmeterol xinafoate monotherapy has strong anticancer activity.
Survey of Lichen Diversity and Abundance in a Florida Scrub in Relation to Various Temporal Stages of Burn Recovery
Authors: Holst Meghan M. , Brandt Cassidy M. , Wolovich Christy K.
Published: October 2024

With the increased use of prescribed burns in recent years, it is critical to understand their impacts not only on their primary target species, but also on the entire biological community. Lichen have intricate symbioses with other neighboring organisms and provide important ecosystem services. In prairie and grassland environments, the prescribed burns may result in the extirpation of some ground-dwelling species of lichen. However, the impacts of fire schedules on the lichen recovery in Florida scrublands remains unknown. The dry, sandy scrub ecosystem houses Florida’s only federally endangered lichen, the Florida Perforate Lichen (Cladonia perforata). As scrub communities are adapted to the presence of fire, prescribed burns are now a routine management practice. Lichen has a key role in early plant succession following fire, influencing the health of Florida scrub. We used a modified Feest’s method to survey the effects of fire regime on terrestrial lichen abundance and diversity in the Lakeland Highlands Scrub, an area of scrub habitat in Polk County in Central Florida. The speed and comparable accuracy of Feest’s method render it an accessible means of assessing biodiversity for land management in protected areas. We estimated percent cover of lichen and estimated species diversity using the Lichen Diversity Value (LDV) in four areas of scrub and scrubby flatwoods habitat with different burn histories (unburned; and two years, eight years, and ten years since last burn). According to the LDV calculations, diversity is highest in the most extreme temporal groups, contradicting our initial prediction that lichen diversity and abundance would be greatest in the intermediately disturbed areas (two and eight years post-burn). These preliminary data suggest implementing prescribed burns more frequently in this scrub habitat would allow lichen communities a greater opportunity to recover. Our study yields beneficial information to assist future decisions made regarding the frequency of fire regimes within the Florida scrublands habitat. Methods of protecting lichen may also be recommended, such as collecting and removing lichen prior to a burn, and returning those lichen samples to the area after (e.g. “Remove and Return”).
Predicting the Risk of Progression from Barrett’s Esophagus to Esophageal Adenocarcinoma with a Mass-Spectrometry-Based Proteomic Panel
Authors: Cannon Andrew , Hiatt Mark , Ban Igor , Sayad Saed , Karkus Ted , Hartley Christopher
Published: October 2024

Background

Esophageal adenocarcinoma (EAC) is a highly aggressive cancer with poor prognosis, often arising from gastroesophageal reflux disease (GERD) and its precursor, Barrett’s esophagus (BE). Although only a small proportion of individuals with GERD or BE develop EAC, accurately identifying those at high risk is critical for early intervention. Current surveillance methods, such as endoscopy, are invasive and have limited accuracy in predicting malignant transformation. Mass-spectrometry-based proteomics offers a promising alternative by identifying protein biomarkers associated with disease progression.

Method

This study evaluated an eight-protein panel in predicting the risk of progression from BE to BE with high-grade dysplasia or EAC, potentially improving early detection and patient outcomes. A cohort of 107 subjects diagnosed with BE was recruited, and biological samples (tissue biopsies) were collected and labeled by a pathologist. Proteomic analysis was conducted using mass spectrometry to profile protein expression across the samples. A statistical test (t-test) was applied to assess differences in the proteomic panel across BE that progressed on follow-up compared to BE without progression.

Results

The t-test results revealed significant differences in protein expression levels between subjects with BE who progressed to cancer and those who did not. Key proteins, including CNDP2_TVF, DAD1 (detected via the FLE and ADF peptides), and GPI_LQQ, demonstrated strong statistical significance (p < 0.001) for under-expression, suggesting their potential as early biomarkers for identifying individuals at high risk. S100p_YSG also showed meaningful under-expression (p = 0.0111), indicating its relevance in cancer progression pathways. In contrast, LTF_DGA was over-expressed (p = 0.0226), possibly serving as an activator in the progression pathway and offering a novel therapeutic target.

Conclusions

This study identified promising biomarkers on the panel—including CNDP2_TVF, DAD1 (detected via the FLE and ADF peptides), and GPI_LQQ—associated with the development of advanced cancer in BE. Their under-expression could inform novel diagnostic and therapeutic approaches. Integrating these protein profiles with genetic and epigenetic data may provide a more complete understanding of disease progression. Longitudinal studies tracking protein levels over time may also reveal their potential as early cancer markers.
Clinical Relevance and Applicability of the 2022 World Health Organization Classification of Childhood B Lymphoblastic Leukemia in the Context of MRD-Directed Therapy
Authors: Rajpal Sweta , Chatterjee Gaurav , Bhanshe Prasanna , Terse Vishram , Joshi Swapnali , Chaudhary Shruti , Shetty Dhanalaxmi , Mohanty Purvi , Dhamne Chetan , Tembhare Prashant , Srinivasan Shyam , Chichra Akanksha , Malik Nirmalya Roy , Banavali Shripad , Gujral Sumeet , Narula Gaurav , Subramanian PG , Patkar Nikhil
Published: October 2024

WHO5-2022 classification of B-lymphoblastic leukemia (B-ALL) incorporates several novel entities requiring high-throughput sequencing for their accurate characterization. The clinical relevance of this classification in the context of contemporary MRD-directed therapy is unclear. We analyzed 533 pediatric B-ALL uniformly treated with ICiCLe-ALL-14 protocol as defined by WHO2016 and reclassified them as per WHO5-2022 using targeted sequencing, FISH, and cytogenetics. Subtype-defining genetic abnormalities were identified in 81.2% of the cohort as per the WHO5 classification. Among the new subtypes,PAX5alt,MEF2D-r, andBCR::ABL1-like(ABL-class) were associated with an inferior 2-year event-free survival (EFS) of 39.1% (p<0.0001), 53.8% (p=0.024) and 60.6% (p=0.043), respectively. We developed a 3-tier genetic risk stratification model incorporating 15 genetic subtypes and theIKZF1deletion. Children with standard, intermediate, and high genetic risk demonstrated 2-year EFS of 92.6%, 71.0%, and 50.7% (p<0.0001), and 2-year overall survival of 94.3%, 81.9%, and 71.6% (p<0.0001), respectively. Genetic risk further identified heterogeneous outcomes among ICiCLe risk groups (p<0.0001). Standard genetic risk was associated with superior OS and EFS irrespective of MRD status. We demonstrate the applicability of the WHO5 classification in routine practice and create a general framework for incorporating the WHO5 classification in risk-adapted therapy for childhood B-ALL.