bluuebunny/crossref_metadata_2025 huggingface dataset:
Fibrotic Extracellular Matrix Preferentially Induces a Partial Epithelial-Mesenchymal Transition Phenotype in a 3-D Agent Based Model of Fibrosis
Authors: Kim Kristin P. , Lemmon Christopher A.
Published: June 2024

One of the main drivers of fibrotic diseases is epithelial-mesenchymal transition (EMT): a transdifferentiation process in which cells undergo a phenotypic change from an epithelial state to a pro-migratory state. The cytokine transforming growth factor-β1 (TGF-β1) has been previously shown to regulate EMT. TGF-β1 binds to fibronectin (FN) fibrils, which are the primary extracellular matrix (ECM) component in renal fibrosis. We have previously demonstrated experimentally that inhibition of FN fibrillogenesis and/or TGF-β1 tethering to FN inhibits EMT. However, these studies have only been conducted on 2-D cell monolayers, and the role of TGF-β1-FN tethering in 3-D cellular environments is not clear. As such, we sought to develop a 3-D computational model of epithelial spheroids that captures both EMT signaling dynamics and TGF-β1-FN tethering dynamics. We have incorporated the bi-stable EMT switch model developed by Tian et al. (2013) into a 3D multicellular model, capturing both temporal and spatial TGF-β1 signaling dynamics. We show that the addition of TGF-β1 affects cell proliferation, EMT progression, and cell migration. We then incorporate TGF-β1-FN fibril tethering by locally reducing the TGF-β1 diffusion coefficient as a function of EMT to simulate the reduced movement of TGF-β1 when tethered to FN fibrils during fibrosis. We show that incorporation of TGF-β1 tethering to FN fibrils promotes a partial EMT state, independent of exogenous TGF-β1 concentration, indicating a mechanism by which fibrotic ECM can promote a partial EMT state.

Author summary

Epithelial-mesenchymal transition (EMT) is a key cellular process where epithelial cells transform and become mesenchymal. The EMT states are not binary, but instead exhibit a spectrum of partial states where epithelial cells express a combination of epithelial and mesenchymal markers, along with several markers distinct to the partial state. In diseases such as fibrosis and cancer, growing evidence supports the finding that diseased epithelial cells exist primarily in a partial EMT state. However, the mechanisms and signaling factors that drive this partial EMT state in fibrotic diseases is unclear. We use an agent-based model that looks at EMT progression in a population of cells embedded in an ECM environment with controllable fibrotic properties to provide a more systematic approach at studying spatial and temporal changes in the microenvironment that could drive EMT progression and maintain specific EMT phenotypes.
BulkRNABert: Cancer prognosis from bulk RNA-seq based language models
Authors: Gélard Maxence , Richard Guillaume , Pierrot Thomas , Cournède Paul-Henry
Published: June 2024

RNA sequencing (RNA-seq) has become a key technology in precision medicine, especially for cancer prognosis. However, the high dimensionality of such data may restrict classic statistical methods, thus raising the need to learn dense representations from them. Transformers models have exhibited capacities in providing representations for long sequences and thus are well suited for transcriptomics data. In this paper, we develop a pre-trained transformer-based language model through self-supervised learning using bulk RNA-seq from both non-cancer and cancer tissues, following BERT’s masking method. By probing learned embeddings from the model or using parameter-efficient fine-tuning, we then build downstream models for cancer type classification and survival time prediction. Leveraging the TCGA dataset, we demonstrate the performance of our method,BulkRNABert, on both tasks, with significant improvement compared to state-of-the-art methods in the pan-cancer setting for classification and survival analysis. We also show the transfer-learning capabilities of the model in the survival analysis setting on unseen cohorts. Code available athttps://github.com/instadeepai/multiomics-open-research
The role of liprin-α1 phosphorylation in its liquid-liquid phase separation: regulation by PPP2R5D/PP2A holoenzyme
Authors: Mayer Abigail , Derua Rita , Spahn Elijah , Verbinnen Iris , Zhang Yang , Wadzinski Brian , Swingle Mark R. , Honkanen Richard , Janssens Veerle , Xia Houhui
Published: June 2024

Liprin-α1 is a widely expressed scaffolding protein responsible for regulating cellular processes such as focal adhesion, cell motility, and synaptic transmission. Liprin-α1 interacts with many proteins including ELKS, GIT1, liprin-β, and LAR-family receptor tyrosine protein phosphatase. Through these protein-protein interactions, liprin-α1 assembles large higher-order molecular complexes; however, the regulation of this complex assembly/disassembly is unknown. Liquid-liquid phase separation (LLPS) is a process that concentrates proteins within cellular nano-domains to facilitate efficient spatiotemporal signaling in response to signaling cascades. While there is no report that liprin-α1 spontaneously undergoes LLPS, we found that GFP-liprin-α1 expressed in HEK293 cells occasionally forms droplet-like condensates. MS-based interactomics identified Protein Phosphatase 2A (PP2A)/B56δ (PPP2R5D) trimers as specific interaction partners of liprin-α1 through a canonical Short Linear Interaction Motif (SLiM) in its N-terminal dimerization domain. Mutation of this SLiM nearly abolished PP2A interaction, and resulted in significantly increased LLPS. GFP-liprin-α1 showed significantly increased droplet formation in HEK293 cells devoid of B56δ (PPP2R5D knockout), suggesting that PPP2R5D/PP2A holoenzyme inhibits liprin-α1 LLPS. Guided by reported liprin-α1 Ser/Thr phosphorylation sites, we found liprin-α1 phospho-mimetic mutant at serine 763 (S763E) is sufficient to drive its LLPS. Domain mapping studies of liprin-α1 indicated that the intrinsically disordered region, the N-terminal dimerization domain, and the SAM domains are all necessary for liprin-α1 LLPS. Finally, expression of p.E420K, a human PPP2R5D variant causing Houge-Janssens Syndrome type 1 (also known as Jordan’s Syndrome), significantly compromised suppression of liprin-α1 LLPS. Our work identified B56δ-PP2A holoenzyme as an inhibitor of liprin-α1 LLPS via regulation at multiple phosphorylation sites.
WITHDRAWN: Extracting Auditory Emotion in Noise: A distributed auxiliary auditory network supporting affect processing of non-predictably obscured vocalisations
Authors: Swanborough Huw , Frühholz Sascha
Published: June 2024

Withdrawal Statement

The authors have withdrawn their manuscript owing to data encoding fault causing incorrect analysis. Therefore, the authors do not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding author.
Mitochondrial dysfunction: unraveling the elusive biology behind anti-TNF response during ulcerative colitis
Authors: Kioroglou Dimitrios , Peña-Cearra Ainize , Corraliza Ana M. , Seoane Iratxe , Castelo Janire , Panés Julian , Gómez-Irwin Laura , Rodríguez-Lago Iago , de Zarate Jone Ortiz , Fuertes Miguel , Martín-Ruiz Itziar , Gonzalez Monika , Aransay Ana Mª , Salas Azucena , Rodríguez Héctor , Anguita Juan , Abecia Leticia , Marigorta Urko M.
Published: June 2024

Background

Recent studies hint at mitochondrial genes influencing UC patient response to anti-TNF treatment. We evaluated this hypothesis by following a targeted strategy to identify gene expression that captures the relationship between mitochondrial dysregulation and response to treatment. Our objective was to initially examine this relationship in colon samples and subsequently assess whether the resulting signal persists in the bloodstream.

Methods

We analyzed the transcriptome of colon samples from an anti-TNF treated murine model characterized by impaired mitochondrial activity and treatment resistance. We then transferred the findings that linked mitochondrial dysfunction and compromised treatment response to an anti-TNF treated UC human cohort. We next matched differential expression in the blood using monocytes from peripheral blood of controls and IBD patients, and we evaluated a classification process at baseline with whole blood samples from UC patients.

Results

In human colon samples, the derived gene-set from the murine model showed differential expression, primarily enriched metabolic pathways, and exhibited similar classification capacity as genes enriching inflammatory pathways. Moreover, the evaluation of the classification signal using blood samples from UC patients at baseline highlighted the involvement of mitochondrial homeostasis in treatment response.

Conclusion

Our results highlight the involvement of metabolic pathways and mitochondrial homeostasis in determining treatment response and their ability to provide promising classification signals with detection levels in both colon and bloodstream.
Mendelian randomization for multiple exposures and outcomes with Bayesian Directed Acyclic Graphs exploration and causal effects estimation
Authors: Zuber Verena , Cronjé Toinét , Cai Na , Gill Dipender , Bottolo Leonardo
Published: June 2024

Current Mendelian randomization (MR) methods do not reflect complex relationships among multiple exposures and outcomes as is typical for real-life applications. We introduce MrDAG the first MR method to model dependency relations within the exposures, the outcomes, and between them to improve causal effects estimation. MrDAG combines three causal inference strategies in a unified manner. It uses genetic variation as instrumental variables to account for unmeasured confounders. It performs structure learning to detect and orientate the direction of the dependencies within exposures and outcomes. Finally, interventional calculus is employed to derive principled causal effect estimates. MrDAG was motivated to unravel how lifestyle and behavioural exposures impact mental health. It highlights education and smoking as key effective points of intervention given their down-stream effects on mental health. These insights would have been difficult to delineate without modelling the causal paths between multiple exposures and outcomes at once.
Dicarbonyl stress debilitates mesothelial defense against metastasizing ovarian cancer
Authors: Mishra Satyarthi , Vidhipriya Kottpalli , Gopikrishnan Anchita , Mishra Sudiksha , Prasanna CVS , Sen Prosenjit , Bhat Ramray
Published: June 2024

Chronic metabolic disorders and aging result in accumulation of active dicarbonyls that glycate biomolecules rendering them dysfunctional. Although metabolic aberrations are known to be epidemiologically associated with faster cancer progression, cell biological determinants of such associations remain elusive. The formation of micro-metastases in epithelial ovarian cancer involves its colonization of visceral peritonea through clearance of mesothelia that line the coelom. In this study, we observe that cocultures of immortalized human coelomic MeT-5A mesothelia with human ovarian cancer cells OVCAR-3 and SK-OV-3 show greater infiltration by the latter when exposed to increasing concentrations of the dicarbonyl methylglyoxal (MG). Treatment with increasing concentrations of MG caused death and senescence within human and murine serosal mesothelia. Cells showed higher levels of advanced glycation end products, dysregulated occludens junction protein ZO-1, and disrupted localization of cortical filamentous actin and its regulator ezrin, indicating poor inter-cell adhesion. Time lapse imaging also showed impaired migration for MG-treated single mesothelia and for their collective monolayers. Agent-based computer modeling of coculture dynamics predicted that a combined effect of confluence and migration allows inter-adherent mesothelia to contain the spread of colonizing cancer cells, which was confirmed through coculture time lapses of cancer colonization within higher and lower mesothelial densities. We found ovarian cancer cells showed higher levels of glyoxalase-1 (GLO-1) enzyme, which catabolizes MG, suggesting how they escaped its cytotoxic effects. Consistent with this, treatment of OVCAR-3 with MG concurrently with pharmacological inhibition of GLO-1 showed greater cell death. Our results suggest dicarbonyl stress helps colonizing cancer cells overcome the resistance of natural homoeostatic barriers and its inhibition may, in supplementation with chemotherapy, stem metastasis.
Variation in season length and development time is sufficient to drive the emergence and coexistence of social and solitary behavioral strategies
Authors: Ruttenberg Dee M. , Levin Simon A. , Wingreen Ned S. , Kocher Sarah D.
Published: June 2024

Season length and its associated variables can influence the expression of social behaviors, including the occurrence of eusociality in insects. Eusociality can vary widely across environmental gradients, both within and between different species. Numerous theoretical models have been developed to examine the life history traits that underlie the emergence and maintenance of eusociality, yet the impact of seasonality on this process is largely uncharacterized. Here, we present a theoretical model that incorporates season length and offspring development time into a single, individual-focused model to examine how these factors can shape the costs and benefits of social living. We find that longer season lengths and faster brood development times are sufficient to favor the emergence and maintenance of a social strategy, while shorter seasons favor a solitary one. We also identify a range of season lengths where social and solitary strategies can coexist. Moreover, our theoretical predictions are well-matched to the natural history and behavior of two flexibly-eusocial bee species, suggesting our model can make realistic predictions about the evolution of different social strategies. Broadly, this work reveals the crucial role that environmental conditions can have in shaping social behavior and its evolution and underscores the need for further models that explicitly incorporate such variation to study evolutionary trajectories of eusociality.
Plasticity and evolution of metabolic division of labour within families
Authors: Bladon EK , Hakala SM , Kilner RM , LeBoeuf AC
Published: June 2024

Fluids produced by parents for dependent young, such as milk or regurgitate, carry molecules that assist offspring with growth, immunity and digestion, allowing the metabolic burden of development to be shared between parents and offspring. We tested whether this division of metabolic labour changes plastically and evolves when offspring are experimentally deprived of their parents’ metabolic assistance. In the burying beetleNicrophorus vespilloidesparents deposit oral fluids on their carrion nest during pre-hatching care, and facultatively transfer fluids to larvae through oral trophallaxis as post-hatching care. We analysed the oral fluid proteomes of replicate experimental populations that had been evolving for 50 generations with or without post-hatching care, and which were then allowed to raise larvae with or without post-hatching care for one experimental generation. We found that parents and larvae plastically and evolutionarily adjusted the proteins in their oral fluids when we prevented post-hatching care. When reared in the absence of post-hatching care, larvae that evolved without post-hatching care were also more capable of consuming carrion proteins than larvae that had evolved with post-hatching care, and had higher survival. Our results suggest that metabolic division of labour within families is plastically modulated, and that the extent of socially modulated plasticity can evolve rapidly when social conditions change.
Phasic alertness generates urgency and amplifies competition between evidence accumulators
Authors: Tromp Jeshua , Wurm Franz , Lucchi Federica , de Kleijn Roy , Nieuwenhuis Sander
Published: June 2024

Although phasic alertness generally benefits cognitive performance, it often increases the interference caused by distracting information, resulting in impaired decision-making and cognitive control. However, it is unclear why phasic alertness has these negative effects. Here, we present a novel, biologically-informed account, according to which phasic alertness generates an evidence-independent urgency signal. This urgency signal shortens overall response times, but also amplifies competition between evidence accumulators, thus slowing down decision-making and impairing cognitive control. The key assumptions of this account are supported with pupil measurements and electrophysiological data from human decision-makers performing an arrow flanker task. We also show that a computational model of the flanker task that incorporates time-varying urgency can reproduce the behavioral effects of phasic alertness, but only when the evidence accumulators compete with each other through lateral inhibition. Our results reveal a close interplay between dynamic changes in urgency, cognitive control and evidence accumulation.
Rapid and Stimulus-Specific Deviance Detection in the Human Inferior Colliculus
Authors: Wetekam Johannes , Gotta Nell , López-Jury Luciana , Hechavarría Julio , Kössl Manfred
Published: June 2024

Auditory deviance detection, the neural process by which unexpected stimuli are identified within repetitive acoustic environments, is crucial for survival. While this phenomenon has been extensively studied in the cortex, recent evidence indicates that it also occurs in subcortical regions, including the inferior colliculus (IC). However, compared to animal studies, research on subcortical deviance detection in humans is often constrained by methodological limitations, leaving several important questions unanswered. This study aims to overcome some of these limitations by employing auditory brainstem responses (ABRs) to investigate the earliest neural correlates of deviance detection in humans, with a focus on the IC. We presented healthy participants of either sex with low- and high-frequency chirps in an oddball paradigm and observed significant deviance detection effects in the ABR, specifically when low-frequency chirps were used as deviants within a context of high-frequency standards. These effects manifested as larger and faster ABRs to deviant stimuli, with the strongest responses occurring at higher stimulation rates. Our findings suggest that the human IC exhibits rapid, stimulus-specific deviance detection with differential modulation of response amplitude and latency. The data indicate that the temporal dynamics of novelty detection in humans align well with the data reported in animals, helping to bridge the gap between animal and human research. By uncovering previously unknown characteristics of subcortical deviance detection in humans, this study highlights the value of ABR recordings with excellent temporal resolution in investigating subcortical deviance detection processes.

Significance statement

Auditory deviance detection enables the brain to identify unexpected stimuli in a repetitive environment, but its subcortical mechanisms in humans remain comparatively underexplored. Using auditory brainstem responses (ABRs), our study reveals two key findings about deviance detection in the human inferior colliculus (IC). First, we show subcortical deviance detection at latencies under 10 ms, bridging a longstanding gap between human and animal research. Second, deviance detection in the IC is rapid, emerging within three or fewer standard repetitions, with differential modulation of ABR amplitude and latency. These findings improve our understanding of the temporal dynamics of auditory processing in the human IC and highlight the value of ABR recordings in studying subcortical deviance detection mechanisms.
Hyperporous encapsulation of microbes for whole cell biocatalysis and biomanufacturing
Authors: Zhang Jingyi , Chang Keziah , Tay Joyce , Tiong Elaine , Heng Elena , Seah Theresa , Lim Yi Wee , Peh Guangrong , Lim Yee Hwee , Wong Fong Tian , Beh Cyrus W.
Published: June 2024

Compared to traditional synthetic chemical processes, biocatalysts offer a more sustainable and eco-friendly approach to producing complex molecules. In particular, whole-cell biocatalysts boast numerous advantages, including scalable, self-containing co-factor recycling systems, the use of cost-effective raw materials, and reduced purification costs. However, challenges arise when working with microbial consortia for biotransformation cascades. Our encapsulation strategy addresses these challenges by controlling microbial cell populations through physical constraints, offering a promising approach in biomanufacturing.

In this work, we describe the immobilization of cells in a hyper-porous hydrogel block, which provides ample nutrient access while simplifying media changes. We encapsulatedE. colicells in a hydrogel matrix with suitable mechanical properties, effectively limiting their proliferation while sustaining recombinant GFP production. Furthermore, we successfully maintained different microbial strains spatially in a single porous hydrogel block for at least 10 days, demonstrating the potential of this method for achieving stable co-culture. Finally, we demonstrated the application of immobilizedE. colifor co-culture fermentation. The immobilization ofE. coliheterologously expressing RadH halogenase significantly improved the efficiency of genistein halogenation in a co-culture with genistein-producingStreptomycescompared to its non-immobilized counterpart.
Rituximab-IgG2 is a phagocytic enhancer in antibody-based immunotherapy of B-cell lymphoma by altering CD47 expression
Authors: Nguyen Oanh T.P. , Lara Sandra , Ferro Giovanni , Peipp Matthias , Kleinau Sandra
Published: June 2024

Antibody-dependent phagocytosis (ADP) by monocytes and macrophages contributes significantly to the efficacy of many therapeutic monoclonal antibodies (mAbs), including anti-CD20 rituximab (RTX) targeting CD20+B-cell non-Hodgkin lymphomas (NHL). However, ADP is constrained by various immune checkpoints, notably the anti-phagocytic CD47 molecule, necessitating strategies to overcome this resistance.

The IgG2 isotype of RTX induces CD20-mediated apoptosis in B-cell lymphoma cells, and significantly enhances Fc receptor-mediated phagocytosis when used in combination with RTX-IgG1 or RTX-IgG3 mAbs, as previously described. Here, we report that the apoptotic effect of RTX-IgG2 on lymphoma cells contributes to changes in the tumor cell’s CD47 profile by reducing its overall expression and altering its surface distribution. Furthermore, when RTX-IgG2 is combined with other lymphoma-targeting mAbs, such as anti-PD-L1 or anti-CD59, it significantly enhances the ADP of lymphoma cells compared to single mAb treatment.

In summary, RTX-IgG2 acts as a potent phagocytic enhancer by promoting Fc-receptor mediated phagocytosis through apoptosis and reduction of CD47 in malignant CD20+B-cells. RTX-IgG2 represents a valuable therapeutic component in enhancing the effectiveness of different mAbs targeting B-cell NHL.
Highly-sensitive reporter cell line for detection of interferon types I-III and their neutralization by antibodies
Authors: Groen Kevin , Kuratli Roger , Vasou Andri , Huber Michael , Hughes David J. , Hale Benjamin G.
Published: June 2024

Interferons (IFNs) are a critical component of innate immune defenses and limit viral disease severity. To advance studies on IFNs and their neutralization by pathogenic autoantibodies, we generated a Renilla luciferase-based reporter cell line capable of detecting the activities of IFN-Is, IFN-II, and IFN-IIIs. The reporter cell line exhibits a 125-to 2000-fold higher sensitivity to IFNs than a commonly-used alternative biological reporter system, and allows for a rapid and simple live-cell workflow for detecting low titer amounts of neutralizing anti-IFN antibodies.
TheDlk1-Dio3noncoding RNA cluster coordinately regulates mitochondrial respiration and chromatin structure to establish proper cell state for muscle differentiation
Authors: Pinheiro Amanda , Petty Christopher A. , Cabrera Kevin , Tost Eric P. , Gower Adam C. , Marano Madison , Leviss Ethan M. , Boberg Matthew J. , Mahendran Jawahar , Bock Payton M. , Stephens Chelsea E. , Fetterman Jessica L. , Naya Francisco J.
Published: June 2024

The coordinate regulation of metabolism and epigenetics to establish cell state-specific gene expression patterns during lineage progression is a central aspect of cell differentiation, but the factors that regulate this elaborate interplay are not well-defined. The imprintedDlk1-Dio3noncoding RNA (ncRNA) cluster has been associated with metabolism in various progenitor cells, suggesting it functions as a regulator of metabolism and cell state. Here, we directly demonstrate that theDlk1-Dio3ncRNA cluster coordinates mitochondrial respiration and chromatin structure to maintain proper cell state. Stable muscle cell lines were generated harboring two distinct deletions in the proximal promoter region resulting in either greatly upregulated or downregulated expression of the entireDlk1-Dio3ncRNA cluster. Both mutant lines displayed impaired muscle differentiation along with altered mitochondrial respiration and genome-wide changes in chromatin accessibility and histone methylation. Global gene expression patterns and pathway analyses indicated a reprogramming of myogenic cell state creating a differentiated-like phenotype in proliferating myoblasts. Our results strongly suggest theDlk1-Dio3ncRNA locus is a nodal regulator coordinating metabolic activity and the epigenome to maintain proper cell state in the myogenic lineage.

Summary statement

Muscle cell state is regulated by the imprintedDlk1-Dio3noncoding RNA locus through its coordinate control of mitochondrial activity and histone modifications.
The persistence of locally adapted polymorphisms under mutation swamping
Authors: Sakamoto Takahiro , Whiting James R. , Yeaman Samuel
Published: June 2024

Locally adapted traits can exhibit a wide range of genetic architectures, from pronounced divergence at a few loci to small allele frequency shifts at many loci. The type of architecture that evolves depends strongly on migration rate, as weakly selected loci experience swamping and do not make stable contributions to divergence. Simulations from previous studies showed that even when mutations are strongly selected and should resist migration swamping, the architecture of adaptation can collapse and become transient at high mutation rates. Here, we use an analytical two-population model to study how this “mutation swamping” phenomenon depends upon population size, strength of selection, and parameters determining mutation effects. To do this, we developed a mathematical theory based on the diffusion approximation to predict the threshold mutation rate above which swamping occurs, and find that this performs well across wide range of parameter space, based on comparisons with individual-based simulations. The mutation swamping threshold depends most strongly on the average effect size of mutations, and weakly on the strength of selection, but is only minimally affected by population size. Across a wide range of parameter space, we observe that mutation swamping occurs when the trait-wide mutation rate is 10−3–10−2, suggesting that this phenomenon is potentially relevant to complex traits with a large mutational target. On the other hand, based on the apparent stability of genetic architecture in many classic examples of local adaptation, our theory suggests that per-trait mutation rates are often relatively low.
AAV-mediated gene transfer of WDR45 corrects neurologic deficits in the mouse model of beta-propeller protein-associated neurodegeneration
Authors: Carisi Maria Carla , Shamber Claire , Bishop Martha , Sangster Madison , Chandrachud Uma , Meyerink Brandon , Pilaz Louis Jean , Grishchuk Yulia
Published: June 2024

Beta-propeller protein-associated neurodegeneration (BPAN) is an ultra-rare, X-linked dominant, neurodegenerative disease caused by loss-of-function mutations in theWDR45gene. It manifests in neurodevelopmental delay and seizures followed by secondary neurologic decline with dystonia/parkinsonism and dementia in adolescence and early adulthood and is characterized by progressive accumulation of iron in the basal ganglia.WDR45encodes β-propeller-shaped scaffold protein, or WIPI4, which plays an important role in autophagosome formation. While the mechanisms of how WIPI4 loss of function results in neurologic decline and brain pathology have not yet been established, findings of lower autophagic activity provide a direct link between impaired autophagy and neurologic disease in BPAN. Here we performed phenotypical characterization of a novel mouse model of BPAN, WDR45_ex9+1g>a mouse. We identified hyperactive behavior and reduction of autophagy markers in brain tissue inWDR45_ex9+1g>a hemizygous males as early as at 2 months of age. Given the early onset and spectrum of neurologic symptoms such as hyper-arousal and attention deficits in human patients, this model presents a disease-relevant phenotype and can be used in preclinical studies. We used this mouse model for a proof-of-concept study to evaluate whether AAV-mediated CNS-targeted gene transfer ofWDR45can provide therapeutic benefit and be considered a therapeutic paradigm for BPAN. We observed successful expression of humanWDR45transcripts and WIPI4 protein in the brain tissue, rescue of hyperactive behavior, and correction of autophagy markers in the brain tissue. This data demonstrates thatWDR45gene transfer can be a promising therapeutic strategy for BPAN.
Drugs targeting microRNAs that regulate DNA damage sensing and repair mechanisms:A computational drug discovery approach
Authors: Ravindranath S.B , Vratin S. , Lakshmi B.S. , Ramirez D.C. , Gomez Mejiba S.E.
Published: June 2024

ABSTRACT

DNA damage-sensing (DDS) and DNA damage-repair (DDR) mechanisms are essential for the fidelity of genetic information transmission. Failure to accomplish an effective DDS/DDR mechanism can lead to cell death or otherwise to cell transformation and cancer development. microRNAs (miRs) are short noncoding RNAs that primarily function as micromanagers of gene expression. Herein, we aimed to investigate the links between miRs and the translation of specific mRNAs encoding proteins involved in genomic DDS and DDR and to screen drugs that have high binding affinity to the selected miRs, which may serve as cancer therapeutics. To accomplish these aims, we used a variety of computational methods spanning data analysis, molecular modeling, and simulation tools (i.e.,PyRx, Biopython, ViennaRNA, RNAComposer, AutoDock Vina, OpenBabel, PyMOL, Discovery Studio, MarvinSketch). The genes and miRNAs involved in the DDS and DDR mechanisms were retrieved from either the literature or various online databases (e.g.,miRDB). miR data were further cleaned and prepared using scripts, and various libraries were used to obtain their 3-D structures. Genes interacting with miRs were enriched based on multiple database annotations using Enrichr KG. Then, we used docking analyses to virtually screen compounds to serve as ligands for the miRs. Finally, we generated gene-disease-miR-drug networks to study the linkages between the compounds and miR molecules under investigation. For the first time, we were able to identify five compounds that could be repurposed for downregulating miRs that are linked to inhibition of translation of mRNA involved in the DDS and DDR processes. The gathered candidate drugs can be useful for preventing cell transformation and cancer development.
Amniotic fluid stem cell extracellular vesicles promote lung development via TGF-beta modulation in a fetal rat model of oligohydramnios
Authors: Doktor Fabian , Figueira Rebeca Lopes , Fortuna Victoria , Biouss George , Stasiewicz Kaya , Obed Mikal , Khalaj Kasra , Antounians Lina , Zani Augusto
Published: June 2024

Oligohydramnios (decreased amniotic fluid volume for gestational age) is a severe condition associated with high morbidity and mortality mainly due to fetal pulmonary hypoplasia. Currently, there are limited treatment options to promote fetal lung development. Administration of stem cells and their derivates have shown promising regenerative properties for several fetal and neonatal diseases related to arrested lung development. Herein, we first characterized pulmonary hypoplasia secondary to oligohydramnios in a surgical rat model. Experimental induction of oligohydramnios led to impaired lung growth, branching morphogenesis (fewer airspaces with decreasedFgf10,Nrp1,Ctnnb1expression), proximal/distal progenitor cell patterning (decreased Sox2 and Sox9 expression), and TGF-β signaling. We then tested antenatal administration of extracellular vesicles derived from amniotic fluid stem cells (AFSC- EVs). In oligohydramnios lungs, AFSC-EV administration improved lung branching morphogenesis and airway progenitor cell patterning at least in part through the release of miR-93-5p. Our experiments suggest that AFSC-EV miR-93-5p blocked SMAD 7, resulting in upregulation of pSMAD2/3 and restoration of TGF-β signaling. Conversely, oligohydramnios lungs treated with antagomir 93-5p transfected AFSC- EVs had decreased branching morphogenesis and TGF-β signaling. This is the first study reporting that antenatal administration of stem cell derivatives could be a potential therapy to rescue lung development in fetuses with oligohydramnios.

Highlights

Pulmonary hypoplasia secondary to oligohydramnios in fetal rats is characterized by impaired TGF-β signaling.

AFSC-EV administration improves fetal lung branching morphogenesis and airway progenitor cell patterning.

AFSC-EV effects are mediated at least in part via modulation of TGF-β signaling by the release of miR-93-5p from AFSC-EVs.
Designing a novel Scaffold-Based Multi-Epitope Vaccine to Combat Melioidosis Caused by Burkholderia pseudomallei: AnIn-silicoand Immunoinformatics approach
Authors: Rahman Shakilur , Das Ardhendu , Das Amit Kumar , Hazra Ditipriya , Roychowdhury Amlan
Published: June 2024

Burkholderia pseudomallei, the gram-negative bacteria causing melioidosis, is becoming a serious threat to healthcare settings. In recent years,B. pseudomalleihas been identified as an emerging and significant etiological agent responsible for localized pyogenic infections primarily observed in India and South Asia. At present, no vaccine against melioidosis is available in the treatment system. This study has undertaken anin-silicoreverse vaccinology approach to design a novel multi-epitope vaccine for treatingB. pseudomallei-mediated infections. B-cell and T-cell epitopes have been predicted and stitched to develop a multi-epitope vaccine. The predicted vaccine is found to be non-toxic, non-allergic, and immunogenic in nature. Immune simulation results indicate that the designed vaccine can generate an immune response resembling a real-life scenario. The 610 amino-acid long vaccine construct has been codon-optimized and could be cloned in the E. coli K12 system. These findings from this immunoinformatics study offer a foundation for developing a tailored, safe, and potent vaccine targetingB. pseudomallei.
Emergence of alternative stable states in microbial communities undergoing horizontal gene transfer
Authors: Hong Juken , Xue Wenzhi , Wang Teng
Published: June 2024

Microbial communities living in the same environment often display alternative stable states, each characterized by a unique composition of species. Understanding the origin and determinants of microbiome multistability has broad implications in environments, human health and microbiome engineering. However, despite its conceptual importance, how multistability emerges in complex communities remains largely unknown. Here, we focused on the role of horizontal gene transfer (HGT), one important aspect mostly overlooked in previous studies, on the stability landscape of microbial populations. Combining mathematical modeling and numerical simulations, we demonstrate that, when mobile genes only affect bacterial growth rates, increasing HGT rate in general promote the emergence of alternative stable states in complex microbiota. We further extend our analysis to scenarios where HGT changes interspecies interactions, microbial communities are subjected to strong environmental selections and microbes live in metacommunities consisting of multiple local habitats. We also discuss the role of different mechanisms, including interspecies interaction strength, the growth rate effects of MGEs, MGE epistasis and microbial death rates in shaping the multistability of microbial communities undergoing HGT. These results reveal how different dynamic processes collectively shape community multistability and diversity. Our results provide key insights for the predictive control and engineering of complex microbiota.
Optimizing Cost-Effective Gene Expression Phenotyping Approaches in Cattle Using 3′ mRNA Sequencing
Authors: Mohamed Ruwaa I. , Ault-Seay Taylor B. , Moisa Sonia , Beever Jonathan , Ríus Agustín G. , Rowan Troy
Published: June 2024

Background

Genetic and genomic selection programs require large numbers of phenotypes observed for animals in shared environments. Direct measurements of phenotypes like meat quality, methane emission, and disease susceptibility are difficult and expensive to measure at scale but are critically important to livestock production. Our work leans on our understanding of the “Central Dogma” of molecular genetics to leverage molecular intermediates as cheaply-measured proxies of organism-level phenotypes. The rapidly declining cost of next-generation sequencing presents opportunities for population-level molecular phenotyping. While the cost of whole transcriptome sequencing has declined recently, its required sequencing depth still makes it an expensive choice for wide-scale molecular phenotyping. We aim to optimize 3′ mRNA sequencing (3′ mRNA-Seq) approaches for collecting cost-effective proxy molecular phenotypes for cattle from easy-to-collect tissue samples (i.e., whole blood). We used matched 3′ mRNA-Seq samples for 15 Holstein male calves in a heat stress trail to identify the 1) best library preparation kit (Takara SMART-Seq v4 3′ DE and Lexogen QuantSeq) and 2) optimal sequencing depth (0.5 to 20 million reads/sample) to capture gene expression phenotypes most cost-effectively.

Results

Takara SMART-Seq v4 3′ DE outperformed Lexogen QuantSeq libraries across all metrics: number of quality reads, expressed genes, informative genes, differentially expressed genes, and 3′ biased intragenic variants. Serial downsampling analyses identified that as few as 8.0 million reads per sample could effectively capture most of the between-sample variation in gene expression. However, progressively more reads did provide marginal increases in recall across metrics. These 3′ mRNA-Seq reads can also capture animal genotypes that could be used as the basis for downstream imputation. The 10 million read downsampled groups called an average of 104,386 SNPs and 20,131 INDELs, many of which segregate at moderate minor allele frequencies in the population.

Conclusion

This work demonstrates that 3′ mRNA-Seq with Takara SMART-Seq v4 3′ DE can provide an incredibly cost-effective (<$25/sample) approach to quantifying molecular phenotypes (gene expression) while discovering sufficient variation for use in genotype imputation. Ongoing work is evaluating the accuracy of imputation and the ability of much larger datasets to predict individual animal phenotypes.
Does the PolyJet Printing Technology Affect Mechanical Properties of 3D Printed Synthetic Tissue?
Authors: Kohnle Samantha , Bermel Emily , Severseike Leah , Bhatia Varun
Published: June 2024

Within the medical field, there are multiple opportunities in which 3D printed anatomical models could be utilized such as physician training, surgical planning, education, and R&D testing. Because of this, it is vital to choose materials that most closely mechanically mimic the tissues that would be seen within the simulated model. Stratasys currently has a line of Digital Anatomy (DA) printers that contain predetermined compositions and mixtures called anatomical presets to mimic soft tissue materials such as liver, myocardium, aortic, and epicardium tissue. Different compositions of these printed materials have been previously printed on the J750 Digital Anatomy printer and have undergone mechanical testing. Stratasys is releasing a new printer called J5 Digital Anatomy printer that will also have the capabilities of printing anatomical presets. To compare any differences between the two printer sample types, these mechanical tests were repeated on the J5 DA printer.

Mechanical testing included stiffness testing of printed liver samples, compliance testing of printed myocardium samples, and lubricity testing of printed cardiac tissue samples. Stiffness of J5 DA liver and J750 DA liver samples were similar with slight variation seen in more rigid J5 DA samples; however, both printer samples still fell within the stiffness range observed in porcine liver tissue. Compliance testing showed comparable stiffness between J5 DA and J750 DA myocardium samples; however, J5 DA samples tended to be slightly less stiff making them more similar to porcine myocardium stiffness. Thinner J5 DA samples were more variable when compared to J750 DA samples; however, this was minimal variability when compared to that experienced in porcine tissue. Lubricity testing showed comparable coefficients of friction between J5 DA and J750 DA samples with the exception of Mineral oil and Dry lubricants. J5 DA cardiac samples saw smaller coefficients of friction; however, these still fell within the range of aortic and epicardium coefficients of frictions. Because of these results, it can be concluded that the J5 DA printer samples are comparable to J750 DA printer samples and are alternatives to animal tissue benchtop testing depending on the application.
Functionally Adaptive Structural Basis Sets of the Brain: A Dynamic Fusion Approach
Authors: Duda Marlena , Chen Jiayu , Belger Aysenil , Ford Judith , Mathalon Daniel , Preda Adrian , Turner Jessica , Erp Theo Van , Pearlson Godfrey , Calhoun Vince D.
Published: June 2024

The precise relationship between brain structure and function has been investigated through a multitude of lenses, but one detail that is held constant across most neuroimaging studies in this space is the identification of a singular structural basis set of the brain, upon which functional activation signals can be reconstructed to examine the linkage between structure and function. Such basis sets can be considered “functionally independent”, as they are derived through structural data alone and have no explicit association to functional data. Recent work in multimodal fusion has facilitated a more integrated view of structure-function linkages by enabling the equal contribution of both modalities to the joint decomposition, resulting in components that are independent within modality but co-vary closely across modalities. These existing symmetric fusion approaches thus identify structural bases given an associated functional context. In this work we consider an additional layer of precision to the investigation of structure-function coupling by studying these context-dependent linkages in a time-resolved manner. In other words, we ask which features of brain structure become (or remain) salient given the dynamically changing functional contexts (i.e., dynamic functional connectivity states, task structure, etc.) the brain may pass through during a given fMRI scan. We introduce “dynamic fusion”, an ICA-based symmetric fusion approach that enables flexible, time-resolved linkages between brain structure and dynamic brain function. We show evidence that temporally resolved, and functionally contextualized, structural basis sets can accurately reflect dynamic functional processes and capture diagnostically relevant structure- functional coupling while detecting nuanced functionally-driven structural components that cannot be captured with traditionally computed structural bases. Lastly, differential analysis of component stability across repeated scans from a control cohort reveals organization of static and dynamic structure/function coupling falls along unimodal/transmodal hierarchical lines.
Quantum theory of a potential biological magnetic field sensor: radical pair mechanism in flavin adenine dinucleotide biradicals
Authors: Sotoodehfar Amirhosein , Rishabh  , Zadeh-Haghighi Hadi , Simon Christoph
Published: June 2024

Recent studiesin vitroandin vivosuggest that flavin adenine dinucleotide (FAD) on its own might be able to act as a biological magnetic field sensor. Motivated by these observations, in this study, we develop a detailed quantum theoretical model for the radical pair mechanism (RPM) for the flavin adenine biradical within the FAD molecule. We perform molecular dynamics simulations to determine the distance between the radicals on FAD, which we then feed into a quantum master equation treatment of the RPM. In contrast to previous semi-classical models which are limited to the low-field and high-field cases, our quantum model can predict the full magnetic field dependence of the transient absorption signal. Our model’s predictions are consistent with experiments.
Variants in tubule epithelial regulatory elements mediate most heritable differences in human kidney function
Authors: Loeb Gabriel B. , Kathail Pooja , Shuai Richard , Chung Ryan , Grona Reinier J. , Peddada Sailaja , Sevim Volkan , Federman Scot , Mader Karl , Chu Audrey , Davitte Jonathan , Du Juan , Gupta Alexander R. , Ye Chun Jimmie , Shafer Shawn , Przybyla Laralynne , Rapiteanu Radu , Ioannidis Nilah , Reiter Jeremy F.
Published: June 2024

Kidney disease is highly heritable; however, the causal genetic variants, the cell types in which these variants function, and the molecular mechanisms underlying kidney disease remain largely unknown. To identify genetic loci affecting kidney function, we performed a GWAS using multiple kidney function biomarkers and identified 462 loci. To begin to investigate how these loci affect kidney function, we generated single-cell chromatin accessibility (scATAC-seq) maps of the human kidney and identified candidatecis-regulatory elements (cCREs) for kidney podocytes, tubule epithelial cells, and kidney endothelial, stromal, and immune cells. Kidney tubule epithelial cCREs explained 58% of kidney function SNP-heritability and kidney podocyte cCREs explained an additional 6.5% of SNP-heritability. In contrast, little kidney function heritability was explained by kidney endothelial, stromal, or immune cell-specific cCREs. Through functionally informed fine-mapping, we identified putative causal kidney function variants and their corresponding cCREs. Using kidney scATAC-seq data, we created a deep learning model (which we named ChromKid) to predict kidney cell type-specific chromatin accessibility from sequence. ChromKid and allele specific kidney scATAC-seq revealed that many fine-mapped kidney function variants locally change chromatin accessibility in tubule epithelial cells. Enhancer assays confirmed that fine-mapped kidney function variants alter tubule epithelial regulatory element function. To map the genes which these regulatory elements control, we used CRISPR interference (CRISPRi) to target these regulatory elements in tubule epithelial cells and assessed changes in gene expression. CRISPRi of enhancers harboring kidney function variants regulatedNDRG1andRBPMSexpression. Thus, inherited differences in tubule epithelialNDRG1andRBPMSexpression may predispose to kidney disease in humans. We conclude that genetic variants affecting tubule epithelial regulatory element function account for most SNP-heritability of human kidney function. This work provides an experimental approach to identify the variants, regulatory elements, and genes involved in polygenic disease.