bluuebunny/crossref_metadata_2025 huggingface dataset:
A broad cathepsin inhibitor blocks crystal-stimulated inflammasome-dependent and -independent inflammation, and gout arthritis
Authors: Orellano Laura Alejandra Ariza , Zeng Chunhui , Zhu Jiyun , Bogyo Matthew , Rock Kenneth L. , Lai Jiann-Jyh
Published: July 2024

In the disease gout, monosodium urate (MSU) crystals nucleate in joints and cause acute painful arthritis that can damage the affected joints. Similarly, the deposition of other crystals or irritant particles in tissues elicits an inflammatory response that can cause disease. These various particles stimulate macrophages to produce the proinflammatory cytokine interleukin 1β (IL-1β), which is a major driver of the ensuing inflammation. Here we show that in vivo and in vitro, broad spectrum cathepsin inhibitors, like VBY-825, blocked the activation of inflammasomes, which are known to be essential in generating bioactive IL-1β in response to crystals. In addition, the cathepsin inhibitors blocked an inflammasome-independent pathway that also generates mature IL-1β and which contributed substantially to crystal-stimulated inflammation in vivo. Through these effects, the cathepsin inhibitors markedly reduced gout arthritis and inflammation to the unrelated crystal silica, which is the etiologic agent in the disease silicosis. The cathepsin inhibitors didn’t affect any of the inflammatory processes after bioactive IL-1β was present in tissues. They also didn’t inhibit LPS-stimulated inflammationin mice, or TNF-⍺ production from macrophages. These findings provide proof of concept that cathepsin inhibitors are a novel class of anti-inflammatories that can inhibit crystal-stimulated disease with unique mechanisms of action.
Visual quality control withCytoMDS, a Bioconductor package for low dimensional representation of cytometry sample distances
Authors: Hauchamps Philippe , Delandre Simon , Temmerman Stéphane T. , Lin Dan , Gatto Laurent
Published: July 2024

Quality Control (QC) of samples is an essential preliminary step in cytometry data analysis. Notably, identification of potential batch effects and outlying samples is paramount, to avoid mistaking these effects for true biological signal in downstream analyses. However, this task can prove to be delicate and tedious, especially for datasets with many samples.

Here, we presentCytoMDS, a Bioconductor package implementing a dedicated method for low dimensional representation of cytometry samples composed of marker expressions for up to millions of single cells. This method allows a global representation of all samples of a study, with one single point per sample, in such a way that projected distances can be visually interpreted. It usesEarth Mover’s Distancefor assessing dissimilarities between multi-dimensional distributions of marker expression, andMulti Dimensional Scalingfor low dimensional projection of distances. Some additional visualization tools, both for projection quality diagnosis and for user interpretation of the projection coordinates, are also provided in the package.

We demonstrate the strengths and advantages ofCytoMDSfor QC of cytometry data on three real biological datasets, revealing the presence of low quality samples, batch effects and biological signal between sample groups.
UNRAVELING THE LUNG VASCULAR REMODELING IN PULMONARY HYPERTENSION USING A QUANTITATIVE DIGITAL PATHOLOGY SOFTWARE
Authors: Serdjebi Cindy , Chandes Florine , Biernat Marzena , Lepoivre Bastien , Salvail Dany , Laurent Charles-E.
Published: July 2024

Pulmonary arterial hypertension (PAH) is a rare chronic life-threatening disorder, characterized by the elevation of the mean pulmonary arterial pressure above 20 mmHg at rest. Histologically, PAH induces lung vascular remodeling, with the thickening of vessel wall. The conventional histological analysis commonly used in non-clinical models to assess lung vascular remodeling relies on manual measurements of representative lung vessels and is time-consuming. We have developed a fully automated reader-independent software (MorphoQuant-Lung) to both specifically detect vessels and measure vascular wall components from a-SMA rat lung sections. Analysis was performed on monocrotaline-and Sugen/hypoxia-induced PH rat models, treated or not with Sildenafil. The software requires 3-5 minutes to detect up to 1500 vessels per section, classify them per size, quantify intima, media and wall thicknesses, and calculate their level of occlusion. A comparison of our digital analysis results with those of the pathologist’s conventional visual analysis was performed for wall thickness and lumen radius showing a strong correlation between the two techniques (r: 0.80 and r: 0.88) regardless of the rat model. In addition, the occlusion estimated by automated analysis also strongly correlated with the mean pulmonary arterial pressure and the pulmonary vascular resistance (r ranging from 0.71 to 0.83) in both rat models. The added value of the present digital analysis paves the way for a more in-depth understanding of the PAH physiopathology in preclinical research and provides a robust and reliable tool for efficient therapeutic drug development.
Imaging Intra- and Extracellular Conductivity using MR based Conductivity Tensor Imaging
Authors: Rana Neha , Katoch Nitish
Published: July 2024

Imaging electrical conductivity may reveal relationships between biological tissues, cellular structures, and physiological processes. Biological tissues are primarily composed of major ions such as Na+ and K+, with varying concentrations and mobility within the cellular structures. These tissues consist of intracellular and extracellular fluids separated by cell membranes, and their electrical conductivity can be expressed as a function of ion concentration and mobility. This study introduces Conductivity Tensor Imaging (CTI) to independently reconstruct the electrical conductivity of intra- and extracellular compartments in biological tissues using MRI. We validated this method using a conductivity phantom with three compartments filled with electrolytes and/or giant vesicle suspensions. These vesicles mimic cell-like materials with thin insulating membranes, providing a realistic model for cellular structures. Measurements showed that high-frequency conductivity closely matched low-frequency conductivity in normal electrolytes. However, in the giant vesicle compartment, the conductivity of extracellular (EC) and intracellular (IC) regions correlated with cell volume fraction. In vivo human brain imaging using CTI revealed significant EC and IC conductivity variations across different brain regions, corresponding to underlying cellular compositions and structures. CTI introduces a novel MR contrast mechanism to distinctly measure IC and EC conductivities. Our findings highlight the potential of CTI to enhance our understanding of brain microstructure and its physiological processes through detailed conductivity mapping. This method signifies a notable advancement in non-invasive imaging, providing novel insights into the electrical properties of biological tissues and their implications for biophysical properties.
Aedes aegypti VLG-1challenges the assumed antiviral nature ofVagogenes
Authors: Couderc Elodie , Crist Anna B. , Daron Josquin , Varet Hugo , van Hout Femke A. H. , Miesen Pascal , Palatini Umberto , Dabo Stéphanie , Vial Thomas , Lambrechts Louis , Merkling Sarah H.
Published: July 2024

Arthropod-borne viruses (arboviruses) such as dengue virus (DENV) and Zika virus (ZIKV) pose a significant threat to global health. Novel approaches to control the spread of arboviruses focus on harnessing the antiviral immune system of their primary vector, theAedes aegyptimosquito. In arthropods, genes of theVagofamily are often presented as analogs of mammalian cytokines with potential antiviral functions, but the role ofVagogenes upon virus infection inAe. aegyptiis largely unknown. We conducted a phylogenetic analysis of theVagogene family in Diptera, which led us to focus on aVago-like gene that we namedVLG-1. Using CRISPR/Cas9-mediated gene editing, we generated aVLG-1mutant line ofAe. aegypti, which revealed a broad impact ofVLG-1on the mosquito transcriptome, affecting several biological processes potentially related to viral replication, including the oxidative stress response. Surprisingly, experimental viral challenge of theVLG-1mutant line indicated a modest proviral role for this gene during DENV and ZIKV infectionsin vivo. In the absence ofVLG-1, virus dissemination throughout the mosquito’s body was slightly impaired, albeit not altering virus transmission rates. Our results challenge the conventional understanding ofVago-like genes as antiviral factors and underscore the need for furtherin vivoresearch to elucidate the molecular mechanisms underlying mosquito-arbovirus interactions.
Phosphodiesterase 3 inhibitors boost bone outgrowth
Authors: Kawabe Takaaki , Ichimura Atsuhiko , Yasue Tomoki , Li Jianhong , Kim Ga Eun , Ishikawa Haruki , Uda Yohei , Ito Hiromu , Nishi Miyuki , Takeshima Hiroshi
Published: July 2024

C-type natriuretic peptide (CNP) stimulates skeletal growth by acting on the growth plates of long bones, and a CNP variant is clinically used for achondroplasia treatment. We previously reported that CNP stimulates the autonomic Ca2+influx mediated by TRPM7 channels in growth plate chondrocytes to facilitate extracellular matrix synthesis for bone growth. Here, we report that phosphodiesterase 3 (PDE3) inhibitors facilitate the Ca2+influx and promote bone outgrowth. The representative PDE3 inhibitor cilostazol elevated cGMP levels and activated cell-surface K+channels probably due to protein kinase G-mediated phosphorylation in growth-plate chondrocytes. The resulting hyperpolarization likely facilitated TRPM7-mediated Ca2+influx by increasing the Ca2+-driving force. Moreover, cilostazol simulated the elongation of cultured bones and enlarged the body size of juvenile mice. Several PDE3 inhibitors have been used for clinical treatment of thrombosis, heart failure and asthma, while our observations suggest that the repositioning of PDE3 inhibitors would provide novel medications for syndromes involving short stature.
Characterisation of aphid antixenosis in aphid-resistant ancestor wheat,Triticum monococcum
Authors: Borg Alexander N. , Vuts József , Caulfield John C. , Withall David M. , Foulkes M. John , Birkett Michael A
Published: July 2024

BACKGROUND

Due to the increasing presence of insecticide resistance across cereal aphid populations, new aphid management strategies, including the engineering of host resistance to aphids into commercial wheat varieties, are required. Previous studies have identified ancestor wheat,Triticum monococcumaccessions MDR045 and MDR049, with resistance against the grain aphid,Sitobion avenae. To test the hypothesis that resistance can be accounted for by antixenosis (reduced attractiveness of host plants)viathe release of repellent volatile organic compounds (VOCs), we explored the response ofS. avenaeto MDR045 and MDR049 followingS. avenaeherbivory, using behaviour and electrophysiology experiments.

RESULTS

In four-arm olfactometry assays, alateS. avenaeshowed aphid-density dependent reduced preference to VOC extracts fromT. monococcumMDR045 and MDR049. By contrast, alateS. avenaeshowed aphid-density dependent increased preference to extracts from hexaploid wheat,T. aestivumvar Solstice andT. monococcumMDR037. Coupled gas chromatography-electroantennography (GC- EAG), using the antennae of alateS. avenae, located 24 electrophysiologically active compounds across all tested accessions. Synthetic blends created from 21 identified EAG-active compounds confirmed bioactivity of corresponding VOC extracts in four-arm olfactometry assays against alateS. avenae.

CONCLUSION

Our data suggest that resistance ofT. monococcumMDR045 and MDR049 toS. avenaecan be at least partially accounted for by antixenosis, through antennal perception of specific repellent VOC blends induced byS. avenaefeeding behaviour.
Activated NK cells with a predominance of inhibitory receptors and a decidual-like phenotype expand after autologous HSCT in children with tumors
Authors: Astarloa-Pando Gabirel , Polanco-Alonso Diego , Sandá Víctor , Orrantia Ane , Amarilla-Irusta Ainhoa , Pérez-Fernández Silvia , Pérez-Garay Raquel , Sevilla Arrate , Lopez-Pardo Ainara , Tijero Aritz , Úriz José J. , Rey Mercedes , Astigarraga Itziar , Manzanares-Martin Bárbara , Bediaga Naiara G. , Amo Laura , Zenarruzabeitia Olatz , Borrego Francisco
Published: July 2024

Early immune reconstitution after autologous hematopoietic stem cell transplantation (autoHSCT) is associated with a better outcome in a variety of cancers. NK cells constitute the first lymphocyte subset to recover in the blood after autoHSCT. We have in-depth characterized them in pediatric patients with different tumors and found that, immediately after autoHSCT, NK cells transiently acquired a decidual-like phenotype, were more immature and activated, and exhibited an increased expression of inhibitory receptors, while activating receptors levels were diminished. This activated and decidual-like phenotype was characterized by increased CD56, CD9, CD49a, CD151, CD38, HLA-DR and CD55 expression. We also determined plasma levels of several cytokines and found that their concentrations were associated with the observed changes in NK cells phenotype.In vitroexperiments, including flow cytometry and single-cell RNA sequencing (scRNA-seq), recapitulated the changes observed in NK cells early after autoHSCT. Specifically, results revealed that the combination of IL-15 and TGF-β induced, at least partially, this distinctive phenotype on NK cells after autoHSCT. Finally, we have observed a positive correlation between relapse and the percentage of CD56dimNK cells shortly after autoHSCT in our cohort of pediatric patients. Altogether, our work is of relevance to understand the physiopathology of NK cells during the immune system reconstitution after autoHSCT in children and potentially help in the management of these patients.
Upregulation of a nonsense mediated decay (NMD) insensitive CFTR mRNA isoform has therapeutic potential for the treatment of 3’ CFTR PTC variants
Authors: Allaire Normand E. , Armstrong Mathew , Yoon Jae Seok , Bhatt Priyanka , Harrington Jan , Cheng Yi , Valley Hillary , Macadino Caitlin , Bihler Hermann , Sivachenko Andrey , Mense Martin , Cotton Calvin
Published: July 2024

Background

Nonsense or Premature Termination Codon (PTC) mutations of theCFTRgene are pathogenic and found in ∼10% of North American people with cystic fibrosis. PTC mutations induce Nonsense-Mediated mRNA Decay (NMD), leading to a substantial (∼80-90%) reduction in full-length mRNA. This reduction is a key contributor to PTC mutation-related pathology. Various approaches to evade NMD and preserve the impacted mRNA transcript have been explored but have not progressed to clinical development, leaving NMD a significant hurdle for PTC readthrough therapy.

Methods

Antisense oligonucleotides (ASOs) were tiled across intron 22 splice donor (SD) and acceptor (SA) sites of theCFTRgene. Immortalized airway cells were treated with SD and SA ASOs, and those yielding the greatest increase in aCFTRNMD-insensitive mRNA isoform (e22 trunc mRNA) were tested in combinations. Top SD/SA ASO pairs were assessed for their impact on e22 trunc mRNA via ddPCR, e22 trunc protein via western blot, and CFTR-mediated chloride (Cl-) transport via transepithelial electrophysiological measurements in immortalized and primary human bronchial epithelial (hBE) cell cultures.

Results

We demonstrate that e22 trunc mRNA generates a truncated CFTR protein whose Cl-transport function can be enhanced with elexacaftor/tezacaftor/ivacaftor (ETI) treatment. ASO and ETI treatment in combination restore ∼20% and 25% of wild-type CFTR Cl-transport function in immortalized epithelial and primary hBE cells homozygous forCFTRW1282X, respectively.

Conclusions

This study lays the groundwork for advancing ASO-mediated upregulation of e22 trunc mRNA and protein as a therapeutic approach for cystic fibrosis caused by 3’-terminalCFTRPTC mutations.
PENGUIN: A rapid and efficient image preprocessing tool for multiplexed spatial proteomics
Authors: Sequeira A. M. , Ijsselsteijn M. E. , Rocha M. , de Miranda Noel F.C.C.
Published: July 2024

Multiplex spatial proteomic methodologies can provide a unique perspective on the molecular and cellular composition of complex biological systems. Several challenges are associated to the analysis of imaging data, in particular regarding the normalization of signal-to-noise ratios across images and background noise subtraction. However, straightforward and user-friendly solutions for denoising multiplex imaging data that are applicable to large datasets are still lacking. We have developed PENGUIN –Percentile Normalization GUI Image deNoising: a rapid and efficient image preprocessing tool for multiplexed spatial proteomics. In comparison to existing approaches, PENGUIN stands out by eliminating the need for manual annotation or machine learning model training. It effectively preserves signal intensity differences and reduces noise, thereby enhancing downstream tasks like cell segmentation and phenotyping. PENGUIN’s simplicity, speed, and user-friendly interface, deployed both as script and as a Jupyter notebook, facilitate parameter testing and image processing. We illustrate the effectiveness of PENGUIN by comparing it with conventional image processing techniques and solutions tailored for multiplex imaging data. This comparison underscores PENGUIN’s capability to produce high-quality imaging data efficiently and consistently.
Dsg2 truncation causes a lethal barrier breakdown in mice
Authors: Kugelmann Daniela , Butz Elisabeth S. , Ponce Alexander Garcia , Radeva Mariya Y. , Neubauer Jessica , Hiermaier Matthias , Siadjeu Christian , Burkard Natalie , Egu Desalegn , Horn Anja K. E. , Schmitz Christoph , Vuopala Katri S. , Kuismin Outi , Schlegel Nicolas , Waschke Jens
Published: July 2024

Inflammatory bowel diseases (IBD) such as Crohn’s disease (CD) have a complex aetiology with alterations of both the intestinal epithelial barrier and the IL23/IL17 immune response. Here, we investigated the role of a novel mutation in the desmosomal cadherin desmoglein 2 gene (DSG2) in the pathogenesis of IBD. DSG2 is known to regulate intestinal epithelial barrier integrity. Genetic analysis of a CD patient revealed a novel likely pathogenicDSG2mutation leading to a truncated protein lacking part of the intracellular domain. We generated an enterocyte-specific mouse model, recapitulating the human mutation to study how the cytoplasmic truncation ofDsg2affects intestinal barrier properties systemically. Moreover, we analysed the intestinal genetic profile in these mice and compared it to IBD patients. We describe a first CD patient with a rare mutation in theDSG2gene causing cytoplasmic truncation with affects Dsg2 mobility. Mice with enterocyte-specific Dsg2 truncation suffered from a lethal intestinal barrier defect and presented a skewed IL17 response similar to CD patients. We identified the desmosomal cadherin Dsg2 as a regulator of the skewed IL17 response. These data indicate that desmosomes regulate inflammation similar to psoriasis which explains why the same novel immune therapies are effective for both diseases.
The Soybean Cyst Nematode Effector Cysteine Protease 1 (CPR1) Targets a Mitochondrial Soybean Branched-Chain Amino Acid Aminotransferase (GmBCAT1) for Degradation
Authors: Margets Alexandra , Foster Jessica , Kumar Anil , Maier Tom R. , Masonbrink Rick , Mejias Joffrey , Baum Thomas J. , Innes Roger W.
Published: July 2024

The soybean cyst nematode (SCN;Heterodera glycines) facilitates infection by secreting a repertoire of effector proteins into host cells to establish a permanent feeding site composed of a syncytium of root cells. Among the diverse proteins secreted by the nematode, we were specifically interested in identifying proteases to pursue our goal of engineering decoy substrates that elicit an immune response when cleaved by an SCN protease. We identified a cysteine protease that we named Cysteine Protease 1 (CPR1), which was predicted to be a secreted effector based on transcriptomic data obtained from SCN esophageal gland cells, presence of a signal peptide, and lack of transmembrane domains. CPR1 is conserved in all isolates of SCN sequenced to date, suggesting it is critical for virulence. Transient expression of CPR1 inNicotiana benthamianaleaves suppressed cell death induced by a constitutively active nucleotide binding leucine-rich repeat protein, RPS5, indicating that CPR1 inhibits effector-triggered immunity. CPR1 localizes in part to the mitochondria when expressedin planta. Proximity-based labeling in transgenic soybean roots, co-immunoprecipitation, and cleavage assays identified a branched-chain amino acid aminotransferase from soybean (GmBCAT1) as a substrate of CPR1. Silencing of theCPR1transcript in the nematode reduced penetration frequency in soybean roots while the expression ofCPR1in soybean roots enhanced susceptibility. Our data demonstrates that CPR1 is a conserved effector protease with a direct target in soybean roots, highlighting it as a promising candidate for decoy engineering.
Comparison of Conventional Cytomorphology, Automated Cell Counting, and FTIR Spectroscopy for Detection of CNS Involvement in Acute Leukaemia
Authors: esohe lasaki abiodun , ADEGBE Samson
Published: July 2024

Abstract

Background

The incidence of central nervous system (CNS) involvement in pediatric leukemia patients presents significant diagnostic challenges. This study compares the diagnostic capabilities of Fourier Transform Infrared (FTIR) Spectroscopy with conventional cytomorphology and automated cell counting to detect CNS involvement in pediatric leukemia.

Methods

A cohort of pediatric patients diagnosed with leukemia was assessed at Altınbaş University Medical Park Hospital. Cerebrospinal fluid (CSF) samples were analyzed using FTIR spectroscopy and compared with outcomes from conventional cytomorphology and automated cell counting to evaluate diagnostic efficacy and accuracy.

Results

FTIR spectroscopy demonstrated a higher sensitivity in detecting biochemical markers of CNS involvement than conventional methods. Distinct spectral profiles enabled the identification of specific biochemical changes associated with CNS leukemia.

Conclusions

FTIR spectroscopy offers a promising alternative to traditional diagnostic methods, providing rapid, non-invasive, and accurate detection of CNS involvement, which is crucial for timely and effective treatment of pediatric leukemia.
Multiomics data analysis identifies TM4SF4 as a cell surface target in hepatocellular carcinoma
Authors: Wong Kah Keng , Ab. Hamid Suzina Sheikh
Published: July 2024

The clinical application of cellular immunotherapy in hepatocellular carcinoma (HCC) is impeded by the lack of a cell surface target frequently expressed in HCC cells and with minimal presence in normal tissues to reduce on-target, off-tumor toxicity. In thisin silicoanalysis, a longlist of genes (n=12,948) expressed in HCCs according to The Human Protein Atlas database were examined. The aim was to identify the optimal cell surface target, without being shed into circulation, in HCCs and with restrictive expression profile in other normal human tissues. A total of eight genes were shortlisted and they were subsequently ranked according to the combination of their transcript and protein expression levels in HCC cases (n=791) derived from four independent datasets (TCGA, CNHPP, GSE14520, and CHCC). TM4SF4 was the top-ranked target with the highest expression in HCCs. TM4SF4 demonstrated more favorable expression profile with significantly lower expression in normal human tissues but more highly expressed in HCC cases compared with seven other common HCC therapeutic targets. Furthermore, scRNA-seq (GSE149614 and GSE134355) and immunohistochemistry (HPA) datasets showed that TM4SF4 was absent in immune cell populations but highly expressed in the bile duct canaliculi of hepatocytes, a region that is inaccessible to immune cells. In scRNA-seq dataset of HCCs (GSE149614),TM4SF4expression was positively associated with mitochondrial components and oxidative phosphorylation Gene Ontologies in HCC cells (n=15,787 cells), suggesting its potential roles in mitochondrial-mediated oncogenic effects in HCC. Taken together, TM4SF4 is proposed as a promising cell surface target in HCC.
EFL-3/E2F7 modulates Wnt signalling through repressing the LIT-1 Nemo-like kinase during asymmetric epidermal cell division inCaenorhabditis elegans
Authors: Ferrando-Marco Mar , Barkoulas Michalis
Published: July 2024

The E2F family of transcription factors is conserved in higher eukaryotes and plays pivotal roles in controlling gene expression during the cell cycle. Most canonical E2Fs associate with members of the Dimerisation Partner (DP) family to activate or repress target genes. However, atypical repressors, such as E2F7 and E2F8, lack DP interaction domains and their functions are less understood. We report here that EFL-3, the E2F7 homologue ofC. elegans, regulates epidermal stem cell differentiation. We show that phenotypic defects inefl-3mutants depend on the Nemo-like kinaselit-1.EFL-3 represseslit-1expression through direct binding to alit-1intronic element. Increased LIT-1 expression inefl-3mutants reduces POP-1/TCF nuclear distribution, and consequently alters Wnt pathway activation. Our findings provide a mechanistic link between an atypical E2F family member and NLK duringC. elegansasymmetric cell division, which may be conserved in other animals.

Highlights

EFL-3 is enriched in anterior daughter cells following asymmetric seam cell division.

efl-3mutants show defects in cell differentiation and seam cell fate maintenance.

EFL-3 directly represseslit-1/NLK expression.

EFL-3-mediatedlit-1repression alters POP-1 nuclear levels, linking EFL-3 to Wnt signalling.
Responses to visual motion of neurons in the extrastriate visual cortex of macaque monkeys with experimental amblyopia
Authors: Van Grootel Tom J. , Raghavan R. T. , Kelly Jenna G. , Movshon J. Anthony , Kiorpes Lynne
Published: July 2024

Amblyopia is a developmental disorder that results from abnormal visual experience in early life. Amblyopia typically reduces visual performance in one eye. We studied the representation of visual motion information in area MT and nearby extrastriate visual areas in two monkeys made amblyopic by creating an artificial strabismus in early life, and in a single age-matched control monkey. Tested monocularly, cortical responses to moving dot patterns, gratings, and plaids were qualitatively normal in awake, fixating amblyopic monkeys, with primarily subtle differences between the eyes. However, the number of binocularly driven neurons was substantially lower than normal; of the neurons driven predominantly by one eye, the great majority responded only to stimuli presented to the fellow eye. The small population driven by the amblyopic eye showed reduced coherence sensitivity and a preference for faster speeds in much the same way as behavioral deficits. We conclude that, while we do find important differences between neurons driven by the two eyes, amblyopia does not lead to a large scale reorganization of visual receptive fields in the dorsal stream when tested through the amblyopic eye, but rather creates a substantial shift in eye preference toward the fellow eye.
Evolutionarily conserved principles of ESCRT-III-mediated membrane remodelling revealed by a two-subunit Asgard archaeal system
Authors: Souza Diorge P. , Espadas Javier , Chaaban Sami , Moody Edmund R. R. , Hatano Tomoyuki , Balasubramanian Mohan , Williams Tom A. , Roux Aurélien , Baum Buzz
Published: July 2024

ESCRT-III proteins assemble into composite polymers that undergo stepwise changes in composition and structure to deform membranes across the tree of life. Here, using a phylogenetic analysis we demonstrate that the two ESCRT-III proteins present in our closest archaeal relatives are evolutionarily related to B-type and A-type eukaryotic paralogues, which initiate and execute membrane remodelling, respectively. This deep homology is reflected in ESCRT-III structure and function as demonstrated by the fact that ESCRT-IIIB assembles into parallel arrays on planar membranes to initiate membrane deformation, and is required to recruit ESCRT-IIIA to generate composite polymers. ESCRT-IIIA homopolymers can then remodel membranes into tubes, as a likely prelude to scission. Taken together, this analysis reveals a set of conserved principles governing ESCRT-III-dependent membrane remodelling that first emerged with the evolution of a two-component ESCRT-III system in the Asgard archaea, and which continue to underlie complex multi-component, ESCRT-III-dependent membrane remodelling in eukaryotes.
TheEx VivoInfection of the Peripheral Bovine Mononuclear Cells (PBMCs) and the Bovine Spleen Cells with the Bovine Coronavirus (BCoV) Induced a Differential Expression of the Host Cytokine Genes Profiles and Modulates the Virus Replication
Authors: Shah Abid Ullah , Hemida Maged H
Published: July 2024

The adaptive immune response during BCoV infection of peripheral blood mononuclear cells (PBMCs), the bovine spleen cells, and their isolated T lymphocytes was not studied well. Our study confirmed successful BCoV infection in PBMCs and spleen T cells. This was evidenced by measuring genome copy numbers using real-time PCR, expression levels of BCoV spike and nucleocapsid proteins via western blot and immunofluorescence assays, and virus infectivity titration by plaque assay. In infected PBMCs, CD4 T-cell levels were 1.45-fold higher, and CD8 T-cell levels were 1.6-fold lower compared to sham-infected cells. Conversely, infected splenocytes showed a 0.88-fold decrease in CD4 T-cells and a 1.88-fold increase in CD8 T-cells. The cytokine gene expression analysis revealed that BCoV infection activated type 1 interferon and upregulated IL-6 expression in PBMCs and splenocytes. These findings demonstrate that BCoV successfully infects immune cells from PBMCs and spleen, inducing differential host cytokine gene expression favors virus replication.
tRNA modification profiling reveals epitranscriptome regulatory networks inPseudomonas aeruginosa
Authors: Sun Jingjing , Wu Junzhou , Yuan Yifeng , Fan Leon , Chua Wei Lin Patrina , Ling Yan Han Sharon , Balamkundu Seetharamsing , Dwijapriya  , Suen Suen Hazel Chay , de Crécy-Lagard Valérie , Dziergowska Agnieszka , Dedon Peter C.
Published: July 2024

Transfer RNA (tRNA) modifications have emerged as critical posttranscriptional regulators of gene expression affecting diverse biological and disease processes. While there is extensive knowledge about the enzymes installing the dozens of post-transcriptional tRNA modifications – the tRNA epitranscriptome – very little is known about how metabolic, signaling, and other networks integrate to regulate tRNA modification levels. Here we took a comprehensive first step at understanding epitranscriptome regulatory networks by developing a high-throughput tRNA isolation and mass spectrometry-based modification profiling platform and applying it to aPseudomonas aeruginosatransposon insertion mutant library comprising 5,746 strains. Analysis of >200,000 tRNA modification data points validated the annotations of predicted tRNA modification genes, uncovered novel tRNA-modifying enzymes, and revealed tRNA modification regulatory networks inP. aeruginosa. Platform adaptation for RNA-seq library preparation would complement epitranscriptome studies, while application to human cell and mouse tissue demonstrates its utility for biomarker and drug discovery and development.
Antagonistic effects of actin-specific toxins onSalmonellaTyphimurium invasion into mammalian cells
Authors: Heisler David B. , Kudryashova Elena , Hitt Regan , Williams Blake , Dziejman Michelle , Gunn John , Kudryashov Dmitri S.
Published: July 2024

Competition between bacterial species is a major factor shaping microbial communities. In this work, we explored the hypothesis that competition between bacterial pathogens can be mediated through antagonistic effects of bacterial effector proteins on host systems, particularly the actin cytoskeleton. UsingSalmonellaTyphimurium invasion into cells as a model, we demonstrate that invasion is inhibited if the host actin cytoskeleton is disturbed by any of the four tested actin-specific toxins:Vibrio choleraeMARTX actin crosslinking and Rho GTPase inactivation domains (ACD and RID, respectively), TccC3 fromPhotorhabdus luminescens, andSalmonella’sown SpvB. We noticed that ACD, being an effective inhibitor of tandem G-actin binding assembly factors, is likely to inhibit the activity of anotherVibrioeffector, VopF. In reconstituted actin polymerization assays confirmed by live-cell microscopy, we confirmed that ACD potently halted the actin nucleation and pointed-end elongation activities of VopF, revealing competition between these twoV. choleraeeffectors. Together, the results suggest bacterial effectors from different species that target the same host machinery or proteins may represent an effective but largely overlooked mechanism of indirect bacterial competition in host-associated microbial communities. Whether the proposed inhibition mechanism involves the actin cytoskeleton or other host cell compartments, such inhibition deserves investigation and may contribute to a documented scarcity of human enteric co-infections by different pathogenic bacteria.
Prenylation controls proliferation in human pluripotent stem cell-derived cardiomyocytes
Authors: Batho Christopher A.P. , Reid Janice D. , Robinson Harley R. , Szappanos Henrietta Cserne , Devilée Lynn A.C. , Hoyte Sharon M. , Johnston Rebecca L. , Ziegman Rebekah , Hassan Sarah , Soday Lior , Fitzsimmons Rebecca L. , Foster Simon R. , Ng Dominic C. H. , Tate Edward , Porrello Enzo R. , Parker Benjamin L. , Mills Richard J. , Hudson James E.
Published: July 2024

Induction of cardiomyocyte proliferation to replace damaged heart tissue is a promising therapeutic approach. A recent drug screen revealed that cardiomyocytes require the mevalonate pathway for proliferation, although the specific mechanisms are unknown. In this study, we use human pluripotent stem cell-derived cardiomyocytes and cardiac organoids to further interrogate the role of the mevalonate pathway in cardiomyocyte proliferation. Chemical and genetic perturbations of the mevalonate pathway indicated that the post-translational modification, prenylation, regulates cardiomyocyte proliferation. We use prenyl probes and mass spectrometry to identify a catalogue of 40 prenylated proteins in human cardiac cells, including proteins where prenylated function had not yet been investigated. We show that multiple prenylated proteins control cardiomyocyte proliferation including RRAS2 and NAP1L4. We demonstrate that prenylation has differential effects on distinct proteins, with RRAS2 prenylation controlling membrane localization and NAP1L4 prenylation regulating cardiomyocyte mitosis and centrosome homeostasis. Together, these data show that protein prenylation is required for cardiomyocyte proliferation through multiple targets and these processes may need to be re-activated for cardiac regeneration.
Single-cell proteomics of Arabidopsis leaf mesophyll identifies drought stress-related proteins
Authors: Fulcher James M. , Dawar Pranav , Balasubramanian Vimal Kumar , Williams Sarah M. , Nadeau Kyle D. , Winkler Tanya E. , Markillie Lye Meng , Mitchell Hugh D. , Ahkami Amir H. , Paša-Tolić Ljiljana , Zhu Ying
Published: July 2024

The application of single-cell omics tools to biological systems can provide unique insights into diverse cellular populations and their heterogeneous responses to internal and external perturbations. Thus far, most single-cell studies in plant systems have been limited to RNA-sequencing approaches, which only provide indirect readouts of cellular functions. Here, we present a single-cell proteomics workflow for plant cells that integrates tape-sandwich protoplasting, piezoelectric cell sorting, nanoPOTS sample preparation, and FAIMS-based MS data acquisition method for label-free single-cell proteomics analysis of Arabidopsis leaf mesophyll cells. From a single leaf protoplast, over 3,000 proteins were quantified with high precision. The workflow is demonstrated to identify stress associated changes in protein abundance by analyzing >80 protoplasts from well-watered and water-deficit stressed plants. Additionally, we describe a new approach for constructing covarying protein networks at the single-cell level and demonstrate how single-cell protein covariation analysis can reveal previously unrecognized protein functions while also capturing stress-induced changes in protein-protein dynamics.

Highlights

This study describes the first application of scProteomics to study abiotic stress-induced proteome regulation in leaf mesophyll cells

From a single Arabidopsis mesophyll protoplast, ∼2800 proteins on average were quantified with high precision using label free scProteomics

scProteomics of water-deficit Arabidopsis leaves revealed known and novel proteins involved in drought response

Single-protoplast proteomics revealed water deficit-induced changes in protein covariation networks independent of changes in abundance
The microcephaly protein WDR62 regulates cellular purine metabolism through the HSP70/HSP90 chaperone machinery
Authors: Morris Matthew J. , Yeap Yvonne Y. , Chen Chi , Millard S. Sean , Pagan Julia K. , Ng Dominic C. H.
Published: July 2024

Inherited mutations in WD repeat-containing protein 62 (WDR62) are associated with microcephaly (MCPH2). While WDR62 plays important roles in mitosis and centriole biogenesis, additional WDR62 functions may cause abnormal brain growth. Here, we reveal a novel WDR62 role in the molecular chaperone network regulating purine metabolism. In response to hyperosmotic stress, WDR62 redistributes to purinosomes—phase-separated membraneless assemblies of purine metabolic enzymes and their chaperones. While WDR62 is not needed for purinosome formation, its loss disrupts purine homeostasis, resulting in the accumulation of purine nucleotide intermediates and a reduction in the levels of hypoxanthine-guanine phosphoribosyl transferase (HPRT), a key purine salvage enzyme. We link this to WDR62’s interaction with Bcl2-associated athanogene 2 (BAG2), a co-chaperone that modulates the function of HSP70/90. In cells lacking WDR62, BAG2 levels are elevated and HPRT stability is reduced. Knocking down BAG2 in these cells restores HPRT levels, underscoring the crucial role of WDR62-BAG2 interactions in chaperone-mediated stability and turnover of metabolic pathway enzymes. Notably, common microcephaly-associated mutations in WDR62 alter its interaction with BAG2, suggesting that purine metabolic defects resulting from WDR62 mutations may underlie microcephaly in humans.
De novocancer mutations frequently associate with recurrent chromosomal abnormalities during long-term human pluripotent stem cell culture
Authors: Al Delbany Diana , Ghosh Manjusha S , Krivec Nusa , Huygebaert Anfien , Regin Marius , Duong Chi Mai , Lei Yingnan , Sermon Karen , Olsen Catharina , Spits Claudia
Published: July 2024

Human pluripotent stem cells (hPSC) are pivotal in regenerative medicine, yet theirin vitroexpansion often leads to genetic abnormalities, raising concerns about their safety in clinical applications. This study analyzed ten human embryonic stem cell lines across multiple passages to elucidate the dynamics of chromosomal abnormalities and single nucleotide variants (SNVs) in 380 cancer-related genes. Prolongedin vitroculture resulted in 80% of the lines acquiring gains of chromosomes 20q or 1q, both known for conferringin vitrogrowth advantage. 70% of lines also acquired other copy number variants (CNVs) outside the recurrent set. Additionally, we detected 122 SNVs in 88 genes, with all lines acquiring at least onede novoSNV during culture. Our findings show higher loads of both CNVs and SNVs at later passages which are due to the cumulative acquisition of mutations over a longer time in culture and not to an increased rate of mutagenesis over time. Importantly, we observed that SNVs and rare CNVs follow the acquisition of chromosomal gains in 1q and 20q, while most of the low-passage and genetically balanced samples were devoid cancer-associated mutations. This suggests that the recurrent chromosomal abnormalities are the potential drivers for the acquisition of other mutations.
Increased BMI associated with decreased breastfeeding initiation in Million Veteran Program participants
Authors: Lankester Joanna , Guarischi-Sousa Rodrigo , Hilliard Austin T ,   VA Million Veteran Program, Shere Labiba , Husary Marya , Crowe Susan , Tsao Philip S , Rehkopf David H , Assimes Themistocles L
Published: July 2024

Background

Breastfeeding has been associated with maternal and infant health benefits but has been inversely associated with body mass index (BMI) prepartum. Breastfeeding and BMI are both linked to socioeconomic factors.

Methods

Data from parous female participants with available breastfeeding information from the Million Veteran Program cohort was included. BMI at enrollment and earliest BMI available were extracted, and polygenic scores (PGS) for BMI were calculated. We modeled breastfeeding for one month or more as a function of BMI at enrollment; earliest BMI where available pre-pregnancy; and PGS for BMI. We conducted Mendelian randomization for breastfeeding initiation using PGS as an instrumental variable.

Results

A higher BMI predicted a lower likelihood of breastfeeding for one month or more in all analyses. A +5 kg/m2BMI pre-pregnancy was associated with a 24% reduced odds of breastfeeding, and a +5 kg/m2genetically predicted BMI was associated with a 17% reduced odds of breastfeeding.

Conclusions

BMI predicts a lower likelihood of breastfeeding for one month or longer. Given the high success of breastfeeding initiation regardless of BMI in supportive environments as well as potential health benefits, patients with elevated BMI may benefit from additional postpartum breastfeeding support.
Large-scale analysis of the medical discourse on rheumatoid arthritis: complementing a socio-anthropologic analysis
Authors: Santoro Mario , Nardini Christine
Published: July 2024

The medical discourse, entails the analysis of the modalities, far from unbiased, by which hypotheses and results are laid out in the dissemination of findings in scientific publications, giving different emphases on the background, relevance, robustness, and assumptions that the audience should take for granted. While this concept is extensively studied in socio-anthropology, it remains generally overlooked within the scientific community conducting the research. Yet, analyzing the discourse is crucial for several reasons: to frame policies that take into account an appropriately large screen of medical opportunities, to avoid overseeing promising but less walked paths, to grasp different types of representations of diseases, therapies, patients, and other stakeholders, understanding and being aware of how these very terms are conditioned by time, culture and so on. While socio-anthropologists traditionally use manual curation methods, automated approaches like topic modeling offer a complementary way to explore the vast and ever-growing body of medical literature. In this work, we propose a complementary analysis of the medical discourse regarding the therapies offered for rheumatoid arthritis using topic modeling and large language model-based emotion and sentiment analysis.
Duodenal organoids from metabolic dysfunction-associated steatohepatitis patients exhibit altered digestive homeostasis
Authors: Hadefi Alia , Leprovots Morgane , Dinsart Gilles , Marefati Maryam , Vermeersch Marjorie , Monteyne Daniel , Pérez-Morga David , Lefort Anne , Libert Frédérick , Verset Laurine , Liefferinckx Claire , Moreno Christophe , Devière Jacques , Trépo Eric , Garcia Marie-Isabelle
Published: July 2024

Background and Aims

Metabolic dysfunction-associated steatohepatitis (MASH) is a progressive liver disease that can lead to fibrosis, cirrhosis, and hepatocellular carcinoma. Though MASH is closely tied to metabolic risk factors, the underlying pathogenic mechanisms remain scarcely understood. Recent research underscores the importance of the gut-liver axis in its pathogenesis, an aspect less explored in human studies. Here, we investigated whether the duodenal epithelium of MASH patients, could exhibit intrinsic dysfunctions.

Methods

Duodenal epithelial organoids were generated from 16 MASH patients and 14 healthy controls. Biopsies and patient-derived organoid transcriptomes were then analyzed to evaluate if specific intestinal pathways were differentially modulated in MASH subjects. Functional assays were performed to assess the duodenal epithelial digestive potential and barrier functionality.

Results

Organoid formation efficiency was similar between control-derived epithelial organoids (CDEOs) and MASH-derived epithelial organoids (MDEOs) (71% and 69%, respectively). Despite global heterogeneity in growth patterns, MDEOs frequently exhibited cystic spheroid morphology. MDEOs displayed altered digestive homeostasis associated with reduced mature absorptive cell fate, but they retained their lipid metabolic capacity, possibly mediated by lipid oxidation in stem/progenitor cells. Additionally, MDEOs misexpressed components of tight and adherens junctions and desmosomes compared to controls. However, MDEOs maintained pore and leak pathway integrity, indicating that the duodenal epithelial barrier remained functionally preserved under tested conditions.

Conclusions

This study provides evidence that the duodenal epithelium of MASH patients exhibits significant alterations in its digestive and barrier functions. This study sheds light on the intricate dynamics of duodenal epithelial alterations in MASH, highlighting potential therapeutic avenues for restoring intestinal homeostasis.
Nitrogen Availability and Utilisation of Oligopeptides by Yeast in Industrial Scotch Grain Whisky Fermentation
Authors: Berg Hidde Yaël , Arju Georg , Nisamedtinov Ildar
Published: July 2024

Scotch grain whisky is produced with a substantial proportion of unmalted grains, which can result in nitrogen deficiency for yeast in the fermentable grain mash. This study examined nitrogen source availability and utilisation by three commercial whisky strains (Saccharomyces cerevisiae) during Scotch grain whisky fermentation, focusing on oligopeptides. Peptide uptake kinetics in synthetic whisky mash with defined peptides showed that oligopeptides of up to nine amino acids were taken up by the strains, albeit with some variability between the strains. The study found that peptides with appropriate molecular weights could replace free amino acids without negatively affecting fermentation kinetics. Moreover, fermentation performance improved when additional nitrogen was provided via peptides rather than diammonium phosphate. Analysis of industrial grain mash indicated that despite low initial yeast assimilable nitrogen, residual proteolytic activity from malt increased nitrogen availability during fermentation. Approximately 30% of the nitrogen consumed by yeast during grain mash fermentation was derived from peptides. LC-HRMS peptide analysis revealed complex dynamics of peptide formation, degradation, and utilisation. This study highlights the importance of oligopeptides in ensuring optimal fermentation efficiency in Scotch grain mash and similar substrates.