bluuebunny/crossref_metadata_2025 huggingface dataset:
DNA methylation entropy is associated with DNA sequence features and developmental epigenetic divergence
Authors: Fang Yuqi , Ji Zhicheng , Zhou Weiqiang , Abante Jordi , Koldobskiy Michael A. , Ji Hongkai , Feinberg Andrew P.
Published: December 2022

Epigenetic information defines tissue identity and is largely inherited in development through DNA methylation. While studied mostly for mean differences, methylation also encodes stochastic change, defined as entropy in information theory. Analyzing allelespecific methylation in 48 human tissue sample datasets, we find that methylation entropy is associated with specific DNA binding motifs, regulatory DNA, and CpG density. Then applying information theory to 42 mouse embryo methylation datasets, we find that time- and tissue-specific patterns of development are more strongly correlated with methylation entropy than with mean, and methylation entropy is associated with sequence and chromatin features conserved with human. Moreover, methylation entropy is directly related to gene expression variability in development, suggesting a role for epigenetic entropy in developmental plasticity.
Glucosinolate catabolism maintains glucosinolate profiles and transport in sulfur-starvedArabidopsis
Authors: Zhang Liu , Kawaguchi Ryota , Enomoto Takuro , Nishida Sho , Burow Meike , Maruyama-Nakashita Akiko
Published: December 2022

Glucosinolates (GSL) are sulfur (S)-rich specialized metabolites produced by plants of the Brassicales order. Our previous study found that in Arabidopsis seedlings, S deficiency (−S) promoted GSL catabolism by activating two ß-glucosidases (BGLU), BGLU28 and BGLU30. The induced GSL catabolism was a survival strategy for seedlings grown under −S, because S released from GSL was reincorporated into primary S metabolites which are essential for plant growth. However, as GSL profile in plants vary among growth stages and organs, we set out to test a potential contribution of BGLU28/30-dependent GSL catabolism at the reproductive growth stage. Thus, in this study, we assessed growth, metabolic, and transcriptional phenotypes of maturebglu28/30double mutants grown under different S conditions. Our results showed that compared to wild-type plants grown under −S, maturebglu28/30mutants displayed impaired growth and accumulated increased levels of GSL in their mature seeds, siliques, flowers, and rosette leaves of before bolting plants. In contrast, the levels of primary S-containing metabolites, glutathione and cysteine, were decreased in mature seeds. Furthermore, the transport of GSL from rosette leaves to the reproductive organs was stimulated in thebglu28/30mutants under −S. Transcriptome analysis revealed that genes related to other biological processes, such as phytohormone signaling and plant response to heat, responded differentially to −S in thebglu28/30mutants. Altogether, these findings broadened our understanding of the roles of BGLU28/30-dependent GSL catabolism in plant adaptation to nutrient stress.

One-sentence summary

Disruption of glucosinolate catabolic genes,BGLU28andBGLU30, in sulfur-starved matureArabidopsisimpaired growth, affected glucosinolate distribution, and altered transcriptional profiles.
Immunomodulation of Neutrophil Granulocyte Functions by Bacterial Polyphosphates
Authors: Krenzlin Viola , Schöche Johannes , Walachowski Sarah , Reinhardt Christoph , Radsak Markus P. , Bosmann Markus
Published: December 2022

Polyphosphates are highly conserved, linear polymers of monophosphates that reside in all living cells. Bacteria produce long chains containing hundreds to thousands of phosphate units, which can interfere with host defense to infection.

Here, we report that intratracheal long-chain polyphosphate administration to C57BL/6J mice resulted in the release of proinflammatory cytokines and influx of Ly6G+polymorphonuclear neutrophils in the bronchoalveolar lavage fluid causing a disruption of the physiologic endothelial-epithelial small airway barrier and histologic signs of lung injury. Polyphosphate-induced effects were attenuated after neutrophil depletion in mice. In isolated murine neutrophils, long-chain polyphosphates modulated cytokine release induced by lipopolysaccharides (LPS) from gram-negative bacteria or lipoteichoic acid from gram-positive bacteria. In addition, long-chain polyphosphates induced immune evasive effects in human neutrophils. In detail, long-chain polyphosphates down-regulated CD11b and curtailed the phagocytosis ofE. coliparticles by neutrophils. Polyphosphates modulated the migration capacity by inducing CD62L shedding resulting in CD62Llowand CD11blowneutrophils. The release of IL-8 induced by LPS was also significantly reduced. Pharmacologic blockade of PI3K with wortmannin antagonized long-chain polyphosphate-induced effects on LPS-induced IL-8 release.

In conclusion, polyphosphates govern immunomodulation in murine and human neutrophils suggesting polyphosphates as a therapeutic target for bacterial infections to restore innate immune defense.
Can hubs of the human connectome be identified consistently with diffusion MRI?
Authors: Gajwani Mehul , Oldham Stuart J. , Pang James C. , Arnatkevičiūtė Aurina , Tiego Jeggan , Bellgrove Mark A. , Fornito Alex
Published: December 2022

Recent years have seen a surge in the use of diffusion MRI to map connectomes in humans, paralleled by a similar increase in processing and analysis choices. Yet these different steps and their effects are rarely compared systematically. Here, in a healthy young adult population (n=294), we characterized the impact of a range of analysis pipelines on one widely studied property of the human connectome; its degree distribution. We evaluated the effects of 40 pipelines (comparing common choices of parcellation, streamline seeding, tractography algorithm, and streamline propagation constraint) and 44 group-representative connectome reconstruction schemes on highly connected hub regions. We found that hub location is highly variable between pipelines. The choice of parcellation has a major influence on hub architecture, and hub connectivity is highly correlated with regional surface area in most of the assessed pipelines (ρ>0.70 in 69% of the pipelines), particularly when using weighted networks. Overall, our results demonstrate the need for prudent decision-making when processing diffusion MRI data, and for carefully considering how different processing choices can influence connectome organization.

Author Summary

The increasing use of diffusion MRI for mapping white matter connectivity has been matched by a similar increase in the number of ways to process the diffusion data. Here, we assess how diffusion processing affects hubs across 1760 pipeline variations. Many processing pipelines do not show a high concentration of connectivity within hubs. When present, hub location and distribution vary based on processing choices. The choice of probabilistic or deterministic tractography has a major impact on hub location and strength. Finally, node strength in weighted networks can correlate highly with node size. Overall, our results illustrate the need for prudent decision-making when processing and interpreting diffusion MRI data.

Code and data availability

All the data used in this study is openly available on Figshare athttps://doi.org/10.26180/c.6352886.v1. Scripts to analyze these data are available on GitHub athttps://github.com/BMHLab/DegreeVariability.

Competing Interests

The authors declare that they have no competing interests.
Antibiotic-degrading resistance changes bacterial community structure via species-specific responses
Authors: Pathak Ayush , Angst Daniel C. , León-Sampedro Ricardo , Hall Alex R.
Published: December 2022

Some bacterial resistance mechanisms degrade antibiotics, potentially protecting neighbouring susceptible cells from antibiotic exposure. We do not yet understand how such effects influence bacterial communities of more than two species, which are typical in nature. Here, we used experimental multispecies communities to test the effects of clinically important pOXA-48-plasmid-encoded resistance on community-level responses to antibiotics. We found resistance in one community member reduced antibiotic inhibition of other species, but some benefitted more than others. Further experiments with supernatants and pure-culture growth assays showed the susceptible species profiting most from detoxification were those that grew best at degraded antibiotic concentrations (greater than zero, but lower than the starting concentration). This pattern was also observed on agar surfaces. By contrast, we found no evidence of a role for higher-order interactions or horizontal plasmid transfer in community-level responses to detoxification in our experimental communities. Our findings suggest carriage of an antibiotic-degrading resistance mechanism by one species can drastically alter community-level responses to antibiotics, and the identities of the species that profit most from antibiotic detoxification are predicted by their intrinsic ability to grow at degraded antibiotic concentrations.
Friction patterns guide actin network contraction
Authors: Colin Alexandra , Orhant-Prioux Magali , Guérin Christophe , Savinov Mariya , Scarfone Ilaria , Roux Aurelien , De La Cruz Enrique M. , Mogilner Alex , Théry Manuel , Blanchoin Laurent
Published: December 2022

The shape of cells is the outcome of the balance of inner forces produced by the actomyosin network and the resistive forces produced by cell adhesion to their environment. The specific contributions of contractile, anchoring and friction forces to network deformation rate and orientation are difficult to disentangle in living cells where they influence each other. Here, we reconstituted contractile acto-myosin networksin vitroto study specifically the role of the friction forces between the network and its anchoring substrate. To modulate the magnitude and spatial distribution of friction forces, we micropatterned actin nucleation promoting factors on glass or on a lipid bilayer. We adapted their concentrations on each surface to induce the assembly of actin networks of similar densities, and compare the deformation of the network toward the centroid of the pattern shape upon myosin-induced contraction. We found that actin network deformation was faster and more coordinated on lipid bilayers than on glass, showing the resistance of friction to network contraction. To further study the role of the spatial distribution of these friction forces, we designed heterogeneous micropatterns made of glass and lipids. The deformation upon contraction was no longer symmetric but biased toward the region of higher friction. Furthermore, we showed that the pattern of friction could robustly drive network contraction and dominate the contribution of asymmetric distributions of myosins. Therefore, we demonstrate that during contraction both the active and resistive forces are essential to direct the actin network deformation.

Significance statement

Cell shape changes are controlled by complex sets of mechanical forces of various origins. Numerous studies have been dedicated to the role of active forces, originating from molecular motors and filament polymerization, but much less is known about the guiding role of resistive forces. Here we show that a non-uniform distribution of friction forces between a contracting acto-myosin network and its underlying substrate can direct its deformation as it contracts. Our results suggest that the contribution of resistive forces, such as anchoring forces but also less specific viscous forces along cell surface, can be as significant as those of active forces in driving network deformation and should be considered in mechanical models describing the regulation of cell shape and movements.
SARS-CoV-2 Variant-Specific Differences in Inhibiting the Effects of the PKR-Activated Integrated Stress Response
Authors: Christ Wanda , Klingström Jonas , Tynell Janne
Published: December 2022

The integrated stress response (ISR) is a eukaryotic cell pathway that triggers translational arrest and the formation of stress granules (SGs) in response to various stress signals, including those caused by viral infections. The SARS-CoV-2 nucleocapsid protein has been shown to disrupt SGs, but SARS-CoV-2 interactions with other components of the pathway remains poorly characterized. Here, we show that SARS-CoV-2 infection triggers the ISR through activation of the eIF2α-kinase PKR while inhibiting a variety of downstream effects. In line with previous studies, SG formation was efficiently inhibited and the induced eIF2α phosphorylation only minimally contributed to the translational arrest observed in infected cells. Despite ISR activation and translational arrest, expression of the stress-responsive transcripts ATF4 and CHOP was not induced in SARS-CoV-2 infected cells. Finally, we found variant-specific differences in the activation of the ISR between ancestral SARS-CoV-2 and the Delta and Omicron BA.1 variants in that Delta infection induced weaker PKR activation while Omicron infection induced higher levels of p-eIF2α and greatly increased SG formation compared to the other variants. Our results suggest that different SARS-CoV-2 variants can affect normal cell functions differently, which can have an impact on pathogenesis and treatment strategies.
Diagnosis with Confidence: Deep Learning for Reliable Classification of Squamous Lesions of the Upper Aerodigestive Tract
Authors: Lubrano Mélanie , Bellahsen-Harrar Yaëlle , Berlemont Sylvain , Atallah Sarah , Vaz Emmanuelle , Walter Thomas , Badoual Cécile
Published: December 2022

Background

Diagnosis of head and neck (HN) squamous dysplasias and carcinomas is critical for patient care cure and follow-up. It can be challenging, especially for grading intraepithelial lesions. Despite recent simplification in the last WHO grading system, the inter- and intra-observer variability remains substantial, particularly for non-specialized pathologists, exhibiting the need for new tools to support pathologists.

Methods

In this study we investigated the potential of deep learning to assist the pathologist with automatic and reliable classification of HN lesions following the 2022 WHO classification system. We created, for the first time, a large-scale database of histological samples (>2000 slides) intended for developing an automatic diagnostic tool. We developed and trained a weakly supervised model performing classification from whole slide images (WSI). We evaluated our model on both internal and external test sets and we defined and validated a new confidence score to assess the predictions which can be used to identify difficult cases.

Results

Our model demonstrated high classification accuracy across all lesion types on both internal and external test sets (respectively average AUC: 0.878 (95% CI:[0.834-0.918]) and 0.886 (95% CI: [0.813-0.947])) and the confidence score allowed for accurate differentiation between reliable and uncertain predictions.

Conclusions

Our results demonstrate that the model, associated with confidence measurements, can help in the difficult task of classifying head and neck squamous lesions by limiting variability and detecting ambiguous cases, taking us one step closer to a wider adoption of AI-based assistive tools.
Viability of carcass removal as an option for offsetting the incidental take of golden eagles (Aquila chrysaetos) at wind energy facilities
Authors: Lonsdorf Eric V. , Gerber James S. , Ray Deepak , Slater Steven J. , Allison Taber D.
Published: December 2022

As wind energy expands to achieve the United States’ net zero emission goals, compensatory mitigation will be required to offset negative impacts to birds and bats. The golden eagle (Aquila chrysaetos) is particularly susceptible to collision with wind turbines but only one option for offsetting mortalities has been approved by the U.S. Fish and Wildlife Service despite many sources of anthropogenic-caused mortality. Here, we update a previously developed vehicle-collision model with empirical data and integrate a resource equivalency analysis so that removal of road-killed game animals can be used as mitigation to offset incidental mortality. We parameterized the golden eagle behavior parameters using camera-traps placed at roadside carcasses. We quantified the effects of different carcass-removal schemes based on vehicle and carcass characteristics observed for the state of Wyoming. Our model results indicate that while eagles saved per carcass removed depends on removal interval and vehicle traffic volume, carcass removal is a viable mitigation strategy; up to seven eagles could be saved per year in some counties. While some uncertainty remains about the precise credit received from each carcass removed, delaying the inclusion of additional mitigation methods prevents opportunities for conservation action. An adaptive management program could be a way forward where management and monitoring are combined to further improve estimates of mitigation credit.
Decorrelation Time Mapping as an Analysis Tool for Nanobubble-Based Contrast Enhanced Ultrasound Imaging
Authors: Wegierak Dana , Cooley Michaela , Perera Reshani , Wulftange William J. , Gurkan Umut A. , Kolios Michael C. , Exner Agata A.
Published: December 2022

Nanobubbles (NBs) are nanoscale (∼100-500 nm diameter) ultrasound (US) contrast agents that enable new robust applications of contrast enhanced US and US-mediated therapy. Due to their sub-micron size, high particle density, and highly deformable shell, NBs exhibit unique properties. In pathological states of heightened vascular permeability, such as in tumours, NBs can extravasate, enabling extravascular applications not currently possible with clinically available microbubbles (∼1000-10,000 nm diameter). This ability can be explored to develop imaging biomarkers to improve tumour detection. There is a need for an imaging method that can rapidly and effectively separate intravascular versus extravascular NB signal when imaged using nonlinear dynamic contrast enhanced US. Herein, we demonstrated the use of decorrelation time (DT) mapping to achieve this goal. Twoin vitromodels were used to explore the roles of NB velocity and diffusion on DTs. Mice bearing prostate specific membrane antigen (PSMA) expressing flank tumours (n = 7) were injected with bubble agents to evaluate thein vivopotential of this technique. The DT was calculated at each pixel of nonlinear contrast videos to produce DT maps. Across all models, long DT correlated with slowly moving or entrapped NBs while short DT correlated with flowing NBs. DT maps were sensitive to NBs in tumour tissue with high average DT in tumour regions (∼10 s) compared to surrounding normal tissue (∼1 s). Molecular NB targeting to PSMA extended DT (17 s) compared to non-targeted NBs (12 s), demonstrating sensitivity to NB adherence dynamics. Overall, DT mapping ofin vivoNB dynamics produced detailed information of tumour tissue and showed potential for quantifying extravascular NB kinetics. This new NB-contrast enhanced US-based biomarker can be useful in molecular ultrasound imaging, with improved sensitivity and specificity of target tissue detection and potential for use as a predictor of vascular permeability and the enhanced permeability and retention (EPR) effect in tumours.
An improved reference of the grapevine genome supports reasserting the origin of the PN40024 highly-homozygous genotype
Authors: Velt Amandine , Frommer Bianca , Blanc Sophie , Holtgräwe Daniela , Duchêne Éric , Dumas Vincent , Grimplet Jérôme , Hugueney Philippe , Lahaye Marie , Kim Catherine , Matus José Tomás , Navarro-Payá David , Orduña Luis , Tello-Ruiz Marcela K. , Vitulo Nicola , Ware Doreen , Rustenholz Camille
Published: December 2022

The genome sequence assembly of the diploid and highly homozygousV. viniferagenotype PN40024 serves as the reference for many grapevine studies. Despite several improvements of the PN40024 genome assembly, its current version PN12X.v2 is quite fragmented and only represents the haploid state of the genome with mixed haplotypes. In fact, despite the PN40024 genome is nearly homozygous, it still contains various heterozygous regions. Taking the opportunity of the improvements that long-read sequencing technologies offer to fully discriminate haplotype sequences and considering that severalVitissp. genomes have recently been assembled with these approaches, an improved version of the reference, called PN40024.v4, was generated.

Through incorporating long genomic sequencing reads to the assembly, the continuity of the 12X.v2 scaffolds was highly increased. The number of scaffolds decreased from 2,059 to 640 and the number of N bases was reduced by 88%. Additionally, the full alternative haplotype sequence was built for the first time, the chromosome anchoring was improved and the amount of unplaced scaffolds were reduced by half. To obtain a high-quality gene annotation that outperforms previous versions, a liftover approach was complemented with an optimized annotation workflow forVitis. Integration of the gene reference catalogue and its manual curation have also assisted in improving the annotation, while defining the most reliable estimation to date of 35,230 genes. Finally, we demonstrate that PN40024 resulted from selfings of cv. ‘Helfensteiner’ (cross of cv. ‘Pinot noir’ and ‘Schiava grossa’) instead of a single ‘Pinot noir’. These advances will help maintaining the PN40024 genome as a gold-standard reference also contributing in the eventual elaboration of the grapevine pangenome.
Dysfunctional Hippocampal-Prefrontal Network Underlies a Multidimensional Neuropsychiatric Phenotype following Early-Life Seizure
Authors: Ruggiero Rafael Naime , Marques Danilo Benette , Rossignoli Matheus Teixeira , De Ross Jana Batista , Prizon Tamiris , Beraldo Ikaro Jesus Silva , Bueno-Junior Lezio Soares , Kandratavicius Ludmyla , Peixoto-Santos Jose Eduardo , Aguiar Cleiton Lopes , Leite João Pereira
Published: December 2022

Brain disturbances during development can have a lasting impact on neural function and behavior. Seizures during this critical period are linked to significant long-term consequences such as neurodevelopmental disorders, cognitive impairments, and psychiatric symptoms, resulting in a complex spectrum of multimorbidity. The hippocampus-prefrontal cortex (HPC-PFC) circuit emerges as a potential common link between such disorders. However, the mechanisms underlying these outcomes and how they relate to specific behavioral alterations are unclear. We hypothesized that specific dysfunctions of hippocampal-cortical communication due to early-life seizure would be associated with distinct behavioral alterations observed in adulthood. Here, we performed a multilevel study to investigate behavioral, electrophysiological, histopathological, and neurochemical long-term consequences of early-lifeStatus epilepticusin male rats. We show that adult animals submitted to early-life seizure (ELS) present working memory impairments and sensorimotor disturbances, such as hyperlocomotion, poor sensorimotor gating, and sensitivity to psychostimulants despite not exhibiting neuronal loss. Surprisingly, cognitive deficits were linked to an aberrant increase in the HPC-PFC long-term potentiation (LTP) in a U-shaped manner, while sensorimotor alterations were associated with heightened neuroinflammation, as verified by glial fibrillary acidic protein (GFAP) expression, and altered dopamine neurotransmission. Furthermore, ELS rats displayed impaired HPC-PFC theta-gamma coordination and an abnormal brain state during active behavior resembling rapid eye movement (REM) sleep oscillatory dynamics. Our results point to impaired HPC- PFC functional connectivity as a possible pathophysiological mechanism by which ELS can cause cognitive deficits and psychiatric-like manifestations even without neuronal loss, bearing translational implications for understanding the spectrum of multidimensional developmental disorders linked to early-life seizures.
Plasma concentrations of anti-inflammatory cytokine TGF-β are associated with hippocampal structure related to explicit memory performance in older adults
Authors: Raschick Matthias , Richter Anni , Fischer Larissa , Knopf Lea , Schult Annika , Yakupov Renat , Behnisch Gusalija , Guttek Karina , Düzel Emrah , Dunay Ildiko Rita , Seidenbecher Constanze I. , Schraven Burkhart , Reinhold Dirk , Schott Björn H.
Published: December 2022

Human cognitive abilities, and particularly hippocampus-dependent memory performance typically decline with increasing age. Immunosenescence, the age-related disintegration of the immune system, is increasingly coming into the focus of research as a considerable factor contributing to cognitive decline. In the present study, we investigated potential associations between plasma levels of pro- and anti-inflammatory cytokines and learning and memory performance as well as hippocampal anatomy in young and older adults. Plasma concentrations of the inflammation marker CRP as well as the pro-inflammatory cytokines IL-6 and TNF-α and the anti-inflammatory cytokine TGF-β1were measured in 142 healthy adults (57 young, 24.47 ± 4.48 years; 85 older, 63.66 ± 7.32 years) who performed tests of explicit memory (Verbal Learning and Memory Test, VLMT; Wechsler Memory Scale, Logical Memory, WMS) with an additional delayed recall test after 24 hours. Hippocampal volumetry and hippocampal subfield segmentation were performed using FreeSurfer, based on T1-weighted and high-resolution T2-weighted MR images. When investigating the relationship between memory performance, hippocampal structure, and plasma cytokine levels, we found that TGF- β1concentrations were positively correlated with the volumes of the hippocampal CA4-dentate gyrus region in older adults. These volumes were in turn positively associated with better performance in the WMS, particularly in the delayed memory test. Our results support the notion that endogenous anti-inflammatory mechanisms may act as protective factors in neurocognitive aging.
Deep learning-enabled design of synthetic orthologs of a signaling protein
Authors: Lian Xinran , Praljak Niksa , Subramanian Subu K. , Wasinger Sarah , Ranganathan Rama , Ferguson Andrew L.
Published: December 2022

Evolution-based deep generative models represent an exciting direction in understanding and designing proteins. An open question is whether such models can represent the constraints underlying specialized functions that are necessary for organismal fitness in specific biological contexts. Here, we examine the ability of three different models to produce synthetic versions of SH3 domains that can support function in a yeast stress signaling pathway. Using a select-seq assay, we show that one form of a variational autoencoder (VAE) recapitulates the functional characteristics of natural SH3 domains and classifies fungal SH3 homologs hierarchically by function and phylogeny. Locality in the latent space of the model predicts and extends the function of natural orthologs and exposes amino acid constraints distributed near and far from the SH3 ligand-binding site. The ability of deep generative models to specify orthologous functionin vivoopens new avenues for probing and engineering protein function in specific cellular environments.
Lateral compression of lipids drives transbilayer coupling of liquid-like protein condensates
Authors: Lee Yohan , Park Sujin , Yuan Feng , Hayden Carl C. , Choi Siyoung Q. , Stachowiak Jeanne C.
Published: December 2022

Liquid-liquid phase separation of proteins has recently been observed on the surfaces of biological membranes, where it plays a role in diverse cellular processes, from assembly of focal adhesions and the immunological synapse, to biogenesis of trafficking vesicles. Interestingly in each of these cases, proteins on both surfaces of the membrane are thought to participate, suggesting that protein phase separation could be coupled across the membrane. To explore this possibility, we used an array of freestanding planar lipid membranes to observe protein phase separation simultaneously on both surfaces of lipid bilayers. When proteins known to engage in phase separation bound to the surfaces of these membranes, two-dimensional, protein-rich phases rapidly emerged. These phases displayed the hallmarks of a liquid, coarsening over time by fusing and re-rounding. Interestingly, we observed that protein-rich domains on one side of the membrane colocalized with those on the other side, resulting in transbilayer coupling. How do liquid-like protein phases communicate across the lipid bilayer? Our results, based on lipid probe partitioning and the differential mobility of proteins and lipids, collectively suggest an entropic coupling mechanism, which relies on the ability of protein phase separation to locally reduce the entropy of the underlying lipid membrane, most likely by increasing lipid packing. Regions of reduced entropy then colocalize across the bilayer to minimize the overall free energy of the membrane. These findings suggest a previously unknown mechanism by which cellular signals originating from one side of the membrane, triggered by protein phase separation, can be transferred to the opposite side.
Multiscale genetic architecture of donor-recipient differences reveals intronic LIMS1 locus mismatches associated with long-term renal transplant survival
Authors: Sun Zeguo , Zhang Zhongyang , Banu Khadija , Gibson Ian , Colvin Robert , Yi Zhengzi , Zhang Weijia , De Kumar Bony , Pell John , Djamali Arjang , Gallon Lorenzo , O’Connell Philip , He Cijiang , Pober Jordan , Heeger Peter , Menon Madhav C
Published: December 2022

Background

Long-term kidney allograft survival remains suboptimal. Emerging evidence indicates donor-recipient (D-R) mismatches outside of human leukocyte antigens (HLA) contribute to graft survival but mechanisms remain unclear, specifically for those mismatches within intronic regions.

Methods

We analyzed genome-wide SNP data of D-R pairs from two well-phenotyped kidney transplant cohorts (median follow-up ~1800 days), Genomics of Chronic Allograft Rejection (GoCAR; n=385) and Clinical Trials in Organ Transplantation 1/17 (CTOT1/17; n=146), quantifying genetic mismatches outside of HLA for every D-R pair at variant, gene, and genome-wide scales.

Results

Unbiased genome-wide screen of GoCAR D-R pairs uncovered the LIMS1 locus as the topranked candidate where D-R mismatches associated with death censored graft loss (DCGL). Independent of HLA, a previously unreported relationship between mismatches at a highly linked, intronic haplotype of 30 SNPs was seen as associated with DCGL, with confirmatory association in intra-ancestry D-Rs. Validation testing within the CTOT-01/17 showed similar associations with DCGL. Haplotype D-R mismatches showed a dosage effect, and the introduction of minor alleles in the donor to major allele-carrying recipients showed a greater risk of DCGL. Both the new LIMS1 haplotype and the previously reported LIMS1 SNP rs893403 are expression quantitative trait loci (eQTL) for the gene GCC2 in recipient immune cells, without alterations in GCC2 or LIMS1 coding sequences. Transcriptome enrichment analyses performed on whole blood and within multiple T cell subsets demonstrated significant associations of GCC2 gene, and of either allelic locus, with regulation of TGF-beta-SMAD signaling, implying a role in Treg function and association with rejection.

Conclusions

Our analysis unravels intronic non-HLA SNP mismatches within LIMS1 that do not induce protein sequence variation but associate with DCGL. By acting as cis-eQTLs for GCC2 expression, these SNPs modulates TGF-beta signaling and T cell function, associating with immune events and graft outcomes. The findings have clinical implications for risk assessment and individualized therapy in kidney transplant recipients.
Evolution and phylogenetic distribution ofendo-α-mannosidase
Authors: Sobala Łukasz F.
Published: December 2022

While glycans underlie many biological processes, such as protein folding, cell adhesion and cell-cell recognition, deep evolution of glycosylation machinery remains an understudied topic. N-linked glycosylation is a conserved process in which mannosidases are key trimming enzymes. One of them is the glycoproteinendo-α-1,2-mannosidase which participates in the initial trimming of mannose moieties from an N-linked glycan inside thecis-Golgi. It is unique as the only endo-acting mannosidase found in this organelle. Relatively little is known about its origins and evolutionary history; so far it was thought to occur only in vertebrates. Here I perform a taxon-rich bioinformatic survey to unravel the evolutionary history of this enzyme, including all major eukaryotic clades and a wide representation of animals. I found the endomannosidase to be vastly more widely distributed in animals than previously thought and in fact present in almost all eukaryotic clades. I tracked protein motif changes in context of the canonical animal enzyme. Additionally, my data show that the two canonical versions of endomannosidase in vertebrates, MANEA and MANEAL, arose at the second round of the two vertebrate genome duplications and indicate presence of a third protein, named here CMANEAL. Finally, I describe a framework where N-glycosylation co-evolved with complex multicellularity. A better understanding of the evolution of core glycosylation pathways is pivotal to understanding biology of eukaryotes in general, and the Golgi apparatus in particular. This systematic analysis of the endomannosidase evolution is one step towards this goal.
Inverse Agonist Activity of Angiotensin II Receptor Blocker Is Crucial for Prevention of Aortic Aneurysm Formation in Marfan Syndrome
Authors: Yagi Hiroki , Akazawa Hiroshi , Liu Qing , Umei Masahiko , Kadowaki Hiroshi , Matsuoka Ryo , Shindo Akito , Okamura Shun , Saga-Kamo Akiko , Takeda Norifumi , Komuro Issei
Published: December 2022

Background

Marfan syndrome (MFS), an inherited disorder caused byFBN1gene mutations, causes fatal aortic aneurysm. Selective angiotensin II (Ang II) type 1 (AT1) receptor blockade is a preventive option for patients with MFS aortopathy, and recent clinical studies demonstrated that the inhibitory effect of an AT1receptor blocker (ARB) losartan on aortic aneurysm growth is equivalent to that of β-blockers. At present, several ARBs are clinically available, and they have drug-specific differences in pharmacological properties. Especially, inverse agonism of ARBs has potential benefits for cardiovascular protection, but its impact on MFS aortopathy remains poorly understood.

Methods

Candesartan-7H is a candesartan derivative which lacks the carboxyl group critical for inverse agonist activity and works as a neutral antagonist for AT1receptor. Candesartan cilexetil (1 mg/kg/day), candesartan-7H (1 mg/kg/day or 20 mg/kg/day), or vehicle was administered toFbn1C1041G/+mice, and aortic aneurysm formation was analyzed using echocardiography, histological staining, andin situMMP assay. Activation of TGF-β signaling and mechanosensitive signaling was studied using western blot and immunohistochemical analysis.

Results

Candesartan cilexetil (1 mg/kg/day) and candesartan-7H (20 mg/kg/day) lowered blood pressures equally inFbn1C1041G/+mice, but that candesartan-7H (1 mg/kg/day) did not. Aortic aneurysmal progression in association with aortic wall thickening, degeneration of elastic fibers, deposition of collagen, MMP activation, and TGF-β signaling activation inFbn1C1041G/+mice was significantly suppressed by treatment with candesartan cilexetil (1 mg/kg/day), but not by candesartan-7H even at 20 mg/kg/day. In addition, candesartan cilexetil, but not candesartan-7H, inhibited up-regulation of mechanical stress–responsive transcriptional factor Egr-1 in ascending aorta ofFbn1C1041G/+mice.

Conclusions

Our findings support a crucial role of inverse agonist activity of ARB for prevention of mechanical stress-induced AT1receptor activation and aortic aneurysm formation in MFS mice.
The Tip60/Ep400 chromatin remodeling complex impacts basic cellular functions in cranial neural crest-derived tissue during early orofacial development
Authors: Gehlen-Breitbach Sebastian , Schmid Theresa , Fröb Franziska , Rodrian Gabriele , Weider Matthias , Wegner Michael , Gölz Lina
Published: December 2022

The cranial neural crest plays a fundamental role in orofacial development and morphogenesis. Accordingly, mutations with impact on the cranial neural crest and its development lead to orofacial malformations such as cleft lip and palate. As a pluripotent and dynamic cell population, the cranial neural crest undergoes vast transcriptional and epigenomic alterations throughout the formation of facial structures pointing to an essential role of factors regulating chromatin state or transcription levels. Using CRISPR/Cas9-guided genome editing and conditional mutagenesis in the mouse, we here show that inactivation of Kat5 and Ep400 as the two essential enzymatic subunits of the Tip60/Ep400 chromatin remodeling complexes severely affects carbohydrate and amino acid metabolism in cranial neural crest cells. The resulting decrease in protein synthesis, proliferation and survival leads to a drastic reduction of cranial neural crest cells early in fetal development and a loss of most facial structures in the absence of either protein. Following heterozygous loss of Kat5 in neural crest cells palatogenesis was impaired. These findings point to a decisive role of the Tip60/Ep400 chromatin remodeling complex in facial morphogenesis and lead us to conclude that the orofacial clefting observed in patients with heterozygous KAT5 missense mutations is at least in part due to disturbances in the cranial neural crest.
Gene regulatory network inference using mixed-norms regularized multivariate model with covariance selection
Authors: Mbebi Alain J. , Nikoloski Zoran
Published: December 2022

Despite extensive research efforts, reconstruction of gene regulatory networks (GRNs) from transcriptomics data remains a pressing challenge in systems biology. While non-linear approaches for reconstruction of GRNs show improved performance over simpler alternatives, we do not yet have understanding if joint modelling of multiple target genes may improve performance, even under linearity assumptions. To address this problem, we propose two novel approaches that cast the GRN reconstruction problem as a blend between regularized multivariate regression and graphical models that combine the L2,1-norm with classical regularization techniques. We used data and networks from the DREAM5 challenge to show that the proposed models provide consistently good performance in comparison to contenders whose performance varies with data sets from simulation and experiments from model unicellular organismsEscherichia coliandSaccharomyces cerevisiae. Since the models’ formulation facilitates the prediction of master regulators, we also used the resulting findings to identify master regulators over all data sets as well as their plasticity across different environments. Our results demonstrate that the identified master regulators are in line with experimental evidence from the model bacteriumE. coli. Together, our study demonstrates that simultaneous modelling of several target genes results in improved inference of GRNs and can be used as an alternative in different applications.

Author summary

Reconstruction of cellular networks based on snapshots of molecular profiles of the network components has been one of the key challenges in systems biology. In the context of reconstruction of gene regulatory networks (GRNs), this problem translates into inferring regulatory relationships between transcription factor coding genes and their targets based on, often small, number of expression profiles. While unsupervised nonlinear machine learning approaches have shown better performance than regularized linear regression approaches, the existing modeling strategies usually do predictions of regulators for one target gene at a time. Here, we ask if and to what extent the joint modeling of regulation for multiple targets leads to improvement of the accuracy of the inferred GRNs. To address this question, we proposed, implemented, and compared the performance of models cast as a blend between regularized multivariate regression and graphical models that combine the L2,1-norm with classical regularization techniques. Our results demonstrate that the proposed models, despite relying on linearity assumptions, show consistently good performance in comparison to existing, widely used alternatives.
Engaging Men Through HIV Self-Testing with Differentiated Care to Improve ART Initiation and Viral Suppression among Men in Malawi (ENGAGE): a study protocol for a randomized control trial
Authors: Choko Augustine Talumba , Coates Thomas J , Mphande Misheck , Balakasi Kelvin , Robson Isabella , Phiri Khumbo , Phiri Sam , Kulich Michal , Sweat Micheal , Cornell Morna , Hoffmann Risa , Dovel Kathryn
Published: December 2022

Background Men experience twice the mortality of women while on ART in sub-Saharan Africa (SSA) largely due to late HIV diagnosis and poor retention. Here we propose to conduct an individually randomized control trial (RCT) to investigate the impact of three-month home-based ART (hbART) on viral suppression among men who were not engaged in care. Methods and Design A programmatic, individually randomized non-blinded, non-inferiority-controlled trial design (ClinicalTrials.orgNCT04858243). Through medical chart reviews we will identify non-engaged men living with HIV, ≥15years of age who are not currently engaged in ART care, including (1) men who have tested HIV-positive and have not initiated ART within 7 days; (2) men who have initiated ART but are at risk of immediate default; and (3) men who have defaulted from ART. With 1:1 computer block randomization to either hbART or facility-based ART (fbART) arms, we will recruit men from 10-15 high-burden health facilities in central and southern Malawi. The hbART intervention will consist of 3 home-visits in a 3-month period by a certified male study nurse ART provider. In the fbART arm, male participants will be offered counseling at male participants home, or a nearby location that is preferred by participants, followed with an escort to the local health facility and facility navigation. The primary outcome is the proportion of men who are virally suppressed at 6-months after ART initiation. Assuming primary outcome achievement of 24.0% and 33.6% in the two arms, 350 men per arm will provide 80% power to detect the stated difference. Discussion Identifying effective ART strategies that are convenient and accessible for men in SSA is a priority in the HIV world. Men may not (re-)engage in facility-based care due to a myriad of barriers. Two previous trials investigated the impact of hbART on viral suppression in the general population whereas this trial focuses on men. Additionally, this trial involves a longer duration of hbART i.e., three months compared to two weeks allowing men more time to overcome the initial psychological denial of taking ART.
Functional genomic mechanisms of opioid action and opioid use disorder: a systematic review of animal models and human studies
Authors: Falconnier Camille , Caparros-Roissard Alba , Decraene Charles , Lutz Pierre-Eric
Published: December 2022

In the past two decades, over-prescription of opioids for pain management has driven a steep increase in opioid use disorder (OUD) and death by overdose, exerting a dramatic toll on western countries. OUD is a chronic relapsing disease associated with a lifetime struggle to control drug consumption, suggesting that opioids trigger long-lasting brain adaptations, notably through functional genomic and epigenomic mechanisms. Current understanding of these processes, however, remain scarce, and have not been previously reviewed systematically. To do so, the goal of the present work was to synthesize current knowledge on genome-wide transcriptomic and epigenetic mechanisms of opioid action, in primate and rodent species. Using a prospectively registered methodology, comprehensive literature searches were completed in PubMed, Embase, and Web of Science. Of the 2709 articles identified, 73 met our inclusion criteria and were considered for qualitative analysis. Focusing on the 5 most studied nervous system structures (nucleus accumbens, frontal cortex, whole striatum, dorsal striatum, spinal cord; 44 articles), we also conducted a quantitative analysis of differentially expressed genes, in an effort to identify a putative core transcriptional signature of opioids. Only one gene, Cdkn1a, was consistently identified in eleven studies, and globally, our results unveil surprisingly low consistency across published work, even when considering most recent single-cell approaches. Analysis of putative sources of variability detected significant contributions from species, brain structure, duration of opioid exposure, strain, time-point of analysis, and batch effects, but not type of opioid. To go beyond those limitations, we leveraged threshold-free methods to illustrate how genome-wide comparisons may generate new findings and hypotheses. Finally, we discuss current methodological development in the field, and their implication for future research and, ultimately, better care.
A quantitative and site-specific atlas of the in vivo citrullinome reveals widespread existence of citrullination
Authors: Rebak Alexandra S. , Hendriks Ivo A. , Buch-Larsen Sara C. , Elsborg Jonas D. , Kirsch Rebecca , Doncheva Nadezhda T. , Jensen Lars J. , Christophorou Maria , Nielsen Michael L.
Published: December 2022

Citrullination is the conversion of peptidyl-arginine into the non-coded amino acid citrulline. Despite its importance in physiology and disease, global identification of citrullinated proteins and precise modification sites has remained challenging. Here, we employed quantitative mass spectrometry-based proteomics to generate a comprehensive atlas of citrullination sites in a physiologically relevant cell type. Collectively, we identified 14.056 citrullination sites within 4.008 proteins and quantified their regulation upon inhibition of the citrullinating enzyme PADI4. Using this rich dataset, we uncover general mechanistic and cell biological principles of citrullination function, while providing site-specific and quantitative information on thousands of PAD4 substrates within cells. Our findings include signature histone marks and numerous modifications on transcriptional regulators and chromatin-related signaling effectors. Additionally, we identify precise citrullination sites on an extensive list of known autoantigens. Collectively, we describe systems attributes of the human citrullinome and provide a resource framework for understanding citrullinaiton at the mechanistic level.
The Beta secretase BACE1 drives fibroblasts activation in Systemic Sclerosis through the APP/β-catenin/Notch signalling axis
Authors: Wasson Christopher W. , Lorenzis Enrico De , Clavane Eva M. , Ross Rebecca L. , Walker Kieran A. , Caballero-Ruiz Begoña , Antinozzi Cristina , Wells Rebecca , Migneco Gemma , Brown Jane M. Y. , Riobo-Del Galdo Natalia A. , Luigi Luigi Di , McKimmie Clive S. , Del Galdo Francesco , Meakin Paul J.
Published: December 2022

The beta-amyloid precursor protein cleaving enzyme 1 (BACE1) is well known for its role in the development of Alzheimer’s disease. Recent publications, including our own, have demonstrated a role for this enzyme in other chronic diseases. The aim of this study was to investigate the role of BACE1 in the autoimmune disease systemic sclerosis (SSc). BACE1 protein levels were elevated in SSc patient skin. Inhibition of BACE1 with small molecule inhibitors or siRNA blocked SSc and fibrotic stimuli mediated fibroblast activation. Furthermore, we show that BACE1 regulation of dermal fibroblast activation is dependent on β-catenin and Notch signalling. The Neurotropic factor BDNF negatively regulates BACE1 expression and activity in dermal fibroblasts. Finally, sera from SSc patients show higher Aβ and lower BDNF levels compared to healthy controls. The ability of BACE1 to regulate SSc fibroblast activation reveals a new therapeutic target in SSc. Several BACE1 inhibitors have been shown to be safe in clinical trials for Alzheimer’s disease and could be repurposed to ameliorate fibrosis progression.