Systems Biology

Genome-scale annotation of protein binding sites via language model and geometric deep learning

Wed, 2024-04-17 06:00

Elife. 2024 Apr 17;13:RP93695. doi: 10.7554/eLife.93695.

ABSTRACT

Revealing protein binding sites with other molecules, such as nucleic acids, peptides, or small ligands, sheds light on disease mechanism elucidation and novel drug design. With the explosive growth of proteins in sequence databases, how to accurately and efficiently identify these binding sites from sequences becomes essential. However, current methods mostly rely on expensive multiple sequence alignments or experimental protein structures, limiting their genome-scale applications. Besides, these methods haven't fully explored the geometry of the protein structures. Here, we propose GPSite, a multi-task network for simultaneously predicting binding residues of DNA, RNA, peptide, protein, ATP, HEM, and metal ions on proteins. GPSite was trained on informative sequence embeddings and predicted structures from protein language models, while comprehensively extracting residual and relational geometric contexts in an end-to-end manner. Experiments demonstrate that GPSite substantially surpasses state-of-the-art sequence-based and structure-based approaches on various benchmark datasets, even when the structures are not well-predicted. The low computational cost of GPSite enables rapid genome-scale binding residue annotations for over 568,000 sequences, providing opportunities to unveil unexplored associations of binding sites with molecular functions, biological processes, and genetic variants. The GPSite webserver and annotation database can be freely accessed at https://bio-web1.nscc-gz.cn/app/GPSite.

PMID:38630609 | DOI:10.7554/eLife.93695

Categories: Literature Watch

STMND1 is A Phylogenetically Ancient Stathmin which Localizes to Motile Cilia and Exhibits Nuclear Translocation that Is Inhibited When Soluble Tubulin Concentration Increases

Wed, 2024-04-17 06:00

Mol Biol Cell. 2024 Apr 17:mbcE23120514. doi: 10.1091/mbc.E23-12-0514. Online ahead of print.

ABSTRACT

Stathmins are small, unstructured proteins that bind tubulin dimers and are implicated in several human diseases, but whose function remains unknown. We characterized a new stathmin, STMND1 (Stathmin Domain Containing 1) as the human representative of an ancient sub-family. STMND1 features a N-terminal myristoylated and palmitoylated motif which directs it to membranes and a tubulin-binding stathmin-like domain (SLD) that contains an internal nuclear localization signal. Biochemistry and proximity labeling showed that STMND1 binds tubulin, and live imaging showed that tubulin binding inhibits translocation from cellular membranes to the nucleus. STMND1 is highly expressed in multiciliated epithelial cells, where it localizes to motile cilia. Overexpression in a model system increased the length of primary cilia. Our study suggests that the most ancient stathmins have cilium-related functions that involve sensing soluble tubulin. [Media: see text] [Media: see text].

PMID:38630521 | DOI:10.1091/mbc.E23-12-0514

Categories: Literature Watch

Teneurin C-terminal associated peptide (TCAP)-1 attenuates the development and expression of naloxone-precipitated morphine withdrawal in male Swiss Webster mice

Wed, 2024-04-17 06:00

Psychopharmacology (Berl). 2024 Apr 17. doi: 10.1007/s00213-024-06582-0. Online ahead of print.

ABSTRACT

RATIONALE: Corticotropin-releasing factor (CRF), the apical stress-inducing hormone, exacerbates stress and addictive behaviors. TCAP-1 is a peptide that directly inhibits both CRF-mediated stress and addiction-related behaviors; however, the direct action of TCAP-1 on morphine withdrawal-associated behaviors has not previously been examined.

OBJECTIVE: To determine whether TCAP-1 administration attenuates behavioral and physiological consequences of morphine withdrawal in mice.

METHODS: Mice were administered via subcutaneous route TCAP-1 either before or after initial morphine exposure, after which jumping behavior was quantified to assess the effects of TCAP-1 on naloxone-precipitated morphine withdrawal. As a comparison, mice were treated with nonpeptide CRF1 receptor antagonist CP-154,526. In one experiment, plasma corticosterone (CORT) was also measured as a physiological stress indicator.

RESULTS: Pretreatment with TCAP-1 (10-250 nmol/kg) before morphine treatment significantly inhibited the development of naloxone-precipitated withdrawal. TCAP-1 (250-500 nmol/kg) treatment administered after morphine treatment attenuated the behavioral expression of naloxone-precipitated withdrawal. TCAP-1 (250 nmol/kg) treatment during morphine treatment was more effective than the optimal dosing of CP-154,526 (20 mg/kg) at suppressing the behavioral expression of naloxone-precipitated withdrawal, despite similar reduction of withdrawal-induced plasma CORT level increases.

CONCLUSIONS: These findings establish TCAP-1 as a potential therapeutic candidate for the prevention and treatment of morphine withdrawal.

PMID:38630316 | DOI:10.1007/s00213-024-06582-0

Categories: Literature Watch

Astrocytic uptake of posttranslationally modified amyloid-β leads to endolysosomal system disruption and induction of pro-inflammatory signaling

Wed, 2024-04-17 06:00

Glia. 2024 Apr 17. doi: 10.1002/glia.24539. Online ahead of print.

ABSTRACT

The disruption of astrocytic catabolic processes contributes to the impairment of amyloid-β (Aβ) clearance, neuroinflammatory signaling, and the loss of synaptic contacts in late-onset Alzheimer's disease (AD). While it is known that the posttranslational modifications of Aβ have significant implications on biophysical properties of the peptides, their consequences for clearance impairment are not well understood. It was previously shown that N-terminally pyroglutamylated Aβ3(pE)-42, a significant constituent of amyloid plaques, is efficiently taken up by astrocytes, leading to the release of pro-inflammatory cytokine tumor necrosis factor α and synapse loss. Here we report that Aβ3(pE)-42, but not Aβ1-42, gradually accumulates within the astrocytic endolysosomal system, disrupting this catabolic pathway and inducing the formation of heteromorphous vacuoles. This accumulation alters lysosomal kinetics, lysosome-dependent calcium signaling, and upregulates the lysosomal stress response. These changes correlate with the upregulation of glial fibrillary acidic protein (GFAP) and increased activity of nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB). Treatment with a lysosomal protease inhibitor, E-64, rescues GFAP upregulation, NF-κB activation, and synapse loss, indicating that abnormal lysosomal protease activity is upstream of pro-inflammatory signaling and related synapse loss. Collectively, our data suggest that Aβ3(pE)-42-induced disruption of the astrocytic endolysosomal system leads to cytoplasmic leakage of lysosomal proteases, promoting pro-inflammatory signaling and synapse loss, hallmarks of AD-pathology.

PMID:38629411 | DOI:10.1002/glia.24539

Categories: Literature Watch

Disentangling the effects of sulfate and other seawater ions on microbial communities and greenhouse gas emissions in a coastal forested wetland

Wed, 2024-04-17 06:00

ISME Commun. 2024 Mar 26;4(1):ycae040. doi: 10.1093/ismeco/ycae040. eCollection 2024 Jan.

ABSTRACT

Seawater intrusion into freshwater wetlands causes changes in microbial communities and biogeochemistry, but the exact mechanisms driving these changes remain unclear. Here we use a manipulative laboratory microcosm experiment, combined with DNA sequencing and biogeochemical measurements, to tease apart the effects of sulfate from other seawater ions. We examined changes in microbial taxonomy and function as well as emissions of carbon dioxide, methane, and nitrous oxide in response to changes in ion concentrations. Greenhouse gas emissions and microbial richness and composition were altered by artificial seawater regardless of whether sulfate was present, whereas sulfate alone did not alter emissions or communities. Surprisingly, addition of sulfate alone did not lead to increases in the abundance of sulfate reducing bacteria or sulfur cycling genes. Similarly, genes involved in carbon, nitrogen, and phosphorus cycling responded more strongly to artificial seawater than to sulfate. These results suggest that other ions present in seawater, not sulfate, drive ecological and biogeochemical responses to seawater intrusion and may be drivers of increased methane emissions in soils that received artificial seawater addition. A better understanding of how the different components of salt water alter microbial community composition and function is necessary to forecast the consequences of coastal wetland salinization.

PMID:38628812 | PMC:PMC11020224 | DOI:10.1093/ismeco/ycae040

Categories: Literature Watch

Internuclear ophthalmoplegia following radial artery cardiac catheterization approach: An unusual presentation

Wed, 2024-04-17 06:00

Saudi J Ophthalmol. 2023 Jul 24;38(1):64-66. doi: 10.4103/sjopt.sjopt_2_23. eCollection 2024 Jan-Mar.

ABSTRACT

Internuclear ophthalmoplegia (INO) may happen following percutaneous coronary intervention and angiography. However, no reports of INO during radial artery angioplasty were reported yet. We report a rare case in a 47-year-old man presenting with diplopia after radial artery angioplasty. Although the symptoms were resolved after 60 days, diagnosing this obstacle is necessary to reduce the patient and physician's anxiety.

PMID:38628413 | PMC:PMC11017003 | DOI:10.4103/sjopt.sjopt_2_23

Categories: Literature Watch

<em>Rhizobium</em> symbiosis improves amino acid and secondary metabolite biosynthesis of tungsten-stressed soybean (<em>Glycine max</em>)

Wed, 2024-04-17 06:00

Front Plant Sci. 2024 Apr 2;15:1355136. doi: 10.3389/fpls.2024.1355136. eCollection 2024.

ABSTRACT

The industrially important transition metal tungsten (W) shares certain chemical properties with the essential plant micronutrient molybdenum and inhibits the activity of molybdoenzymes such as nitrate reductase, impacting plant growth. Furthermore, tungsten appears to interfere with metabolic processes on a much wider scale and to trigger common heavy metal stress response mechanisms. We have previously found evidence that the tungsten stress response of soybeans (Glycine max) grown with symbiotically associated N2-fixing rhizobia (Bradyrhizobium japonicum) differs from that observed in nitrogen-fertilized soy plants. This study aimed to investigate how association with symbiotic rhizobia affects the primary and secondary metabolite profiles of tungsten-stressed soybean and whether changes in metabolite composition enhance the plant's resilience to tungsten. This comprehensive metabolomic and proteomic study presents further evidence that the tungsten-stress response of soybean plants is shaped by associated rhizobia. Symbiotically grown plants (N fix) were able to significantly increase the synthesis of an array of protective compounds such as phenols, polyamines, gluconic acid, and amino acids such as proline. This resulted in a higher antioxidant capacity, reduced root-to-shoot translocation of tungsten, and, potentially, also enhanced resilience of N fix plants compared to non-symbiotic counterparts (N fed). Taken together, our study revealed a symbiosis-specific metabolic readjustment in tungsten-stressed soybean plants and contributed to a deeper understanding of the mechanisms involved in the rhizobium-induced systemic resistance in response to heavy metals.

PMID:38628363 | PMC:PMC11020092 | DOI:10.3389/fpls.2024.1355136

Categories: Literature Watch

Double-digest restriction-associated DNA sequencing-based genotyping and its applications in sesame germplasm management

Wed, 2024-04-17 06:00

Plant Genome. 2024 Apr 17:e20447. doi: 10.1002/tpg2.20447. Online ahead of print.

ABSTRACT

Sesame (Sesamum indicum L.) is an ancient oilseed crop belonging to the family Pedaliaceae and a globally cultivated crop for its use as oil and food. In this study, 2496 sesame accessions, being conserved at the National Genebank of ICAR-National Bureau of Plant Genetic Resources (NBPGR), were genotyped using genomics-assisted double-digest restriction-associated DNA sequencing (ddRAD-seq) approach. A total of 64,910 filtered single-nucleotide polymorphisms (SNPs) were utilized to assess the genome-scale diversity. Applications of this genome-scale information (reduced representation using restriction enzymes) are demonstrated through the development of a molecular core collection (CC) representing maximal SNP diversity. This information is also applied in developing a mid-density panel (MDP) comprising 2515 hyper-variable SNPs, representing almost equally the genic and non-genic regions. The sesame CC comprising 384 accessions, a representative set of accessions with maximal diversity, was identified using multiple criteria such as k-mer (subsequence of length "k" in a sequence read) diversity, observed heterozygosity, CoreHunter3, GenoCore, and genetic differentiation. The coreset constituted around 15% of the total accessions studied, and this small subset had captured >60% SNP diversity of the entire population. In the coreset, the admixture analysis shows reduced genetic complexity, increased nucleotide diversity (π), and is geographically distributed without any repetitiveness in the CC germplasm. Within the CC, India-originated accessions exhibit higher diversity (as expected based on the center of diversity concept), than those accessions that were procured from various other countries. The identified CC set and the MDP will be a valuable resource for genomics-assisted accelerated sesame improvement program.

PMID:38628142 | DOI:10.1002/tpg2.20447

Categories: Literature Watch

Collision induced unfolding and molecular dynamics simulations of norovirus capsid dimers reveal strain-specific stability profiles

Wed, 2024-04-17 06:00

Phys Chem Chem Phys. 2024 Apr 17. doi: 10.1039/d3cp06344e. Online ahead of print.

ABSTRACT

Collision induced unfolding (CIU) is a method used with ion mobility mass spectrometry to examine protein structures and their stability. Such experiments yield information about higher order protein structures, yet are unable to provide details about the underlying processes. That information can however be provided using molecular dynamics simulations. Here, we investigate the gas-phase unfolding of norovirus capsid dimers from the Norwalk and Kawasaki strains by employing molecular dynamics simulations over a range of temperatures, representing different levels of activation, together with CIU experiments. The dimers have highly similar structures, but their CIU reveals different stability that can be explained by the different dynamics that arises in response to the activation seen in the simulations, including a part of the sequence with previously observed strain-specific dynamics in solution. Our findings show how similar protein variants can be examined using mass spectrometric techniques in conjunction with atomistic molecular dynamics simulations to reveal differences in stability as well as differences in how and where unfolding takes place upon activation.

PMID:38628116 | DOI:10.1039/d3cp06344e

Categories: Literature Watch

Isotopically nonstationary metabolic flux analysis of plants: recent progress and future opportunities

Wed, 2024-04-17 06:00

New Phytol. 2024 Apr 16. doi: 10.1111/nph.19734. Online ahead of print.

ABSTRACT

Metabolic flux analysis (MFA) is a valuable tool for quantifying cellular phenotypes and to guide plant metabolic engineering. By introducing stable isotopic tracers and employing mathematical models, MFA can quantify the rates of metabolic reactions through biochemical pathways. Recent applications of isotopically nonstationary MFA (INST-MFA) to plants have elucidated nonintuitive metabolism in leaves under optimal and stress conditions, described coupled fluxes for fast-growing algae, and produced a synergistic multi-organ flux map that is a first in MFA for any biological system. These insights could not be elucidated through other approaches and show the potential of INST-MFA to correct an oversimplified understanding of plant metabolism.

PMID:38628036 | DOI:10.1111/nph.19734

Categories: Literature Watch

Superparamagnetic Iron Oxide Nanoparticles Reprogram the Tumor Microenvironment and Reduce Lung Cancer Regrowth after Crizotinib Treatment

Tue, 2024-04-16 06:00

ACS Nano. 2024 Apr 16. doi: 10.1021/acsnano.3c08335. Online ahead of print.

ABSTRACT

ALK-positive NSCLC patients demonstrate initial responses to ALK tyrosine kinase inhibitor (TKI) treatments, but eventually develop resistance, causing rapid tumor relapse and poor survival rates. Growing evidence suggests that the combination of drug and immune therapies greatly improves patient survival; however, due to the low immunogenicity of the tumors, ALK-positive patients do not respond to currently available immunotherapies. Tumor-associated macrophages (TAMs) play a crucial role in facilitating lung cancer growth by suppressing tumoricidal immune activation and absorbing chemotherapeutics. However, they can also be programmed toward a pro-inflammatory tumor suppressive phenotype, which represents a highly active area of therapy development. Iron loading of TAMs can achieve such reprogramming correlating with an improved prognosis in lung cancer patients. We previously showed that superparamagnetic iron oxide nanoparticles containing core-cross-linked polymer micelles (SPION-CCPMs) target macrophages and stimulate pro-inflammatory activation. Here, we show that SPION-CCPMs stimulate TAMs to secrete reactive nitrogen species and cytokines that exert tumoricidal activity. We further show that SPION-CCPMs reshape the immunosuppressive Eml4-Alk lung tumor microenvironment (TME) toward a cytotoxic profile hallmarked by the recruitment of CD8+ T cells, suggesting a multifactorial benefit of SPION-CCPM application. When intratracheally instilled into lung cancer-bearing mice, SPION-CCPMs delay tumor growth and, after first line therapy with a TKI, halt the regrowth of relapsing tumors. These findings identify SPIONs-CCPMs as an adjuvant therapy, which remodels the TME, resulting in a delay in the appearance of resistant tumors.

PMID:38626916 | DOI:10.1021/acsnano.3c08335

Categories: Literature Watch

Nextflow pipeline for Visium and H&amp;E data from patient-derived xenograft samples

Tue, 2024-04-16 06:00

Cell Rep Methods. 2024 Apr 10:100759. doi: 10.1016/j.crmeth.2024.100759. Online ahead of print.

ABSTRACT

We designed a Nextflow DSL2-based pipeline, Spatial Transcriptomics Quantification (STQ), for simultaneous processing of 10x Genomics Visium spatial transcriptomics data and a matched hematoxylin and eosin (H&E)-stained whole-slide image (WSI), optimized for patient-derived xenograft (PDX) cancer specimens. Our pipeline enables the classification of sequenced transcripts for deconvolving the mouse and human species and mapping the transcripts to reference transcriptomes. We align the H&E WSI with the spatial layout of the Visium slide and generate imaging and quantitative morphology features for each Visium spot. The pipeline design enables multiple analysis workflows, including single or dual reference genome input and stand-alone image analysis. We show the utility of our pipeline on a dataset from Visium profiling of four melanoma PDX samples. The clustering of Visium spots and clustering of H&E imaging features reveal similar patterns arising from the two data modalities.

PMID:38626768 | DOI:10.1016/j.crmeth.2024.100759

Categories: Literature Watch

Characterizing glucokinase variant mechanisms using a multiplexed abundance assay

Tue, 2024-04-16 06:00

Genome Biol. 2024 Apr 16;25(1):98. doi: 10.1186/s13059-024-03238-2.

ABSTRACT

BACKGROUND: Amino acid substitutions can perturb protein activity in multiple ways. Understanding their mechanistic basis may pinpoint how residues contribute to protein function. Here, we characterize the mechanisms underlying variant effects in human glucokinase (GCK) variants, building on our previous comprehensive study on GCK variant activity.

RESULTS: Using a yeast growth-based assay, we score the abundance of 95% of GCK missense and nonsense variants. When combining the abundance scores with our previously determined activity scores, we find that 43% of hypoactive variants also decrease cellular protein abundance. The low-abundance variants are enriched in the large domain, while residues in the small domain are tolerant to mutations with respect to abundance. Instead, many variants in the small domain perturb GCK conformational dynamics which are essential for appropriate activity.

CONCLUSIONS: In this study, we identify residues important for GCK metabolic stability and conformational dynamics. These residues could be targeted to modulate GCK activity, and thereby affect glucose homeostasis.

PMID:38627865 | DOI:10.1186/s13059-024-03238-2

Categories: Literature Watch

From buds to shoots: insights into grapevine development from the Witch's Broom bud sport

Tue, 2024-04-16 06:00

BMC Plant Biol. 2024 Apr 16;24(1):283. doi: 10.1186/s12870-024-04992-y.

ABSTRACT

BACKGROUND: Bud sports occur spontaneously in plants when new growth exhibits a distinct phenotype from the rest of the parent plant. The Witch's Broom bud sport occurs occasionally in various grapevine (Vitis vinifera) varieties and displays a suite of developmental defects, including dwarf features and reduced fertility. While it is highly detrimental for grapevine growers, it also serves as a useful tool for studying grapevine development. We used the Witch's Broom bud sport in grapevine to understand the developmental trajectories of the bud sports, as well as the potential genetic basis. We analyzed the phenotypes of two independent cases of the Witch's Broom bud sport, in the Dakapo and Merlot varieties of grapevine, alongside wild type counterparts. To do so, we quantified various shoot traits, performed 3D X-ray Computed Tomography on dormant buds, and landmarked leaves from the samples. We also performed Illumina and Oxford Nanopore sequencing on the samples and called genetic variants using these sequencing datasets.

RESULTS: The Dakapo and Merlot cases of Witch's Broom displayed severe developmental defects, with no fruit/clusters formed and dwarf vegetative features. However, the Dakapo and Merlot cases of Witch's Broom studied were also phenotypically different from one another, with distinct differences in bud and leaf development. We identified 968-974 unique genetic mutations in our two Witch's Broom cases that are potential causal variants of the bud sports. Examining gene function and validating these genetic candidates through PCR and Sanger-sequencing revealed one strong candidate mutation in Merlot Witch's Broom impacting the gene GSVIVG01008260001.

CONCLUSIONS: The Witch's Broom bud sports in both varieties studied had dwarf phenotypes, but the two instances studied were also vastly different from one another and likely have distinct genetic bases. Future work on Witch's Broom bud sports in grapevine could provide more insight into development and the genetic pathways involved in grapevine.

PMID:38627633 | DOI:10.1186/s12870-024-04992-y

Categories: Literature Watch

Transcriptional rewiring of an evolutionarily conserved circadian clock

Tue, 2024-04-16 06:00

EMBO J. 2024 Apr 16. doi: 10.1038/s44318-024-00088-3. Online ahead of print.

ABSTRACT

Circadian clocks temporally coordinate daily organismal biology over the 24-h cycle. Their molecular design, preserved between fungi and animals, is based on a core-oscillator composed of a one-step transcriptional-translational-negative-feedback-loop (TTFL). To test whether this evolutionarily conserved TTFL architecture is the only plausible way for achieving a functional circadian clock, we adopted a transcriptional rewiring approach, artificially co-opting regulators of the circadian output pathways into the core-oscillator. Herein we describe one of these semi-synthetic clocks which maintains all basic circadian features but, notably, it also exhibits new attributes such as a "lights-on timer" logic, where clock phase is fixed at the end of the night. Our findings indicate that fundamental circadian properties such as period, phase and temperature compensation are differentially regulated by transcriptional and posttranslational aspects of the clockworks.

PMID:38627599 | DOI:10.1038/s44318-024-00088-3

Categories: Literature Watch

A spatiotemporal atlas of mouse liver homeostasis and regeneration

Tue, 2024-04-16 06:00

Nat Genet. 2024 Apr 16. doi: 10.1038/s41588-024-01709-7. Online ahead of print.

ABSTRACT

The mechanism by which mammalian liver cell responses are coordinated during tissue homeostasis and perturbation is poorly understood, representing a major obstacle in our understanding of many diseases. This knowledge gap is caused by the difficulty involved with studying multiple cell types in different states and locations, particularly when these are transient. We have combined Stereo-seq (spatiotemporal enhanced resolution omics-sequencing) with single-cell transcriptomic profiling of 473,290 cells to generate a high-definition spatiotemporal atlas of mouse liver homeostasis and regeneration at the whole-lobe scale. Our integrative study dissects in detail the molecular gradients controlling liver cell function, systematically defining how gene networks are dynamically modulated through intercellular communication to promote regeneration. Among other important regulators, we identified the transcriptional cofactor TBL1XR1 as a rheostat linking inflammation to Wnt/β-catenin signaling for facilitating hepatocyte proliferation. Our data and analytical pipelines lay the foundation for future high-definition tissue-scale atlases of organ physiology and malfunction.

PMID:38627598 | DOI:10.1038/s41588-024-01709-7

Categories: Literature Watch

Correction: In vivo genome-wide CRISPR screening identifies CITED2 as a driver of prostate cancer bone metastasis

Tue, 2024-04-16 06:00

Oncogene. 2024 Apr 16. doi: 10.1038/s41388-024-03031-2. Online ahead of print.

NO ABSTRACT

PMID:38627522 | DOI:10.1038/s41388-024-03031-2

Categories: Literature Watch

ATP13A3 variants promote pulmonary arterial hypertension by disrupting polyamine transport

Tue, 2024-04-16 06:00

Cardiovasc Res. 2024 Apr 16:cvae068. doi: 10.1093/cvr/cvae068. Online ahead of print.

ABSTRACT

AIMS: Potential loss-of-function variants of ATP13A3, the gene encoding a P5B-type transport ATPase of undefined function, were recently identified in pulmonary arterial hypertension (PAH) patients. ATP13A3 is implicated in polyamine transport but its function has not been fully elucidated. Here, we sought to determine the biological function of ATP13A3 in vascular endothelial cells and how PAH-associated variants may contribute to disease pathogenesis.

METHODS AND RESULTS: We studied the impact of ATP13A3 deficiency and overexpression in endothelial cell (EC) models (human pulmonary ECs, blood outgrowth ECs (BOECs) and HMEC-1 cells), including a PAH patient-derived BOEC line harbouring an ATP13A3 variant (LK726X). We also generated mice harbouring an Atp13a3 variant analogous to a human disease-associated variant to establish whether these mice develop PAH.ATP13A3 localised to the recycling endosomes of human ECs. Knockdown of ATP13A3 in ECs generally reduced the basal polyamine content and altered the expression of enzymes involved in polyamine metabolism. Conversely, overexpression of wild-type ATP13A3 increased polyamine uptake. Functionally, loss of ATP13A3 was associated with reduced EC proliferation, increased apoptosis in serum starvation and increased monolayer permeability to thrombin. Assessment of five PAH-associated missense ATP13A3 variants (L675V, M850I, V855M, R858H, L956P) confirmed loss-of-function phenotypes represented by impaired polyamine transport and dysregulated EC function. Furthermore, mice carrying a heterozygous germ-line Atp13a3 frameshift variant representing a human variant spontaneously developed a PAH phenotype, with increased pulmonary pressures, right ventricular remodelling and muscularisation of pulmonary vessels.

CONCLUSION: We identify ATP13A3 as a polyamine transporter controlling polyamine homeostasis in ECs, deficiency of which leads to EC dysfunction and predisposes to PAH. This suggests a need for targeted therapies to alleviate the imbalances in polyamine homeostasis and EC dysfunction in PAH.

PMID:38626311 | DOI:10.1093/cvr/cvae068

Categories: Literature Watch

Alfaxalone is an effective anesthetic for the electrophysiological study of anoxia-tolerance mechanisms in western painted turtle pyramidal neurons

Tue, 2024-04-16 06:00

PLoS One. 2024 Apr 16;19(4):e0298065. doi: 10.1371/journal.pone.0298065. eCollection 2024.

ABSTRACT

Anoxia in the mammalian brain leads to hyper-excitability and cell death; however, this cascade of events does not occur in the anoxia-tolerant brain of the western painted turtle, Chrysemys picta belli. The painted turtle has become an important anoxia-tolerant model to study brain, heart, and liver function in the absence of oxygen, but being anoxia-tolerant likely means that decapitation alone is not a suitable method of euthanasia. Many anesthetics have long-term effects on ion channels and are not appropriate for same day experimentation. Using whole-cell electrophysiological techniques, we examine the effects of the anesthetic, Alfaxalone, on pyramidal cell action potential amplitude, threshold, rise and decay time, width, frequency, whole cell conductance, and evoked GABAA receptors currents to determine if any of these characteristics are altered with the use of Alfaxalone for animal sedation. We find that Alfaxalone has no long-term impact on action potential parameters or whole-cell conductance. When acutely applied to naïve tissue, Alfaxalone did lengthen GABAA receptor current decay rates by 1.5-fold. Following whole-animal sedation with Alfaxalone, evoked whole cell GABAA receptor current decay rates displayed an increasing trend with 1 and 2 hours after brain sheet preparation, but showed no significant change after a 3-hour washout period. Therefore, we conclude that Alfaxalone is a suitable anesthetic for same day use in electrophysiological studies in western painted turtle brain tissue.

PMID:38626211 | DOI:10.1371/journal.pone.0298065

Categories: Literature Watch

Retraction Note: Gintonin Mitigates MPTP-Induced Loss of Nigrostriatal Dopaminergic Neurons and Accumulation of α-Synuclein via the Nrf2/HO-1 Pathway

Tue, 2024-04-16 06:00

Mol Neurobiol. 2024 Apr 16. doi: 10.1007/s12035-024-04175-8. Online ahead of print.

NO ABSTRACT

PMID:38625622 | DOI:10.1007/s12035-024-04175-8

Categories: Literature Watch

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