Biology subjects

Thompson, J. W.

Publications and source records attributed to Thompson, J. W..

18 recordsLinked to original sources

bioRxiv2026

E3 ubiquitin ligase SYVN1 mediates K63-linked ubiquitination of DDX3X to activate Macrophage NLRP3 Inflammasome

DDX3X (DEAD box helicase 3, X linked) is a common and essential component for both stress granules and NLRP3 inflammasome assembly and their activation; however, the upstream cellular stress signals driving DDX3X to activate the contrasting cellular pathway remain unclear. We identified the pivotal role of the E3 ubiquitin ligase SYVN1(Synoviolin) as the upstream regulator of DDX3X and thereby controlling NLRP3 activation and stress granule assembly. We observed SYVN1 silencing in macrophages prevented both NLRP3 driven inflammation and stress granule formation. SYVN1 deficiency prevented LPS induced inflammatory lung injury and increased the survival rate of the mice. SYVN1 sustains DDX3X gene expression and promotes stimulus-dependent ubiquitination of DDX3X. Under inflammatory conditions, SYVN1 mediated 63 linked ubiquitination of DDX3X, a requirement for NLRP3 inflammasome activation. Conversely, stress conditions reduced K63 linked DDX3X ubiquitination in coordination with activity of the deubiquitinase OTUB1 (OTU domain-containing ubiquitin aldehyde-binding protein 1). Thus, the balance between SYVN1 and OTUB1 functioned to optimize DDX3X activity and activation of NLRP3 or stress granule. These findings show the upstream role of SYVN1 OTUB1 axis in integrating cellular stress signals to decide the cell fate and suggest that ubiquitination of DDX3X is a potential target for inflammasome driven inflammation.

immunology↗

bioRxiv2026

Gelatin coating enhances flow diverting stent endothelial cell coverage, parent vessel healing and aneurysm occlusion

BackgroundFlow diversion stent treatment of cerebral aneurysms has demonstrated high rates of aneurysm occlusion and long-term durability. However, complete endothelization of the flow diverting stent is required for parent vessel healing which closes the aneurysm and metal stent from the circulation. Therefore, stent coatings which enhance endothelial migration and attachment may increase the rate of aneurysm occlusion and reduce complications associated with flow diversion treatment. Here we investigate the use of gelatin as a stent surface coating to enhance the rate of stent endothelialization and coverage and increase aneurysm healing. MethodsNitinol- Neuroform stents (Stryker, Kalamazoo, MI) and cobalt-chromium-Pipeline Flex flow diverting stents (Medtronic, Minneapolis, MN) were used for this study. The stents were coated with gelatin and endothelial cell attachment, proliferation and stent coverage were determined in vitro and compared to uncoated stent controls. A rabbit elastase-aneurysm model was used to determine the effects of endothelial cell seeded-gelatin coated flow diverting stents on aneurysm obliteration and parent vessel healing. ResultsIn vitro, gelatin coating of nitinol stents did not significantly alter endothelial cell attachment, proliferation, or stent coverage. However, gelatin coating of cobalt-chromium stents significantly increased endothelial cell attachment, proliferation and migration. In fact, gelatin coating significantly (p< 0.001) increased the rate of complete stent endothelization by 33% compared to unmodified controls. In vivo, treating aneurysm with endothelial cell seeded-gelatin coated stents resulted in aneurysm occlusion in 8 of 8 (100%) rabbit aneurysms at 90 days compared to only 4 of 7 (57%) in unmodified controls (p< 0.001). Histologically, there were trends in increased neoarterial wall thickness across the aneurysm neck and neointimal formation in the parent artery. Angiographic assessment demonstrated strong parent and side branch patency. ConclusionsGelatin coating enhances EC attachment and stent coverage which is dependent upon the type of stent. Endothelial cell seeded-gelatin coated-flow diverting stents allowed 100% aneurysm obliteration and neoarterial formation without affecting side branch patency or parent artery perfusion. Gelatin coating therefore represents a valuable strategy to enhance stent cellularization and aneurysm occlusion rates.

neuroscience↗

bioRxiv2025

Development and validation of a streamlined workflow for proteomic analysis of proteins and post-translational modifications from dried blood

It is increasingly recognized that the omic analysis of whole blood has applications for precision medicine and disease phenotyping. Despite this realization, whole blood is generally viewed as a challenging analytical matrix in comparison to plasma or serum. Moreover, proteomic analyses of whole blood proteomics have almost exclusively focused on (non)targeted analyses of protein abundances and much less on post-translational modifications (PTMs). Here, we developed a streamlined workflow for processing twenty microliters of venous blood collected by volumetric absorptive microsampling that incorporates serial trypsinization, N-glycopeptide and phosphopeptide enrichment and avoids laborious sample dry-down or cleanup steps. Up to 10,000 analytes (reported as protein groups, glycopeptidoforms and phosphosites) were quantified by liquid chromatography-tandem mass spectrometry (LC-MS/MS) in approximately 2 h of MS acquisition time. Using these methods, we explored the stability of "dried" and "wet" blood proteomes, as well as effects of ex vivo inflammatory stimulus or phosphatase inhibition. Multi-omics factor analysis enabled facile identification of analytes that contributed to inter-individual variability of the blood proteomes, including N-glycopeptides that distinguish immunoglobulin heavy constant alpha 2 allotypes. Collectively, our results help to establish feasibility and best practices for the integrated MS-based quantification of proteins and PTMs from dried blood.

biochemistry↗

bioRxiv2025

Rapamycin enhances VEGFA and VSMC contractile protein expression in MSCs via mTORC1 inhibition

IntroductionIntracranial aneurysm (ICA) rupture is the most common cause of non-traumatic subarachnoid hemorrhage, a devastating type of stroke. Vascular smooth muscle (VSMC) and endothelial cell (EC) dysfunction and death play important roles in the etiology of ICA formation, rupture and treatment failure. Mesenchymal stem cells (MSCs) have been extensively investigated for their therapeutic potential in vascular diseases. The mammalian target of rapamycin (mTOR) is a key regulatory pathway involved in cellular functions controlling intracellular anabolic and regulatory processes. Rapamycin, a specific mTOR complex 1 inhibitor, is widely used in the clinical management of cardiac and vascular pathologies. In this study, we explored MSCs potential to express VSMC and EC markers under the influence of rapamycin. MethodsHuman MSCs were treated with rapamycin for 2, 5, and 10 days, and cell death and proliferation determined by MTT analysis. Protein expression and phosphorylation levels were determined by western blot analysis. Calcein AM and PI staining was used to determine cell viability, and morphology. ResultsMTT and Calcein AM analysis demonstrated that prolonged rapamycin treatment did not affect MSC viability but was found to reduce MSC proliferation and cause a nearly threefold increase in cell size compared to controls. Rapamycin treatment increased expression of the VSMC protein markers, -SMA, and transgelin and was required to maintain elevated expression levels both proteins. In contrast, selective inhibition of mTORC2 with JR-AB2-01 caused a decrease in -SMA and trangelin expression, suggesting mTORC1 regulation of -SMA and transgelin expression, rather than mTORC2. Rapamycin treated MSC were also found to induce cell sprouting between adjacent cells. MSCs were found not to express endothelial protein markers under either basal conditions or following rapamycin treatment. However, rapamycin treatment was found to increase VEGFA expression, a known promoter of angiogenesis. ConclusionRapamycin has the potential to increase VSMC protein expression in MSCs by its action on mTORC1. The ability of rapamycin to increase VEGFA expression in MSCs could allow for a novel MSC-based therapeutic intervention in cerebral aneurysm management which could aid in ICA healing and reducing rupture risk.

neuroscience↗

bioRxiv2025

Coil and flow diverting stents as drug delivery platforms for cerebral aneurysm treatment

Cerebral aneurysm occlusion with coils and flow diverting stents has become the first line treatment for both unruptured and ruptured cerebral aneurysms. As these technologies have advanced, there have been changes in device shape and surface coating to enhance aneurysm embolization while reducing stent thrombogenicity. Drug eluting stents have been used with great success in the targeted delivery of rapamycin, a mTOR complex 1 inhibitor to prevent restenosis in coronary and peripheral artery disease. However, few studies have investigated the use of coils and stents as delivery platforms for sustained drug release to cerebral aneurysm tissue. In this study, we used the bio-compatible and degradable polymers, gelatin and PLGA and a simple evaporative coating technique to investigate the release of rapamycin over time from coated platinum coils and Pipeline flow diverting stents. Rapamycin coated coils were incubated with human vascular endothelial cells in vitro to confirm therapeutic levels of rapamycin release. The rate of rapamycin release was similar in both gelatin and PLGA coated coils and was sustained for more than three weeks. Rapamycin was bioactive, at a therapeutic dose and inhibited mTOR complex 1 in human brain endothelial cells treated with a rapamycin coated coil. The relative degree of mTOR complex 1 inhibition was greater in PLGA compared to gelatin coated coils. Coating flow diverting stents with a rapamycin-PLGA coating demonstrated continuous rapamycin release over a 35 day period. Reducing the percent PLGA polymer concentration caused a robust and sustainable release of rapamycin. The PLGA coating was resilient enough to allow device recapturing without affecting rapamycin eluting rates or device deployment and expansion. This work provides a simple, feasible and tunable method to coat occlusion devices for preclinical studies investigating targeted drug delivery for improved parent vessel healing and aneurysm obliteration.

bioengineering↗

bioRxiv2025

Cerebral vascular tortuosity and aneurysm formation and rupture: a novel vessel tortuosity scale

Cerebral aneurysm (CA) rupture is the most common cause of nontraumatic subarachnoid hemorrhage. Recent data suggests that tortuosity is associated with aneurysm formation and rupture risk. We aimed to determine if tortuosity correlates with CA development and rupture in a mouse CA model and to develop a novel tortuosity scale to be used for in vivo CA studies. A highly validated, elastase-mouse CA model was used to assess cerebral vessel tortuosity with CA formation and rupture in sham and elastase groups. A 4-point ordinal scale was created to evaluate predictive capacity for vessel tortuosity level and CA formation and rupture. Nearly all sham animals (92%) had little to no vessel tortuosity on the visual scale (median, IQR: 1, [1-2]), compared to 24% in the elastase groups (2, [2-3]) (p=0.001). Sham cohorts had zero animals with highly tortuous vessels, while 3.5mU and 35mU cohorts had >35% of animals with significant visual tortuosity, p=0.003 and p<0.000, respectively. CA formation and rupture was higher in the elastase groups compared to the sham group (p=0.002). Both the visual scale and tortuosity index significantly predicted CA formation (p<0.001) and rupture (p<0.001). A novel tortuosity scale is highly predictive of CA formation and rupture in vivo. It may offer a new measurement to better understand vessel stress in the pathogenesis and progression of CAs.

neuroscience↗

bioRxiv2024

SPE-CZE-MS quantifies zeptomole concentrations ofphosphorylated peptides

Capillary zone electrophoresis (CZE) is gaining attention in the field of single-cell proteomics for its ultra-low-flow and high-resolution separation abilities. Even more sample-limited yet rich in biological information are phosphoproteomics experiments, as the phosphoproteome composes only a fraction of the whole cellular proteome. Rapid analysis, high sensitivity, and maximization of sample utilization are paramount for single-cell analysis. Some challenges of coupling CZE analysis with mass spectrometry analysis (MS) of complex mixtures include 1. sensitivity due to volume loading limitations of CZE and 2. incompatibility of MS duty cycles with electrophoretic timescales. Here, we address these two challenges as applied to single-cell equivalent phosphoproteomics experiments by interfacing a microchip-based CZE device integrated with a solid-phase-extraction (SPE) bed with the Orbitrap Astral mass spectrometer. Using 225 phosphorylated peptide standards and phosphorylated peptide-enriched mouse brain tissue, we investigate microchip-based SPE-CZE functionality, quantitative performance, and complementarity to nano-LC-MS (nLC-MS) analysis. We highlight unique SPE-CZE separation mechanisms that can empower fit-for-purpose applications in single-cell-equivalent phosphoproteomics.

systems biology↗

bioRxiv2024

Interlaboratory comparison of standardised metabolomics and lipidomics analyses in human and rodent blood using the MxP(R) Quant 500 kit

Metabolomics and lipidomics are pivotal in understanding phenotypic variations beyond genomics. However, quantification and comparability of mass spectrometry (MS)-derived data are challenging. Standardised assays can enhance data comparability, enabling applications in multi-center epidemiological and clinical studies. Here we evaluated the performance and reproducibility of the MxP(R) Quant 500 kit across 14 laboratories. The kit allows quantification of 634 different metabolites from 26 compound classes using triple quadrupole MS. Each laboratory analysed twelve samples, including human plasma and serum, lipaemic plasma, NIST SRM 1950, and mouse and rat plasma, in triplicates. 505 out of the 634 metabolites were measurable above the limit of detection in all laboratories, while eight metabolites were undetectable in our study. Out of the 505 metabolites, 412 were observed in both human and rodent samples. Overall, the kit exhibited high reproducibility with a median coefficient of variation (CV) of 14.3 %. CVs in NIST SRM 1950 reference plasma were below 25 % and 10 % for 494 and 138 metabolites, respectively. To facilitate further inspection of reproducibility for any compound, we provide detailed results from the in-depth evaluation of reproducibility across concentration ranges using Deming regression. Interlaboratory reproducibility was similar across sample types, with some species-, matrix-, and phenotype-specific differences due to variations in concentration ranges. Comparisons with previous studies on the performance of MS-based kits (including the AbsoluteIDQ p180 and the Lipidyzer) revealed good concordance of reproducibility results and measured absolute concentrations in NIST SRM 1950 for most metabolites, making the MxP(R) Quant 500 kit a relevant tool to apply metabolomics and lipidomics in multi-center studies.

biochemistry↗

bioRxiv2023

Functional glycoproteomics by integrated network assembly and partitioning

The post-translational modification (PTM) of proteins by O-linked {beta}-N-acetyl-D-glucosamine (O-GlcNAcylation) is widespread across the proteome during the lifespan of all multicellular organisms. However, nearly all functional studies have focused on individual protein modifications, overlooking the multitude of simultaneous O-GlcNAcylation events that work together to coordinate cellular activities. Here, we describe Networking of Interactors and SubstratEs (NISE), a novel, systems-level approach to rapidly and comprehensively monitor O-GlcNAcylation across the proteome. Our method integrates affinity purification-mass spectrometry (AP-MS) and site-specific chemoproteomic technologies with network generation and unsupervised partitioning to connect potential upstream regulators with downstream targets of O-GlcNAcylation. The resulting network provides a data-rich framework that reveals both conserved activities of O-GlcNAcylation such as epigenetic regulation as well as tissue-specific functions like synaptic morphology. Beyond O-GlcNAc, this holistic and unbiased systems-level approach provides a broadly applicable framework to study PTMs and discover their diverse roles in specific cell types and biological states.

cell biology↗

bioRxiv2022

Acarbose suppresses symptoms of mitochondrial disease in a mouse model of Leigh Syndrome

Mitochondrial diseases represent a spectrum of disorders caused by impaired mitochondrial function ranging in severity from mortality during infancy to progressive adult-onset disease. Mitochondrial dysfunction is also recognized as a molecular hallmark of the biological aging process. Rapamycin, a drug that increases lifespan and health during normative aging also increases survival and reduces neurological symptoms in a mouse model of the severe mitochondrial disease Leigh Syndrome. The Ndufs4 knockout (Ndufs4-/-) mouse lacks the complex I subunit NDUFS4 and shows rapid onset and progression of neurodegeneration mimicking patients with Leigh Syndrome. Here we show that another drug that extends lifespan and delays normative aging in mice, acarbose, also suppresses symptoms of disease and improves survival of Ndufs4-/- mice. Unlike rapamycin, acarbose rescues disease phenotypes independently of mTOR inhibition. Furthermore, rapamycin and acarbose have additive effects in delaying neurological symptoms and increasing maximum lifespan in Ndufs4-/- mice. We find that acarbose remodels the intestinal microbiome and alters the production of short chain fatty acids. Supplementation with tributyrin, a source of butyric acid, recapitulates some effects of acarbose on lifespan and disease progression. This study provides the first evidence that alteration of the gut microbiome may impact severe mitochondrial disease and provides further support for the model that biological aging and severe mitochondrial disorders share underlying common mechanisms.

biochemistry↗

bioRxiv2021

Centrosomal Enrichment and Proteasomal Degradation of SYS-1/-β-catenin Requires the Microtubule Motor Dynein

The C. elegans Wnt/{beta}-catenin Asymmetry (W{beta}A) pathway utilizes asymmetric regulation of SYS- 1/{beta}-catenin and POP-1/TCF coactivators. W{beta}A differentially regulates gene expression during cell fate decisions, specifically by asymmetric localization of determinants in mother cells to produce daughters biased towards their appropriate cell fate. Despite the induction of asymmetry, {beta}-catenin localizes symmetrically to mitotic centrosomes in both mammals and C. elegans. Due to the mitosis-specific localization of SYS-1 to centrosomes and enrichment of SYS-1 at kinetochore microtubules when SYS-1 centrosomal loading is disrupted, we investigated active trafficking in SYS-1 centrosomal localization. Here, we demonstrate that trafficking by microtubule motor dynein is required to maintain SYS-1 centrosomal enrichment, by dynein RNAi-mediated decreases in SYS-1 centrosomal enrichment and by temperature-sensitive allele of the dynein heavy chain. Conversely, we observe depletion of microtubules by nocodazole treatment or RNAi of dynein-proteasome adapter ECPS-1 exhibits increased centrosomal enrichment of SYS-1. Moreover, disruptions to SYS-1 or negative regulator microtubule trafficking are sufficient to significantly exacerbate SYS-1 dependent cell fate misspecifications. We propose a model whereby retrograde microtubule-mediated trafficking enables SYS-1 enrichment at centrosomes, enhancing its eventual proteasomal degradation. These studies support the link between centrosomal localization and enhancement of proteasomal degradation, particularly for proteins not generally considered centrosomal.

cell biology↗

bioRxiv2020

Quantitative proteomics links the LRRC59 interactome to mRNA translation on the ER membrane

Protein synthesis on the endoplasmic reticulum (ER) requires the dynamic coordination of resident membrane proteins and cytoplasmic translation factors. While ER membrane proteins functioning in ribosome association, mRNA anchoring, and protein translocation, have been identified, little is known regarding the higher order organization of ER-localized translation. Here we utilized proximity proteomics to identify neighboring protein networks for the ribosome interactors SEC61{beta}, RPN1, SEC62, and LRRC59. Whereas the SEC61{beta} and RPN1 BioID reporters revealed translocon-associated networks, the SEC62 and LRRC59 reporters identified divergent interactome networks of previously unexplored functions. Notably, the SEC62 interactome is enriched in redox-linked proteins and ER luminal chaperones, whereas the LRRC59 interactome is enriched in SRP pathway components, translation factors, and ER-localized RNA-binding proteins. Analysis of the LRRC59 interactome by native immunoprecipitation identified similar protein and functional enrichments. Combined, these data reveal a functional domain organization for the ER and suggest a key role for LRRC59 in the organization of mRNA translation on the ER. SummaryHannigan et al. characterize the protein interactomes of four ER ribosome-binding proteins, providing evidence that ER-bound ribosomes reside in distinct molecular environments. Their data link SEC62 to ER redox regulation and chaperone trafficking, and suggest a role for LRRC59 in SRP-coupled protein synthesis.

cell biology↗

bioRxiv2020

Alterations in Acylcarnitines, Amines, and Lipids Inform about Mechanism of Action of Citalopram/Escitalopram in Major Depression

Selective serotonin reuptake inhibitors (SSRIs) are the first-line treatment for major depressive disorder (MDD), yet their mechanisms of action are not fully understood and their therapeutic benefit varies among individuals. We used a targeted metabolomics approach utilizing a panel of 180 metabolites to gain insights into mechanisms of action and response to citalopram/escitalopram. Plasma samples from 136 participants with MDD enrolled into the Mayo Pharmacogenomics Research Network Antidepressant Medication Pharmacogenomic Study (PGRN-AMPS) were profiled at baseline and after 8 weeks of treatment. After treatment, we saw increased levels of short-chain acylcarnitines and decreased levels of medium- and long-chain acylcarnitines, suggesting an SSRI effect on {beta}-oxidation and mitochondrial function. Amines - including arginine, proline, and methionine-sulfoxide - were upregulated while serotonin and sarcosine were downregulated, suggesting an SSRI effect on urea cycle, one-carbon metabolism and serotonin uptake. Eighteen lipids within the phosphatidylcholine (PC aa and ae) classes were upregulated. Changes in several lipid and amine levels correlated with changes in 17-item Hamilton Rating Scale for Depression scores (HRSD17). Differences in metabolic profiles at baseline and post-treatment were noted between participants who remitted (HRSD17[≤]7) and those who gained no meaningful benefits (<30% reduction in HRSD17). Remitters exhibited a) higher baseline levels of C3, C5, alpha-aminoadipic acid, sarcosine and serotonin; and b) higher week-8 levels of PC aa C34:1, PC aa C34:2, PC aa C36:2 and PC aa C36:4. These findings suggest that mitochondrial energetics - including acylcarnitine metabolism, transport and its link to {beta}-oxidation - and lipid membrane remodeling may play roles in SSRI treatment response.

neuroscience↗

bioRxiv2019

finFindR: Computer-assisted Recognition and Identification of Bottlenose Dolphin Photos in R

O_LIPhotographic identification is an essential research and management tool for studying population size and dynamics of common bottlenose dolphins (Tursiops truncatus). Photographic identification involves recognizing individuals based on unique dorsal fin markings. Manual identification of dolphins, while successful, is labor-intensive and time-consuming. To shorten processing times, we developed a series of neural networks that finds fins, assesses their unique characteristics, and matches them to an existing catalog.\nC_LIO_LIOur software, finFindR, shortens photo-ID processing times by autonomously finding and isolating (i.e., \"cropping\") dolphin fins in raw field photographs, tracing the trailing edge of fins in cropped images, and producing a sorted list of likely identities from a catalog of known individuals. The program then presents users with the top 50 most likely matching identities, allowing users to view side-by-side image pairs and make final identity determinations.\nC_LIO_LIDuring testing on two sets of novel images, finFindR placed the correct individual in the first position of its ordered list in 88% (238/272 and 354/400) of test cases. finFindR placed the correct identity among the top 10 ranked images in 94% of test cases, and among the top 50 ranked images in 97% of test cases. Hence, if a match does not exist in the first 50 images of finFindRs ordered list, researchers can be almost certain (~97%) that a match does not exist in the entire catalog.\nC_LIO_LIDuring a head-to-head blind test of the human-only and finFindR-assisted matching methods, two experienced photo-ID technicians both achieved 97% correct identification of identities when matched against a catalog containing over 2,000 known individuals. However, the manual-only technician examined 124 images on average before making a match, while the technician using finFindR examined only 10 images on average before finding a match.\nC_LIO_LIWe conclude that finFindR will facilitate equal or improved match accuracy while greatly reducing the number of examined photos. The faster matches, automated detection, and automated cropping afforded by finFindR will greatly reduce typical photo-ID processing times.\nC_LI

bioinformatics↗

bioRxiv2019

Acylcarnitine Metabolomic Profiles Inform Clinically-Defined Major Depressive Phenotypes

BackgroundAcylcarnitines have important functions in mitochondrial energetics and {beta}-oxidation, and have been implicated to play a significant role in metabolic functions of the brain. This retrospective study examined whether plasma acylcarnitine profiles can help biochemically distinguish the three phenotypic subtypes of major depressive disorder (MDD)--(core depression (CD+), anxious depression (ANX+), and neurovegetative symptoms of melancholia (NVSM+))--following treatment with a selective serotonin reuptake inhibitor (SSRI).\n\nMethodsDepressed outpatients (n=240) from the Mayo Clinic Pharmacogenomics Research Network were treated with citalopram or escitalopram for eight weeks. Plasma samples collected at baseline and eight weeks post-treatment were profiled for multiple-, short-, medium- and long-chain acylcarnitine levels using AbsoluteIDQ(R)p180-Kit and LC-MS. Linear mixed effects models were used to examine whether acylcarnitine levels discriminate the clinical phenotypes at baseline or eight weeks post-treatment, and whether temporal changes in acylcarnitine profiles differ between groups.\n\nResultsAt baseline, significantly lower concentrations of short- and long-chain acylcarnitines were found in CD+ and NVSM+ compared to ANX+, and the short-chain acylcarnitines remained lower after eight weeks. At eight weeks, the medium- and long-chain acylcarnitines were significantly lower in NVSM+ compared to ANX+. Regarding changes baseline to week eight, short-chain acylcarnitine levels significantly increased in CD+ and ANX+, and medium- and long-chain acylcarnitines significantly decreased in NVSM+ and CD+.\n\nConclusionsIn depressed patients treated with SSRIs, {beta}-oxidation and mitochondrial energetics as evaluated by levels and changes in acylcarnitines may provide the biochemical basis of the clinical heterogeneity of MDD, especially when combined with clinical characteristics.

biochemistry↗

bioRxiv2019

The Alzheimer’s Disease Metabolome: Effects of Sex and APOE ε4 genotype

Recent studies have provided evidence that late-onset Alzheimers disease (AD) can in part be considered a metabolic disease. Besides age, female sex and APOE {varepsilon}4 genotype represent strong risk factors for AD. They also both give rise to large metabolic differences, suggesting that metabolic aspects of AD pathogenesis may differ between males and females and between APOE {varepsilon}4 carriers and non-carriers. We systematically investigated group-specific metabolic alterations by conducting stratified association analyses of 140 metabolites measured in serum samples of 1,517 AD neuroimaging initiative subjects, with AD biomarkers for A{beta} and tau pathology and neurodegeneration. We observed substantial sex differences in effects of 15 metabolites on AD biomarkers with partially overlapping differences for APOE {varepsilon}4 status groups. These metabolites highlighted several group-specific alterations not observed in unstratified analyses using sex and APOE {varepsilon}4 as covariates. Combined stratification by both variables uncovered further subgroup-specific metabolic effects limited to the group with presumably the highest AD risk: APOE {varepsilon}4+ females. Pathways linked to the observed metabolic alterations suggest that females experience more expressed impairment of mitochondrial energy production in AD than males. These findings indicate that dissecting metabolic heterogeneity in AD pathogenesis may enable grading of the biomedical relevance of specific pathways for specific subgroups. Extending our approach beyond simple one- or two-fold stratification may thus guide the way to personalized medicine.\n\nSignificance statementResearch provides substantial evidence that late-onset Alzheimers disease (AD) is a metabolic disease. Besides age, female sex and APOE{varepsilon}4 genotype represent strong risk factors for AD, and at the same time give rise to large metabolic differences. Our systematic investigation of sex and APOE {varepsilon}4 genotype differences in the link between metabolism and measures of pre-symptomatic AD using stratified analysis revealed several group-specific metabolic alterations that were not observed without sex and genotype stratification of the same cohort. Pathways linked to the observed metabolic alterations suggest females are more affected by impairment of mitochondrial energy production in AD than males, highlighting the importance of tailored treatment approaches towards a precision medicine approach.

bioinformatics↗

bioRxiv2019

Pathogen-encoded evasion of CXCL10 and T cell responses

Clearance of intracellular pathogens, such as Leishmania (L.) major, depends on a well-regulated adaptive T cell response. Here we describe a pathogen-encoded mechanism to alter T cell recruitment by suppressing CXCL10, a chemokine that recruits CD4+ and CD8+ T cells by signaling through the CXCR3 receptor. L. major suppresses CXCL10 through the virulence factor and protease, glycoprotein-63 (gp63). GP63 cleaves CXCL10 after amino acid A81, impairing T-cell chemotaxis in vitro. GP63 from either extracellular promastigotes or intracellular amastigotes is capable of cleaving CXCL10. Consistent with CXCL10 cleavage during infection, we observed GP63-mediated impairment of activated CD8+ T-cells in the draining lymph nodes of C57BL/6JWT mice. Correspondingly, in C57BL/6JWT mice, gp63 deletion resulted in slower lesion development and a smaller maximum lesion size. However, infection in C57BL/6Jcxcr3-/- mice revealed the delay to lesion development required CXCR3 signaling. Finally, Salmonella enterica and Chlamydia trachomatis infection also suppress CXCL10, demonstrating convergent evolution of this immune evasion strategy in diverse intracellular pathogens. Understanding mechanisms of CXCL10 evasion may facilitate the development of novel therapeutic strategies to treat intracellular pathogens. Author SummaryLeishmaniasis is an infectious disease that affects over one million people annually. It is caused by intracellular parasites that have evolved to evade the hosts attempts to eliminate the parasite. The most common form of disease, cutaneous leishmaniasis, causes disfiguring skin lesions if the host immune system does not appropriately respond to the infection. A family of molecules called chemokines are critical for the recruitment of specific subsets of immune cells required to eliminate infection. Here, we demonstrate a novel mechanism that the parasite Leishmania (L.) major employs to disrupt the immune response by interfering with chemokine signaling. By this strategy, L. major uses a protease to cleave chemokines known to recruit T-cells required for fighting off infection. We show that L. major cleavage of these immune signals changes the recruitment of CD8+ T-cells and alters disease progression in mice. Finally, we observe that multiple common human intracellular pathogens, including Chlamydia trachomatis and Salmonella enterica, interfere with the same chemokines, suggesting a strong selective pressure to avoid this component of the immune response. Our study provides new insights into how intracellular pathogens interact with the host immune response to enhance pathogen survival and exacerbate disease outcomes.

microbiology↗

bioRxiv2018

Altered Bile Acid Profile Associates with Cognitive Impairment in Alzheimer’s Disease – An Emerging Role for Gut Microbiome

IntroductionIncreasing evidence suggests a role for the gut microbiome in central nervous system disorders and specific role for the gut-brain axis in neurodegeneration. Bile acids (BA), products of cholesterol metabolism and clearance, are produced in the liver and are further metabolized by gut bacteria. They have major regulatory and signaling functions and seem dysregulated in Alzheimer disease (AD).\n\nMethodsSerum levels of 15 primary and secondary BAs and their conjugated forms were measured in 1,464 subjects including 370 cognitively normal older adults (CN), 284 with early mild cognitive impairment (MCI), 505 with late MCI, and 305 AD cases enrolled in the AD Neuroimaging Initiative. We assessed associations of BA profiles including selected ratios with diagnosis, cognition, and AD-related genetic variants, adjusting for cofounders and multiple testing.\n\nResultsIn AD compared to CN, we observed significantly lower serum concentrations of a primary BA (cholic acid CA) and increased levels of the bacterially produced, secondary BA, deoxycholic acid (DCA), and its glycine and taurine conjugated forms. An increased ratio of DCA:CA, which reflects 7-dehydroxylation of CA by gut bacteria, strongly associated with cognitive decline, a finding replicated in serum and brain samples in the Rush Religious Orders and Memory and Aging Project. Several genetic variants in immune response related genes implicated in AD showed associations with BA profiles.\n\nConclusionWe report for the first time an association between altered BA profile, genetic variants implicated in AD and cognitive changes in disease using a large multicenter study. These findings warrant further investigation of gut dysbiosis and possible role of gut liver brain axis in the pathogenesis of AD.

neuroscience↗