Biology subjects

Yee, A.

Publications and source records attributed to Yee, A..

10 recordsLinked to original sources

bioRxiv2026

The impact of alpha synuclein overexpression on nigrostriatal transmission

Accumulation of wild type synuclein in dopamine neurons of the Substantia Nigra pars compacta is a pathological hallmark of Parkinson's disease (PD), which commonly precedes neurodegeneration. Yet how synuclein accumulation affects nigrostriatal neurotransmission early in the progression of PD remains poorly understood. In addition to axonal dopamine release, SNc neurons also co-release GABA and glutamate from striatal axon terminals and release dopamine from their somatodendritic region. However, the selective vulnerability of these distinct functions to increased synuclein remains largely unexplored. Here, we selectively overexpressed wild type human synuclein in SNc dopamine neurons to examine impacts on nigrostriatal and somatodendritic transmission and correlated these changes to impairments in locomotion. We found that dopamine release in the dorsolateral striatum was robustly reduced, while transmission to postsynaptic medium spiny neurons remained intact. Glutamate co-release from dopamine terminals onto both medium spiny neurons and cholinergic interneurons was selectively impaired, while GABA co-release was unaffected. Conversely, somatodendritic dopamine release within the SNc was completely abolished by synuclein overexpression. Together, these findings identify selective deficits in nigrostriatal neurotransmission associated with wild type synuclein accumulation prior to overt degeneration and raise the possibility of compensatory adaptations shaping the early functional consequences of synuclein pathology in PD.

neuroscience↗

bioRxiv2026

Distinct forms of dopamine transmission control locomotion and learning

The neuromodulator dopamine is essential for voluntary movement and learning from experience. While these behaviors often occur simultaneously and rely on overlapping nigrostriatal dopamine circuits, they are also separable and can manifest independently. How a single neuromodulatory system controls such disparate aspects of behavior in parallel remains poorly understood. Here we show that striatal dopamine is released through two spatially and functionally distinct modes that are independently regulated and serve distinct behavioral roles. Eliminating dopamine release underlying bulk extracellular accumulation reveals a spatially restricted mode of transmission that maintains phasic dopamine receptor activation on striatal projection neurons. We find that selective loss of diffuse dopamine impairs striatal circuit excitability and reduces locomotion, while point-to-point transmission is sufficient to maintain striatal spine density and support motor and associative learning. We propose that the geometry of dopamine release determines its behavioral output, a principle that explains the breadth of dopamines functions and more broadly elucidates how neurons multiplex different forms of information.

neuroscience↗

bioRxiv2025

Tissue Kallikrein 1 cleaves complement factor C3 and activates the alternative complement pathway

Hematopoietic stem cell transplant-associated thrombotic microangiopathy (HSCT-TMA), characterized by microvascular endothelial damage and severe renal injury, negatively affects HSCT survivorship with high mortality and long-term renal morbidity. After HSCT, innate immunity and inflammation are often dysregulated. The alternative complement pathway (AP) of the innate immune system is overactivated in HSCT-TMA, but the mechanisms of its initiation are poorly described. Complement component C3 of the AP can be cleaved by proteases outside of the AP. Because mRNA expression of tissue kallikrein 1 (KLK1), an inflammatory serine protease that produces kinins, has been found to be markedly elevated in the renal endothelium of inflamed mice, we hypothesized that increased KLK1 activity during inflammation contributes to AP overactivation and endothelial injury in HSCT-TMA. We assessed AP activation, KLK1 activity, endothelial injury, and renal function in HSCT-TMA experimental models and disease settings and investigated C3 cleavage and AP activation by KLK1. We found that patients with HSCT-TMA had significantly increased AP activation and decreased KLK1 inactivation at TMA diagnosis compared to pre-HSCT. Mice challenged with HSCT-TMA triggers cyclosporine A (CsA) and lipopolysaccharide (LPS) exhibited increased AP activation, renal endothelial injury, and impaired renal function in the setting of decreased KLK1 inactivation. We further demonstrated that KLK1 cleaved AP component C3 to C3b that functionally activated the AP. Our data indicate a noncanonical mechanism for AP activation by KLK1 in settings of HSCT-TMA. Key PointsO_LITissue kallikrein (KLK1) functionally cleaves complement factor C3. C_LIO_LIReduced KLK1 inhibition is associated with activation of the alternative pathway of complement. C_LI O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=111 SRC="FIGDIR/small/674260v1_ufig1.gif" ALT="Figure 1"> View larger version (13K): org.highwire.dtl.DTLVardef@8f260aorg.highwire.dtl.DTLVardef@a6511org.highwire.dtl.DTLVardef@7160f6org.highwire.dtl.DTLVardef@194d36d_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical Abstract.C_FLOATNO HSCT-TMA triggers (e.g. inflammation, immunosuppression) upregulate expression of the inflammatory serine protease KLK1, which cleaves C3 to initiate AP activation and amplification, leading to renal endothelial injury. Created with BioRender.com under its Academic License Terms with Baylor College of Medicine. C_FIG

molecular biology↗

bioRxiv2024

The Alzheimers Disease Risk Genes MS4A4A And MS4A6A Cooperate to Negatively Regulate Trem2 and Microglia states

Genetic variations in MS4A4A and MS4A6A are linked to the regulation of cerebrospinal fluid soluble TREM2 (sTREM2) levels and are associated with Alzheimers disease (AD) risk and progression. Using CRISPR knockout and MS4A4A-degrading antibodies in primary human microglia, non-human primates (NHP), and a xenotransplantation model of amyloid pathology, we provide evidence that MS4A4A and MS4A6A are negative regulators of both the transmembrane and soluble TREM2 proteins. They also negatively regulate microglia proliferation, survival, metabolism, lysosomal function, energetics, phagocytosis, and disease-fighting states. Mechanistically, we find that MS4A4A exerts negative regulation by interacting with MS4A6A and protecting it from degradation. MS4A6A in turn forms a complex with and blocks the co-receptor DAP12, which is required for the stability, cell surface localization, and signaling of TREM2 and other receptors. Taken together, the data indicate that MS4A4A and MS4A6A are cooperating, post-transcriptional negative regulators of TREM2 and microglial function, and potential drug targets for AD.

neuroscience↗

bioRxiv2023

Platelet Activating Factor Activity Modulates Hyperoxic Neonatal Lung Injury Severity

Hyperoxia-induced inflammation contributes significantly to developmental lung injury and bronchopulmonary dysplasia (BPD) in preterm infants. Platelet activating factor (PAF) is known to be a major driver of inflammation in lung diseases such as asthma and pulmonary fibrosis, but its role in BPD has not been previously investigated. Therefore, to determine whether PAF signaling independently modulates neonatal hyperoxic lung injury and BPD pathogenesis, lung structure was assessed in 14 day-old C57BL/6 wild-type (WT) and PAF receptor knockout (PTAFR KO) mice that were exposed to 21% (normoxia) or 85% O2 (hyperoxia) from postnatal day 4. Lung morphometry showed that PTAFR KO mice had attenuated hyperoxia-induced alveolar simplification when compared to WT mice. Functional analysis of gene expression data from hyperoxia-exposed vs. normoxia-exposed lungs of WT and PTAFR KO showed that the most upregulated pathways were the hypercytokinemia/hyperchemokinemia pathway in WT mice, NAD signaling pathway in PTAFR KO mice, and agranulocyte adhesion and diapedesis as well as other pro-fibrotic pathways such as tumor microenvironment and oncostatin-M signaling in both mice strains, indicating that PAF signaling may contribute to inflammation but may not be a significant mediator of fibrotic processes during hyperoxic neonatal lung injury. Gene expression analysis also indicated increased expression of pro-inflammatory genes such as CXCL1, CCL2 and IL-6 in the lungs of hyperoxia-exposed WT mice and metabolic regulators such as HMGCS2 and SIRT3 in the lungs of PTAFR KO mice, suggesting that PAF signaling may modulate BPD risk through changes in pulmonary inflammation and/or metabolic reprogramming in preterm infants.

pathology↗

bioRxiv2022

Deep mutational scanning and massively parallel kinetics of plasminogen activator-1 functional stability

Plasminogen activator inhibitor-1 (PAI-1), a member of the serine protease inhibitor (SERPIN) superfamily of proteins, is unique among SERPINs for exhibiting a spontaneous conformational change to a latent or inactive state. The functional half-life for this transition at physiologic temperature and pH is ~1-2 h. To better understand the molecular mechanisms underlying this transition, we now report on the analysis of a comprehensive PAI-1 variant library expressed on filamentous phage and selected for functional stability after 48 h at 37 {degrees}C. Of the 7,201 possible single amino acid substitutions in PAI-1, we identify 439 that increase the functional stability of PAI-1 beyond that of the wild-type protein and 1,549 that retain inhibitory activity toward PAI-1s canonical target protease (urokinase-like plasminogen activator, uPA), while exhibiting functional stability less than or equal to that of wild-type PAI-1. Missense mutations that increase PAI-1 functional stability are concentrated in highly flexible regions within the PAI-1 structure. Finally, we developed a method for simultaneously measuring the functional half-lives of hundreds of PAI-1 variants in a multiplexed, massively parallel manner, quantifying the functional half-lives for 697 single missense variants of PAI-1 by this approach. Overall, these findings provide novel insight into the mechanisms underlying PAI-1s latency transition and provide a database for interpreting human PAI-1 genetic variants.

biochemistry↗

bioRxiv2021

Deep mutational scanning of the plasminogen activator inhibitor-1 functional landscape

The serine protease inhibitor (SERPIN) plasminogen activator inhibitor-1 (PAI-1) is a key regulator of the fibrinolytic system, inhibiting the serine proteases tissue- and urokinase-type plasminogen activator (tPA and uPA, respectively). Missense variants may render PAI-1 non-functional through misfolding, leading to its turnover as a protease substrate, or to a more rapid transition to the latent/inactive state. Deep mutational scanning was performed to evaluate the impact of amino acid sequence variation on PAI-1 inhibition of uPA using an M13 filamentous phage display system. The effects of single amino acid substitutions on PAI-1s functional inhibition of its canonical target proteases, tPA and uPA, have been determined for only a small fraction of potential mutations. To construct a more comprehensive dataset, a mutagenized PAI-1 library, encompassing [~]70% of potential single amino acid substitutions, was displayed on M13 filamentous phage. From this library, the relative effects of 27% of all possible missense variants on PAI-1 inhibition of urokinase-type plasminogen activator were determined using high-throughput DNA sequencing with 826 missense variants demonstrating conserved inhibitory activity and 1137 resulting in loss of PAI-1 function. Comparison of these deep mutational scanning results to predictions from PolyPhen-2 and SIFT demonstrate the limitations of these algorithms, consistent with similar reports for other proteins. Comparison to common human PAI-1 gene variants present in the gnomAD database is consistent with evolutionary selection against loss of PAI-1 function. These findings provide insight into structure-function relationships for PAI-1 and other members of the SERPIN superfamily.

biochemistry↗

bioRxiv2021

Phage Display Broadly Identifies Inhibitor-reactive Regions in von Willebrand Factor

BackgroundCorrection of von Willebrand factor (VWF) deficiency with replacement products containing VWF can lead to the development of anti-VWF alloantibodies (i.e., VWF inhibitors) in patients with severe von Willebrand disease (VWD). ObjectiveLocate inhibitor-reactive regions within VWF using phage display. MethodsWe screened a phage library displaying random, overlapping fragments covering the full length VWF protein sequence for binding to a commercial anti-VWF antibody or to immunoglobulins from three type 3 VWD patients who developed VWF inhibitors in response to treatment with plasma-derived VWF. Immunoreactive phage clones were identified and quantified by next generation DNA sequencing (NGS). ResultsNGS markedly increased the number of phage analyzed for locating immunoreactive regions within VWF following a single round of selection and identified regions not recognized in previous reports using standard phage display methods. Extending this approach to characterize VWF inhibitors from three type 3 VWD patients (including two siblings homozygous for the same VWF gene deletion) revealed patterns of immunoreactivity distinct from the commercial antibody and between unrelated patients, though with notable areas of overlap. Alloantibody reactivity against the VWF propeptide is consistent with incomplete removal of the propeptide from plasma-derived VWF replacement products. ConclusionThese results demonstrate the utility of phage display and NGS to characterize diverse anti-VWF antibody reactivities.

pathology↗

bioRxiv2020

A fast genetically encoded fluorescent sensor for faithful in vivo acetylcholine detection in mice, fish, worms and flies

Here we design and optimize a genetically encoded fluorescent indicator, iAChSnFR, for the ubiquitous neurotransmitter acetylcholine, based on a bacterial periplasmic binding protein. iAChSnFR shows large fluorescence changes, rapid rise and decay kinetics, and insensitivity to most cholinergic drugs. iAChSnFR revealed large transients in a variety of slice and in vivo preparations in mouse, fish, fly and worm. iAChSnFR will be useful for the study of acetylcholine in all animals.

neuroscience↗

bioRxiv2019

The in vivo endothelial cell translatome is highly heterogeneous across vascular beds

Endothelial cells (ECs) are highly specialized across vascular beds. However, given their interspersed anatomic distribution, comprehensive characterization of the molecular basis for this heterogeneity in vivo has been limited. By applying endothelial-specific translating ribosome affinity purification (EC-TRAP) combined with high-throughput RNA sequencing analysis, we identified pan EC-enriched genes and tissue-specific EC transcripts, which include both established markers and genes previously unappreciated for their presence in ECs. In addition, EC-TRAP limits changes in gene expression following EC isolation and in vitro expansion, as well as rapid vascular bed-specific shifts in EC gene expression profiles as a result of the enzymatic tissue dissociation required to generate single cell suspensions for fluorescence-activated cell sorting (FACS) or single cell RNA sequencing analysis. Comparison of our EC-TRAP to published single cell RNA sequencing data further demonstrates considerably greater sensitivity of EC-TRAP for the detection of low abundant transcripts. Application of EC-TRAP to examine the in vivo host response to lipopolysaccharide (LPS) revealed the induction of gene expression programs associated with a native defense response, with marked differences across vascular beds. Furthermore, comparative analysis of whole tissue and TRAP-selected mRNAs identified LPS-induced differences that would not have been detected by whole tissue analysis alone. Together, these data provide a resource for the analysis of EC-specific gene expression programs across heterogeneous vascular beds under both physiologic and pathologic conditions.\n\nSignificanceEndothelial cells (ECs), which line all vertebrate blood vessels, are highly heterogeneous across different tissues. The present study uses a genetic approach to specifically tag mRNAs within ECs of the mouse, thereby allowing recovery and sequence analysis to evaluate the EC-specific gene expression program directly from intact organs. Our findings demonstrate marked heterogeneity in EC gene expression across different vascular beds under both normal and disease conditions, with a more accurate picture than can be achieved using other methods. The data generated in these studies advance our understanding of EC function in different blood vessels and provide a valuable resource for future studies.

genomics↗