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Beenken, K. E.

Publications and source records attributed to Beenken, K. E..

4 recordsLinked to original sources

Scaling of Neuronal Growth and Excitability Through Separable mTORC1 and mTORC2 Pathways

As neurons grow, they must regulate intrinsic excitability to maintain an appropriate level of spiking based on synaptic inputs. Using gene knockouts, phosphoproteomics, and electrophysiology we show PTEN regulates neuronal growth and intrinsic excitability through separable downstream mechanisms. Pten loss induces cellular hypertrophy, increased excitatory synaptic input, reduced fast afterhyperpolarization, and burst firing. Deleting the mTORC1 scaffold, Raptor, rescues overgrowth and synaptic input but fails to normalize firing, while deleting Akt or the mTORC2 scaffold, Rictor, restores firing without rescuing growth. This dissociation identifies an AKT-mTORC2 mechanism that regulates voltage-gated calcium and BK potassium channels to set spike repolarization and burst firing. In vivo, Pten knockout produces altered network synchrony, lethal seizures, and impaired object and location behavior; Raptor co-deletion display non-lethal hyperexcitability with improved object-location coupling. The biological and pathophysiological significance of these mechanisms is demonstrated by overlap of the PTEN-regulated phosphoproteome with ASD and epilepsy.

neuroscience↗

A transcriptomic-driven segmentation and cell simulation framework for high-resolution spatial transcriptomics and cell-cell communication

The Visium HD spatial transcriptomics platform enables transcriptome-wide profiling at near-single-cell resolution. However, accurate segmentation of cells to define spatial boundaries relies heavily on histological images. Previous approaches struggle to define cells when the tissues have high cell density, are inflamed, or are mineralized, leading to transcriptomic bleed-through and inaccurate clustering. To address this, we developed TENGU (Transcript-signal Enrichment and Grouping Unit), a comprehensive end-to-end bioinformatic software package. Unlike existing tools, TENGU employs a transcript-first segmentation approach, prioritizing transcript-signal density as the primary modality and utilizing histological images only as a secondary supplement in unresolved regions. These initial boundaries are further optimized through a novel transcriptomic-driven cell simulation algorithm. Iterative refinement of boundaries based on localized gene expression probabilities effectively minimizes spatial scattering and preserves biologically distinct molecular signatures. The pipeline seamlessly integrates tissue segmentation, high-resolution cell-type annotation, and basic spatially aware cell-cell communication (CCC) analysis. We rigorously benchmarked TENGU against the 10X Genomics and Bin2cell pipelines for cell segmentation across diverse and technically challenging microenvironments. TENGU demonstrated superior transcriptomic distinctness in the murine brain, successfully captured matrix-embedded osteocytes, and localized critical osteoimmune CCC networks (Tgfb and Il1a) in a murine model of osteomyelitis. TENGU also resolved species-specific, pro-tumorigenic signaling hubs (MDK-SDC4) within a highly compacted human colorectal cancer xenograft. By mitigating the constraints of traditional image-dependent segmentation, TENGU provides a highly adaptable and robust computational framework that empowers researchers to accurately decode the complex functional micro-anatomy of both healthy and pathological tissues.

bioinformatics↗

Lipolysis of host triacylglyceride-rich lipoproteins creates a toxic microenvironment for Staphylococcus aureus

Staphylococcus aureus secretes lipases that hydrolyze glycerol esters to mitigate host detection and scavenge fatty acids for membrane synthesis, but exposure to host-derived polyunsaturated fatty acids (PUFA) can be toxic. Here, we show that host hyperlipidemia protects against S. aureus osteomyelitis by engaging this vulnerability. Using a mouse model of severe hyperlipidemia, we show that PUFA-enriched plasma triacylglycerides are associated with reduced bacterial burden and bone destruction from injury-associated osteomyelitis. In vitro, human triacylglyceride-rich lipoproteins (TRL) exhibit potent bactericidal activity against post-exponential S. aureus that requires lipase activity of glycerol ester hydrolase (geh). Pre-exponential exposure to TRL suppressed agr quorum-sensing, blunting geh expression and toxicity; however, bactericidal activity of TRL could be restored by exogenous lipoprotein lipase. Together, these findings reveal TRL as active antimicrobial particles whose toxicity is unmasked by lipolysis and suggest that modulation of host lipid metabolism may provide new therapeutic opportunities for chronic S. aureus infection.

microbiology↗

The major role of sarA in limiting Staphylococcus aureus extracellular protease production is correlated with decreased virulence in diverse clinical isolates in osteomyelitis

We previously demonstrated that MgrA, SarA, SarR, SarS, SarZ, and Rot bind at least three of the four promoters associated with genes encoding primary extracellular proteases in Staphylococcus aureus. We also showed that mutation of sarA results in a greater increase in protease production, and decrease in biofilm formation, than mutation of the loci encoding any of these other proteins. However, these conclusions were based on in vitro studies. Thus, the goal of the experiments reported here was to determine the relative impact of the regulatory loci encoding these proteins in vivo. To this end, we compared the virulence of mgrA, sarA, sarR, sarS, sarZ, and rot mutants in a murine osteomyelitis model. Mutants were generated in the methicillin-resistant USA300 strain LAC and the methicillin-sensitive USA200 strain UAMS-1. As assessed based on an overall osteomyelitis pathology score derived from the incidence of bone fracture, bacterial burdens in the bone, cortical bone destruction, and reactive bone formation, mutation of mgrA and rot limited virulence to a statistically significant extent in UAMS-1, but not in LAC. In contrast, the sarA mutant exhibited reduced virulence in both strains. This illustrates the importance of considering diverse clinical isolates when evaluating the impact of regulatory mutations on virulence. The reduced virulence of the sarA mutant was correlated with reduced cytotoxicity for osteoblasts and osteoclasts, reduced biofilm formation, and reduced sensitivity to the antimicrobial peptide indolicidin, all of which were directly attributable to increased protease production in both LAC and UAMS-1. This suggests that these in vitro phenotypes, either alone or in combination with each other, may be useful in prioritizing additional mutants for in vivo evaluation. Most importantly, they illustrate the significance of limiting protease production in vivo in S. aureus, and confirm that SarA plays the primary role in this regard. Author SummaryStaphylococcus aureus causes a diverse array of infections due to its ability to produce an arsenal of virulence factors. Among these are extracellular proteases, which serve several purposes on behalf of the bacterium. However, it has become increasingly apparent that it is also critical to limit the production of these proteases to prevent them from compromising the S. aureus virulence factor repertoire. Many regulatory loci have been implicated in this respect, but it is difficult to draw relative conclusions because few reports have made direct comparisons, and fewer still have done so in vivo. We addressed this by assessing the impact on virulence of six regulatory loci previously implicated in protease production. We did this in the clinical context of osteomyelitis using mutants generated in two divergent clinical isolates. Our results confirm significant strain-dependent differences, reinforcing the importance of considering such diverse clinical isolates when evaluating targets for potential therapeutic intervention. In this respect, only mutation of sarA attenuated virulence in both strains. This illustrates the importance of limiting protease production as a means of post-translational regulatory control in S. aureus and confirms that sarA plays a predominant role in this regard.

microbiology↗