Biology subjects

Sprenger, K. G.

Publications and source records attributed to Sprenger, K. G..

8 recordsLinked to original sources

bioRxiv2026

Investigating the therapeutic potential of soluble TREM2 interactions with Transgelin-2 in Alzheimer's disease

Triggering receptor expressed on myeloid cells 2 (TREM2) is a regulator of microglial function in Alzheimer's disease (AD), and its soluble ectodomain (sTREM2) has emerged as a potential neuroprotective factor. Recent work shows that sTREM2 exerts protective effects through direct interaction with neuronal transgelin-2 (TG2) and modulates downstream tau pathology, yet the molecular basis of this interaction remains unknown. Here, we use all-atom molecular dynamics simulations to define the structural mechanisms of sTREM2-TG2 binding. We identify an electrostatically driven interface centered on the TG2 calponin homology domain. This surface is engaged by a binding motif on sTREM2 in which charged anchoring residues are flanked by hydrophobic contacts. We further show that the AD-risk TREM2R47H variant maintains a more open, solvent-exposed CDR2 loop that redistributes interfacial contacts while preserving overall binding affinity, offering a structural explanation for reports that R47H does not exacerbate tau pathology in tauopathy models. Leveraging these insights, we design optimized sTREM2-derived peptides that outperform a previously reported therapeutic peptide in binding persistence, energetics, and recapitulation of native TG2 contacts, supporting engagement at the epitope through which sTREM2 suppresses tau phosphorylation. Taken together, our results define a mechanistic framework for the sTREM2-TG2 axis in AD and establish a structure-guided strategy for developing peptide modulators of this interaction.

bioengineering↗

bioRxiv2026

ApoE Lipidation State Directs Immunometabolic Reprogramming of Human Microglia

IntroductionApoE4 is the strongest genetic risk factor for Alzheimers disease (AD). Emerging evidence suggests that ApoE4 increases AD risk by disrupting microglial metabolism and function. However, whether ApoE lipidation state contributes to microglial dysfunction remains poorly understood. MethodsHuman microglia were treated with lipid-free or lipid-bound ApoE3 or ApoE4. Label-free live-cell holotomography and global proteomics were used to assess isoform- and lipidation-specific effects on lipid droplet dynamics, mitochondrial morphology, and microglial phenotype. ResultsApoE4 treatment resulted in fewer but enlarged lipid droplets and increased mitochondrial fragmentation compared to ApoE3, effects that were enhanced by lipid-bound ApoE4. Proteomic analyses revealed a strong type I interferon response in cells exposed to lipid-free ApoE, which was exacerbated by lipid-free ApoE4. DiscussionThese findings indicate that lipid-bound ApoE4 drives metabolic reprogramming, whereas lipid-free ApoE4 promotes inflammatory signaling, identifying ApoE lipidation as a critical modifier of ApoE4-associated AD risk.

neuroscience↗

bioRxiv2025

Lipoprotein lipase requires a flexible lid and stable C-terminal, both maintained by ApoC-II peptide binding

Lipoprotein lipase (LPL) is the rate-limiting enzyme responsible for hydrolyzing triglycerides in circulating lipoproteins. Reduced LPL activity contributes to hypertriglyceridemia, a major cardiovascular risk factor. LPL activity is thought to depend on the conformation of the lid domain, the lipid pore, N- and C-terminal domains (NTD, CTD), and stabilization of these domains by endogenous activators such as apolipoprotein C-II (ApoC-II). Despite major clinical significance, the structure-function relationship of LPLs functional domains and cofactors remain incompletely understood. To address this, we performed the longest known (1-{micro}s) molecular dynamics simulations of LPL independently and in complex with an ApoC-II mimetic peptide (ApoC-II-P). For the first time, we show that LPLs flexible lid can adopt multiple orientations, transitioning between open and closed states that regulate lipid pore access and catalytic activity. We also observed flipping of [~]180{degrees} by the CTD, a unique characteristic that dictates LPL activity when not in a closed lid state. Furthermore, ApoC-II-P stabilizes LPL by bridging its NTD and CTD, while maintaining an optimal lid orientation. Biochemical and cellular assays corroborate these findings, demonstrating that ApoC-II-P enhances LPL hydrolysis and supports noncanonical LPL functions. Together, these insights reveal previously unrecognized mechanisms governing LPL regulation and activity dynamics.

molecular biology↗

bioRxiv2025

Prioritizing Stability-enhancing Mutations using a Protein Language Model in conjunction with Physics-Based Predictions

Mutational protein engineering, as currently practiced in the biotechnology and pharmaceutical industries, is both tedious and expensive. Computationally driven protein design has the potential to expedite the process and generate high-quality variants at a lower cost. Using datasets of 174824 mutations for 180 proteins, we benchmark the effectiveness of a protein language model (PLM), Evolutionary Scale Modeling (ESM), alongside a physics-based method (PBM), namely molecular mechanics energies with generalized Born and surface area continuum solvation (MM/GBSA), as triaging tools for identifying and prioritizing target positions and specific mutations that improve protein thermodynamic stability. We found prediction biases in each method but also determined that these biases can be mitigated by applying the two methods in a complementary manner. We propose a hybrid mutation prioritization and selection strategy that achieves better accuracy than either method alone. Through re-ranking, the combined prioritization strategy attained a higher overall average ROC AUC of 0.744 across the dataset compared to either MM/GBSA alone (0.684) or ESM Log Odds alone (0.597).

biophysics↗

bioRxiv2025

Antibodies blocking PlGF or VEGF interactions with the NRP1 receptormediate anti-proliferative effects

Antibodies blocking the function of vascular endothelial growth factor A (VEGFA) remain a promising therapeutic strategy, especially when combined with check-point inhibitors, but their efficacy is limited by tumor resistance. This can occur via multiple mechanisms, including upregulation of placental growth factor 2 (PlGF-2), an alternative ligand for VEGF receptor 1 (VEGFR1) and neuropilin receptor 1 (NRP1). Activity of both growth factors is mediated by interactions with multiple receptors and extra-cellular matrix components, which complicates efforts to understand their contributions to cancer progression. To complement existing antibodies, we discovered those blocking interactions between PlGF-2 or VEGFA and their shared NRP1 receptor in the presence of heparin. Limiting angiogenesis to promote vascular normalization is one mechanism of anti-VEGF protection; here, anti-VEGFA antibodies blocking interactions with VEGFR1 and NRP1 reduced HUVEC tube formation in a physiological angiogenesis model. By contrast, antibodies binding PlGF-2 or VEGFA to block NRP1 significantly reduced proliferation of Caki-I kidney carcinoma cells in vitro, indicating this receptor mediates additional effects. Interestingly, one antibody exhibited dual-reactive binding to VEGFA and PlGF-2, suggesting a novel therapeutic strategy to prevent PlGF-driven VEGF-resistance. Overall, these antibodies define new mechanisms to disrupt PlGF activity and support a role for NRP1 in cell proliferation. Key ResultsO_LINew antibodies binding VEGFA or PlGF selectively block NRP1-receptor interactions. C_LIO_LIAntibody blockade of VEGFA binding to NRP1 reduced HUVEC angiogenesis. C_LIO_LIBlocking growth factor interactions with NRP1 reduced Caki-I renal carcinoma proliferation. C_LIO_LIIdentified an antibody with dual-reactive binding to VEGFA and PlGF. C_LI

biochemistry↗

bioRxiv2024

The flexible stalk domain of sTREM2 modulates its interactions with phospholipids in the brain

The microglial surface protein Triggering Receptor Expressed on Myeloid Cells 2 (TREM2) plays a critical role in mediating brain homeostasis and inflammatory responses in Alzheimers disease (AD). The soluble form of TREM2 (sTREM2) exhibits neuroprotective effects in AD, though the underlying mechanisms remain elusive. Moreover, differences in ligand binding between TREM2 and sTREM2, which have major implications for their roles in AD pathology, remain unexplained. To address these knowledge gaps, we conducted the most computationally intensive molecular dynamics simulations to date of (s)TREM2, exploring their interactions with key damage- and lipoprotein-associated phospholipids and the impact of the AD-risk mutation R47H. Our results demonstrate that the flexible stalk domain of sTREM2 serves as the molecular basis for differential ligand binding between sTREM2 and TREM2, facilitated by its role in modulating the dynamics of the Ig-like domain and altering the accessibility of canonical ligand binding sites. We identified a novel ligand binding site on sTREM2, termed the Expanded Surface 2, which emerges due to competitive binding of the stalk with the Ig-like domain. Additionally, we observed that the stalk domain itself functions as a site for ligand binding, with increased binding frequency in the presence of R47H. This suggests that sTREM2s neuroprotective role in AD may, at least in part, arise from the stalk domains ability to rescue dysfunctional ligand binding caused by AD-risk mutations. Lastly, our findings indicate that R47H-induced dysfunction in TREM2 may result from both diminished ligand binding due to restricted complementarity-determining region 2 loop motions and an impaired ability to differentiate between ligands, proposing a novel mechanism for loss-of-function. In summary, these results provide valuable insights into the role of sTREM2 in AD pathology, laying the groundwork for the design of new therapeutic approaches targeting (s)TREM2 in AD.

bioengineering↗

bioRxiv2021

Regulatory approved monoclonal antibodies contain framework mutations predicted from human antibody repertoires

Monoclonal antibodies (mAbs) are an important class of therapeutics used to treat cancer, inflammation, and infectious diseases. Identifying highly developable mAb sequences in silico could greatly reduce the time and cost required for therapeutic mAb development. Here, we present position-specific scoring matrices (PSSMs) for antibody framework mutations developed using natural human antibody repertoire sequences. Our analysis shows that natural human antibody repertoire-based PSSMs are consistent across individuals and demonstrate high correlations between related germlines. We show that mutations in existing therapeutic antibodies can be accurately predicted solely from natural human antibody sequence data. mAbs developed using humanized mice had more human-like FR mutations than mAbs originally developed by hybridoma technology. A quantitative assessment of entire framework regions of therapeutic antibodies revealed that there may be potential for improving the properties of existing therapeutic antibodies by incorporating additional mutations of high frequency in natural human antibody repertoires. In addition, high frequency mutations in natural human antibody repertoires were predicted in silico to reduce immunogenicity in therapeutic mAbs due to the removal of T cell epitopes. Several therapeutic mAbs were identified to have common, universally high-scoring framework mutations, and molecular dynamics simulations revealed the mechanistic basis for the evolutionary selection of these mutations. Our results suggest that natural human antibody repertoires may be useful as predictive tools to guide mAb development in the future.

immunology↗

bioRxiv2020

Optimizing immunization protocols to elicit broadly neutralizing antibodies

Natural infections and vaccination with a pathogen typically stimulates the production of potent antibodies specific for the pathogen through a Darwinian evolutionary process known as affinity maturation. Such antibodies provide protection against reinfection by the same strain of a pathogen. A highly mutable virus, like HIV or influenza, evades recognition by these strain-specific antibodies via the emergence of new mutant strains. A vaccine that elicits antibodies that can bind to many diverse strains of the virus - known as broadly neutralizing antibodies (bnAbs) - could protect against highly mutable pathogens. Despite much work, the mechanisms by which bnAbs emerge remain uncertain. Using a computational model of affinity maturation, we studied a wide variety of vaccination strategies. Our results suggest that an effective strategy to maximize bnAb evolution is through a sequential immunization protocol, wherein each new immunization optimally increases the pressure on the immune system to target conserved antigenic sites, thus conferring breadth. We describe the mechanisms underlying why sequentially driving the immune system increasingly further from equilibrium, in an optimal fashion, is effective. The optimal protocol allows many evolving B cells to become bnAbs via diverse evolutionary paths. Significance StatementThe global health burden could be substantially alleviated by the creation of universal vaccines against highly mutable pathogens like HIV and influenza. Broadly-neutralizing antibodies (bnAbs) are encouraging targets for such vaccines, because they can bind to diverse strains of highly mutable pathogens. BnAbs typically develop only rarely upon natural infection, after the immune system has been exposed to many mutated versions of a pathogen. Thus, sequentially administering multiple different pathogen-like proteins (antigens) is a promising strategy to elicit bnAbs through vaccination. However, it remains unclear how best to design and administer these antigens. We explore this matter using physics-based simulations, and provide new mechanistic insights into antibody evolution that could guide the creation of universal vaccines against highly mutable pathogens.

biophysics↗