MARTin-an open-source platform for microarray analysis

eSylites: Synthetic Probes for Visualization and Topographic Mapping of Single Excitatory Synapses

The spatiotemporal organization of the postsynaptic density (PSD) is a fundamental determinant of synaptic transmission, information processing, and storage in the brain. The major bottleneck that prevents the direct and precise representation of the nanometer-scaled organization of excitatory glutamatergic synapses is the size of antibodies, nanobodies, and the genetically encoded fluorescent tags. Here, we introduce small, high affinity synthetic probes for simplified, high contrast visualization of excitatory synapses without the limitations of larger biomolecules. In vitro binding quantification together with microscopy-based evaluation identified eSylites, a series of fluorescent bivalent peptides comprising a dye, linker, and sequence composition that show remarkable cellular target selectivity. Applied on primary neurons or brain slices at nanomolar concentrations, eSylites specifically report PSD-95, the key orchestrator of glutamate receptor nanodomains juxtaposed to the presynaptic glutamate release sites that mediate fast synaptic transmission. The eSylite design minimizes a spatial dye offset and thereby enables visualization of PSD-95 with improved localization precision and further time-resolved discrimination. In particular, we find that individual dendritic spines can contain separate nanodomains enriched for either PSD-95 or its closest homologues, PSD-93 or SAP102. Collectively, these data establish eSylites as a broadly applicable tool for simplified excitatory synapse visualization, as well as a high-end microscopy compatible probe for resolving the PSD organization with unprecedented resolution.

High-Throughput Tiling of Essential mRNAs Increases Potency of Antisense Antibiotics

Antimicrobial resistance is outpacing drug discovery, creating an urgent need for precision-based strategies to counteract resistant pathogens. Peptide nucleic acid (PNA)-based antisense molecules offer a promising approach by selectively inhibiting essential bacterial mRNAs, but their design rules for optimal efficacy remain incompletely understood. Here, a scalable high-throughput platform is developed for the nanomolar-scale one-shot synthesis of PNAs as carrier peptide conjugates (PPNAs). Parallel synthesis of up to 1,536 PPNAs composed of up to 21 PNA or peptide building blocks enabled systematic, base-by-base analysis of RNA hybridization, mRNA inhibition, and antimicrobial activity across nine essential genes in uropathogenic Escherichia coli. The accuracy and robustness of this high-throughput tiling platform are demonstrated through in-depth analysis of the acpP mRNA and identify potent antisense inhibitors of rpsH, ftsZ, and murA. This approach provides an efficient and scalable route to design and optimize PNA-based antimicrobials, facilitating empirical testing across diverse bacterial targets. By enabling large-scale exploration of the relevant mRNA sequence space, the sequence tiling platform accelerates the discovery of antisense-based antimicrobials, offering a scalable strategy to develop precision therapies against various pathogens and combat resistance.

Molecular dissection of an immunodominant epitope in Kv1.2-exclusive autoimmunity

Introduction

Subgroups of autoantibodies directed against voltage-gated potassium channel (Kv) complex components have been associated with immunotherapy-responsive clinical syndromes. The high prevalence and the role of autoantibodies directly binding Kv remain, however, controversial. Our objective was to determine Kv autoantibody binding requirements and to clarify their contribution to the observed immune response.

Methods

Binding epitopes were studied in sera (n = 36) and cerebrospinal fluid (CSF) (n = 12) from a patient cohort positive for Kv1.2 but negative for 32 common neurological autoantigens and controls (sera n = 18 and CSF n = 5) by phospho and deep mutational scans. Autoantibody specificity and contribution to the observed immune response were resolved on recombinant cells, cerebellum slices, and nerve fibers.

Results

83% of the patients (30/36) within the studied cohort shared one out of the two major binding epitopes with Kv1.2-3 reactivity. Eleven percent (4/36) of the serum samples showed no binding. Fingerprinting resolved close to identical sequence requirements for both shared epitopes. Kv autoantibody response is directed against juxtaparanodal regions in peripheral nerves and the axon initial segment in central nervous system neurons and exclusively mediated by the shared epitopes.

Discussion

Systematic mapping revealed two shared autoimmune responses, with one dominant Kv1.2-3 autoantibody epitope being unexpectedly prevalent. The conservation of the molecular binding requirements among these patients indicates a uniform autoantibody repertoire with monospecific reactivity. The enhanced sensitivity of the epitope-based (10/12) compared with that of the cell-based detection (7/12) highlights its use for detection. The determined immunodominant epitope is also the primary immune response visible in tissue, suggesting a diagnostic significance and a specific value for routine screening.