Biology subjects

Soderling, S. H.

Publications and source records attributed to Soderling, S. H..

12 recordsLinked to original sources

bioRxiv2026

In vivo Proximity & Spatial Proteomics with CRISPR Screening Identify STXBP1 as a Protective Modifier of a-synuclein Toxicity in Dopamine Neurons.

Parkinsons disease (PD) is a disease of adults involving the loss of dopaminergic neurons after a long, asymptomatic, prodromal period. -synuclein, LRRK2, and VPS35 are linked to familial PD, however, how these mutations predispose dopamine neurons to death during the early prodromal phases remains unclear. Here, we used in vivo native proximity proteomics (iBioID) and dopaminergic neuron-specific subcellular proteomics across multiple PD models to uncover early alterations preceding neuronal loss. Our analyses identified convergent disruptions in synaptic protein abundance, indicating that presynaptic trafficking defects are early events in PD pathogenesis. Using a targeted CRISPR-based genetic screen in dopamine neurons, we demonstrated that mimicking this misregulation of STXBP1 amplifies vulnerability to -synuclein, implicating it as a previously underappreciated toxicity buffering factor. These findings highlight convergent mechanisms that sensitize dopamine neuronal degeneration and that presynaptic vesicle SNARE-complex proteins could serve as key targets for disease-modifying therapies in PD and related neurodegenerative disorders. HighlightsO_LIIn vivo native-BioID mapping of multiple Parkinsons disease (PD) protein interactomes revealed a convergent presynaptic network. C_LIO_LIiBioID analysis on mutant PD proteins (-synuclein A30P, LRRK2 G2019S, VPS35 D620N) uncovered mutation-specific shifts in local proximity networks, notably in endocytic and vesicle recycling pathways. C_LIO_LISpatial proteomics (iBioCoFrac) of dopamine neurons in vivo identified functional modules with reduced levels of key synaptic proteins in PD models. C_LIO_LIComparative proteomics using iBioCoFrac revealed synaptic vesicle regulation as a primary site of molecular convergence and early molecular signatures in dopamine neurons across multiple PD mouse models. C_LIO_LIAn in vivo CRISPR screen pinpointed the presynaptic protein Stxbp1/Munc18-1 as an -synuclein toxicity modifier in dopaminergic neurons. C_LI

neuroscience↗

bioRxiv2025

Protein Language Model-Aligned Spectra Embeddings for De Novo Peptide Sequencing

We consider the problem of de novo peptide sequencing in tandem mass spectrometry, where the goal is to predict the underlying peptide sequence given a spectrums fragment peaks and precursor information. We present PLMNovo, a constrained learning framework that leverages pre-trained protein language models (PLMs) to guide the training process. In particular, we cast peptide-spectrum matching as a constrained optimization problem that enforces alignment between spectrum and peptide embeddings produced by a spectrum encoder and a PLM, respectively. We use a Lagrangian primal-dual algorithm to train the spectrum encoder and the peptide decoder by solving the proposed constrained learning problem, while optionally fine-tuning the pre-trained PLM. Through numerical experiments on established benchmarks, we demonstrate that PLMNovo outperforms several state-of-the-art deep learning-based de novo sequencing algorithms.

bioinformatics↗

bioRxiv2025

Deep Learning-coupled Proximity Proteomics to Deconvolve Kinase Signaling In Vivo

Deconvolving the substrates of hundreds of kinases linked to phosphorylation networks driving cellular behavior is a fundamental, unresolved biological challenge, largely due to the poorly understood interplay of kinase selectivity and substrate proximity. We introduce KolossuS, a deep learning framework leveraging protein language models to decode kinase-substrate specificity. KolossuS achieves superior prediction accuracy and sensitivity across mammalian kinomes, enabling proteome-wide predictions and evolutionary insights. By integrating KolossuS with CRISPR-based proximity proteomics in vivo, we capture kinase-substrate recognition and spatial context, obviating prior limitations. We show this combined framework identifies kinase substrates associated with physiological states such as sleep, revealing both known and novel Sik3 substrates during sleep deprivation. This novel integrated computational-experimental approach promises to transform systematic investigations of kinase signaling in health and disease.

cell biology↗

bioRxiv2024

Miniaturizing, Modifying, and Augmenting Nature's Proteins with Raygun

Proteins have evolved over billions of years through extensive and coordinated substitutions, insertions and deletions (indels). Computational protein design cannot yet fully mimic natures ability to engineer new proteins from existing templates. Protein language models generate informative per-residue representations, but leveraging them to execute large-scale, function-preserving mutations and indels has remained beyond reach. We introduce Raygun, a generative AI framework that unlocks efficient miniaturization, modification, and augmentation of proteins, using a novel probabilistic encoding of protein sequences constructed from language model embeddings. Emulating evolution, Raygun shrinks proteins by 10-25% (sometimes over 50%) while preserving predicted structural integrity and fidelity, introduces extensive sequence diversity while preserving functional sites, and can expand proteins beyond their natural size. These capabilities unlock new opportunities in gene therapy and biotechnology. In cell-based validation, Raygun successfully miniaturized fluorescent proteins, two of which are smaller than 96% of fluorescent proteins reported in FPbase, as well as TurboID, a synthetic biotin ligase widely adopted for proteomics. It also successfully expanded Epidermal Growth Factor (EGF), a natural binding partner to the EGFR protein, generating EGF variants with higher binding affinity than the wildtype. Rayguns conceptual innovations in template-based protein design reveal that protein function can be encoded in a length-independent space. This fundamental insight bridges protein representation learning with evolutionary biology and could unlock the development of more efficient molecular tools and biological therapeutics.

bioinformatics↗

bioRxiv2024

Presynaptic Rac1 in the hippocampus selectively regulates working memory

One of the most extensively studied members of the Ras superfamily of small GTPases, Rac1 is an intracellular signal transducer that remodels actin and phosphorylation signaling networks. Previous studies have shown that Rac1-mediated signaling is associated with hippocampal-dependent working memory and longer-term forms of learning and memory and that Rac1 can modulate forms of both pre- and postsynaptic plasticity. How these different cognitive functions and forms of plasticity mediated by Rac1 are linked, however, is unclear. Here, we show that spatial working memory is selectively impaired following the expression of a genetically encoded Rac1-inhibitor at presynaptic terminals, while longer-term cognitive processes are affected by Rac1 inhibition at postsynaptic sites. To investigate the regulatory mechanisms of this presynaptic process, we leveraged new advances in mass spectrometry to identify the proteomic and post-translational landscape of presynaptic Rac1 signaling. We identified serine/threonine kinases and phosphorylated cytoskeletal signaling and synaptic vesicle proteins enriched with active Rac1. The phosphorylated sites in these proteins are at positions likely to have regulatory effects on synaptic vesicles. Consistent with this, we also report changes in the distribution and morphology of synaptic vesicles and in postsynaptic ultrastructure following presynaptic Rac1 inhibition. Overall, this study reveals a previously unrecognized presynaptic role of Rac1 signaling in cognitive processes and provides insights into its potential regulatory mechanisms.

animal behavior and cognition↗

bioRxiv2023

Identification of new ciliary signaling pathways in the brain and insights into neurological disorders

Primary cilia are conserved sensory hubs essential for signaling transduction and embryonic development. Ciliary dysfunction causes a variety of developmental syndromes with neurological features and cognitive impairment, whose basis mostly remains unknown. Despite connections to neural function, the primary cilium remains an overlooked organelle in the brain. Most neurons have a primary cilium; however, it is still unclear how this organelle modulates brain architecture and function, given the lack of any systemic dissection of neuronal ciliary signaling. Here, we present the first in vivo glance at the molecular composition of cilia in the mouse brain. We have adapted in vivo BioID (iBioID), targeting the biotin ligase BioID2 to primary cilia in neurons. We identified tissue-specific signaling networks enriched in neuronal cilia, including Eph/Ephrin and GABA receptor signaling pathways. Our iBioID ciliary network presents a wealth of neural ciliary hits that provides new insights into neurological disorders. Our findings are a promising first step in defining the fundamentals of ciliary signaling and their roles in shaping neural circuits and behavior. This work can be extended to pathological conditions of the brain, aiming to identify the molecular pathways disrupted in the brain cilium. Hence, finding novel therapeutic strategies will help uncover and leverage the therapeutic potential of the neuronal cilium.

neuroscience↗

bioRxiv2023

Astrocytic LRRK2 Controls Synaptic Connectivity through ERM Phosphorylation

Astrocytes are highly complex cells that mediate critical roles in synapse formation and maintenance by establishing thousands of direct contacts with synapses through their perisynaptic processes. Here, we found that the most common Parkinsonism gene mutation, LRRK2 G2019S, enhances the phosphorylation of the ERM proteins (Ezrin, Radixin, and Moesin), components of the perisynaptic astrocyte processes in a subset of cortical astrocytes. The ERM hyperphosphorylation was accompanied by decreased astrocyte morphological complexity and reduced excitatory synapse density and function. Dampening ERM phosphorylation levels in LRRK2 G2019S mouse astrocytes restored both their morphology and the excitatory synapse density in the anterior cingulate cortex. To determine how LRRK2 mutation impacts Ezrin interactome, we used an in vivo BioID proteomic approach, and we found that astrocytic Ezrin interacts with Atg7, a master regulator of autophagy. The Ezrin/Atg7 interaction is inhibited by Ezrin phosphorylation, thus diminished in LRRK2 G2019S astrocytes. Importantly, the Atg7 function is required to maintain proper astrocyte morphology. Our data provide a molecular pathway through which the LRRK2 G2019S mutation alters astrocyte morphology and synaptic density in a brain-region-specific manner.

neuroscience↗

bioRxiv2022

Chemico-genetic Analysis of Native Autism Proteomes Reveals Shared Biology Predictive of Functional Modifiers

One of the main drivers of autism spectrum disorder is risk alleles within hundreds of genes, which may interact within shared but unknown protein complexes. Here we develop a scalable genome-editing-mediated approach to target 14 high-confidence autism risk genes within the mouse brain for proximity-based endogenous proteomics, achieving high specificity spatial interactomes compared to prior methods. The resulting native proximity interactomes are enriched for human genes dysregulated in the brain of autistic individuals and reveal unexpected and highly significant interactions with other lower-confidence autism risk gene products, positing new avenues to prioritize genetic risk. Importantly, the datasets are enriched for shared cellular functions and genetic interactions that may underlie the condition. We test this notion by spatial proteomics and CRISPR-based regulation of expression in two autism models, demonstrating functional interactions that modulate mechanisms of their dysregulation. Together, these results reveal native proteome networks in vivo relevant to autism, providing new inroads for understanding and manipulating the cellular drivers underpinning its etiology.

neuroscience↗

bioRxiv2022

A prefrontal to lateral entorhinal pathway disrupts memory.

While the neural circuits underlying memory encoding, storage, and retrieval are well characterized, the circuits that act to disrupt memory are enigmatic. Here we find that silencing a projection from the prefrontal cortex to the lateral entorhinal cortex surprisingly improves spatial working memory and contextual memory. We then found that the same cell type shows increased activity during errors in a spatial working memory test. Finally we found that optogenetic activation of the same activity patterns can disrupt working memory performance. By using a combination of intersectional genetic and in vivo imaging techniques we advance evidence that a novel prefrontal-entorhinal pathway critically participates in memory disruption.

neuroscience↗

bioRxiv2021

Excitatory synaptogenesis in the anterior cingulate cortex is required for effort/reward evaluation

Synaptogenesis is essential for circuit development; however, it is unknown whether it is critical for the establishment and performance of goal-directed voluntary behaviors. Here, we show that operant-conditioning via lever-press for food reward-training in mice induces excitatory synapse formation onto a subset of Anterior Cingulate Cortex neurons projecting to the dorsomedial striatum (ACC->DMS). Training-induced synaptogenesis is controlled by the Gabapentin/Thrombospondin receptor 2{delta}-1, which is an essential neuronal protein for proper intracortical excitatory synaptogenesis. Using germline and conditional knockout mice, we found that deletion of 2{delta}-1 in the adult ACC->DMS circuit diminishes training-induced excitatory synaptogenesis. Surprisingly, this manipulation did not impact learning but instead resulted in a profound increase in effort exertion without affecting sensitivity to reward value or changing contingencies. Bidirectional optogenetic manipulation of ACC->DMS neurons rescued or phenocopied the behaviors of the 2{delta}-1 cKO mice highlighting the importance of synaptogenesis within this cortico-striatal circuit in regulating effort exertion.

neuroscience↗

bioRxiv2020

Action potential-coupled Rho GTPase signaling drives presynaptic plasticity

In contrast to their postsynaptic counterparts, the contributions of activity-dependent cytoskeletal signaling to presynaptic plasticity remain controversial and poorly understood. To identify and evaluate these signaling pathways, we conducted a proteomic analysis of the presynaptic cytomatrix using in vivo biotin identification (iBioID). The resultant proteome was heavily enriched for actin cytoskeleton regulators, including Rac1, a Rho GTPase that activates the Arp2/3 complex to nucleate branched actin filaments. Strikingly, we find Rac1 and Arp2/3 are closely associated with presynaptic vesicle membranes and negatively regulate synaptic vesicle replenishment at both excitatory and inhibitory synapses. Using optogenetics and fluorescence lifetime imaging, we show this pathway bidirectionally sculpts short-term synaptic depression and that its presynaptic activation is coupled to action potentials by voltage-gated calcium influx. Thus, this study provides a new proteomic framework for understanding presynaptic physiology and uncovers a previously unrecognized mechanism of actin-regulated short-term presynaptic plasticity that is conserved across cell types.

neuroscience↗

bioRxiv2018

Restoring striatal WAVE-1 improves maze exploration performance of GluN1 knockdown mice

NMDA receptors are important for cognition and are implicated in neuropsychiatric disorders. GluN1 knockdown (GluN1KD) mice have reduced NMDA receptor levels, striatal spine density deficits, and cognitive impairments. However, how NMDA depletion leads to these effects is unclear. Since Rho GTPases are known to regulate spine density and cognition, we examined the levels of RhoA, Rac1, and Cdc42 signaling proteins. Striatal Rac1-pathway components are reduced in GluN1KD mice, with Rac1 and WAVE-1 deficits at 6 and 12 weeks of age. Concurrently, medium spiny neuron (MSN) spine density deficits are present in mice at these ages. To determine whether WAVE-1 deficits were causal or compensatory in relation to these phenotypes, we intercrossed GluN1KD mice with WAVE-1 overexpressing (WAVE-Tg) mice to restore WAVE-1 levels. GluN1KD-WAVE-Tg hybrids showed rescue of striatal WAVE-1 protein levels and MSN spine density, as well as selective behavioral rescue in the Y-maze and 8-arm radial maze tests. GluN1KD-WAVE-Tg mice expressed normalized WAVE-1 protein levels in the hippocampus, yet spine density of hippocampal CA1 pyramidal neurons was not significantly altered. Our data suggest a nuanced role for WAVE-1 effects on cognition and a delineation of specific cognitive domains served by the striatum. Rescue of striatal WAVE-1 and MSN spine density may be significant for goal-directed exploration and associated long-term memory in mice.

neuroscience↗