Biology subjects

Soni, D. M.

Publications and source records attributed to Soni, D. M..

5 recordsLinked to original sources

bioRxiv2026

Optimization and Characterization of SHIP1 Ligands for Cellular Target Engagement and Activity in Alzheimer's Disease Models

Src homology 2 domain-containing inositol 5-phosphatase 1 (SHIP1), encoded by the gene INPP5D, is a lipid phosphatase that negatively regulates immune receptor signaling in hematopoietic cells and microglia. Here, we describe a pyridyl-pyrazole-piperidine scaffold and the lead compound 3-((2-chlorobenzyl)oxy)-5-(1-(piperidin-4-yl)-1H-pyrazol-4-yl)pyridine (32), which demonstrates SHIP1 target engagement, brain exposure, and evidence of a central pharmacodynamic response in vivo. Structure-activity relationship studies, guided by biochemical and cellular assays using multiple human and murine protein constructs and cells, identified SHIP1-active ligands. A thermal shift assay using full-length SHIP1 was used to assess compounds for cellular target engagement, while studies in IL-4 conditioned THP-1 cells was used to demonstrate changes in downstream AKT signaling. Targeted lipidomics revealed changes in the overall phosphoinositide pool consistent with SHIP1 target engagement and reduction of phospho-AKT levels. In a protein-lipid overlay assay, compound 32 induced changes in the relative association of SHIP1 with multiple phosphatidylinositols on a membrane surface. In high-content cellular imaging assays, compound 32 enhanced the uptake of myelin/membrane debris and fibrillar amyloid by primary murine microglia, phenocopying a genetic model with reduced SHIP1 expression. Finally, oral administration of compound 32 resulted in brain exposure sufficient to alter gene expression and reduce IL-1{beta} levels as pharmacodynamic markers of microglial activation and neuroinflammation in an amyloidosis mouse model of Alzheimers disease. Collectively, these results define a scaffold with SHIP1 target engagement, CNS exposure, and in vivo activity, providing a foundation for the optimization of brain-penetrant SHIP1 ligands suitable for further mechanistic studies and therapeutic development for the treatment of Alzheimers disease.

pharmacology and toxicology↗

bioRxiv2023

In vivo validation of late-onset Alzheimer's disease genetic risk factors

Structured AbstractO_ST_ABSIntroductionC_ST_ABSGenome-wide association studies have identified over 70 genetic loci associated with late-onset Alzheimers disease (LOAD), but few candidate polymorphisms have been functionally assessed for disease relevance and mechanism of action. MethodsCandidate genetic risk variants were informatically prioritized and individually engineered into a LOAD-sensitized mouse model that carries the AD risk variants APOE4 and Trem2*R47H. Potential disease relevance of each model was assessed by comparing brain transcriptomes measured with the Nanostring Mouse AD Panel at 4 and 12 months of age with human study cohorts. ResultsWe created new models for 11 coding and loss-of-function risk variants. Transcriptomic effects from multiple genetic variants recapitulated a variety of human gene expression patterns observed in LOAD study cohorts. Specific models matched to emerging molecular LOAD subtypes. DiscussionThese results provide an initial functionalization of 11 candidate risk variants and identify potential preclinical models for testing targeted therapeutics.

neuroscience↗

bioRxiv2023

SHIP1 modulation and proteome characterization of microglia

Microglia, the resident macrophage in brain, has gained significant attention due to their involvement in neurodegenerative diseases. Disease associated microglia (DAM) have been identified at sites of amyloid-beta plaques and neurodegeneration. Understanding microglial states in the aging brain has become crucial, especially with the discovery of numerous Alzheimers disease (AD) risk and protective variants in genes such as TREM2, CD33, APOE, ABCA7, PLCG2, and INPP5D, which are essential to microglia function1. Here we present a thorough examination of microglia-like cell lines and primary mouse microglia at the proteomic and transcriptomic levels to help illuminate the roles these genes and the proteins they encode play in various cell states. This analysis serves as a guide to the exploration of potential therapeutic targets in the context of neurodegeneration. INPP5D, which encodes the SHIP1 protein, is essential for microglia function. SHIP1 has emerged as a target of interest having been nominated as a therapeutic target by three teams within the Accelerating Medicines Partnership for Alzheimers Disease (AMP-AD)2. In this study, we compared the proteomic profiles of wildtype, SHIP1 heterozygous knockout, and homozygous knockout primary microglia. Our findings revealed significant proteomic alterations only in the homozygous knockout of the SHIP1 gene, revealing its impact on the microglial proteome. Additionally, we compared the proteomic and transcriptomic profiles of BV2 and HMC3 cells with primary mouse microglia because these cell lines are often used as microglial cellular models. Our results demonstrated a substantial similarity between the proteome of BV2 cells and mouse primary cells, while notable differences were observed between BV2 and human HMC3 cells, with some shared characteristics. Since SHIP1 functions as a lipid phosphatase that modulates phosphatidylinositol (PI) species, we conducted lipidomic analysis to quantify different phosphatidylinositols (PIs), phosphatidylinositol monophosphate (PIPs), and polyphosphoinositides (PPIs) in the HMC3 and BV2 cells. Under basal conditions, PI(3,4,5)P3 and PI(3,4)P2 species were detected at extremely low levels, making confident quantification challenging; however, PIP species within the overall pool were significantly changed upon SHIP1 overexpression in HMC3. This in-depth proteomic analysis of both mouse and human microglia, complemented by targeted lipidomic studies, enhances our understanding of these cellular models. The similarities between primary mouse microglia and the BV2 cell line is especially encouraging, supporting the use of this model for further investigations into the role that SHIP1 and other potential drug targets may play in the regulation of microglial states.

neuroscience↗

bioRxiv2022

Plcg2M28L interacts with high fat-high sugar diet to accelerate Alzheimers disease-relevant phenotypes in mice

Obesity is recognized as a significant risk factor for Alzheimers disease (AD). Studies have supported the notion that obesity accelerates AD-related pathophysiology in mouse models of AD. The majority of studies to date have focused on the use of early-onset AD models. Here we evaluate the impact of genetic risk factors on late-onset AD (LOAD) in mice fed a high fat/high sugar diet. We focused on three mouse models created through the IU/JAX/Pitt MODEL-AD Center, LOAD1, LOAD1.Plcg2M28L and LOAD1.Mthfr677C>T. At 2 months of age, animals were placed on a high fat/high sugar diet (HFD) that induces obesity, or a control diet (CD) that does not, until 12 months of age. Throughout the study, blood was collected to assess cholesterol and glucose. Positron emission tomography/computed tomography (PET/CT) was completed prior to sacrifice to image for glucose utilization and brain perfusion. At the completion of the study, blood and brains were collected for analysis. As expected, animals fed the HFD, regardless of genotype or sex, showed a significant increase in body weight compared to those fed the CD. Glucose and cholesterol increased as a function of HFD as well. Interestingly, LOAD1.Plcg2M28L demonstrated an increase in microglia density as well as alterations in regional brain glucose and perfusion when on a HFD. These changes were not observed in LOAD1 or LOAD1.Mthfr677C>T animals when fed a HFD. Furthermore, LOAD1.Plcg2M28L but not LOAD1.Mthfr677C>T or LOAD1 animals showed transcriptomics correlations to human AD modules. Our results show HFD affects brain health in a genotype-specific manner. Further insight into this process may have significant implications in the development of lifestyle interventions for treatment of AD.

neuroscience↗

bioRxiv2021

AD Informer Set: Chemical tools to facilitate Alzheimer's disease drug discovery

IntroductionThe portfolio of novel targets to treat Alzheimers disease (AD) has been enriched by the AMP-AD program. MethodsA cheminformatics-driven effort enabled identification of existing small molecule modulators for many protein targets nominated by AMP-AD and suitable positive control compounds to be included in the set. ResultsWe have built an annotated set of 171 small molecule modulators, including mostly inhibitors, targeting 98 unique proteins that have been nominated by AMP-AD consortium members as novel targets for AD treatment. These small molecules vary in their quality and should be considered chemical tools that can be used in efforts to validate therapeutic hypotheses, but which would require further optimization. A physical copy of the AD Informer Set can be ordered via the AD Knowledge Portal. DiscussionSmall molecule tools that enable target validation are important tools for the translation of novel hypotheses into viable therapeutic strategies for AD.

neuroscience↗