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SHIP1 modulation and proteome characterization of microglia
Erpan Ahat1, Zanyu Shi2, Shaoyou Chu3
1Eli Lilly and Company, Indianapolis, USA.
Abstract:
Understanding microglial states in the aging brain has become crucial, especially with the discovery of numerous Alzheimer's disease (AD) risk and protective variants in genes such as INPP5D and TREM2, which are essential to microglia function in AD. Here we present a thorough examination of microglia-like cells and primary mouse microglia at the proteome and transcriptome levels to illuminate the roles these genes and the proteins they encode play in various cell states. First, we compared the proteome profiles of wildtype and INPP5D (SHIP1) knockout primary microglia. Our findings revealed significant proteome alterations only in the homozygous SHIP1 knockout, revealing its impact on the microglial proteome. Additionally, we compared the proteome and transcriptome profiles of commonly used in vitro microglia BV2 and HMC3 cells with primary mouse microglia. Our results demonstrated a substantial similarity between the proteome of BV2 and mouse primary cells, while notable differences were observed between BV2 and human HMC3. Lastly, we conducted targeted lipidomic analysis to quantify different phosphatidylinositols (PIs) species, which are direct SHIP1 targets, in the HMC3 and BV2 cells. This in-depth omics analysis of both mouse and human microglia enhances our systematic understanding of these microglia models. SIGNIFICANCE: Given the growing urgency of comprehending microglial function in the context of neurodegenerative diseases and the substantial therapeutic implications associated with SHIP1 modulation, we firmly believe that our study, through a rigorous and comprehensive proteomics, transcriptomics and targeted lipidomic analysis of microglia, contributes to the systematic understanding of microglial function in the context of neurodegenerative diseases.
Insights
Investigating microglial function in aging and Alzheimer's disease (AD) is key. This study used omics analysis to reveal SHIP1's impact on microglial proteomes and compare cell models, aiding neurodegenerative disease research.
Area of Science:
- Neuroscience
- Immunology
- Genetics
Background:
- Microglial function is critical in aging and neurodegenerative diseases like Alzheimer's.
- Genes like INPP5D (SHIP1) and TREM2 influence microglial roles in Alzheimer's disease.
- Understanding microglial states is essential for therapeutic development.
Purpose of the Study:
- To comprehensively examine microglia-like cells and primary microglia using proteome and transcriptome analyses.
- To elucidate the roles of INPP5D (SHIP1) and its encoded proteins in different microglial cell states.
- To compare commonly used in vitro microglia models (BV2, HMC3) with primary mouse microglia.
Main Methods:
- Proteomic and transcriptomic profiling of wildtype and INPP5D (SHIP1) knockout primary mouse microglia.
- Comparative proteomic and transcriptomic analysis of BV2, HMC3, and primary mouse microglia.
- Targeted lipidomic analysis of phosphatidylinositol (PI) species in HMC3 and BV2 cells.
Main Results:
- Homozygous SHIP1 knockout significantly altered the primary microglial proteome.
- BV2 cells showed proteomic similarity to primary mouse microglia, unlike human HMC3 cells.
- SHIP1 directly impacts phosphatidylinositol species, key targets identified in HMC3 and BV2 cells.
Conclusions:
- This omics analysis provides a systematic understanding of microglial models and function.
- Findings highlight SHIP1's significant role in microglial proteome regulation.
- The study enhances comprehension of microglial function in neurodegenerative diseases and potential therapeutics.
