InCytokine, an Open-Source Software, Reveals a TREM2 Variant-Specific Cytokine Signature

Area of Science:

• Immunology
• Neuroscience
• Bioinformatics

Background:

• Cytokine and chemokine profiling is crucial for understanding disease mechanisms.
• Protein array technologies generate valuable data for disease research.
• Existing analysis tools may lack robustness or user-friendliness.

Purpose of the Study:

• To introduce InCytokine, an open-source tool for semiquantitative analysis of protein array data.
• To enable robust, reproducible, and scalable analysis of cytokine and chemokine profiling data.
• To investigate the role of TREM2 variants in inflammatory signaling.

Main Methods:

• Development of InCytokine with automated spot detection, alignment, normalization, and quality control.
• Profiling of wild-type, TREM2 knockout, and TREM2 R47H variant microglia.
• Stimulation with lipopolysaccharide and sulfatide, followed by differential expression analysis.
• Corroboration using transcriptional profiling (RNA sequencing).

Main Results:

• InCytokine provides consistent and reliable readouts from protein array assays.
• TREM2 variants exhibit unique sulfatide-specific and genotype-specific cytokine signatures.
• Distinct inflammatory profiles were observed in TREM2 variants, suggesting roles in cardio-metabolic and Alzheimer's disease.
• Good concordance was found between protein array and RNA sequencing data.

Conclusions:

• InCytokine is a user-friendly web application for rapid, reproducible, and scalable protein array data analysis.
• TREM2 variants modulate inflammatory signaling pathways relevant to neurodegenerative and metabolic diseases.
• The tool facilitates drug and biomarker discovery in pharmaceutical settings.