Immune cell annotation in the single-cell studies: technologies, challenges, and integrative solutions

Area of Science:

• Immunology
• Genomics
• Proteomics

Background:

• Single-cell RNA sequencing (scRNA-seq) offers high-resolution immune cell profiling.
• Challenges in immune cell annotation arise from mRNA-protein expression discrepancies.
• These discrepancies are driven by biological variability and technical limitations, impacting cell classification.

Purpose of the Study:

• To review challenges in immune cell annotation using scRNA-seq.
• To examine mechanisms behind mRNA-protein expression divergence.
• To evaluate current and emerging single-cell profiling technologies and computational strategies.

Main Methods:

• Literature review of immune cell annotation challenges.
• Analysis of biological and technical factors causing mRNA-protein mismatches.
• Evaluation of transcriptomic, proteomic, and multimodal single-cell profiling technologies.
• Assessment of computational approaches for multi-omics data integration.

Main Results:

• mRNA-protein discrepancies pose significant challenges for accurate immune cell annotation.
• Multimodal approaches, like Cellular Indexing of Transcriptomes and Epitopes by Sequencing (CITE-seq), integrate transcriptomic and proteomic data.
• Standardized multimodal profiling is crucial for reliable annotation and advancing immunological research.

Conclusions:

• Addressing mRNA-protein discrepancies is vital for precise immune cell classification.
• Multimodal profiling technologies offer a solution to single-modality limitations.
• Integrated computational strategies are essential for leveraging multi-omics data in immunology.