Single-cell RNA sequencing (scRNA-seq) allows transcriptomic profiling at the level of individual cells, enabling researchers to capture cellular heterogeneity that bulk RNA sequencing cannot. The method isolates single cells – via microfluidics, droplets, or plate-based methods – and sequences their mRNA to reconstruct gene expression profiles cell-by-cell [1]. 
 
scRNA-seq 𝗜𝘀 transformative 𝗳𝗼𝗿 𝗜𝗺𝗺𝘂𝗻𝗼𝗹𝗼𝗴𝘆 
The immune system is heterogeneous, dynamic, and context-dependent. scRNA-seq enables: 
• Mapping of immune cell subsets beyond classical markers, including novel DCs subclasses, unconventional T cell types 
• Characterization of activation, exhaustion, and memory states in T and NK cells during infection, cancer, or chronic inflammation [2] 
• Profiling myeloid populations such as tumor-associated macrophages (TAMs), polarization spectrum, not strictly M1 or M2 subtypes 
• Deciphering cytokine and chemokine networks, identifying the cells responsible for immunosuppression or immunopathology 
 
Applications 𝗶𝗻 𝗜𝗺𝗺𝘂𝗻𝗼𝗹𝗼g𝘆 a𝗻𝗱 𝗜𝗺𝗺𝘂𝗻o-𝗢𝗻𝗰𝗼𝗹𝗼𝗴𝘆 
1. Tumor Microenvironment Analysis 
scRNA-seq is capable of revealing immunosuppressive niches, spatially organized T cell dysfunction programs, and tumor–immune crosstalk that determines therapeutic resistance [3]. 
2. CAR-T and Cellular Therapy Development 
By profiling engineered immune cells before and after infusion, scRNA-seq helps researchers determine: 
how CAR-T cells interact with suppressive tumor compartments. 
3. Vaccine and Infection Research 
scRNA-seq identifies antigen-specific T and B cell responses at high resolution, elucidating clonal expansion, somatic hypermutation patterns, and effector/memory differentiation pathways. 
4. Autoimmunity and Inflammation 
In diseases such as RA or IBD, scRNA-seq reveals dysregulated immune populations responsible for tissue damage. 
 
𝗤𝘂𝗲𝘀𝘁𝗶𝗼𝗻 𝗳𝗼𝗿 𝘁𝗵𝗲 𝗔𝘂𝗱𝗶𝗲𝗻𝗰𝗲 
If you could profile any immune population at single-cell resolution e.g. CAR-T cells, TAMs, exhausted CD8⁺ T cells, mucosal immunity, which would you choose? 
 
Stay tuned for 𝗗𝗮𝘆 𝟴𝟭: 𝗗𝗲𝗰𝗼𝗱𝗶𝗻𝗴 𝗘p𝗶𝗴𝗲𝗻𝗲𝘁𝗶𝗰 𝗟𝗮𝗻𝗱𝘀c𝗮p𝗲𝘀 w𝗶𝘁𝗵 𝗔𝗧𝗔𝗖-𝘀𝗲𝗾: 𝗙𝗿𝗼𝗺 𝗥𝗲𝗴𝘂𝗹𝗮𝘁𝗼𝗿𝘆 𝗘𝗹𝗲𝗺𝗲𝗻𝘁𝘀 𝘁𝗼 𝗜𝗺𝗺𝘂𝗻𝗲 𝗙𝘂𝗻𝗰𝘁𝗶𝗼𝗻 
 
𝗥𝗲𝗳𝗲𝗿𝗲𝗻𝗰𝗲𝘀 
1. DOI: 10.1038/nmeth.4636 
2. DOI: 10.1038/s41591-019-0522-3 
3. DOI: 10.1126/science.aad0501 
 
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