Flow Cytometry Analysis: Limitations and precautions for cell isolation from in vivo samples


**Flow cytometry** is a highly popular technique for a detailed analysis of cellular characteristics and functions. Especially when analyzing cells taken directly from in vivo samples, this technology is extremely appealing. However, this approach has several constraints and limitations. In this blog, we will elaborate on the primary challenges of cell separation from in vivo samples and flow cytometry analysis, and how to effectively address them.

Main Constraints and Points to Note:

  1. Cell Damage: Physical or enzymatic separation processes can potentially affect the morphology or function of cells. Specifically, there might be alterations in the cell surface markers.
    Countermeasure: By selecting an appropriate separation method and minimizing the processing time, damage to cells can be significantly reduced.
  2. Incomplete Separation: Not all tissue types and cell types separate with the same efficiency.
    Countermeasure: It’s crucial to select the optimal separation protocol tailored to the sample’s characteristics.
  3. Loss of Inter-Cellular Interactions: In the in vivo state, inter-cellular interactions and the microenvironment play essential roles.
    Countermeasure: Considering co-cultivation of cells or cultivating under specific conditions can help replicate some inter-cellular interactions.
  4. Impact of Dead Cells: There might be an increase in dead cells during the separation process, potentially affecting the analysis results.
    Countermeasure: Consider using dead cell removal kits and cultivating at an appropriate cell concentration to minimize the impact of dead cells.
  5. Background Noise: With separation from tissues, there’s a possibility of extracellular debris and fragments being present in the sample.
    Countermeasure: Proper centrifugation and filtering can help in removing debris and fragments.
  6. Variability in Marker Expression: When cells are separated from the in vivo state, there could be fluctuations in the expression of their surface markers and intracellular molecules.
    Countermeasure: Quickly analyzing cells after separation or optimizing preservation conditions can keep these fluctuations to a minimum.
  7. Time Constraints: Particularly when dealing with human or animal samples, if the time from sample collection to analysis becomes extended, the state of the cells might change.
    Countermeasure: Streamlining the process from sample collection to analysis and completing it in the shortest possible time is essential.
  8. Sample Constraints: Some tissues and cells may be challenging to separate and analyze.
    Countermeasure: It’s crucial to refer to literature and research in advance and choose methods suitable for specific samples.
  9. Complexity of Multi-Color Analysis: When using many fluorochromes simultaneously, there might be issues with spectral overlap and correction.
    Countermeasure: By correcting spectral overlap and selecting the appropriate fluorochromes, accurate analysis can be conducted.

Flow cytometry is an incredibly powerful tool. With the right techniques and considerations, it’s possible to obtain high-quality data. Please refer to the above constraints and countermeasures to aim for more reliable analyses.