Preserving the True Immune Landscape: Eliminating Enzymatic Artifacts in Inflammation Research

Preserving the True Immune Landscape in Inflammation Research

Inflammation is a critical process involving complex interactions between innate and adaptive immune cells, stromal populations, and the surrounding tissue microenvironment. Triggered by infection, injury, or dysregulated signaling, inflammation serves to eliminate harmful stimuli and initiate repair. Yet persistent or maladaptive inflammation enables chronic disease, including autoimmunity, cardiovascular disorders, neurodegenerative conditions, and cancer.

Deciphering inflammation at the single-cell level is essential for mapping the cell-cell interactions underlying disease mechanisms that can be targeted for therapeutic interventions. Advances in flow cytometry and single-cell RNA sequencing (scRNA-seq) now allow unprecedented resolution in defining cellular phenotypes, activation states, and signaling networks. However, these technologies depend on a critical assumption: that the cells being analyzed truly reflect their in-situ biology.

Cell Sample Preparation: The Critical Variable

The first step in most single-cell workflows is dissociating tissue into single-cell suspensions. Conventional methods rely on enzymatic digestion (e.g., collagenases, proteases, DNases) to degrade extracellular matrices. While efficient at liberating cells, these methods often compromise biological fidelity.

Evidence of Enzymatic Artifacts

Multiple studies demonstrate that enzymatic digestion alters both surface marker integrity and transcriptional states:

• Surface marker degradation – High-dose dispase impairs detection of essential T cell markers such as CD4, CD8, and CD62L¹, with these effects persisting even after 24 hours in culture². Enzymatic cocktails combining collagenase and dispase also reduce detection of markers like CD69 and CD103 in inflamed lung tissue. Importantly, these methods are also less efficient at preserving CD19, a canonical B cell marker, compared to mechanical dissociation.
• Altered cellular phenotypes – B cell marker B220 and chemokine receptor CXCR5 show reduced expression post-digestion, while dendritic cell activation markers (CD40, CD80, CD86) may appear artificially elevated ³.
• Transcriptional stress artifacts – Standard enzymatic digestion at 37 °C induces immediate early genes (IEGs) such as Fos and Jun, mimicking activation across multiple tissues⁴. Cold-active proteases at 6 °C reduce but do not eliminate this artifact.

For inflammation research — where identifying subtle immune subset differences (e.g., classical vs. non-classical monocytes) and transient activation states is critical — these artifacts can obscure biological truth and overlook key immune cell interactions.

Acoustic Dissociation: Preserving Biology at the Point of Isolation

The Cellsonics SimpleFlow™ system applies controlled acoustic energy to dissociate tissues without enzymes or elevated temperature. This gentle, acoustic-generated movement preserves epitope integrity, maintains receptor conformation, and minimizes induction of artificial stress responses.

Key Advantages of acoustic dissociation for Inflammation Research

• Marker Preservation – Immune epitopes (e.g., CD19, CD45, CD64, CD138 ) remain intact, enabling accurate flow cytometry.
• Broad Cell Recovery – Acoustic dissociation supports recovery of lymphocytes, macrophages, dendritic cells, endothelial cells, and progenitors from inflamed tissues, including kidney, brain, and tumors.
• Native in vivo cell status and poise – Acoustic dissociation doesn’t illegitimately activate cells and/or alter their phenotype that can lead to misinterpretation of the cellular activity, activation status and biological poise.

Demonstrating Marker preservations across multiple tissues with acoustic dissociation

Figure 1. Enzymatic dissociation skews macrophage marker detection and phenotype compared to acoustic processing.

Flow cytometry plots show macrophages (MerTK⁺, CD64⁺) from mouse spleen prepared with enzymatic (left) or acoustic (SimpleFlow™, right) dissociation. Enzymatic treatment shifts the macrophage population with altered CD64 and MerTK staining, consistent with cleavage, masking, or induction of marker expression. MerTK, enriched in reparative M2 macrophages, can be upregulated by enzymatic dissociation through release of M-CSF and IL-10, promoting an artifactual M2-like phenotype. Similarly, CD64 (FcγRI), a high-affinity IgG receptor that mediates immune complex clearance and supports inflammation resolution, may be upregulated due to enzyme-induced macrophage activation.

Importantly, the spleen cells were pulled from healthy mice under normal physiological conditions , so minimal macrophage stimulation would be expected. 

Figure 2. Acoustic dissociation preserves CD19 marker integrity compared to enzymatic digestion.

Murine kidney B cell recovery and marker preservation were evaluated following acoustic dissociation via the SimpleFlow™ or standard enzymatic digestion.

• Left panel: Median fluorescence intensity (MFI) of CD19 was significantly higher in cells prepared by acoustic dissociation, indicating improved preservation of the CD19 epitope (***p < 0.001).
• Right panel: The proportion of CD19⁺ cells among live cells was similar between conditions (ns, not significant).

Figure 3. Enzyme-free dissociation preserves CD138 expression on B lineage cells.

 Median fluorescence intensity (MFI) of CD138, a plasma cell marker, was compared across two dissociation methods in mouse spleen.

• Acoustic dissociation (SimpleFlow™) preserved the highest CD138 signal, indicating intact epitope detection.
• Enzymatic dissociation caused a marked reduction in CD138 detection, consistent with degradation of proteoglycan-rich epitopes.

These results demonstrate that plasma cell markers like CD138 are particularly vulnerable to enzymatic degradation, which can lead to underestimation of antibody-secreting cell populations in inflamed tissues. By preserving CD138 expression, SimpleFlow™ enables more accurate phenotyping of plasma cells and their contribution to immune responses in inflammation and cancer.

Figure 4. Enzymatic dissociation reduces CD45 detection across immune cells.

Median fluorescence intensity (MFI) of CD45, a pan-leukocyte marker, was compared after acoustic and enzymatic dissociation from murine spleen tissue.

• Acoustic methods preserved strong CD45 signal intensity, ensuring robust detection of total immune populations.
• Enzymatic dissociation caused a notable reduction in CD45 signal, indicating cleavage or masking of this core epitope.

Because CD45 is critical for identifying and gating total leukocytes, enzymatic degradation can bias downstream analyses of immune composition, leading to underestimation of cell recovery in inflamed or tumor tissues. In contrast, SimpleFlow™ acoustic dissociation maintains CD45 integrity, ensuring accurate quantification of the entire immune compartment.

Conclusion

Accurate characterization of the immune landscape in inflammation research depends on preserving cellular phenotypes, interacting cells and activation states at the point of isolation. Traditional enzymatic digestion, while efficient, introduces artifacts that obscure true biology— degrading critical markers, altering phenotypes, and inducing artificial stress signatures. The Cellsonics SimpleFlow™ acoustic dissociation system overcomes these limitations by maintaining epitope integrity, supporting broad immune cell recovery, and minimizing transcriptional artifacts. By enabling researchers to resolve fragile and rare populations, discriminate subtle activation states, and capture authentic immune dynamics, SimpleFlow™ ensures that single-cell analyses reflect in-situ biology. Preserving the true immune landscape not only enhances data quality but also accelerates discovery of new therapeutic targets and strategies across autoimmune, infectious, and cancer immunology.

Citations

1. Autengruber A, Gereke M, Hansen G, Hennig C, Bruder D. Impact of enzymatic tissue disintegration on the level of surface molecule expression and immune cell function. Eur J Microbiol Immunol (Bp). 2012 Jun;2(2):112-20. doi: 10.1556/EuJMI.2.2012.2.3. Epub 2012 Jun 13. PMID: 24672679; PMCID: PMC3956959.
2. Bondonese A, Craig A, Fan L, Valenzi E, Bain W, Lafyatis R, Sembrat J, Chen K, Snyder ME. Impact of enzymatic digestion on single cell suspension yield from peripheral human lung tissue. Cytometry A. 2023 Oct;103(10):777-785. doi: 10.1002/cyto.a.24777. Epub 2023 Jul 27. PMID: 37449375; PMCID: PMC10592386.
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