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This protocol for PBMC collection and cryopreservation has been successfully implemented by individuals with and without prior research laboratory training. In our application, FACS and RNA-sequencing of highly viable monocytes purified from stored PBMCs resulted in high-quality sequences.
A major strength of this protocol is its accessibility. The technique presented in the protocol utilizes tubes pre-packed with a solid-density gradient medium. As a result, whole blood can be collected directly into the tube and then immediately processed to isolate PBMCs. A relatively small number of premade solutions and specialized equipment is needed, facilitating collaboration between the research laboratory, where reagents may be prepared, and the clinical laboratory, where samples are collected and processed. The written and video protocols are geared towards operators at any level of training.
While this protocol utilizes fresh whole blood to isolate PBMCs and, therefore, has a relatively high expected yield and purity of >90%, it may not be suitable for applications necessitating exceptionally high purities of >98%26,27. Moreover, density gradient centrifugation tubes can be costly to obtain, especially if a large number of samples need to be collected.
Alternative methods of PBMC collection include the use of a liquid density gradient medium or immunomagnetic depletion28,29. Briefly, the former involves layering a pre-made density gradient medium under heparinized whole blood followed by centrifugation. The latter utilizes magnetically tagged antibodies to label non-PBMCs, which are then retained in a magnetic column while unlabeled PBMCs pass through unaffected.
Relative to the presented protocol, the use of a liquid density gradient medium is both less costly and necessitates much less material due to the lack of density gradient centrifugation tubes; PBMC isolation can be performed in a standard 50 mL tube8. However, this technique is more elaborate, has a longer processing time, and may be subject to a higher risk of user error. Heparin must be precisely added to avoid over-dilution and the density gradient medium must be layered carefully in the correct amounts to ensure good PBMC separation26.
Relative to the presented protocol, the use of immunomagnetic depletion offers higher yield and purity, reduced handling due to lack of centrifugation, a faster processing time, and necessitates much less material30,31,32. However, the main downside is that this method is the costliest of the three methods described, especially at scale.
While this protocol is robust, certain critical steps may require additional attention. Throughout the protocol, ensure that samples are not mixed and are placed into the appropriately labelled tubes, especially when working with multiple patients or conditions simultaneously. For step 1.4, ensure that no PBMCs are discarded; excess plasma will only decrease the concentration of PBMCs, which is less critical in maintaining sample viability and quality. Separately, the presence of precipitates in collected PBMCs suggests that pieces of the density gradient medium were dislodged. Pipette more gently in step 1.5 to prevent this issue. In steps 1.10 and 3.6, ensure that the centrifuged cell pellet is not discarded. Working expeditiously is critical for step 1.12 and 3.3 as Solution 3 contains DMSO, which is toxic to cells at room temperature33. It is also important to note that storage of PBMCs in liquid nitrogen is recommended over storage at -80°C. Long-term storage at -80°C has been associated with decreased cell viability and altered gene expression34,35.
This protocol may be adapted according to experimental needs. The addition of flavopiridol, an inhibitor of RNA polymerase and mRNA synthesis, in Solutions 2 and 3 is intended to prevent any handling and stress induced artifact with RNA-sequencing36. However, flavopiridol may be omitted if functional or ex vivo studies utilizing PBMCs are desired.
Plasma collected from EDTA tubes will become contaminated with EDTA, a chelating agent. As a result, EDTA plasma is unsuitable for assays involving coagulation or calcium ions37,38. If desired, the plasma layer in the density gradient medium tubes post-centrifugation can instead be collected in step 1.4. These tubes contain sodium heparin as an anticoagulant which can be removed with the addition of heparinase39. Notably, heparin inhibits reverse transcriptase and PCR amplification, making the collected plasma unsuitable for PCR experiments without the addition of a heparin-blocking agent40.
The collected buffy coat from EDTA tubes is not stored in a solution containing DMSO or flavopiridol. DMSO is important in reducing ice crystal formation and cell death41. Flavopiridol is important for the inhibition of RNA synthesis36. Thus, the buffy coat is unsuitable for ex vivo and transcriptomic analyses. If desired, steps 1.6 to 1.15 can be performed using collected buffy coat in order to maximize cell viability and inhibit RNA synthesis.
While this protocol was designed for RNA-sequencing, additional potential applications of PBMCs collected and cryopreserved using this protocol include cell culture, gene editing, ex-vivo functional studies, single cell analyses, phenotyping by flow cytometry or cytometry by time of flight, isolation of DNA/RNA or proteins, slides for immunohistochemistry, amongst others.