CryoSCAPE: Scalable immune profiling using cryopreserved whole blood for multi-omic single cell and functional assays
Abstract Background The field of single cell technologies has rapidly advanced our comprehension of the human immune system, offering unprecedented insights into cellular heterogeneity and immune function. While cryopreserved peripheral blood mononuclear cell (PBMC) samples enable deep characterizat...
Saved in:
| Main Authors: | , , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
BMC
2025-01-01
|
| Series: | Journal of Translational Medicine |
| Online Access: | https://doi.org/10.1186/s12967-024-06010-z |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1841559165114253312 |
|---|---|
| author | Alexander T. Heubeck Cole Phalen Neel Kaul Peter J. Wittig Jessica Garber Morgan Weiss Palak C. Genge Zachary Thomson Claire Gustafson Julian Reading Peter J. Skene |
| author_facet | Alexander T. Heubeck Cole Phalen Neel Kaul Peter J. Wittig Jessica Garber Morgan Weiss Palak C. Genge Zachary Thomson Claire Gustafson Julian Reading Peter J. Skene |
| author_sort | Alexander T. Heubeck |
| collection | DOAJ |
| description | Abstract Background The field of single cell technologies has rapidly advanced our comprehension of the human immune system, offering unprecedented insights into cellular heterogeneity and immune function. While cryopreserved peripheral blood mononuclear cell (PBMC) samples enable deep characterization of immune cells, challenges in clinical isolation and preservation limit their application in underserved communities with limited access to research facilities. We present CryoSCAPE (Cryopreservation for Scalable Cellular And Proteomic Exploration), a scalable method for immune studies of human PBMC with multi-omic single cell assays using direct cryopreservation of whole blood. Results Comparative analyses of matched human PBMC from cryopreserved whole blood and density gradient isolation demonstrate the efficacy of this methodology in capturing cell proportions and molecular features. The method was then optimized and verified for high sample throughput using fixed single cell RNA sequencing and liquid handling automation with a single batch of 60 cryopreserved whole blood samples. Additionally, cryopreserved whole blood was demonstrated to be compatible with functional assays, enabling this sample preservation method for clinical research. Conclusions The CryoSCAPE method, optimized for scalability and cost-effectiveness, allows for high-throughput single cell RNA sequencing and functional assays while minimizing sample handling challenges. Utilization of this method in the clinic has the potential to democratize access to single-cell assays and enhance our understanding of immune function across diverse populations. |
| format | Article |
| id | doaj-art-b0460ba1b1bf4b0e945764d5fc32a7cc |
| institution | Kabale University |
| issn | 1479-5876 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | BMC |
| record_format | Article |
| series | Journal of Translational Medicine |
| spelling | doaj-art-b0460ba1b1bf4b0e945764d5fc32a7cc2025-01-05T12:44:32ZengBMCJournal of Translational Medicine1479-58762025-01-0123111710.1186/s12967-024-06010-zCryoSCAPE: Scalable immune profiling using cryopreserved whole blood for multi-omic single cell and functional assaysAlexander T. Heubeck0Cole Phalen1Neel Kaul2Peter J. Wittig3Jessica Garber4Morgan Weiss5Palak C. Genge6Zachary Thomson7Claire Gustafson8Julian Reading9Peter J. Skene10Allen Institute for ImmunologyAllen Institute for ImmunologyAllen Institute for ImmunologyAllen Institute for ImmunologyAllen Institute for ImmunologyWestern University of Health Sciences, College of Osteopathic Medicine of the Pacific NorthwestAllen Institute for ImmunologyAllen Institute for ImmunologyAllen Institute for ImmunologyAllen Institute for ImmunologyAllen Institute for ImmunologyAbstract Background The field of single cell technologies has rapidly advanced our comprehension of the human immune system, offering unprecedented insights into cellular heterogeneity and immune function. While cryopreserved peripheral blood mononuclear cell (PBMC) samples enable deep characterization of immune cells, challenges in clinical isolation and preservation limit their application in underserved communities with limited access to research facilities. We present CryoSCAPE (Cryopreservation for Scalable Cellular And Proteomic Exploration), a scalable method for immune studies of human PBMC with multi-omic single cell assays using direct cryopreservation of whole blood. Results Comparative analyses of matched human PBMC from cryopreserved whole blood and density gradient isolation demonstrate the efficacy of this methodology in capturing cell proportions and molecular features. The method was then optimized and verified for high sample throughput using fixed single cell RNA sequencing and liquid handling automation with a single batch of 60 cryopreserved whole blood samples. Additionally, cryopreserved whole blood was demonstrated to be compatible with functional assays, enabling this sample preservation method for clinical research. Conclusions The CryoSCAPE method, optimized for scalability and cost-effectiveness, allows for high-throughput single cell RNA sequencing and functional assays while minimizing sample handling challenges. Utilization of this method in the clinic has the potential to democratize access to single-cell assays and enhance our understanding of immune function across diverse populations.https://doi.org/10.1186/s12967-024-06010-z |
| spellingShingle | Alexander T. Heubeck Cole Phalen Neel Kaul Peter J. Wittig Jessica Garber Morgan Weiss Palak C. Genge Zachary Thomson Claire Gustafson Julian Reading Peter J. Skene CryoSCAPE: Scalable immune profiling using cryopreserved whole blood for multi-omic single cell and functional assays Journal of Translational Medicine |
| title | CryoSCAPE: Scalable immune profiling using cryopreserved whole blood for multi-omic single cell and functional assays |
| title_full | CryoSCAPE: Scalable immune profiling using cryopreserved whole blood for multi-omic single cell and functional assays |
| title_fullStr | CryoSCAPE: Scalable immune profiling using cryopreserved whole blood for multi-omic single cell and functional assays |
| title_full_unstemmed | CryoSCAPE: Scalable immune profiling using cryopreserved whole blood for multi-omic single cell and functional assays |
| title_short | CryoSCAPE: Scalable immune profiling using cryopreserved whole blood for multi-omic single cell and functional assays |
| title_sort | cryoscape scalable immune profiling using cryopreserved whole blood for multi omic single cell and functional assays |
| url | https://doi.org/10.1186/s12967-024-06010-z |
| work_keys_str_mv | AT alexandertheubeck cryoscapescalableimmuneprofilingusingcryopreservedwholebloodformultiomicsinglecellandfunctionalassays AT colephalen cryoscapescalableimmuneprofilingusingcryopreservedwholebloodformultiomicsinglecellandfunctionalassays AT neelkaul cryoscapescalableimmuneprofilingusingcryopreservedwholebloodformultiomicsinglecellandfunctionalassays AT peterjwittig cryoscapescalableimmuneprofilingusingcryopreservedwholebloodformultiomicsinglecellandfunctionalassays AT jessicagarber cryoscapescalableimmuneprofilingusingcryopreservedwholebloodformultiomicsinglecellandfunctionalassays AT morganweiss cryoscapescalableimmuneprofilingusingcryopreservedwholebloodformultiomicsinglecellandfunctionalassays AT palakcgenge cryoscapescalableimmuneprofilingusingcryopreservedwholebloodformultiomicsinglecellandfunctionalassays AT zacharythomson cryoscapescalableimmuneprofilingusingcryopreservedwholebloodformultiomicsinglecellandfunctionalassays AT clairegustafson cryoscapescalableimmuneprofilingusingcryopreservedwholebloodformultiomicsinglecellandfunctionalassays AT julianreading cryoscapescalableimmuneprofilingusingcryopreservedwholebloodformultiomicsinglecellandfunctionalassays AT peterjskene cryoscapescalableimmuneprofilingusingcryopreservedwholebloodformultiomicsinglecellandfunctionalassays |