Researchers from the Centro Nacional de Análisis Genómico (CNAG-CRG) have substantially broadened the applicability of single cell genomics by combining cell and tissue cryopreservation with workflows of this emerging research field.

The study, published in Genome Biology, has found that single cells from cryopreserved samples show indistinguishable gene expression profiles compared to freshly processed samples. This work has major implications in single cell study designs since current techniques rely on the availability of fresh starting material, excluding experiments without direct access to specialized equipment. “Cryopreservation could be a game-changer on how future single cell projects are designed” says Dr. Holger Heyn, senior author of the study and leader of the CNAG-CRG Single Cell Genomics team, who has had the collaboration of researchers from other Spanish and international centers.

Single Cell Genomics – or the capability to sequence and analyze individual cells- is currently revolutionizing our knowledge about complex tissues. Identifying molecular profiles of individual cells provides unprecedented insights into the way organisms, like the human body, are built and function. “The in depth characterization of complex tissues does not only impact on our understanding of life itself, but also sharpens our view on the biology of diseases, such as Alzheimer’s or cancer” adds Dr. Heyn.

The study analyzed more than 1,000 single cells either freshly prepared or cryopreserved up to 6 months. The researchers tested the most popular single cell sequencing strategies and could not detect a systematic bias introduced by the freezing procedure. Analyzing cell lines from different species and primary samples, including blood, colon and tumor samples, they illustrated the broad application spectrum of the method. According to the study, cryopreserved material can be readily combined with conventional single cell sequencing methods and the authors foresee its implementation as standard technique in this type of analysis. Dr. Ivo Gut, director of the CNAG-CRG says “this is an important technological development in the field of single cell analysis, particularly in the context of international initiatives, such as the Human Cell Atlas, that aims to create comprehensive reference maps of all human cells as a basis for both understanding human health and diagnosing, monitoring, and treating disease.”

The researchers showed that entire tissues can be cryopreserved, avoiding the immediate separation of single cells that hindered sample collection at less-well equipped locations and outside of facility’s working hours. In this regard, single cell analyses were challenging to apply in clinical settings and stored patient material could not be processed. The use of cryopreservation could drastically influence sample accessibility. “We can now store patient material along the course of treatment without the need of immediate sample processing. Indeed, we collaborate with hospitals that started to prospectively archive samples with cryoprotectants - providing us access to samples that were previously out of scope.” explains Dr. Heyn.

While the researchers previously disconnected sampling from the center’s specialized procedures by transferring isolated cells in plates, cryopreservation introduces another level of flexibility. It also allows, for example, the joint processing of time course experiments, which, to date, were greatly affected by technical artefacts. “The so-called batch effects that occur when samples are processed at different time points greatly confound analysis and often lead to false-positive results. Cryopreservation enables the joint processing of samples in the same batch, avoiding such problems and greatly supporting subsequent comparative analyses” explains Dr. Heyn and adds “the published method tackles technical challenges as well as a major bottleneck in sample accessibility. We hence expect a paradigm shift in single cell research that broadens its scope while increasing the robustness of the results.”  

Work of reference:

Single-cell transcriptome conservation in cryopreserved cells and tissues

Post by Holger Heyn in BioMed Central’s blog