Advancing wide implementation of precision oncology: A liquid nitrogen‐free snap freezer preserves molecular profiles of biological samples

• Published in: Cancer medicine (Malden, MA) MA), 2023-05, Vol.12 (9), p.10979-10989
• Main Authors: Wijngaart, Hanneke, Jagga, Sahil, Dekker, Henk, Goeij, Richard, Piersma, Sander R., Pham, Thang V., Knol, Jaco C., Zonderhuis, Babs M., Holland, Harry J., Jiménez, Connie R., Verheul, Henk M. W., Vanapalli, Srinivas, Labots, Mariette
• Format: Article
• Language: English
• Subjects: Aluminum; biopsies; Biopsy; Cancer; Cancer research; cooling; Cryopreservation - methods; Freezing; Humans; Liver; Mass spectroscopy; Medical research; multi‐omics; Neoplasms - genetics; Nitrogen; Oncology; Patients; Peptides; Precision Medicine; precision oncology; Proteins; Ribonucleic acid; RNA; snap freezing; Temperature; Transcriptomics; Tumor cell lines; Tumors
• ISSN: 2045-7634; 2045-7634
• DOI: 10.1002/cam4.5781

Purpose In precision oncology, tumor molecular profiles guide selection of therapy. Standardized snap freezing of tissue biospecimens is necessary to ensure reproducible, high‐quality samples that preserve tumor biology for adequate molecular profiling. Quenching in liquid nitrogen (LN2) is the golden standard method, but LN2 has several limitations. We developed a LN2‐independent snap freezer with adjustable cold sink temperature. To benchmark this device against the golden standard, we compared molecular profiles of biospecimens. Methods Cancer cell lines and core needle normal tissue biopsies from five patients' liver resection specimens were used to compare mass spectrometry (MS)‐based global phosphoproteomic and RNA sequencing profiles and RNA integrity obtained by both freezing methods. Results Unsupervised cluster analysis of phosphoproteomic and transcriptomic profiles of snap freezer versus LN2‐frozen K562 samples and liver biopsies showed no separation based on freezing method (with Pearson's r 0.96 (range 0.92–0.98) and >0.99 for K562 profiles, respectively), while samples with +2 h bench‐time formed a separate cluster. RNA integrity was also similar for both snap freezing methods. Molecular profiles of liver biopsies were clearly identified per individual patient regardless of the applied freezing method. Two to 25 s freezing time variations did not induce profiling differences in HCT116 samples. Conclusion The novel snap freezer preserves high‐quality biospecimen and allows identification of individual patients' molecular profiles, while overcoming important limitations of the use of LN2. This snap freezer may provide a useful tool in clinical cancer research and practice, enabling a wider implementation of (multi‐)omics analyses for precision oncology. We studied a novel snap freezer and showed similar protein‐ and RNA‐based molecular profiles of biological samples including individual patient tissues as obtained with the golden standard of LN2 quenching. Importantly, this snap freezer overcomes several practical limitations of LN2 and may provide a useful tool enabling wider implementation of (multi‐)omics analyses for precision oncology.