PT  - JOURNAL ARTICLE
AU  - Nancy G. Azizian
AU  - Delaney K. Sullivan
AU  - Litong Nie
AU  - Sammy Pardo
AU  - Dana Molleur
AU  - Junjie Chen
AU  - Susan T. Weintraub
AU  - Yulin Li
TI  - Selective Labeling and Identification of the Tumor Cell Proteome of Pancreatic Cancer <em>In Vivo</em>
AID  - 10.1101/2020.05.25.113670
DP  - 2020 Jan 01
TA  - bioRxiv
PG  - 2020.05.25.113670
4099  - http://biorxiv.org/content/early/2020/08/28/2020.05.25.113670.short
4100  - http://biorxiv.org/content/early/2020/08/28/2020.05.25.113670.full
AB  - Pancreatic ductal adenocarcinoma (PDAC) is among the deadliest cancers. Dissecting the tumor cell proteome from that of the non-tumor cells in the PDAC tumor bulk is critical for tumorigenesis studies, biomarker discovery, and development of therapeutics. However, investigating the tumor cell proteome has proven evasive due to the tumor’s extremely complex cellular composition. To circumvent this technical barrier, we have combined bioorthogonal non-canonical amino acid tagging (BONCAT) and data-independent acquisition mass spectrometry (DIA-MS) in an orthotopic PDAC model to specifically identify the tumor cell proteome in vivo. Utilizing the tumor cell-specific expression of a mutant tRNA synthetase transgene, this approach provides tumor cells with the exclusive ability to incorporate an azide-bearing methionine analog into newly synthesized proteins. The azide-tagged tumor cell proteome is subsequently enriched and purified via a bioorthogonal reaction and then identified and quantified using DIA-MS. Applying this workflow to the orthotopic PDAC model, we have identified thousands of proteins expressed by the tumor cells. Furthermore, by comparing the tumor cell and tumor bulk proteomes, we showed that the approach can distinctly differentiate proteins produced by tumor-cells from non-tumor cells within the tumor microenvironment. Our study, for the first time, reveals the tumor cell proteome of PDAC under physiological conditions, providing broad applications for tumorigenesis, therapeutics, and biomarker studies in various human cancers.Competing Interest StatementThe authors have declared no competing interest.