Protocol for constructing in vivo and in vitro models integrating clinical and proteomic subtypes of chordoma

Abstract

Here, we present a protocol for constructing both in vivo and in vitro models of chordoma, integrating clinical and proteomic subtyping to enable a comprehensive analysis. We detail the steps for tissue sample preparation and tandem mass tag proteomic analysis and apply non-negative matrix factorization for molecular classification. Furthermore, we classify chordoma cell lines and establish cell-derived xenograft (CDX) and patient-derived xenograft (PDX) models in mice for investigating drug response. For complete details on the use and execution of this protocol, please refer to Yin et al.¹.

Keywords: Cancer; Cell culture; Cell isolation; Model Organisms; Molecular Biology; Proteomics.

Graphical abstract

Figure 1

The flow chart of the protocol

Figure 2

Demonstration graph of before you begin Figure reprinted with permission from Yin, Huabin et al.

Figure 3

Demonstration graph of TMT proteomic analysis

Figure 4

Demonstration graph of molecular classification based on proteomics Figure reprinted with permission from Yin, Huabin et al.

Figure 5

ESTIMATE analysis of proteomic subtypes ESTIMATE tumor purity (A), stromal score (B), and immune score (C) among the identified three clusters. Figure reprinted with permission from Yin, Huabin et al.

Figure 6

DEPs identification and function enrichment analysis (A) NMF clustering based on the function enrichment analysis of DEPs and clinical features among the identified three clusters. (B) GSEA enrichment analysis of DEPs between Ki-67 > 5% and ≤5% revealed statistic difference. (C) GSVA analysis of DEPs between Ki-67 > 5% and ≤5% based on BP of GO dataset. Abbreviations: DEPs, Differentially Expressed Proteins. Figure reprinted with permission from Yin, Huabin et al.

Figure 7

Demonstration graph of constructing of In vivo and In vitro models