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Transcriptomic analysis of sotorasib-resistant patient-derived xenograft (PDX) lung tumor cells

ABSTRACT: Transcriptomic analysis of sotorasib-resistant patient-derived xenograft (PDX) lung tumor cells

PROVIDER: PRJNA842089 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR19390358.fastq.gz	Fastqsanger.gz
	SRR19390359.fastq.gz	Fastqsanger.gz
	SRR19390360.fastq.gz	Fastqsanger.gz
	SRR19390361.fastq.gz	Fastqsanger.gz
	SRR19390362.fastq.gz	Fastqsanger.gz

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Transcriptomic analysis of sotorasib-resistant patient-derived xenograft (PDX) lung tumor cells

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Project description:There is a strong need to develop patient-derived xenograft (PDX) tumor models for studying new treatment options for gastric cancer (GC). With low engraftment success, few collections of GC PDX have been reported and molecular basis of the model establishment remain largely unknown. Here we established n=27 PDX models from n=100 GC tumors and compared their characteristics to GC patient tumors based on the recent work done by ACRG and TCGA, to evaluate the representativeness and relevance of the collection for drug testing. We show that MSI, CIN and MSS/TP53- tumors were preferentially established as PDX, while MSS/EMT and EBV not and that PDX models retained histology and molecular subtypes of parental tumors. By using synapse database, we identified 48 druggable alterations that could be investigated with the collection. Counting alterations for these 48 genes in PDX compared to TCGA tumors revealed models frequently classified with heavily altered tumors but well preserved genomic alteration patterns specific of each GC subtype. The molecular analysis of n=8/27 tumors and corresponding PDX at passage P1, P2 and P3 revealed variations in somatic alteration content both at single nucleotide and chromosomal level in highly unstable MSI and CIN tumors, with changes occurring mainly at P1. In two cases, we show likely emergence of rare subclones carrying known oncogenic alterations in KRAS and PIK3CA. Significance. This study presents a resource of fully annotated GC PDX models for anticancer agent testing. We show that beside close resemblance of PDX with parental tumors, not all subtypes are established, and that the clonal selection plays a key role the establishment of certain tumors. This may have a bearing on translation of observations into the clinic and underline the need to frequently survey the molecular characteristics of the PDX models.

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