Genomic evolution of non-small cell lung cancer patient-derived xenograft models

Abstract

Patient-derived xenograft (PDX) models of cancer, developed through injection of patient tumour cells into immunocompromised mice, have been widely adopted in preclinical studies, as well as in precision oncology approaches. However, the extent to which PDX models represent the underlying genetic diversity of a patient's tumour and the extent of on-going genomic evolution in PDX models are incompletely understood, particularly in the context of heterogeneous cancers such as non-small cell lung cancer (NSCLC). To investigate the depiction of intratumour heterogeneity by PDX models, we derived 47 new subcutaneous multi-region PDX models from 22 patients with primary NSCLC enrolled in the clinical longitudinal cohort study TRACERx. By analysing whole exome sequencing data from primary tumours and PDX models, we find that PDX establishment creates a genomic bottleneck, with 76% of PDX models being derived from a single primary tumour subclone. Despite this, multiple primary tumour subclones were capable of PDX establishment in regional PDX models, indicating that PDX libraries derived from multiple tumour regions can capture intratumour heterogeneity. Acquisition of somatic mutations continued during PDX model expansion, and was associated with APOBEC- or mismatch repair deficiency-induced mutational signatures in a subset of models. Overall, while NSCLC PDX models retain truncal genomic alterations, the absence of subclonal heterogeneity representative of the primary tumour is a major limitation. Our results emphasise the importance of characterising and monitoring intratumour heterogeneity in the context of pre-clinical cancer studies.

Phenotyping of lymphoproliferative tumours generated in xenografts of non-small cell lung cancer

“…One approach to preventing the formation of lymphoproliferations might therefore be to quantify EBV RNA in starting material to filter out regions most likely to contain these B cells. Our finding that cryopreservation has little impact on NSCLC PDX take rate while not selectively favouring either tumour or B cell proliferations, would allow a time window in which to implement this approach 19 . However, a previous study in NSCLC has suggested that the extent of EBER positivity in tissue did not predict lymphoproliferation formation 15 .…”

“…CD45+ lymphoproliferations in a NSCLC PDX model pipeline PDX generation in NSG mice was performed through subcutaneous injection of multi-region, spatially independent biopsies of NSCLC tumours 19 . Tissue samples were obtained via the lung TRACERx study from patients undergoing surgical resections, with no patients having received neoadjuvant therapy 20 .…”

“…Tissue samples were obtained via the lung TRACERx study from patients undergoing surgical resections, with no patients having received neoadjuvant therapy 20 . Immunohistochemistry (IHC) revealed that 15 xenografts did not express keratin but did express human CD45 19 . Tissue from a further xenograft (CRUK0733 Region 1; R1) was not available but it was determined to be a lymphoproliferation due to its lack of shared mutations with the patient's NSCLC in a targeted sequencing assay, meaning that overall 16/145 (11.0%) of transplanted tumour regions gave rise to lymphoproliferations (Figure 1A; 19 ).…”

“…Immunohistochemistry (IHC) revealed that 15 xenografts did not express keratin but did express human CD45 19 . Tissue from a further xenograft (CRUK0733 Region 1; R1) was not available but it was determined to be a lymphoproliferation due to its lack of shared mutations with the patient's NSCLC in a targeted sequencing assay, meaning that overall 16/145 (11.0%) of transplanted tumour regions gave rise to lymphoproliferations (Figure 1A; 19 ). Following multi-region xenograft establishment, three tumours gave rise to more than one lymphoproliferation from different spatial regions, two of these tumours also gave rise to a NSCLC PDX model from a further spatial tumour region.…”

“…We have recently reported the outcomes from a PDX generation pipeline initiated from multi-regional primary non-small cell lung cancer (NSCLC) tumour tissue within the lung TRACERx prospective cohort study 18 . We found that 16/145 NSCLC transplantations (from 13 of 44 patients) resulted in CD45+ xenograft formation 19 . Here, we report phenotyping of these CD45+ lymphoproliferations using histology, immunohistochemistry, PCR and flow cytometry approaches.…”