Case study: patient-derived clear cell adenocarcinoma xenograft model longitudinally predicts treatment response

Abstract

There has been little progress in the use of patient-derived xenografts (PDX) to guide individual therapeutic strategies. In part, this can be attributed to the operational challenges of effecting successful engraftment and testing multiple candidate drugs in a clinically workable timeframe. It also remains unclear whether the ancestral tumor will evolve along similar evolutionary trajectories in its human and rodent hosts in response to similar selective pressures (i.e., drugs). Herein, we combine a metastatic clear cell adenocarcinoma PDX with a timely 3 mouse x 1 drug experimental design, followed by a co-clinical trial to longitudinally guide a patient's care. Using this approach, we accurately predict response to first- and second-line therapies in so far as tumor response in mice correlated with the patient's clinical response to first-line therapy (gemcitabine/nivolumab), development of resistance and response to second-line therapy (paclitaxel/neratinib) before these events were observed in the patient. Treatment resistance to first-line therapy in the PDX is coincident with biologically relevant changes in gene and gene set expression, including upregulation of phase I/II drug metabolism (CYP2C18, UGT2A, and ATP2A1) and DNA interstrand cross-link repair (i.e., XPA, FANCE, FANCG, and FANCL) genes. A total of 5.3% of our engrafted PDX collection is established within 2 weeks of implantation, suggesting our experimental designs can be broadened to other cancers. These findings could have significant implications for PDX-based avatars of aggressive human cancers.

Fig. 1

Clinical course and molecular profiling of the primary tumor. a Computed tomography scan obtained at the time of diagnosis. The 8.2 × 8.8 cm lobulated metastatic mass in the liver (arrow) and the 8.0 cm centrally necrotic primary tumor mass in the left mesentery (asterisk) are shown. b Representative image of an H&E stained section of the primary tumor. c Copy number count estimates from both exonic (blue) and intragenic or intronic (cyan) reads in Chromosome 17 are shown. d Representative FISH image of the primary tumor using ERBB2/CEP17 dual-color probes. The average ERBB2 signal copy number was 5.1 and the ERBB2/CEP17 ratio was 2.0. e Representative ErbB2 IHC image of the primary tumor. f Sagittal and coronal images of the PET/CT scans before and after treatment with three cycles of paclitaxel and neratinib (second-line treatment). The SUV maximum value for each lesion before and after treatment was, respectively: right lateral abdominal wall musculature, 11.7 and 6.6; posterior 11th rib, 11.2 and 4.1; and the soft tissue abutting the hepatic surgical site, 14.8 and 7.9.

Fig. 2

Time to engraftment and comparison of genome-wide gene expression profiles. a Representative image of an H&E stained section of the PDX. The histologic section is composed of pleomorphic and hyperchromatic tumor cells with cleared to pink cytoplasms, similar to the tumor of origin. The papillary architecture and hyalinized stroma is present but not as prominent as in Fig. 1b due to the cellular density of the PDX. b Probability density function of time to engraftment for 36 small cell lung carcinoma PDXs (SCLC), 27 head and neck squamous cell carcinomas (HNSCC) and 27 lung adenocarcinoma PDXs (LUAD). Red arrow represents the time to engraftment of the index case. Samples obtained from pleural effusion were excluded from this analysis. c Scatter plot, linear regression (dashed red line) and probability density histograms of genome-wide gene transcript levels (16,599 transcripts) in the donor tumor and the PDX. Pearson’s r correlation coefficient is shown. d ERBB2 mRNA levels in the donor tumor and PDX. Data are expressed as the means ± s.e.

Fig. 3

Drug efficacy studies in PDX and treatment resistance. a Schematic of the 3x1 design and treatment arms. b NSG female mice bearing PDX were block randomized into one of four treatment arms as shown. Data are expressed as the means ± s.e. P-values of the χ²-test between vehicle and the treatment groups, cisplatinum, neratinib, and gemcitabine, were 0.03, 0.001, and <0.001, respectively. P-values between the treatment groups cisplatinum/neratinib, cisplatinum/gemcitabine, and neratinib/gemcitabine treatment groups were 0.06, 0.003, and <0.001, respectively. c NSG mice bearing PDX were treated with gemcitabine and nivolumab until treatment resistance was established. d Tumor from the secondarily resistant mouse in c were allowed to grow to ~400-500 mm³ and re-challenged with gemcitabine and nivolumab. e Differential gene expression of equally passaged (P₄) untreated and treatment-resistant PDX. The gray dots represent differentially expressed gene based on P < 0.01 and FDR = 2.5%. f GSEA analysis of treatment-resistant PDX. Gene expression heatmap of genes within the GO Interstand Cross Link Repair pathway for each biological replicate is shown. g PDX from post-gemcitabine/nivolumab treated mice were block randomized into two treatment arms as shown. Neratinib was discontinued at ~100 days from the time of randomization in the paclitaxel plus neratinib arm. Data are expressed as the means ± s.e. The p-value of the χ²-test was 0.003.

Fig. 4

Accelerated and concordant outcomes in mice. A timeline of events in the mouse and patient