Yin J, Duffin A, Dennert K, Donohoe DL, Ahktar P, Rovin RA, Tjoe JA. Concordant genomic vulnerabilities of patient-derived cell line and matched xenograft-derived cell line through whole exome sequencing in breast-brain metastatic cancer. Poster presented at: Aurora Scientific Day; May 20, 2020; virtual webinar hosted in Milwaukee, WI.
Poster presented at: Aurora Scientific Day; May 20, 2020; virtual webinar hosted in Milwaukee, WI.
Background: Brain metastasis (mets) is often associated with the worst prognosis among all disseminated disease, and one of the two main sources of brain mets is the breast, with reported 1-year survival rate of 20% once developed. Breast-to-brain mets (BBM) usually happens in a late stage of breast cancer, and options of treatment are very limited, which becomes a major limitation of life expectancy. Therefore, developing a cost-efficient, robust model that could precisely recapitulate the features of tumor origin would be beneficial to discovery of novel therapeutic strategies to further improve outcomes.
Purpose: Patient-derived xenografts (PDXs) often accurately recapitulate the tumor of origin in terms of genomic landscape, histopathology, and therapeutic response; however, restrictions 362 JPCRR • Volume 7, Issue 4 • Fall 2020 Supplement such as cost, high maintenance, and limited amenability for large-scale screening for potential therapies remain a challenge. To overcome these issues, we established a platform to derive cell lines from both a patient’s BBM tumor and the matched PDX to further investigate the similarity of their pathogenic genomic variants.
Methods: DNAs from the first passage of cells derived from patient tumor along with 2 different passages of cells derived from PDXs were extracted, followed by whole exome sequencing analysis. Raw FASTQ files were quality controlled using FASTQC and then aligned to hg38 using BWA-MEM without trimming. The aligned BAM files were processed using GATK4, following best practice. Mutations were called using mutect2 without normal control. Classification of variants was finally referred to ClinVar.
Results: Cells derived from PDXs (PDXL) has a significantly shorter doubling time than cells derived from patient tumor (PTL). PDXL was able to recapitulate the entire spectrum of PTL’s pathogenic variants. Exome sequencing analyses delineated several pathogenic variants of some common oncogenes and tumor suppressors, which potentially contributed to progression of this tumor. PDXL and PTL have shown consistent response to drugs that target the certain pathogenic variants.
Conclusion: Our patient tumor-PDX cell line platform represents a preclinical tool for functional gene validation and proof-of-concept studies to identify novel druggable vulnerabilities in BBM, which could be further applied to other types of brain mets.