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Pre-clinical validation of an RNA-based precision oncology platform for patient-therapy alignment in a diverse set of human malignancies resistant to standard treatments

ABSTRACT: We use a Master Regular-based precision cancer medicine framework to perform joint analysis of transcriptomic profiles from patients with distinct treatment refractory cancer and drug perturbation transcriptional profiles in cognate cell lines, to predict drug sensitivity. Validation of predictions was performed in patient-derived xenograft (PDX) mice. Pharmacodynamic samples were obtained from PDX mice after the third dose for RNASeq and downstream analysis.

ORGANISM(S): Homo sapiens

PROVIDER: GSE197763 | GEO | 2022/03/09

REPOSITORIES: GEO

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Project description:INTRODUCTION:Advanced gynecologic cancers have a poor prognosis and constitute a major challenge for adequate treatment strategies. By analyzing and targeting molecular alterations, molecular guided treatments may be a viable option for the treatment of advanced gynecologic cancers. PATIENTS AND METHODS:In this single-center, real-world retrospective analysis of our platform for precision cancer medicine (PCM), we describe the molecular profiling of 72 patients diagnosed with different types of advanced gynecologic malignancies. Tumor samples of the patients were examined by next-generation sequencing panel and immunohistochemistry (IHC). RESULTS:In total, we identified 209 genetic aberrations in 72 patients. The ten most frequent alterations were TP53 (n =?42, 20%), KRAS (n =?14, 6.6%), PIK3CA (n =?11, 5.2%), PIK3R1 (n =?9, 4.3%), ATR (n =?8, 3.8%), PTEN (n =?8, 3.8%), BRCA1 (n =?6, 2.8%), NF1 (n =?4, 1.9%), NOTCH1 (n =?4, 1.9%), and POLE (n =?4, 1.9%), which account for more than half of all molecular alterations (52.6%). In 21 (29.1%) patients only one mutation could be detected, and 44 (61.1%) patients had more than one mutation. No molecular alterations were detected in seven (9.7%) patients. IHC detected expression of phosphorylated mammalian target of rapamycin and epidermal growth factor receptor in 58 (80.6%) and 53 (73.6%) patients, respectively. In over two thirds (n =?49, 68.1%), a targeted therapy was suggested, based on the identified genetic aberrations. The most frequently recommended specific treatment was the combination of everolimus with exemestane (n =?18, 25 %). CONCLUSION:Based on our observations, it seems that PCM might be a feasible approach for advanced gynecologic cancers with limited treatment options. IMPLICATIONS FOR PRACTICE:Nowadays molecular profiling of advanced gynecologic malignancies is feasible in the clinical routine. A molecular portrait should be done for every patient with an advanced therapy-refractory gynecologic malignancy to offer molecular-based treatment concepts.

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Pre-clinical validation of an RNA-based precision oncology platform for patient-therapy alignment in a diverse set of human malignancies resistant to standard treatments

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