Circulating Tumor DNA Monitoring and Pharmacogenetics Patients’ Profiling: Pharmacological Implications in Locally Advanced Rectal Cancer and Gastrointestinal Stromal Tumor

Background The standard of care for the management of locally advanced rectal cancer (LARC) relies on chemoradiotherapy (nCRT), followed by surgery. The achievement of a pathological complete response (pCR) after nCRT is observed in up to 30% of patients and is positively associated with a lower risk of local and distant recurrence. The need to discriminate good from poor responder in the early steps of nCRT is urgently required to optimize the therapeutic strategies and improve prognosis. In gastrointestinal stromal tumor (GIST), the development of resistance to first line imatinib treatment represents the leading cause of disease progression and is determined by pharmacodynamics and pharmacokinetics alterations. The chance of interrogating circulating tumor DNA (ctDNA) represents an appealing tool for the real-time monitoring of treatment response in a low-invasive manner and to sustain the decision making for treatment’s personalization in gastrointestinal malignancies. Aims The aims can be summarized as follow: i) Assess whether the presence of copy number aberrations (CNAs) in the cell-free DNA (cfDNA) of LARC patients receiving nCRT might represent an early biomarker of treatment efficacy. ii) Test whether the detection of ctDNA in GIST might help in the identification of disease progression. iii) Assess whether the presence of specific pharmacogenetic variants, as well as the administration of imatinib interacting drug, might explain the pharmacokinetics variability of imatinib. Materials and Methods 84 blood samples were collected from 40 consent LARC patients with available clinical data at the Clinical Pharmacology Unit of IRCCS CRO Aviano. cfDNA was extracted and the presence of CNAs was assessed by means of shallow whole genome sequencing (sWGS) in a tumor-informed manner. The response to nCRT was assessed using the Mandard’s tumor regression grade (TRG) scale. 188 blood samples were collected from 39 consent GIST patients. cfDNA was extracted and the presence of ctDNA was assessed by means of targeted deep sequencing in a panel of GIST relevant genes. Imatinib trough levels were quantified by means of LC-MM/MS validated method and the presence of genetic variants in cytochromes and transporters was assessed on genomic DNA by means of target allele discrimination assays and NGS. Intake of co-administrated drugs was retrieved from clinical records and patients’ interview. Response to imatinib was assessed according to RECIST criteria. Results For all LARC patients the plasma sample collected at the time of diagnosis (T1, n = 40) was available. Further longitudinal plasma samples were collected in the course of nCRT (T2, n = 24) and after nCRT (T3, n = 15). The presence of CNAs was detected in the cfDNA of 6/40 patients (15.0%) at the T1, with a median tumor fraction (TFx) of 10.41% (range 5.89–27.34). When comparing the variation of TFx between T2 and T1, 7/24 evaluable patients (29.2%) showed an increase of the TFx, which was associated with an increased rate of pCR (RR: 3.75; 95% CI 1.47 – 9.56). For GIST patients, ctDNA was detected in 2/9 (22.2%) patients with progressive disease and was informative on the mechanisms of imatinib resistance. Pharmacogenetic profiling was performed on 33 GIST patients and the genotype of CYP2D6 was shown to influence the imatinib plasma exposure, while the concomitant intake of strong CYP3A4 inducers (carbamazepine) and CYP1A2 inhibitors (smoking) were associated with a faster imatinib clearance and risk of under-dosage. Conclusions The identification of CNAs and their quantification by means of TFx estimation is feasible in the cfDNA of LARC patients and preliminary data suggests that an increased TFx in course of nCRT is associated with a higher probability of achieving a pCR. The identification of ctDNA in GIST shows a low sensitivity (22.2%) and a high specificity (100%) in identifying patients with progressive disease and might represent a valuable tool