Feasibility and dynamics of preoperative circulating tumor DNA in patients with gastroesophageal cancer receiving preoperative treatment

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Background: Tumor-informed circulating tumor DNA (ctDNA) testing has shown high sensitivity and specificity for detecting molecular residual disease across solid tumors. However, the requirement of high-quality tissue specimens for upfront sequencing and designing of personalized ctDNA assays can be challenging using preoperative biopsy samples. There is a paucity of data on the feasibility of testing in preop tissue specimens in patients (pts) with gastroesophageal cancer (GEC) as well as its preop dynamics. Methods: We prospectively enrolled pts with locally advanced esophageal, gastroesophageal junctional (GEJ), or gastric cancer who were to receive preop treatment and surgery between 11/2021 and 07/2022. Tumor tissue was analyzed with next-generation sequencing to design a personalized, tumor-informed multiplex PCR assay (Signatera bespoke mPCR NGS assay) for each patient. Peripheral blood was collected for ctDNA analysis at baseline (before preoperative treatment), every 4 weeks until surgery, after surgery (before adjuvant therapy), and then every 4 weeks for patients who received adjuvant chemotherapy or every 3 months for patients who received adjuvant immunotherapy or no active treatment. Results: A total of 17 pts were enrolled, of which 7 had esophageal, 5 had GEJ, and 5 had gastric cancer. Tumor tissues from 14 (82.4%) pts passed quality control (QC), of which 11 were preoperative biopsy samples and 3 were surgically resected tissue. All 14 pts had detectable baseline ctDNA prior to preoperative treatment, with a median at 1.05 mean tumor molecules per mL of plasma (MTM/mL). Of these, 92.8% (13/14) of pts achieved ctDNA clearance by a median of 5 weeks from the start of preoperative treatment. Four pts opted for endoscopy surveillance, of whom 1 pt had transient ctDNA clearance at week 10, but had positive ctDNA at week 14, which persisted as of week 26. Conclusions: In our cohort, locally advanced GEC were ctDNA shedders. Preoperative tumor-informed ctDNA testing was feasible. Further studies to evaluate correlation between ctDNA dynamics and response to treatment are warranted. [Table: see text]

Evaluation of alkyne-modified isoprenoids as chemical reporters of protein prenylation

Protein prenyltransferases catalyze the attachment of C15 (farnesyl) and C20 (geranylgeranyl) groups to proteins at specific sequences localized at or near the C-termini of specific proteins. Determination of the specific protein prenyltransferase substrates affected by the inhibition of these enzymes is critical for enhancing knowledge of the mechanism of such potential drugs. Here, we investigate the utility of alkyne-containing isoprenoid analogs for chemical proteomics experiments by showing that these compounds readily penetrate mammalian cells in culture and become incorporated into proteins that are normally prenylated. Derivatization via Cu(I) catalyzed click reaction with a fluorescent azide reagent allows the proteins to be visualized and their relative levels to be analyzed. Simultaneous treatment of cells with these probes and inhibitors of prenylation reveals decreases in the levels of some but not all of the labeled proteins. Two-dimensional electrophoretic separation of these labeled proteins followed by mass spectrometric analysis allowed several labeled proteins to be unambiguously identified. Docking experiments and density functional theory calculations suggest that the substrate specificity of protein farnesyl transferase may vary depending on whether azide- or alkyne-based isoprenoid analogs is employed. These results demonstrate the utility of alkyne-containing analogs for chemical proteomic applications.