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[Preprint]. 2024 Dec 18:rs.3.rs-5349536.
doi: 10.21203/rs.3.rs-5349536/v1.

Ultra-sensitive, tumor-informed ctDNA profiling in pembrolizumab-treated esophagogastric cancer patients predicts clinical responses

Andrew B Nixon  1 , Fábio C P Navarro  2 , Katherine I Zhou  1 , Charles Abbott  2 , Lee McDaniel  2 , Lauren Howard  3 , J Christopher Brady  1 , Yingmiao Liu  1 , Jingquan Jia  4 , Donna Niedzwiecki  3 , John Strickler  1 , Sean M Boyle  2 , Richard O Chen  2 , Hope Uronis  1
Affiliations

Ultra-sensitive, tumor-informed ctDNA profiling in pembrolizumab-treated esophagogastric cancer patients predicts clinical responses

Andrew B Nixon et al. Res Sq. .

Abstract

To explore whether ultra-sensitive circulating tumor DNA (ctDNA) profiling enables early prediction of treatment response and early detection of disease progression, we applied NeXT Personal, an ultra-sensitive bespoke tumor-informed liquid biopsy platform, to profile tumor samples from the KeyLargo study, a phase II trial in which metastatic esophagogastric cancer (mEGC) patients received capecitabine, oxaliplatin, and pembrolizumab. All 25 patients evaluated were ctDNA-positive at baseline. Minimal residual disease (MRD) events varied from 406,067 down to 1.5 parts per million (PPM) of ctDNA with a median limit of detection of 2.03 PPM. ctDNA dynamics were highly correlated with changes in tumor size (ρ = 0.59, p = 7.3×10-9). Lack of early molecular response (lack of ctDNA decrease) was associated with worse overall survival (OS) (HR 6.6, 95% CI 1.8-24.1, p = 0.005) and progression-free survival (PFS) (HR 15.4, 95% CI 2.7-87.0, p = 0.002). Lack of molecular clearance of ctDNA was associated with worse OS (HR 6.9, 95% CI 1.5-30.8, p = 0.012) and PFS (HR 19.2, 95% CI 2.4-152.8, p = 0.005). Molecular progression (ctDNA increase) preceded imaging-derived progression by a median lead time of 65 days. These results suggest that ultra-sensitive liquid biopsy approaches could improve treatment decision-making for mEGC patients receiving chemotherapy and immunotherapy.

Keywords: ctDNA; gastroesophageal cancer; pembrolizumab; personalized assay; ultra-sensitive detection.

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Conflict of interest statement

Additional Declarations: Competing interest reported. ABN has received research funding from Genentech, Genmab, MedImmune/AstraZeneca, Seattle Genetics, and has received consultant/advisory compensation from Sanofi and Leap Therapeutics. LM has stock in Personalis and other intellectual property. JJ has received research funding from Bayer, Incyte, Roche/Genentech, and Xilis. JS has received research funding or contracted research from Abbvie, Amgen, AStar D3, Bayer, Beigene, Curegenix, Daiichi-Sankyo, Eli Lilly, Erasca, GSK, Leap Therapeutics, Novartis, Pfizer, Revolution Medicines, Roche/ Genentech, Seagen; has received consultant/advisory compensation from Abbvie, Agenus, Astellas, AstraZeneca, Bayer, Beigene, Daiichi-Sankyo, Eli Lilly, GSK, Johnson and Johnson, Jazz Pharmaceuticals, Merck, Natera, Pfizer, Roche/Genentech, Regeneron, Sanofi, Taiho, Takeda, Xilio Therapeutics; and has received stocks from Triumvira Immunologics. HU has received research funding from Adaptimmune, Arcus Biosciences, Bristol-Myers Squibb, Genentech/Roche, Leap Therapeutics, Macrogenics, Merck; and has received consultant/advisory compensation from AstraZeneca and Bristol-Myers Squibb/Medarex. FCPN, CA, LM, SMB, ROC are employed and have received stocks from Personalis, Inc. The other authors declared no conflicts of interest.

Figures

Figure 1
Figure 1
CONSORT diagram.
Figure 2
Figure 2. Ultra-sensitive ctDNA personalized panel design.
A) Graphical depiction of the study strategy. B) Number of somatic variants included in bespoke panels for each patient. C) Distribution of limits of detection (LOD) and of PPM measures (log scale). D) Lollipop plot of all detected PPM measures. High (PPM≥1,000), medium (100≤PPM<1,000), and low (PPM<100) ctDNA levels are respectively depicted in black, dark gray, and light gray.
Figure 3
Figure 3. Cohort clinical and ctDNA overview.
Swimmer plot of 25 patients depicting best overall response (BOR), PFS and OS events, imaging response at each imaging evaluation, and molecular response and plasma ctDNA assessment.
Figure 4
Figure 4. Early ctDNA dynamics differ by RECIST response.
A) Spider plot showing change in ctDNA measurement from baseline over time for patients categorized by best overall response [CR: Complete response (n=2); PR: Partial response (n=14), SD: Stable disease (n=2), PD: Progressive disease (n=5)]. B) Distribution of ctDNA change from baseline to 8 days after treatment initiation (C1D8). C) Distribution of ctDNA change from baseline to approximately 28 days after treatment initiation (C2D1).
Figure 5
Figure 5. ctDNA monitoring allows for early detection of progression.
A) The difference in days between molecular progression and imaging progression. Negative values indicate earlier ctDNA progression. B) Correlation between ctDNA fold change and the fold change of the sum of the longest diameters for target lesions (RECIST 1.1).
Figure 6
Figure 6. ctDNA and tumor size dynamics in select patients.
Longitudinal ctDNA levels and tumor size (expressed as sum of diameters according to RECIST) in four patients whose best overall response by RECIST was: A) CR, B) SD, C) PD, or D) PR.
Figure 7
Figure 7. ctDNA response and clearance as prognostic biomarkers.
Kaplan-Meier and univariable Cox regression analysis of A) PFS and B) OS for patients split by molecular response (mR: ctDNA ratio > 0.5 between baseline and first-time point post 10 days) and molecular non-response (mNR); Kaplan-Meier and univariable Cox regression analysis of C) PFS and D) OS for patients split by ctDNA clearance between baseline and C7D1.
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