Clinical implications of plasma ctDNA features and dynamics in gastric cancer treated with HER2-targeted therapies

Abstract

Background: Gastric cancer (GC) is confronted with limited options for precision medicine. Human epidermal growth factor receptor 2 (HER2) is the principal druggable target of GC, yet proper biomarkers for response/resistance prediction remain unveiled.

Methods: From 40 GC patients received HER2-targeted therapy, a total of 327 peripheral blood plasma specimens was collected including baseline and treatment time points. Circulating tumor DNA (ctDNA) was extracted and sequenced with a target panel of 425 genes. Experimental validation of resistant mutations was carried out in NIH-3T3 cell line.

Results: Genomic features, including ERBB2 copy number variation (CNV), total copy number load, and tumor mutation burdens (TMBs), dynamically changed along with the treatment process and correlated with disease progression. Plasma ctDNA-based diagnosis was more sensitive than conventional computed tomography scanning in 40% of investigated patients, gaining additional time for clinical management. Compared to baseline, new gene alterations were emerged in 12 patients who developed drug resistance during treatment. ERBB2 mutations potentially related to Pyrotinib resistance were identified in plasma ctDNA of one patient and functional analysis of their downstream signaling pathways was carried out in NIH-3T3 cell line. TMB exhibited more power than ERBB2 CNV in predicting treatment responses and prognosis for HER2-targeted therapy in GC patients. Interestingly, survival analysis indicated that patients harboring both HER2 (ERBB2) positivity and high TMB might gain more therapeutic benefits from immune checkpoint inhibitors instead of HER2-targeted regimens that required further studies and validations CONCLUSIONS: Our work showed that the dynamic surveillance of plasma ctDNA genomic features provided instructive information for the precision medication of GC patients.

Keywords: ERBB2 copy number; HER2-targeted therapy; TMB; gastric cancer; immunotherapy; liquid biopsy.

FIGURE 1

ctDNA genomic features dynamically changed in gastric cancer patients received HER2‐targeted therapy. (A) The landscape for all specimens collected at BL, PR, SD, and PD. (B) Comparison of ERBB2 copy number, total copy number load (TCL), and tumor mutation burden (TMB) across all evaluation points. (C) The Spearman correlation of ERBB2 copy number, TCL, and TMB with CEA. (D) The NLR/MLR values across all evaluation points and groups with low‐ or high‐ctDNA genomic features. *P < .05. ns, not significant

FIGURE 2

Genomic features in ctDNA facilitated the early detection of disease progression during HER2‐targeted therapy. (A) The real‐time changes of ctDNA features (ERBB2 copy number, total copy number load [TCL], and tumor mutation burden [TMB]) and CEA for 30 patients who ever reached progressed disease (PD). Computed tomography (CT)‐based PD, ctDNA‐based PD, and CEA‐based PD were marked by separate vertical lines. (B) The advancement of ctDNA‐based PD and CEA‐based PD compared with CT‐based PD in detecting disease progressions for the 30 patients received HER2‐targeted therapy. (C) CT‐scanned images for three representative cases were displayed to compare ctDNA‐based PD with CT‐based PD

FIGURE 3

Emerging genomic aberrations potentially contributed to gastric cancer's (GC) resistance to HER2‐targeted therapy. (A) The distribution of novel gene alterations emerged in 12 patients and their correlation with HER2‐targeted regimens. (B) The biological processes and pathways involved with the emerging genomic aberrations were enriched. (C) The real‐time frequency of primary copy number variations (CNVs), primary mutations, three novel ERBB2 point mutations, and maximum variant allele frequency changed along with the treatments in case 35. PTX, paclitaxel

FIGURE 4

Genomic features served as predictive biomarkers for output of HER2‐targeted therapy. (A) An overview of ERBB2 copy number, total copy number load (TCL), and tumor mutation burden (TMB) for 40 patients at baseline and individually paired responses. (B) ERBB2 copy number, TCL, and TMB information at baseline were used to predict progression‐free survival (PFS) proportions of subsequent HER2‐targeted therapy. (C) PFS was calculated for patients stratified by baseline ERBB2 copy number and TMB. (D) The relative changes of ERBB2 copy number, TCL, and TMB for 40 patients at the first point after treatment started were compared with baseline status. (E) Stratified (left panel) or combined (right panel) information of ERBB2 copy number, TCL, and TMB at the first point were used to predict PFS proportions of HER2‐targeted therapy. E^lowT^low, ERBB2 ^lowTMB^low; E^highT^low, ERBB2 ^highTMB^low; E^lowT^high, ERBB2 ^lowTMB^high; E^highT^high, ERBB2 ^highTMB^high

FIGURE 5

ERBB2 ^highTMB^high patients displayed a more favorable outlook for immunotherapy. (A) Through investigating the ctDNA genomic changes in the HER2‐targeted cohort, the major cancer‐related and immunity‐related pathways displayed a higher enrichment in the ERBB2 ^highTMB^high group. For the immunotherapy cohort, (B) the correlation of PD‐L1 expression, MSI status, and responses after received immune checkpoint inhibitors were compared across ERBB2‐TMB‐stratified patients. (C) Progression‐free survival (PFS) and overall survival (OS) for patients with different ERBB2/TMB status were demonstrated

FIGURE 6

An overview of the workflow and the major conclusions in this study. Through tracking the serial changes of plasma ctDNA from GC patients underwent HER2‐targeted therapy or immunotherapy, our work provided four section of clues that directed the clinical decision‐making of GC