Molecular profiling of a gastroesophageal adenocarcinoma (GEA) multicohort using next-generation sequencing (NGS).
Authors: Terán-Brage Eduardo , Ucha-Hermida José María , Landolfi Stefania , De Sa Gerreiro-Palma Helena María , Tian Tian , Castro-Boix Sandra , Vivancos-Prellezo Ana , Aguilar-Izquierdo Susana , Macarulla Teresa , Acosta-Eyzaguirre Daniel 
Published: January 2025

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Background:
The mutational landscape of GEA is rapidly evolving with the identification of promising molecular targets. However, histological subtypes are insufficient to capture the molecular heterogeneity in these patients (pts). We aim to assess the histopathological and molecular features in a GEA cohort using NGS techniques, and to evaluate the mutational frequency and its prognostic correlation.
Methods:
We conducted a retrospective study on GEA from 2019 to 2024. Immunohistochemistry (IHC) was used to evaluate HER2 expression, microsatellite instability (MSI), Epstein-Barr virus (EBV) and PD-L1 status. In-house and commercial NGS platforms were used to detect molecular alterations from tumor samples. Cox regression model was used to analyze overall survival (OS) based on the clinicopathological and molecular subgroups.
Results:
Using NGS techniques, we identified the following alterations with potential clinical relevance in the 115-pts included: pathogenic mutations in
PIK3CA
(5.2%),
BRCA1/2
(3.5%) and
POLD1
(0.9%), along with copy number alterations (CNA) in
ERBB2
(10.4%),
EGFR
(8.7%),
MET
(5.2%) and
FGFR2
(4.3%) genes, among others. Additionally, a high tumor mutational burden (≥ 13 Mut/Mb) was observed in 6 pts (5.2%). Clinical characteristics are detailed in the table. We detected a higher rate of alterations in
CDH1
(10.42% vs 4.48%; p=0.22) and
PIK3CA
(8.33% vs 2.99%; p=0.20) genes in early (<50y) vs late-onset (≥50y) GEA. Additionally, we identified a significantly higher mutation frequency in diffuse vs intestinal tumors;
ARID1A
(17.6% vs 2.2%; p=0.01) and
CDH1
(11.8% vs 0%; p=0.02) genes. Also, pts with peritoneal involvement showed a greater prevalence of mutations in
CDH1
(12% vs 0%; p=0.04) and
RHOA
(10% vs 0%; p=0.06) compared to those with liver disease. We observed a significantly worse OS in pts with diffuse vs intestinal tumors (15.7m vs 19.1m; p=0.04) and a trend toward shorter survival in pts with
CDKN2A
mutations (11.97m vs 17.83m; p=0.42). Although not significantly, CNA in
ERBB2
were associated with a better prognosis (22.2m vs 16.2m; p=0.09).
Conclusions:
Our results support the utility of NGS platforms in detecting novel molecular targets with prognostic and clinical impact, beyond
ERBB2
. Additionally, we observed poorer prognosis in diffuse subtype tumors, which exhibited a higher frequency of mutations in
ARID1A
and
CDH1
genes.

Clinicopathological characteristics of the 115-pts with GEA.

N=115 (%)

AgeMedian years [range]
54 [18-83]

Sex
Male
69 (60.0)

Tumor site
Gastric
72 (62.6)

Gastroesophageal junction
37 (32.2)

Esophagus
6 (5.2)

Histological subtype
Diffuse or pooly cohesive
51 (44.3)

Intestinal or tubular
46 (40.0)

Others
18 (15.7)

Stage at diagnosis
Advanced
74 (66.9)

Localized
41 (33.1)

Metastatic site
Peritoneum
53 (46.1)

Liver
34 (29.6)

Molecular profile (IHC)
HER2 (+)
20 (17.4)

MSI
5 (4.3)

EBV (+)
2 (1.8)

PDL1 (CPS) ≥1
35 (30.4)