Gene actionability according to the ESMO Scale for Clinical Actionability of molecular Targets (ESCAT) in No Specific Molecular Profile (NSMP) endometrial cancer

Abstract

Background: The No Specific Molecular Profile (NSMP) subtype accounts for ∼30%-40% of endometrial cancer (EC), comprising a heterogeneous group of EC.

Patients and methods: The primary outcome of this study was the prevalence of actionable genomic alterations in NSMP EC, classified according to the European Society for Medical Oncology (ESMO) Scale for Clinical Actionability of molecular Targets (ESCAT). Oncogenic and likely oncogenic alterations, pathways, and co-mutation patterns were reported. The analysis was stratified by risk group according to the European Society of Gynaecological Oncology (ESGO)-ESMO-European SocieTy for Radiotherapy and Oncology (ESTRO) guidelines. Patients with NSMP EC enrolled in the FPG500 comprehensive cancer genome profiling program (NCT06020625) were included.

Results: Two hundred and fifty-three patients with NSMP EC of any International Federation of Gynecology and Obstetrics (FIGO) stage were enrolled between 1 January 2022 and 31 December 2023. Median age was 62 years, and the most frequent histotype was endometrioid (97%). Ninety-five percent of patients were estrogen receptor positive. Two hundred and thirty-three patients (92%) had at least one ESCAT tier I-III alteration. The most frequent variants were in PTEN [88%, 95% confidence interval (CI) 84% to 92%], PIK3CA (42%, 95% CI 36% to 49%), FGFR2 (15%, 95% CI 11% to 20%), and AKT1 (6%, 95% CI 3% to 10%); 4% (95% CI 2% to 8%) of patients had an ESR1 variant, while KRAS G12C was found in 3% (95% CI 1% to 6%) of patients. The majority of PTEN variants were on the R130 hotspot. More frequent PIK3CA hotspot variants were H1047R (9%), E545D/K/Q/A (6%), and E542K (4%). In the overall population, PIK3CA with PIK3R1 (odds ratio [OR] = 0.07, P value = 4.25 × 10^-14), KRAS with CTNNB1 (OR = 0.03, P value = 1.98 × 10^-7), and AKT1 and PTEN (OR = 0.06, P value = 5.73 × 10^-6) were mutually exclusive. Significant co-occurrence was found between PTEN and ARID1A (OR = 6.94, P value = 3.39 × 10^-6) and PTEN with PIK3R1 (OR = 4.36, P value = 0.009). An alteration in the phosphatidylinositol-3 kinase (PI3K) pathway was found in 94% of patients in the overall population and in 98% of patients with an ESCAT tier I-III alteration.

Conclusion: Our findings highlight potentially actionable alterations in NSMP EC patients, supporting the exploration of tailored molecular-matched therapies according to risk groups.

Keywords: ESCAT; No Specific Molecular Profile endometrial cancer; genomic description; target therapy.

Figure 1

STROBE diagram summarizing the NSMP patients included in the study. dMMR, mismatch repair-deficient; FPG, Fondazione Policlinico Gemelli; HT, high-throughput; NSMP, non-specific molecular profile; TSO, TruSight Oncology 500.

Figure 2

Genomic characteristics in the overall cohort stratified by risk groups. (A) Oncoplot displaying variants in the most frequently mutated genes and clinical features. Bar chart on the left represents the mean VAF. When a gene had multiple mutations, variants were prioritized in the following order: frameshift deletions or frameshift insertions, nonsense mutations, splice sites, in-frame deletions or in-frame insertions, missense mutations. (B) Bar plot illustrating the percentage of patients harboring mutations in the most frequently mutated genes, stratified by risk classification. (C) Heatmap of the GO-smoothed mutation matrix. Rows represent genes and columns represent NMF-derived modules, with hierarchical clustering. The color scale indicates the intensity of the smoothed mutation signal for each gene–module pair, with blue reflecting low and red indicating high mutation signal. GO, Gene Ontology; LVSI, lymphovascular space invasion; MSI, microsatellite instability; NMF, non-negative matrix factorization; TMB, tumor mutational burden; VAF, variant allele frequency.

Figure 3

Genomic characteristics according to ESCAT classification. (A) Oncoplot displaying variants in the most frequently mutated genes and clinical features. Bar chart on the left represents the mean VAF. When a gene had multiple mutations, variants were prioritized in the following order: frameshift deletions or frameshift insertions, nonsense mutations, splice sites, in-frame deletions or in-frame insertions, missense mutations. (B) Bar plot illustrating the percentage of patients harboring mutations in the most frequently mutated genes, stratified by risk classification. (C) Multiple correspondence analysis of somatic mutation patterns. The color of the labels and arrows reflects the quality of representation (cos²) of each mutation state (wild-type versus mutated) on the MCA dimensions, while the length of the arrow from the origin indicates the contribution to tumor discrimination along these dimensions, with longer vectors representing mutation states that explain greater variance. (D) Co-occurrence network of ESCAT and non-ESCAT genes, mutated in at least five patients. Edge thickness represents co-mutation frequency, while node size corresponds to mutation frequency. ESCAT and non-ESCAT genes are color coded. Layout: Fruchterman–Reingold (k = 3). ESCAT, European Society for Medical Oncology Scale for Clinical Actionability of molecular Targets; LVSI, lymphovascular space invasion; MCA, multiple correspondence analysis; MSI, microsatellite instability; mut, mutated; TMB, tumor mutational burden; VAF, variant allele frequency; wt, wild-type.

Figure 4

ESCAT gene hotspots and PIK3CA co-mutation network. (A, B) Lollipop plots for PTEN (A) and PIK3CA (B). The x-axis represents the aminoacidic position, while the y-axis indicates the frequency of each variant. The most frequent hotspot mutations are highlighted. (C) Co-occurrence network of PIK3CA mutations. Nodes represent genes, with PIK3CA and its hotspot mutations (Q546, H1047, E545, E542) highlighted. Genes within the PI3K/AKT/mTOR pathway (in-pathway) and genes from other pathways (out-of-pathway) are color coded. Edge thickness represents co-mutation frequency, while node size corresponds to mutation frequency. Layout: spring. ESCAT, European Society for Medical Oncology Scale for Clinical Actionability of molecular Targets; mTOR, mammalian target of rapamycin.