Comprehensive Genomic Profiling of Carcinoma of Unknown Primary Origin: Retrospective Molecular Classification Considering the CUPISCO Study Design

Abstract

Background: Carcinoma of unknown primary origin (CUP) accounts for 2%-5% of newly diagnosed advanced malignancies, with chemotherapy as the standard of care. CUPISCO (NCT03498521) is an ongoing randomized trial using comprehensive genomic profiling (CGP) to assign patients with CUP to targeted or immunotherapy treatment arms based on genomic profiling. We performed a retrospective analysis of CUP cases referred for CGP to determine how many were potentially eligible for enrollment into an experimental CUPISCO arm.

Materials and methods: Centrally reviewed adenocarcinoma and undifferentiated CUP specimens in the FoundationCore database were analyzed using the hybrid capture-based FoundationOne CDx assay (mean coverage, >600×). Presence of genomic alterations, microsatellite instability (MSI), tumor mutational burden (TMB), genomic loss of heterozygosity (gLOH), and programmed death-ligand 1 (PD-L1) positivity were determined.

Results: A total of 96 of 303 patients (31.7%) could be matched to an experimental CUPISCO arm. Key genomic alterations included ERBB2 (7.3%), PIK3CA (6.3%), NF1 (5.6%), NF2 (4.6%), BRAF (4.3%), IDH1 (3.3%), PTEN, FGFR2, EGFR (3.6% each), MET (4.3%), CDK6 (3.0%), FBXW7, CDK4 (2.3% each), IDH2, RET, ROS1, NTRK (1.0% each), and ALK (0.7%). Median TMB was 3.75 mutations per megabase of DNA; 34 patients (11.6%) had a TMB ≥16 mutations per megabase. Three patients (1%) had high MSI, and 42 (14%) displayed high PD-L1 expression (tumor proportion score ≥50%). gLOH could be assessed in 199 of 303 specimens; 19.6% had a score of >16%.

Conclusions: Thirty-two percent of patients would have been eligible for targeted therapy in CUPISCO. Future studies, including additional biomarkers such as PD-L1 positivity and gLOH, may identify a greater proportion potentially benefiting from CGP-informed treatment. Clinical trial identification number. NCT03498521 IMPLICATIONS FOR PRACTICE: The findings of this retrospective analysis of carcinoma of unknown primary origin (CUP) cases validate the experimental treatment arms being used in the CUPISCO study (NCT03498521), an ongoing randomized trial using comprehensive genomic profiling to assign patients with CUP to targeted or immunotherapy treatment arms based on the presence of pathogenic genomic alterations. The findings also suggest that future studies including additional biomarkers and treatment arms, such as programmed death-ligand 1 positivity and genomic loss of heterozygosity, may identify a greater proportion of patients with CUP potentially benefiting from comprehensive genomic profiling-informed treatment.

Keywords: Genetic profiling; Loss of heterozygosity; Molecular targeted therapy; Unknown primary tumors.

Figure 1

CUPISCO study design. ^aBased on eligibility criteria that are summarized at ClinicalTrials.gov: NCT03498521 [46]. Randomization is stratified by gender and response during the induction period (CR + PR vs. SD). Abbreviations: CGP, comprehensive genomic profiling; CR, complete response; CUP, carcinoma of unknown primary origin; EOI, end of induction; EOT, end of treatment; MGT, molecularly guided therapy; MTB, molecular tumor board; PD, progressive disease; PR, partial response; PT, pretreatment; R, randomization; SD, stable disease.

Figure 2

Sample, analysis, and report flow. (A): FFPE tumor sample. (B): Sequencing library preparation. (C): Analysis pipeline. (D): Clinical report. Abbreviation: FFPE, formalin‐fixed, paraffin‐embedded.

Figure 3

Long tail plot of genomic alterations in 303 cases of carcinoma of unknown primary origin. Genes shown have an alteration frequency of 1% or higher. Abbreviations: CN, copy number alteration; RE, rearrangement; SV, short variant.

Figure 4

Long tail plot of genomic alterations in TMB‐high and TMB‐low cases. Genes shown have an alteration frequency of 1% or higher. For each gene, the alteration frequency for TMB‐high and TMB‐low cases is indicated by the left and right bar, respectively. Abbreviations: CN, copy number alteration; RE, rearrangement; SV, short variant; TMB, tumor mutational burden.

Figure 5

Tile plot of overlap of biomarkers gLOH‐high, TMB‐high, PD‐L1‐high, and MSI‐high. Abbreviations: gLOH, genomic loss of heterozygosity; MSI, microsatellite instability; MSS, microsatellite stable; Mut, mutation; PD‐L1, programmed death‐ligand 1; TMB, tumor mutational burden.