Real-Time Genomic Characterization of Metastatic Pancreatic Neuroendocrine Tumors Has Prognostic Implications and Identifies Potential Germline Actionability

Abstract

Purpose: We assessed the usefulness of real-time molecular profiling through next-generation sequencing (NGS) in predicting the tumor biology of advanced pancreatic neuroendocrine tumors (panNETs) and in characterizing genomic evolution.

Methods: Patients with metastatic panNETs were recruited in the routine clinical practice setting (between May 2014 and March 2017) for prospective NGS of their tumors as well as for germline analysis using the Memorial Sloan Kettering-Integrated Mutation Profiling of Actionable Cancer Targets (MSK-IMPACT) sequencing platform. When possible, NGS was performed at multiple time points.

Results: NGS was performed in 96 tumor samples from 80 patients. Somatic alterations were identified in 76 of 80 patients (95%). The most commonly altered genes were MEN1 (56%), DAXX (40%), ATRX (25%), and TSC2 (25%). Alterations could be defined in pathways that included chromatin remodeling factors, histone methyltransferases, and mammalian target of rapamycin pathway genes. Somatic loss of heterozygosity was particularly prevalent (50 of 96 samples [52%]), and the presence of loss of heterozygosity resulted in inferior overall survival (P < .01). Sequencing of pre- and post-treatment samples revealed tumor-grade progression; clonal evolution patterns were also seen (molecular resistance mechanisms and chemotherapy-associated mutagenesis). Germline genetic analysis identified clinically actionable pathogenic or likely pathogenic variants in 14 of 88 patients (16%), including mutations in high-penetrance cancer susceptibility genes (MEN1, TSC2, and VHL).

Conclusion: A clinical NGS platform reveals pertubations of biologic pathways in metastatic panNETs that may inform prognosis and direct therapies. Repeat sequencing at disease progression reveals increasing tumor grade and genetic evolution, demonstrating that panNETs adopt a more aggressive behavior through time and therapies. In addition to frequent somatic mutations in MEN1 and TSC2, germline mutations in these same genes underlie susceptibility to panNETs and highlight the need to re-evaluate whether germline genetic analysis should be performed for all patients with panNETs.

Fig 1.

Genomic landscape of pancreatic neuroendocrine tumors, including the first sequenced sample for each patient (n = 80), as identified by the Memorial Sloan Kettering-Integrated Mutation Profiling of Actionable Cancer Targets. LOH, loss of heterozygosity; Mb, megabyte; mTOR, mammalian target of rapamycin.

Fig 2.

Significant associations between somatic alterations and overall survival.

Fig 3.

Post-treatment samples with high mutational burden after exposure to alkylating agents, as well as acquisition of mutations in the mismatch repair genes. (A) Patient received dacarbazine. (B) Patient received temozolomide.

Fig A1.

Loss of heterozygosity (LOH) and copy-neutral LOH across all autosomes in well-differentiated pancreatic neuroendocrine tumors. LOH was observed recurrently in chromosomes 1, 2, 3, 6, 8, 10, 11, 15, 16, 21, and 22.

Fig A2.

Acquisition of PTEN mutation (Q298*) after treatment with everolimus. POD, progression of disease; PRRT, peptide receptor radionuclide therapy; VAF, variant allele frequency.

Fig A3.

Acquisition of RHEB mutation (Y35S) after treatment with everolimus. (*) Gene was not interrogated in the Memorial Sloan Kettering–Integrated Mutation Profiling of Actionable Cancer Targets version used for next-generation sequencing of the tumor sample. MRI, magnetic resonance imaging; POD, progression of disease; VAF, variant allele frequency.

Fig A4.

After treatment with everolimus, loss of previously seen IGF2 alteration, and acquisition of TSC2 and AKT2 mutations. MRI, magnetic resonance imaging; POD, progression of disease; VAF, variant allele frequency.

Fig A5.

Acquisition of NRAS mutation after treatment with the BRAF V600E inhibitor vemurafenib. (*) Gene was not interrogated in the Memorial Sloan Kettering–Integrated Mutation Profiling of Actionable Cancer Targets version used for next-generation sequencing of the tumor sample. POD, progression of disease; PR, partial response; VAF, variant allele frequency.

Fig A6.

Magnetic resonance imaging of the brain demonstrating bilateral lesions consistent with tubers and radial bands, characteristic of tuberous sclerosis complex.