Mutation profiling in cholangiocarcinoma: prognostic and therapeutic implications

Abstract

Background: Cholangiocarcinoma (CCA) is clinically heterogeneous; intra and extrahepatic CCA have diverse clinical presentations. Next generation sequencing (NGS) technology may identify the genetic differences between these entities and identify molecular subgroups for targeted therapeutics.

Methods: We describe successful NGS-based testing of 75 CCA patients along with the prognostic and therapeutic implications of findings. Mutation profiling was performed using either a) NGS panel of hotspot regions in 46 cancer-related genes using a 318-chip on Ion PGM Sequencer or b) Illumina HiSeq 2000 sequencing platform for 3,769 exons of 236 cancer-related genes plus 47 introns from 19 genes to an average depth of 1000X. Clinical data was abstracted and correlated with clinical outcome. Patients with targetable mutations were referred to appropriate clinical trials.

Results: There were significant differences between intrahepatic (n = 55) and extrahepatic CCA (n = 20) in regard to the nature and frequency of the genetic aberrations (GAs). IDH1 and DNA repair gene alterations occurred more frequently in intrahepatic CCA, while ERBB2 GAs occurred in the extrahepatic group. Commonly occurring GAs in intrahepatic CCA were TP53 (35%), KRAS (24%), ARID1A (20%), IDH1 (18%), MCL1 (16%) and PBRM1 (11%). Most frequent GAs in extrahepatic CCA (n = 20) were TP53 (45%), KRAS (40%), ERBB2 (25%), SMAD4 (25%), FBXW7 (15%) and CDKN2A (15%). In intrahepatic CCA, KRAS, TP53 or MAPK/mTOR GAs were significantly associated with a worse prognosis while FGFR GAs correlated with a relatively indolent disease course. IDH1 GAs did not have any prognostic significance. GAs in the chromatin modulating genes, BAP1 and PBRM1 were associated with bone metastases and worse survival in extrahepatic CCA. Radiologic responses and clinical benefit was noted with EGFR, FGFR, C-met, B-RAF and MEK inhibitors.

Conclusion: There are significant genetic differences between intra and extrahepatic CCA. NGS can potentially identify disease subsets with distinct prognostic and therapeutic implications.

Figure 1. Representative histology of select tumors with the respective GA (40x, 200x).

[A. ERBB2 (S310F) B. ERBB2 (S310F) C. BAP1 (C91*) D. FGFR2-KIAA1598 fusion E. FGFR2-NOL4 fusion].

Figure 2. Ingenuity Pathway Analysis indicates canonical signaling pathways involved in CCA.

Homology noted with more commonly occurring solid tumors including melanoma and glioblastoma.

Figure 3. Schematic of FGFR2-KIAA1598 fusion gene.

These fusions have been proven oncogenic and are potentially susceptible to FGFR inhibitors.

Figure 4. Relationship of Overall Survival with presence of KRAS mutation in cases of Intrahepatic CCA.

Figure 5. Relationship of Overall Survival with presence of TP53 mutation in cases of Intrahepatic CCA.

Figure 6. Relationship of Overall Survival with presence of FGF/FGFR alterations in cases of Intrahepatic CCA.

Figure 7. Relationship of Overall Survival with presence of BAP1 mutation in cases of Extrahepatic CCA (p = 0.007).

Figure 8. A 57 year old male with BAP1 mutated intrahepatic CCA.

Baseline (A) axial and (B) coronal contrast-enhanced CT images demonstrate (A) a 6.9×5.3 cm liver mass involving segments I, II, and IV, and (B) a 5.6 cm sternal metastasis (arrow). Note the sternal metastasis does not extend to the level of the right 3rd rib (arrowhead). Extended left hepatectomy and resection of the sternal metastasis was performed. (C, D) Seven weeks later, contrast-enhanced CT images show a new metastasis in the remnant liver (arrow), and a new 2 cm recurrence (arrowheads) involving the sternum adjacent to the right 3rd rib. (E) Three months later, there is a new 2.2 cm metastasis (arrow) involving the right inferior pubic ramus.

Figure 9. A 69 year old female with KRAS mutated CCA metastatic to the ovaries.

(A) Coronal contrast-enhanced CT image demonstrates a 15.4×12.6×12.2 cm (transverse × craniocaudal × AP) pelvic mass. (B) After two cycles of trametinib + pazopanib therapy, the pelvic mass is slightly decreased to 13.5×11.3×13.4 cm.

Figure 10. A 68 year old female with KRAS wt intrahepatic CCA.

Axial (A) fused PET-CT and (B) unenhanced CT images demonstrate multiple confluent FDG avid liver metastases. After 3 months of erlotinib therapy, (C) axial fused PET-CT and (D) unenhanced CT images show decreased FDG avidity and slightly decreased size of metastases.

Figure 11. A 67 year old male with BRAF mutated intrahepatic CCA, who had progressed on conventional chemotherapy.

Axial (A) fused PET-CT and (B) unenhanced CT images from a PET scan demonstrate FDG avidity of multiple liver metastases. After 8 weeks of BRAF inhibitor therapy, axial (C) fused PET-CT and (D) contrast-enhanced CT images demonstrate lack of FDG avidity and decreased size of liver metastases, e.g., the dominant lesion adjacent to the IVC (arrow) decreased from 3.7 cm to 1.6 cm. After 16 weeks of therapy, axial (E) fused PET-CT and (F) contrast-enhanced CT images demonstrate continued lack of FDG avidity and further decreased size of liver metastases, e.g., the dominant lesion (arrow) now measures 1.3 cm.

Figure 12. A 37 year old female with c-MET amplified CCA, who had progressed on conventional chemotherapy.

At baseline, axial (A) fused PET-CT and (B) unenhanced CT images demonstrate multiple FDG avid liver metastases, in this patient who is status post right hepatectomy. After 4 weeks of therapy, (C) axial fused PET-CT and (D) unenhanced CT images show decreased FDG avidity and size of metastases. A representative segment II mass (arrows) has decreased from 2.6 cm to 2.1 cm.