Mutation Profiling in Cholangiocarcinoma: Prognostic and Therapeutic Implications

<div><p>Background</p><p>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.</p><p>Methods</p><p>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.</p><p>Results</p><p>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). <i>IDH1</i> and DNA repair gene alterations occurred more frequently in intrahepatic CCA, while <i>ERBB2</i> GAs occurred in the extrahepatic group. Commonly occurring GAs in intrahepatic CCA were <i>TP53</i> (35%), <i>KRAS</i> (24%), <i>ARID1A</i> (20%), <i>IDH1</i> (18%), <i>MCL1</i> (16%) and <i>PBRM1</i> (11%). Most frequent GAs in extrahepatic CCA (n = 20) were <i>TP53</i> (45%), <i>KRAS</i> (40%), <i>ERBB2</i> (25%), <i>SMAD4</i> (25%), <i>FBXW7</i> (15%) and <i>CDKN2A</i> (15%). In intrahepatic CCA, <i>KRAS</i>, <i>TP53</i> or <i>MAPK/mTOR</i> GAs were significantly associated with a worse prognosis while <i>FGFR</i> GAs correlated with a relatively indolent disease course. <i>IDH1</i> GAs did not have any prognostic significance. GAs in the chromatin modulating genes, <i>BAP1</i> and <i>PBRM1</i> 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.</p><p>Conclusion</p><p>There are significant genetic differences between intra and extrahepatic CCA. NGS can potentially identify disease subsets with distinct prognostic and therapeutic implications.</p></div

Ingenuity Pathway Analysis indicates canonical signaling pathways involved in CCA.

<p>Homology noted with more commonly occurring solid tumors including melanoma and glioblastoma.</p

Relationship of Overall Survival with presence of <i>KRAS</i> mutation in cases of Intrahepatic CCA.

<p>Relationship of Overall Survival with presence of <i>KRAS</i> mutation in cases of Intrahepatic CCA.</p

A 57 year old male with BAP1 mutated intrahepatic CCA.

<p>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.</p

A 67 year old male with <i>BRAF</i> mutated intrahepatic CCA, who had progressed on conventional chemotherapy.

<p>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.</p

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

<p>(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.</p

Patient demographics and tumor characteristics.

<p>Patient demographics and tumor characteristics.</p

Univariate Analysis of Survival – Extrahepatic CCA.

<p>Univariate Analysis of Survival – Extrahepatic CCA.</p

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

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

Genetic differences identified between Intrahepatic and Extrahepatic CCA

<p>Genetic differences identified between Intrahepatic and Extrahepatic CCA</p