NIPBL::NACC1 Fusion Hepatic Carcinoma

Abstract

Several reports describing a rare primary liver tumor with histologic features reminiscent of follicular thyroid neoplasms have been published under a variety of descriptive terms including thyroid-like, solid tubulocystic, and cholangioblastic cholangiocarcinoma. Although these tumors are considered to represent histologic variants, they lack classic features of cholangiocarcinoma and have unique characteristics, namely immunoreactivity for inhibin and NIPBL::NACC1 fusions. The purpose of this study is to present clinicopathologic and molecular data for a large series of these tumors to better understand their pathogenesis. We identified 11 hepatic tumors with these features. Immunohistochemical and NACC1 and NIPBL fluorescence in situ hybridization assays were performed on all cases. Four cases had available material for whole-genome sequencing (WGS) analysis. Most patients were adult women (mean age: 42 y) who presented with abdominal pain and large hepatic masses (mean size: 14 cm). Ten patients had no known liver disease. Of the patients with follow-up information, 3/9 (33%) pursued aggressive behavior. All tumors were composed of bland cuboidal cells with follicular and solid/trabecular growth patterns in various combinations, were immunoreactive for inhibin, showed albumin mRNA by in situ hybridization, and harbored the NIPBL::NACC1 fusion by fluorescence in situ hybridization. WGS corroborated the presence of the fusion in all 4 tested cases, high tumor mutational burden in 2 cases, and over 30 structural variants per case in 3 sequenced tumors. The cases lacked mutations typical of conventional intrahepatic cholangiocarcinoma. In this report, we describe the largest series of primary inhibin-positive hepatic neoplasms harboring a NIPBL::NACC1 fusion and the first WGS analysis of these tumors. We propose to name this neoplasm NIPBL:NACC1 fusion hepatic carcinoma.

Figure 1:

A fresh gross specimen of NIPBL::NACC1 fusion hepatic carcinoma demonstrates relatively well-circumscribed tumor with abundant hemorrhage and cystic degeneration (A). Microscopy confirms the well-delineated nature of the tumor (B). Most tumors were comprised of varied architectural patterns (C).

Figure 2:

Histologically, NIPBL::NACC1 fusion hepatic carcinomas show variable architectural patterns (A). All tumors contained a component of follicular/microcystic areas with variable dilatation (B,C), many of which contained colloid-like luminal material with peripheral vacuolization (D,E). Other components included solid or insular like growth patterns (F). High power demonstrated monotonous round cells without significant mitotic activity or atypia (E,F).

Figure 3:

Immunohistochemical staining showed diffuse strong staining for CK7 (A) and fairly diffuse moderate-strong intensity for inhibin (B) in all NIPBL::NACC1 fusion hepatic carcinomas. About a half of the cases showed weak or patchy synaptophysin expression (C). Albumin in situ hybridization was positive in all cases (D).

Figure 4:

Extensive spectrum of somatic, germline, and structural variants (SV) in cancer genes revealed by whole genome sequencing of four NIPBL::NACC1 fusion hepatic carcinomas (A). Aging and APOBEC signatures evident in SBS analyses, with three and two cases respectively (B). High TMB was noted in two cases, one of them showing elevated noncoding TMB (C). Different types of structural variants (SVs) are present. A single case exhibits fewer SVs relative to the others, which harbor >30 SVs and an uneven distribution of types (D). SV: Structural Variant. SNV: single nucleotide variant. VUS: variant of unknown significance. SBS: single base substitution.

Figure 5:

Whole genome sequencing demonstrates a NACC1::NIPBL fusion in all four cases (illustrated with different colors), predominantly within intron 1 of NACC1 and intron 18 (intron 19 in one case), a result of more complex structural variants involving other chromosomes such as 5, 19, and 22 as represented in a graphical representation (A). Fluorescence in situ hybridization (FISH) fusion assay showing positive NACC1::NIPBL fusion (B). Positive FISH break-apart assays for NACC1 (C) and NIPBL (D).