Whole-Exome Sequencing Identifies Frequent AHNAK2 Mutations With Prognostic Significance in Undifferentiated Primary Liver Carcinoma.

Abstract

Undifferentiated primary liver carcinoma (UPLC) is an exceedingly rare hepatic malignancy lacking hepatocytic or cholangiocytic differentiation, and its clinicopathologic and molecular characteristics remain poorly defined. We retrospectively analyzed 25 UPLC cases from a single Chinese institution over an 8-year period and performed whole-exome sequencing (WES) to delineate the genomic landscape, combined with multiplex immunofluorescence (mIF), routine histopathology, and immunohistochemistry (IHC) for phenotypic assessment. UPLC exhibits marked histologic and immunophenotypic heterogeneity, with all cases negative for classic hepatobiliary differentiation markers; albumin RNA in situ hybridization (Alb-ISH) demonstrates limited diagnostic utility due to low positivity. Compared with conventional hepatocellular carcinoma (HCC) from the Cancer Genome Atlas (TCGA), UPLC demonstrates a distinct mutational profile, with frequent alterations in 5 key oncogenic pathways (Hippo, NOTCH, WNT, RTK-RAS, and TP53) in 96.0% of cases and a higher mutation frequency of core pathway genes than HCC. TERT promoter hotspot mutations were identified in a subset but showed no association with clinicopathologic features or survival. AHNAK2 was the most frequently mutated gene (68.0%) and is rarely altered in HCC or intrahepatic cholangiocarcinoma (ICC). Patients with AHNAK2 -mutated UPLC had significantly shorter overall survival, elevated tumor mutational burden (TMB), and markedly reduced infiltration of CD4⁺, CD8⁺, CD20⁺, and CD68⁺ immune cells. These findings support the recognition of UPLC as a clinically aggressive and molecularly distinct entity and indicate that the AHNAK2 mutation may serve as a potential prognostic biomarker in this rare malignancy.