# Therapeutic misalignment averted by clonal evolutionary evidence: molecular confirmation of hepatic metastasis in SMARCA4-deficient non-small cell lung cancer initially misdiagnosed as resectable cholangiocarcinoma

## TL;DR

This study uses molecular and clonal analysis to correctly diagnose a rare lung cancer with liver metastasis, initially mistaken for a primary liver cancer.

## Contribution

First genomic evidence of shared and divergent mutations in SMARCA4-dNSCLC and its liver metastasis using clonal evolutionary analysis.

## Key findings

- Both lung and liver tumors shared SMARCA4 and TP53 mutations, confirming a common origin.
- Clonal evolutionary analysis showed lung tumors had more prevalent major and subclones than liver metastases.
- Molecular profiling resolved diagnostic confusion and supported precision therapy.

## Abstract

SMARCA4-deficient non-small cell lung cancer (SMARCA4-dNSCLC) exhibits significant histomorphological diversity and intertumoral heterogeneity. Immunophenotypically, it often lacks lineage-specific markers, making diagnosis challenging, especially in cases of hepatic metastasis. Currently, no reliable method exists to distinguish these metastases from primary hepatic malignancies based on conventional pathology. Therefore, molecular profiling of somatic alterations combined with clonal evolutionary analysis is critical for accurate diagnosis.

Histomorphological and immunophenotypic differences between pulmonary and hepatic lesions were assessed via hematoxylin and eosin staining and immunohistochemistry. Somatic mutational profiles were analyzed using next-generation sequencing, followed by clonal evolutionary analysis to confirm primary lung malignancy and hepatic metastasis.

This study presents a case of SMARCA4-dNSCLC exhibiting notable histomorphological and immunophenotypic divergence between the primary lung tumor and its hepatic metastasis. This heterogeneity led to a misdiagnosis of primary intrahepatic cholangiocarcinoma at another hospital. Molecular analysis showed that both lung and liver tumors harbored consistent SMARCA4 and TP53 mutations. Clonal evolutionary analysis revealed that both major and subclones were more prevalent in the lung tumor than in the liver metastasis. The evolutionary tree topology strongly suggested a unidirectional trajectory from the primary lung tumor to liver metastasis.

This study provides the first genomic evidence of shared and divergent somatic mutations in SMARCA4-dNSCLC and its hepatic metastasis. Clonal evolutionary analysis confirmed the diagnosis of SMARCA4-dNSCLC with hepatic metastasis, resolving diagnostic challenges and supporting precision therapy.

Diagram illustrating the determination of whether a liver tumor is a primary tumor or a metastasis from the lung using morphology, immunohistochemistry (IHC), and next-generation sequencing (NGS) clonal analysis, highlighting genetic similarities and differences in tumor markers such as SMARCA4, P53, ARID2, ABCB1, BUB1B, and CHEK2.