CTSC–RAB38 Potentiates Responsiveness to PD-1 Blockade in Esophageal Squamous Cell Carcinoma

Abstract Immune checkpoint blockade (ICB) shows promise in treating locally advanced esophageal squamous cell carcinoma (ESCC); however, identifying biomarkers for predicting efficacy remains a challenge. Chimeric RNAs offer a potential solution for precision oncology. To investigate the potential of chimeric RNAs as indicators for molecular classification of ESCC and to evaluate their utility in guiding ICB treatment decisions. RNA-seq data from 155 paired ESCC and adjacent normal tissues were analyzed using STAR-Fusion, FusionCatcher, and JAFFA to identify chimeric RNAs, followed by stringent filtering to create a chimeric RNA landscape. A total of 2578 chimeric RNAs were mainly formed through intergenic-splicing, creating 2204 chimeric proteins and 325 neoantigens, which were confirmed by liquid chromatography-mass spectrometry (LC/MS). Moreover, chimeric RNAs can be utilized to facilitate patient stratification. Patients with specific chimeric RNAs, such as BRAF and JAK2, exhibited favorable responses to trametinib or ruxolitinib, and those with more neoantigens may benefit from immunotherapy. Notably, CTSC–RAB38, MTAP–CDKN2B-AS1, and PTK2–AGO2, which possess oncogenic properties, were linked to unfavorable prognoses. CTSC–RAB38, the most recurrent chimeric RNA, formed via cis-splicing between adjacent genes (cis-SAGe), reshaped the tumor microenvironment (TME) by facilitating CD8+ T cell exhaustion to promote tumor growth. In subcutaneous xenograft models, tumors bearing Ctsc–Rab38 responded better to anti-PD1 therapy, highlighting its potential as a biomarker and therapeutic target. These findings indicate that chimeric RNAs can produce novel fusion proteins and neoantigens, disrupt the expression and function of partner genes, and guide clinical treatment stratification in ESCC.