Objective Deep learning signatures (DLS) extracted from CT images can noninvasively reflect tumor heterogeneity and have shown promise in prognostic modeling for esophageal squamous cell carcinoma (ESCC). To develop and validate a CT-based DL model combined with nutritional biomarkers to predict 3-year overall survival (OS) in ESCC, and to investigate transcriptomic differences between DLS-based risk groups. Materials and methods This retrospective multicenter study included 662 postoperative ESCC patients from three hospitals and 16 additional patients from The Cancer Genome Atlas (TCGA). DL features extraction from CT images based on the Crossformer architecture. Skeletal muscle index was measured at the L3 vertebra to assess low skeletal muscle mass (LSMM). Cox regression was used to build clinical, DL, and combined models. Model performance was evaluated using the concordance index (C-index). Transcriptomic analysis of the TCGA cohort was performed to identify metabolic pathway differences between DLS-based risk groups. Results The DL model achieved a C-index of 0.743 (95% CI: 0.683–0.803) in the internal validation cohort and 0.692 (95% CI: 0.576–0.809) in the external cohort. Pathological T and N stages, Neuroaggression, Vascular invasion, and LSMM were identified as independent clinical predictors. The combined model achieved a C-index of 0.753 (95% CI: 0.697–0.808) internally and 0.725 (95% CI: 0.613–0.838) externally. DLS–based risk stratification revealed significant differences in metabolic activity between groups, supporting its biological relevance. Conclusion The combined model enables preoperative OS prediction in ESCC. DLS–based stratification reflects transcriptomic metabolic heterogeneity and enhances the biological interpretability of imaging features. Critical relevance statement This study developed a CT-based DLS and combined it with nutritional markers for prognostic modeling in ESCC. Transcriptomic analysis of DLS-based groups revealed metabolic heterogeneity, enhancing the biological interpretability of the DL model. Key Points <UnorderedList Mark="Bullet"> <ItemContent> A combined DLS and nutritional model enables individualized preoperative survival prediction in ESCC. </ItemContent> <ItemContent> DLS-based risk groups defined by the DLS exhibited transcriptomic differences in key metabolic pathways, revealing biological underpinnings of imaging-based phenotypes. </ItemContent> <ItemContent> Attention map visualization revealed consistent spatial focus on morphologically distinct tumor regions, enhancing the interpretability of deep learning predictions. </ItemContent> </UnorderedList> Graphical Abstract

CT-based deep learning signatures associated with transcriptomic heterogeneity and combined with nutritional biomarkers improve prediction of 3-year overall survival in esophageal squamous cell carcinoma

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2026年1月26日

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Jianye Jia,
Yahui Cheng,
Jiahao Wang,
Genji Bai,
Lei Han,
Lixue Xu,
Yantao Niu

摘要

Objective

Deep learning signatures (DLS) extracted from CT images can noninvasively reflect tumor heterogeneity and have shown promise in prognostic modeling for esophageal squamous cell carcinoma (ESCC). To develop and validate a CT-based DL model combined with nutritional biomarkers to predict 3-year overall survival (OS) in ESCC, and to investigate transcriptomic differences between DLS-based risk groups.

Materials and methods

This retrospective multicenter study included 662 postoperative ESCC patients from three hospitals and 16 additional patients from The Cancer Genome Atlas (TCGA). DL features extraction from CT images based on the Crossformer architecture. Skeletal muscle index was measured at the L3 vertebra to assess low skeletal muscle mass (LSMM). Cox regression was used to build clinical, DL, and combined models. Model performance was evaluated using the concordance index (C-index). Transcriptomic analysis of the TCGA cohort was performed to identify metabolic pathway differences between DLS-based risk groups.

Results

The DL model achieved a C-index of 0.743 (95% CI: 0.683–0.803) in the internal validation cohort and 0.692 (95% CI: 0.576–0.809) in the external cohort. Pathological T and N stages, Neuroaggression, Vascular invasion, and LSMM were identified as independent clinical predictors. The combined model achieved a C-index of 0.753 (95% CI: 0.697–0.808) internally and 0.725 (95% CI: 0.613–0.838) externally. DLS–based risk stratification revealed significant differences in metabolic activity between groups, supporting its biological relevance.

Conclusion

The combined model enables preoperative OS prediction in ESCC. DLS–based stratification reflects transcriptomic metabolic heterogeneity and enhances the biological interpretability of imaging features.

Critical relevance statement

This study developed a CT-based DLS and combined it with nutritional markers for prognostic modeling in ESCC. Transcriptomic analysis of DLS-based groups revealed metabolic heterogeneity, enhancing the biological interpretability of the DL model.

Key Points

A combined DLS and nutritional model enables individualized preoperative survival prediction in ESCC.

DLS-based risk groups defined by the DLS exhibited transcriptomic differences in key metabolic pathways, revealing biological underpinnings of imaging-based phenotypes.

Attention map visualization revealed consistent spatial focus on morphologically distinct tumor regions, enhancing the interpretability of deep learning predictions.

Graphical Abstract