Immune and stromal scoring system associated with tumor microenvironment and prognosis: a gene-based multi-cancer analysis

BACKGROUND: Tumor microenvironment (TME) is associated with tumor progression and prognosis. Previous studies provided tools to estimate immune and stromal cell infiltration in TME. However, there is still a lack of single index to reflect both immune and stromal status associated with prognosis and immunotherapy responses. METHODS: A novel immune and stromal scoring system named ISTMEscore was developed. A total of 15 datasets were used to train and validate this system, containing 2965 samples from lung adenocarcinoma, skin cutaneous melanoma and head and neck squamous cell carcinoma. RESULTS: The patients with high immune and low stromal scores (HL) were associated with low ratio of T cell co-inhibitory/stimulatory molecules and low levels of angiogenesis markers, while the patients with low immune and high stromal scores (LH) had the opposite characteristics. The HL patients had immune-centered networks, while the patients with low immune and low stromal scores (LL) had desert-like networks. Moreover, copy number alteration burden was decreased in the HL patients. For the clinical characteristics, our TME classification was an independent prognostic factor. In the 5 cohorts with immunotherapy, the LH patients were linked to the lowest response rate. CONCLUSIONS: ISTMEscore system could reflect the TME status and predict the prognosis. Compared to previous TME scores, our ISTMEscore was superior in the prediction of prognosis and immunotherapy response. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12967-021-03002-1.