Analysis of Gene Signatures of Tumor Microenvironment Yields Insight Into Mechanisms of Resistance to Immunotherapy

Ben Wang; Mengmeng Liu; Zhujie Ran; Xin Li; Jie Li; Yunsheng Ou

doi:10.3389/fbioe.2020.00348

Analysis of Gene Signatures of Tumor Microenvironment Yields Insight Into Mechanisms of Resistance to Immunotherapy

Front Bioeng Biotechnol. 2020 May 25:8:348. doi: 10.3389/fbioe.2020.00348. eCollection 2020.

Authors

Ben Wang¹, Mengmeng Liu², Zhujie Ran³, Xin Li⁴, Jie Li⁵, Yunsheng Ou¹

Affiliations

¹ Department of Orthopedics, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China.
² Graduated School of Anhui University of Traditional Chinese Medicine, Hefei, China.
³ School of Public Health and Community Medicine, Chongqing Medical University, Chongqing, China.
⁴ Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China.
⁵ Department of Oncology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China.

Abstract

Background: The recent clinical success of immunotherapy represents a turning point in cancer management. But the response rate of immunotherapy is still limited. The inflamed tumor microenvironment has been reported to correlate with response in tumor patients. However, due to the lack of appropriate experimental methods, the reason why the immunotherapeutic resistance still existed on the inflamed tumor microenvironment remains unclear. Materials and Methods: Here, based on single-cell RNA sequencing, we classified the tumor microenvironment into inflamed immunotherapeutic responsive and inflamed non-responsive. Then, phenotype-specific genes were identified to show mechanistic differences between distant microenvironment phenotypes. Finally, we screened for some potential drugs that can convert an unfavorable microenvironment phenotype to a favorable one to aid current immunotherapy. Results: Multiple signaling pathways were phenotypes-specific dysregulated. Compared to non-inflamed microenvironment, the expression of interleukin signaling pathways-associated genes was upregulated in inflamed microenvironment. Compared to inflamed responsive microenvironment, the PPAR signaling pathway-related genes and multiple epigenetic pathways-related genes were, respectively, suppressed and upregulated in the inflamed non-responsive microenvironment, suggesting a potential mechanism of immunotherapeutic resistance. Interestingly, some of the identified phenotype-specific gene signatures have shown their potential to enhance the efficacy of current immunotherapy. Conclusion: These results may contribute to the mechanistic understanding of immunotherapeutic resistance and guide rational therapeutic combinations of distant targeted chemotherapy agents with immunotherapy.

Keywords: immunotherapeutic resistance; immunotherapy; molecular targeted agents; personalized medicine; tumor microenvironment.