On March 26, 2025, the research team led by Professor Zemin Zhang from the Biomedical Pioneering Innovation Center (BIOPIC) at Peking University / Chongqing Medical University published a research article titled “A single-cell atlas reveals immune heterogeneity in anti-PD-1-treated non-small cell lung cancer” in Cell as a Resource paper. This study represents a collaboration with teams from the National Cancer Center/Cancer Hospital of the Chinese Academy of Medical Sciences, Shanghai Pulmonary Hospital, Guangdong Provincial People’s Hospital, the First Affiliated Hospital of Zhengzhou University, Changping Laboratory, Chinese University of Hong Kong, University of Science and Technology of China, and other institutions.

 

Background

Non-small cell lung cancer (NSCLC), including lung squamous carcinoma (LUSC) and lung adenocarcinoma (LUAD), is among the most prevalent and fatal forms of cancer worldwide. For early-stage NSCLC, tumor resection remains the primary treatment modality in clinical practice. However, the surgical approach often fails to detect micro-metastases arising during tumor progression, leaving some patients vulnerable to disease recurrence following surgery. Neoadjuvant therapies, which involve preoperative drug administration, have demonstrated significant breakthroughs in the treatment of NSCLC. Since 2024, clinical studies such as CheckMate-816 have demonstrated that neoadjuvant anti-PD-1 immunotherapy combined with chemotherapy offers remarkable efficacy, achieving a major pathological response (MPR) in approximately 60% of patients, with a significant proportion also achieving complete pathological remission. These advances highlight the potential for curing locally advanced NSCLC, offering new hope for patients.

 

Nevertheless, there are two major unmet clinical challenges in neoadjuvant immunotherapy for NSCLC: (1) Approximately 40% of patients show low responsiveness, and the mechanisms underlying treatment resistance remain unclear; (2) About 20% of patients experience disease relapse despite undergoing neoadjuvant treatment, with no highly accurate biomarkers currently available for identifying patients at higher risk of recurrence. The study by Dr Zhang’s team, published in Cell on March 26, 2025, utilized scRNA/TCR-seq to systematically dissect the immune microenvironment of NSCLC patients following neoadjuvant immunotherapy. The researchers identified mechanisms of resistance in non-MPR patients and developed novel biomarkers to precisely predict relapse risk, providing critical insights for improving clinical management of NSCLC.

 

Figure 1 Key Findings and Study Design

 

The study classified patients based on the relative abundance of immune cell subtypes within their tumors. This analysis revealed five tumor immune microenvironment subtypes (TIME-subtypes) following neoadjuvant immunotherapy: TIME-NK, enriched for FGFBP2+ NK cells; TIME-BE, enriched for B cells and tertiary lymphoid structures; TIME-Teff, enriched for effector T cells; TIME-Treg, enriched for Tregs and terminally exhausted T cells; and TIME-Mye, enriched for myeloid cells. Notably, nearly half of the non-MPR patients exhibited the TIME-Treg subtype, implicating a strong association between Treg enrichment and reduced therapeutic efficacy.

 

Interestingly, this study also revealed that FGFBP2+ NK cells were not only enriched in responders to immunotherapy combined with chemotherapy but also in responders to chemotherapy alone. Furthermore, FGFBP2+ NK-like T cells exhibited extensive clonal expansion and lacked PDCD1 expression, suggesting that FGFBP2+ NK cells may mediate tumor killing via mechanisms distinct from those of conventional CD8+ T cells. In vitro experiments showed that NK cells could target and kill stressed malignant tumor cells following chemotherapy, highlighting the role of FGFBP2+ NK cells in chemotherapy-induced tumor eradication. In addition to the traditional view that chemotherapy predominantly enhances the efficacy of immunotherapy through tumor death and antigen release, this study demonstrated that chemotherapy could also directly activate a subset of NK cells for effective tumor cell killing.

 

Heterogeneity of Resistance Mechanisms in Non-MPR Patients

The study conducted an in-depth analysis of T cell receptor (TCR) clonality in T cells and uncovered two subsets of non-MPR patients with potentially distinct resistance mechanisms. Recent studies suggest that Tex-relevant T cell clones (exhausted T cell-related clones) and CCR8+ Treg clones may approximate tumor antigen-specific CD8+ T cells and tumor antigen-specific Tregs, respectively. By comparing the number and expansion levels of these clonal types across MPR and non-MPR patients, the team identified two categories of non-MPR patients: Treg-hi non-MPR patients, characterized by high numbers of both Tex-relevant and CCR8+ Treg clones, suggesting an association between poor responsiveness and the coexistence of heightened immune activation and immune suppression.Treg-low non-MPR patients, exhibiting low numbers and limited expansion of Tex-relevant clones, indicating insufficient immune activation. By elucidating the heterogeneity of resistance mechanisms among non-MPR patients, the findings provide evidence to guide more precise treatment strategies.

 

Predicting Recurrence Risk Using Exhausted T Cell Progenitors

The study also identified the abundance of progenitor exhausted T cells (Texp) as a robust predictor of postoperative recurrence risk, outperforming traditional pathological response metrics. This valuable biomarker facilitates the identification of high-risk patients at the time of surgery and provides critical insights for tailoring postoperative adjuvant therapies.

 

Significance and Impact

In summary, this study systematically characterized the immune microenvironment heterogeneity in NSCLC patients following neoadjuvant immunotherapy combined with chemotherapy and uncovered potential mechanisms underlying resistance in non-MPR patients. By developing novel biomarkers to predict relapse risk, this research holds both fundamental significance and translational value, paving the way for more effective and personalized clinical management of NSCLC.

 

 

 

Figure 2 - immune heterogeneity in anti-PD-1-treated NSCLC

 

The study was co-authored by Academician Dr. Zemin Zhang from BIOPIC of Peking University / Chongqing Medical University, Professor Shugen Gao from the National Cancer Center/Cancer Hospital of the Chinese Academy of Medical Sciences, Professor Chang Chen from Shanghai Pulmonary Hospital Affiliated To Tongji University, Professor Wenzhao Zhong from Guangdong Provincial People’s Hospital, Professor Yi Zhang from the First Affiliated Hospital of Zhengzhou University, professor Sijin Cheng from Changping Laboratory / Chongqing Medical University, Associate professor Linnian Zhu from BIOPIC of Peking University, Professor Chang Zou from Shenzhen People's Hospital, Associate professor Yunlang She from Shanghai Pulmonary Hospital Affiliated To Tongji University, and Academician Zhigang Tian from the University of Science and Technology of China as corresponding authors. PhD students Zedao Liu, Dr. Zhenlin Yang, Dr. Junqi Wu, PhD students Wenjie Zhang and Yuxuan Sun, Dr. Chao Zhang, Dr. Guangyu Bai, and Professor Li Yang are the study’s co-first authors. This research was supported by Changping Laboratory, National Key Research and Development Program of China, and the National Natural Science Foundation of China.

 

Paper link: https://www.cell.com/cell/fulltext/S0092-8674(25)00291-0