A 7-gene expression signature predicts immune microenvironment remodeling and neoadjuvant chemo-immunotherapy response in lung squamous cell carcinoma

Abstract

Background:

Neoadjuvant chemo-immunotherapy (NCI) has significantly improved outcomes in advanced lung squamous cell carcinoma (LUSC). However, some patients remain resistant to NCI, resulting in poor outcomes. The mechanisms behind this resistance remain unclear.

Methods:

Forty LUSC patients receiving NCI were selected and categorized into major pathological response (MPR) and non-MPR groups based on their pathological response. Pre- and post-treatment samples underwent bulk RNA sequencing (RNA-seq) to assess the composition of immune cell subtypes, including T cells, B cells, NK cells, dendritic cells, and macrophages. A panel of 134 immune cell subtypes were further analyzed to differentiate between “cold” and “hot” tumor immune phenotypes.

Results:

After surgery, 75% of patients achieved MPR, while 25% were classified as non-MPR. In MPR patients, NCI transformed the tumor immune microenvironment (TME) from a “cold” to a “hot” phenotype, characterized by increased anti-tumor immune activity. We identified seven genes potentially linked to NCI response. Among these, HOXC13 was associated with reduced immune-cell infiltration and inferior NCI response. High HOXC13 expression was associated with worse progression-free survival (PFS) and overall survival (OS), as confirmed by the OAK database.

Conclusions:

NCI altered the TME and was linked to treatment response in LUSC. Identifying predictors of immunotherapy efficacy, such as HOXC13, provides potential strategies to overcome resistance in clinical practice.

Introduction

Lung cancer is the leading cause of cancer-related mortality globally, accounting for 18% of all diagnosed cancers (1, 2). Lung squamous cell carcinoma (LUSC) is the second most common type, responsible for 20% to 30% of lung cancer-related deaths (3, 4). As a subtype of non-small cell lung cancer (NSCLC), LUSC includes spindle cell carcinoma (5), and is characterized by a fish-scale-like cell surface. It occurs predominantly in older men and is strongly associated with smoking (6).

For potentially resectable LUSC, surgery remains the cornerstone of treatment; however, for patients with intermediate to advanced LUSC, the surgical resection rate is low (~50%), leading to early postoperative recurrence (7, 8). Given the relative paucity of actionable oncogenic alterations in LUSC (9), opportunities for neoadjuvant targeted therapy are limited. Consequently, neoadjuvant chemo-immunotherapy (NCI) has become the predominant preoperative strategy (10, 11). Immune checkpoint inhibitors (ICIs) targeting programmed cell death protein 1 (PD-1) and its ligand PD-L1 are commonly used in immunotherapy, with favorable response observed in approximately 20% of lung cancer patients (12, 13). NCI combined with surgical treatment has shown a high radical resection rate (87.0%) for locally advanced LUSC, with pathological complete response (pCR) achieved in 26.1% of patients (14). Preclinical studies have demonstrated that ICIs combined with chemotherapy can further enhance the host immune response and inhibit cancer cells immune escape (15), underscoring the clinical promise of NCI. A common indicator of NCI efficacy is the “major pathological response” (MPR), defined as no more than 10% residual viable tumor cells in histopathological sections after treatment (16). Despite these advances, the average MPR rate for neoadjuvant ICIs is approximately 32% (ranging from 18% to 63%) (17), indicating that most patients exhibit resistance (non-MPR), the underlying mechanisms of which remain poorly defined.

In contrast to chemotherapy and targeted therapy, immunotherapy primarily targets the immune microenvironment rather than the tumor cells directly. Immunotherapy has the potential to reverse the tumor’s immunosuppressive microenvironment, trigger the body’s immune response, and ultimately eradicate the tumor (18, 19). Previous case reports have shown that NSCLC patients receiving neoadjuvant immunochemotherapy with MPR exhibited a large number of infiltrating immune cells in tumor tissues, including cytotoxic CD8⁺ T cells, monocyte-derived dendritic cells, and macrophages (20). Hu et al. demonstrated by bulk RNA-seq that neoadjuvant NSCLC tumors harbor an immunosuppressive microenvironment, which immuno-chemotherapy subsequently remodels by promoting the expansion and activation of cytotoxic CD8⁺T cells and CD16⁺NK cells (21). These studies suggest that immunotherapy can convert tumors from an immune “cold” to a “hot” phenotype. However, most investigations of the NSCLC/LUSC tumor immune microenvironment have been cross-sectional or have relied predominantly on post-operative specimens, limiting resolution of how NCI reshapes tumor-immune states from pre- to post-treatment (22). Moreover, in LUSC-where NCI is the prevailing neoadjuvant approach-clinically deployable pre-treatment biomarkers capable of prospectively identifying non-responders remain lacking.

To address these unmet needs, we assembled a cohort of resectable LUSC with paired pre- and post-NCI tumor samples and performed bulk RNA sequencing (RNA-seq) to quantify immune-cell enrichment and phenotypic shifts using signature-based deconvolution. We then applied weighted gene co-expression network analysis (WGCNA) to identify genes/modules associated with NCI efficacy. Together, these analyses delineate dynamic immunologic remodeling across treatment and support an immune-microenvironment-driven, preoperative predictor of NCI response tailored to LUSC.

Methods

The study design is shown in Figure 1. A brief description is given below.

Figure 1

Ethics approval and consent to participate

The study protocol was approved by the Institutional Review Board of Tongji University affiliated Shanghai Pulmonary Hospital (IRB: K24-084Y), and all participants provided written informed consent.

Study population

This retrospective study consecutive enrolled 40 patients with LUSC who received NCI at Shanghai Pulmonary Hospital between January 7, 2020, and September 7, 2022. The key inclusion criteria were: (1) clinical stage IIB-IIIC LUSC diagnosed by imaging and pathology; (2) no prior systemic chemotherapy, radiotherapy, surgery, or targeted therapies; and (3) absence of EGFR, ALK, and other driver gene mutations, with normal organ function. The main exclusion criteria were inoperable tumors after treatment or as a result of clinical incident, immunodeficiency, current systemic immunosuppressive therapy, and active autoimmune or infectious diseases. Additionally, patients lacking paired pre- and post-treatment tissue samples were also excluded.

Patients received 2 to 4 cycles of NCI therapy (PD-1 antibody + chemotherapy) followed by surgery. The study flow chart is depicted in Figure 1. Additionally, we utilized transcriptomic data of patients from the OAK Clinical Trial (NCT02008227) to validate the impact of relevant genes on the efficacy of immunotherapy in lung cancer patients.

Sample collection

Pre-NCI treatment primary tumor tissues were obtained via percutaneous pulmonary, bronchoscopy, or EBUS-guided biopsies. Post-treatment tissues were collected during surgical resection. A total of 40 paired samples were collected for bulk RNA-seq. All specimens were prepared into formalin-fixed and paraffin-embedded (FFPE) blocks by pathologists and stored at room temperature for subsequent analysis.

RNA-seq library construction and sequencing

RNA was extracted from FFPE tissue samples (n = 80) using an FFPE RNA Extraction kit (Amoy Diagnostics, Xiamen, China). Oligo(dT) magnetic beads were used to enrich mRNAs with polyA tails in total RNA, and the fragments were then broken up in a fragmentation buffer that contained divalent cations. Using random hexamer primers and the fragmented mRNA as a template, first- and second-strand cDNAs were synthesized, followed by end repair, poly-A 3’ ends, and splice sites. DNA fragment enrichment, and the NEBNext^® Ultra™ RNA Library Prep Kit for Illumina^® (Illumina, San Diego, CA, USA) were utilized to create the RNA library to build RNA-seq collections. Library quality was assessed on an Agilent Bioanalyzer 2100 system (Agilent Technologies, Palo Alto, CA, USA). Only libraries with an RNA integrity number (RIN) ≥ 6.0 and concentration ≥ 10 ng/µL were processed further. Finally, sequence analysis of RNA-Seq data was performed using the Illumina NovaSeq 6000 platform for the 150-bp end-to-end model. For each sample, a minimum of 10 Gb of clean data was generated, ensuring sufficient coverage for transcriptome profiling and downstream analyses.

Read processing, normalization, batch correction and differential expression

The number of read segments mapped to each gene was calculated using FeatureCounts (1.5.0-p3). The FPKM for each gene was then calculated based on gene length and the number of read segments mapped to that gene was calculated. Raw counts were converted to transcripts per million (TPM), and then transformed to log₂ (TPM + 1) for normalization. Samples with more than 50% of the genes having zero values were excluded. For gene-level differential expression between paired pre- and post-treatment tumors, per-gene differences were assessed using the Wilcoxon signed-rank test (23). Statistical significance was defined as two-sided p<0.05. Given the exploratory and small-sample nature of this study, p-values are reported as nominal alongside effect-size descriptors. All analyses were performed in R (v4.1.0).

Cell type annotation and cluster marker identification

The CIBERSORT algorithm (v1.03) with the LM22 signature matrix was applied to estimate the abundance of immune cell expansion for each sample based on the gene expression file. Immune-infiltration scores of bulk-RNA-seq data were estimated using ssGSEA. The subtypes of tumor immune microenvironment (TME) related cells based on previous studies (24).Immune-infiltration scores were further quantified by ssGSEA using two complementary reference sets—(1) the 29 immune-associated hallmarks from published signatures, and (2) a collection of 134 TME-related cell-type markers (T cells, B cells, NK cells, fibroblasts, dendritic cells, macrophages, etc.) derived from single-cell studies (25–30) (Supplementary Table 2). All ssGSEA enrichment scores were median-scaled across samples, and Louvain clustering on the 29-hallmark matrix partitioned tumors into four microenvironment subtypes: Immune-Enriched/Fibrotic (IE/F), Immune-Enriched (IE), Fibrotic (F), Depleted (D). Finally, based on their overall immune infiltration, the IE/F and IE subtypes were grouped as “hot” tumors, while the F and D subtypes were classified as “cold” tumors (24).

Gene set enrichment analysis

Enrichment analysis was performed using the Cluster Profiler package in R(v4.1.0) (31). The gene set c2.cp.kegg.v7.0.symbols from Molecular Signatures Database (MSigDB) was used for GSEA analysis, and KEGG pathways were screened for significant enrichment with nominal two-sided P value < 0.05.

Weighted gene co-expression network analysis

WGCNA was performed to identify gene modules associated with “cold” and “hot” tumors in the immune microenvironment. Gene expression data (log₂(TPM + 1)) were preprocessed by removing low-variance genes and then quantile-normalized across samples to reduce noise and standardize data distribution. WGCNA was carried out using the “WGCNA” R package.

The network was constructed using a soft-thresholding parameter (β), determined by the lowest power value that resulted in a scale-free topology fit of R²= 0.9. A clustering dendrogram was generated to visualize gene modules, with dynamic module detection performed using the dynamic tree cut method. Modules with high similarity were merged at a mergeCutHeight of 0.20. The minimum module size was set to 30 genes (minModuleSize = 30) to avoid fragmenting smaller but biologically relevant gene clusters. The soft-threshold power β was selected as 4. To identify the modules most strongly associated with immune infiltration scores, Pearson correlation analyses were performed between the module eigengenes (MEs) and “Cold” tumors. The modules with the highest correlation to “Cold” tumors were selected for further analysis.

Statistical analysis

Immune-cell enrichment and pathway/signature scores were compared using Wilcoxon tests: Wilcoxon signed-rank for paired pre- vs post-treatment comparisons within patients, and Wilcoxon rank-sum for between-group comparisons (MPR vs non-MPR). Overall survival (OS) and progression-free survival (PFS) were estimated by the Kaplan–Meier method; group differences were evaluated using the log-rank test. Hazard ratios (HRs) with 95% confidence intervals were obtained from Cox proportional-hazards models (univariable unless otherwise specified). Unless noted otherwise, statistical significance was defined as two-sided p<0.05. Analyses were conducted in R (v4.1.0) using the survival and survminer packages.

Results

Patient characteristics

Between January 7, 2020, and September 7, 2022, 40 eligible patients signed informed consent and were enrolled (Table 1). The median age was 67 years (range 50-76); 97.5% (n = 39) were male, and 2.5% (n = 1) was female. At baseline, 6 patients (15%) had stage IIB disease according to the AJCC^8th edition, while 34 patients (85%) were classified as stage III (including IIIA, IIIB, and IIIC). Subsequently, all patients received NCI therapy (PD-1 antibody plus chemotherapy) followed by surgical resection (Figure 1a). Based on postoperative pathological evaluation, patients were categorized into non-MPR (10 patients, 25%), and MPR (30 patients, 75%). Selected patient characteristics are shown in Figure 1b.

Significantly increased immune infiltration in MPR patients post-NCI

Transcriptome sequencing was performed on tumor samples from MPR and non-MPR groups pre- and post-NCI. Signaling pathway enrichment analysis was subsequently performed on the upregulated gene expression pre- and post-treatment in the MPR and non-MPR groups (|log₂ fold-change|≥ log₂(1.5) & p<0.05). In the MPR group, various pathways associated with immune response and anti-tumor effects showed significant upregulation post-treatment, including allograft rejection, complement system, and inflammatory response (Figure 2b). Downregulated genes were mainly enriched in oncogenic pathways such as, MYC, mTORC1, and glycolysis (Figures 2a, b). These results suggest that NCI activated multiple important immune and antitumor pathways, enhancing tumor immune responses in patients with MPR. Conversely, pathway enrichment analysis of patients in the non-MPR group pre- and post-treatment indicated fewer upregulated pathways. These pathways mainly involved myogenesis, epithelial-mesenchymal transition, and coagulation pathways (Figure 2b). Notably, gene sets annotated to inflammatory response were less prominently represented among upregulated genes in the non-MPR group than in the MPR group, although a modest enrichment signal remained detectable post-NCI (Supplementary Figures S1a, b). To contextualize these patterns, we computed ssGSEA enrichment scores for a panel of 134 immune cell type signature gene sets curated from six single-cell studies and projected them onto bulk RNA-seq, organizing columns by timepoint (pre vs post NCI) and response (MPR vs non-MPR) to visualize group-level shifts (Figure 2c; Supplementary Table 1). In the MPR group, multiple immune-cell-related signatures increased after NCI, whereas such changes were limited in non-MPR.

Figure 2

We next quantified immune-cell enrichment at the patient level. In MPR, enrichment increased after NCI for immature B cells (p<0.01), activated B cells (p<0.01), effector-memory CD8+T cells (p<0.01), and natural killer T cells (p<0.01) (Figure 2d). In non-MPR, no significant pre/post changes were observed across common immune cell (Figure 2d). At baseline, immune-cell enrichment did not differ between MPR and Non MPR group (Supplementary Figure S1c). Post-NCI, MPR tumors displayed higher antitumor immune activity than non-MPR, including activated B cells (p<0.01), activated CD8+T cells (p=0.02), activated dendritic cells (p<0.01), and central-memory CD4+ T cells (p<0.01) (Supplementary Figure S1d).

Collectively, these findings indicate that NCI elicits robust adaptive immune activation in responders, while immune remodeling is blunted in non-responders, aligning with their inferior pathological response.

Immune microenvironment clustering based on 134 single-cell features distinguishes “hot” and “cold” tumors associated with therapeutic response

RNA-seq and immune microenvironment clustering analyses were performed on pre- and post-treatment samples to characterize “cold” and “hot” tumors in LUSC. Figures 3a, b illustrating immune cell enrichment scores in pre- and post-treatment samples, along with dynamic changes in immune cell composition among treatment response groups (MPR and non-MPR). The samples were categorized into three and four subgroups based on immune cell enrichment in pre-treatment and post-treatment samples respectively. According to TME characteristics, these subgroups were labeled as fibrosis (F), immune-enriched, and depleted (D) (Supplementary Figures S2a, b). As shown in Figure 3b, Cluster 1(C1) and 2 (C2) was classified as a “hot” tumor due to higher T cell and NK cell enrichment scores, while Clusters 3 (C3) and 4 (C4) were defined as “cold” tumors with lower B cell and dendritic cell enrichment scores. As for pre-treatment samples, MPR patient were predominantly concentrated in the “hot” tumor cluster, while non-MPR patients were predominantly concentrated in the “cold” tumor cluster (24) (Figure 3a). Post-treatment, MPR patients remained predominantly in “hot” clusters, whereas non-MPR patients persisted in “cold” clusters (Figure 3b; Supplementary Figure S2b).

Figure 3

According to the Sankey plot results, nearly half of the “cold” tumors converted to “hot” post-NCI (Figure 3c; Supplementary Figure S2c). Pre-treatment, MPR and non-MPR patients exhibited a balanced distribution between “cold” and “hot” tumor subpopulations (Figure 3d). Post-treatment, 96.4% of MPR patients were in “hot” clusters, while 75% of non-MPR patients remained in “cold” clusters (Figure 3e; Supplementary Figure S2d), underscoring the link between “hot” phenotypes and treatment response.

Identification of 7 genes associated with the efficacy of NCI

To explore genes associated with NCI efficacy, we compared differentially expressed genes (DEGs) between tumors transitioning from “hot” to “cold” (HC) and those maintaining “cold” tumor (CC) with other subgroups, 267 genes were identified significantly upregulated in HC or CC groups (|Log2FC| > Log2 (1.5), p < 0.05) (Figure 4a). Furthermore, we constructed a gene co-expression network using WGCNA. Initially, we calculated Pearson correlation coefficients between all gene pairs and selected a soft-threshold power of 4 to ensure the network displayed scale-free topology. Then associated the module eigengenes with tumors transitioning from “hot” to “cold” or maintaining ‘cold’ status post-NCI therapy. The results indicated that 4 modules were significantly correlated with “cold” tumors post-NCI therapy (r > 0.3, p < 0.05) (Figure 4b). Additionally, using univariate logistic regression, we identified 1039 genes significantly associated with MPR (p < 0.05, Figure 4c). Seven genes (TNNT1, FOXL2, LMX1B, NEFL, HOXC13, ASS1, and KLK11) were identified as the intersection of the three datasets, defining them as genes associated with NCI efficacy (Figure 4d).

Figure 4

We conducted a detailed analysis of the expression of seven genes and immune cell infiltration pre-NCI, aiming to further explore their relationship with treatment response. Univariate Cox regression analysis demonstrated the difference of these seven genes in NCI response, revealing associations with non-MPR patients (Figure 4e). Receiver operating characteristic (ROC) analysis demonstrated good diagnostic efficacy for predicting non-MPR with an area under ROC curve (AUC) value of 0.837 (Figure 4f). Additionally, leave-one-out cross-validation confirmed that the model still exhibits strong discriminatory performance for MPR (Supplementary Figure S3a).

Figure 5a illustrates the expression levels of these genes in MPR and non-MPR patients, showing significantly higher expression in the non-MPR group. The mean expression of these seven genes was significantly higher in the non-MPR group compared to the MPR groups (p < 0.05, Figure 5b). Based on the median-defined thresholds of seven-gene expression score(cutoff=2.6), the patients were classified into high-expression and low-expression groups, only one non-MPR patient was in the low-expression group (Figure 5c).In multivariable analysis (adjusting for stage, age, and PD-L1 status), the seven-gene high group remained independently associated with non-MPR (OR = 3.24[1.2-12.2], p=0.038, Supplementary Figure S3b).In addition, in the group of seven genes with high expression, the DEGs were mainly enriched in pathways such as mTORC1 signaling, MYC targets, and KRAS signaling (Figure 5d). These pathways are associated with cancer oncogenic pathways. Furthermore, we analyzed the correlation between seven genes and the dynamic changes of various immune cell types pre- and post-NCI. The results indicated that the expression of these seven genes was significantly positively correlated with the CD4. c23 (NME1⁺CCR4^-T), CD8. C17 (NME1⁺T) and CD56dimCD16hi cell type and negatively correlated with other immune cells (Figure 5e). Moreover, the HOXC13 gene exhibited a positive correlation with NK cell types such as CD56dimCD16hi and CD56brightCD16lo and a negative correlation with the dynamic changes of most immune cells. The NEFL gene showed a negative correlation with various T cell types, such as CD8⁺T cell and CD4⁺T cell, while the TNNT1 gene was significantly correlated with CD56dimCD16hi NK cell types (Figure 5e). These correlation analyses revealed the expression patterns of specific genes in various immune cell types, indicating their potential roles in the immune microenvironment.

Figure 5

Validation of seven genes expression levels associated with immunotherapy for LUSC based on public databases

In an independent neoadjuvant cohort of 10 resectable stage II–III LUSC patients (21), we defined 7-gene high expression as high risk using an optimal cutoff (cutoff = 1.5). The high-risk group showed a markedly lower MPR rate than the low-risk group (12.5% vs 100%, p = 0.0667) (Supplementary Figure S3b). Given the limited availability of public neoadjuvant LUSC datasets with pretreatment biopsies, we further assessed the signature in the phase III OAK trial. To further investigate the relationship between the expression levels of the seven genes and immunotherapy efficacy, we confirmed their correlation in a phase III clinical study (OAK trial) comparing immunotherapy versus chemotherapy in NSCLC. In the LUSC immunotherapy group, using the optimal OS-separating cut point to define 7-gene high vs low, patients with high gene expression had shorter PFS (p = 0.004) and OS (p = 0.047) compared to those with low gene expression (Figures 6a, b). However, in the LUSC chemotherapy group, the expression of the seven genes did not affect patient OS and PFS (Supplementary Figure S4a). These findings strongly suggest that the expression of the seven genes was associated with immunotherapy efficacy, with high expression potentially reducing its efficacy.

Figure 6

High expression levels of the seven genes did not impact PFS and OS between immunotherapy (MPDL3280A, Atezolizumab) and chemotherapy (Docetaxel) groups in non-LUSC and NSCLC patients (Supplementary Figures S4b, c). Among non-LUSC and NSCLC patients with low gene expression, there was no significant difference in PFS between immunotherapy and chemotherapy groups. Nevertheless, immunotherapy was found to significantly extend OS in NSCLC patients with low gene expression (p = 0.0034) (Supplementary Figure S4d). These findings suggest that the seven genes could serve as specific immunotherapeutic biomarkers in LUSC.

Furthermore, based on the OAK database, we conducted a univariate Cox regression analysis of the expressions of the seven genes with PFS and OS in NSCLC, LUSC, and LUAD patients (Supplementary Figures S5a, b). Furthermore, using the OAK dataset, we performed univariable Cox regression of the seven-gene expression score for PFS and OS in NSCLC, LUSC, and LUAD (Supplementary Figures S5a, b). Higher seven-gene expression was associated with worse OS (HR = 1.40; 95% CI, 1.04–1.88; p = 0.026) and shorter PFS (HR = 1.34; 95% CI, 1.01–1.77; p = 0.022) (Figure 6c). In multivariable Cox models adjusting for available baseline covariates, the associations remained directionally consistent. Notably, HOXC13 showed a significant association with shorter OS (HR = 1.44; 95% CI, 1.06–1.95; p = 0.018) and a trend toward shorter PFS (HR = 1.29; 95% CI, 0.98–1.69; p = 0.066) (Figure 6c).

Discussion

Immune checkpoint inhibitors have transformed LUSC treatment, extending from metastatic disease to locally advanced, resectable tumors (32). NCI provides the opportunity for early eradication of micrometastatic lesions, thereby enhancing treatment initiation and adherence rates, and potentially eliminating live tumor cells released into the circulation during surgery (33, 34). Hence, NCI may confer additional benefits. Studies have demonstrated that NCI can significantly improve overall survival. In early-stage resectable NSCLC, NCI has achieved a 45% MPR rate (35). However, a majority of patients exhibit inadequate tumor response to immunotherapy, leading to unfavorable treatment outcomes. Therefore, this study investigated mechanisms of suboptimal NCI response in LUSC. We enrolled 40 patients with LUSC who received NCI therapy (PD-1 antibody + chemotherapy) followed by surgical resection. Encouragingly, up to 30% of resected tumors exhibited pCR or MPR, highlighting the anti-tumor efficacy of NCI in LUSC as observed in this study. This finding is consistent with previous studies reporting MPR results (35). Nevertheless, 10% of patients exhibited inadequate tumor response (non-MPR).

The TME comprises malignant cells alongside a heterogeneous mix of non-malignant stromal, vascular, and immune cell populations. With the success of immunotherapy, the role of the TME in tumor development and progression has been extensively studied (36, 37). We speculated that the low efficacy of NCI in LUSC patients could be closely related to the impaired infiltration of immune cells in the tumor. For this reason, tumor tissues pre- and post-treatment were collected for bulk RNA-seq analysis, and the enrichment of immune cells in tumor tissues was compared between the MPR group and the non-MPR group. Interestingly, we found that in the MPR group, after immunotherapy, there was a significant increase in the infiltration of immune cells in the tumor samples compared to pre-treatment. In particular, the infiltration of activated B cells, CD8⁺ T cells, NK cells and macrophages was increased. This result is similar to literature research studies (38, 39). On the one hand, Chen et al. found that in LUSC, the proportion of CD8⁺ T cell subclusters was higher in patients with MPR after immunotherapy (40). On the other hand, immune cells such as dendritic cells and macrophages were found to exhibit higher levels of anti-tumor immune responses in the immune-responsive group than in the non-immune-responsive group (41). In addition, previous studies used PD-L1 blockade to increase CD8⁺ T cell infiltration in lung cancer, and depletion of CD8⁺ T reversed its anti-cancer effect, suggesting that CD8⁺ T has anti-cancer potential (42). B cells can enhance the killing effect of CD8⁺ T lymphocytes on lung stem-like cancer cells (43). While depletion of NK cells and macrophages aggravated tumor progression (44, 45). Thus, in patients with MPR, undergoing NCI activated most of the anti-tumor immune cells to exert a significant anti-cancer effect. On the contrary, in patients with non-MPR, these immune cells were not effectively activated after treatment, resulting in ineffective NCI.

There are significant differences in the remodeling of the immune microenvironment after immunotherapy in patients with different pathological responses. We hypothesized that good responders (MPR patients) might had substantial immune cell activation, whereas poor responders (non-MPR patients) might suffer from a deficiency in the infiltration of immune cells. To further explore the immune cell typing in the samples, we classified the immune cells into subtypes based on the clustering of 134 immune cells. Pre-treatment, the samples were classified into three clusters, with cluster C1 defined as “hot” tumors and clusters C2/C3 defined as “cold” tumors based on immune cell activation. Using the same method, cells from the post-immunotherapy samples were also clustered, with the C1/C2 cluster defined as “hot” tumors and the C3/C4 cluster defined as “cold” tumors. “Hot” tumors were found to be enriched with T- and NK-cell immune cells, which have anticancer effects. In contrast, overall immune cells were not enriched in “cold” tumors. Notably, post-NCI, MPR patients tend to concentrate in the “hot” tumor subpopulation, whereas non-MPR patients concentrate in the “cold” tumor subpopulation. Previous studies have also found that tumors that respond well to immunotherapy are reprogrammed from an immune “cold” phenotype to an immune “hot” phenotype (20, 46, 47), which is consistent with the findings of this work. Patients who respond to immunotherapy exhibit robust in vivo activation and infiltration of effector immune cells, whereas poor responders show minimal immune cell recruitment. Consequently, strategies that enhance intratumoral immune infiltration may help overcome resistance to checkpoint blockade.

Among the seven identified genes associated with NCI response, HOXC13 was found to be oncogenic in previous reports (48). Over expression of HOXC13 promoted the proliferation of lung adenocarcinoma cells and facilitated cell cycle progression (49). Furthermore, in glioblastoma, the correlation between HOXC13 expression and immune cell infiltration (50). High expression of HOXC13 expression suppressed infiltration of γδ T cells and plasma cells (51). Interestingly, this study also found a negative correlation between HOXC13 expression and enrichment of mostly immune cells such as T cells and B cells. HOXC13 was associated with OS and showed a trend toward association with PFS in immunotherapy-treated LUSC, supporting HOXC13 as a candidate marker related to immunotherapy outcomes. However, its prognostic role in LUSC appears limited, warranting further investigation. Specifically, targeting HOXC13 expression to increase immune cell activation could potentially enhance the efficacy of NCI. Mechanistically, HOXC13 may suppress immune infiltration through several tumor-intrinsic programs. First, HOXC13 has been shown to remodel the tumor–immune microenvironment by regulating innate sensing/IFN programs (cGAS–STING–IRF3 axis) and chemokines, implying that dysregulated HOXC13 can blunt type-I IFN signaling and T-cell-supportive cytokines (51). Second, HOXC13 can reprogram epigenetics (e.g.,upregulating DNMT3A) and cell-cycle/glycolytic pathways, a milieu linked to reduced antigen visibility and non-inflamed states (52). Third, tissue data in other cancers suggest an inverse association with CD8⁺ T-cell presence, consistent with an immune-excluded phenotype (53). Collectively, these lines of evidence support a model in which HOXC13 shapes immune quality (type-I IFN tone, antigen presentation/epigenetics, chemokine milieu) rather than merely altering bulk immune-cell quantities.

High ASS1 expression remodels the tumor microenvironment by driving a purine‐rich metabolic state that suppresses immunoproteasome activity and neoantigen presentation, resulting in diminished CD8⁺ T-cell infiltration and poor ICI response. Pharmacologic inhibition of purine synthesis in ASS1-high tumors restores a more immunogenic milieu and significantly enhances anti-PD-1 efficacy (54).TNNT1 (55), FOXL2 (56), LMX1B (57), NEFL (58), and KLK1 (59) regulate key aspects of tumor biology, including epithelial-mesenchymal transition, proliferation, metastasis, tumor grade, and extracellular matrix remodeling. These genes may indirectly influence the immune microenvironment, although direct evidence is still lacking. While their roles in tumor progression, metastasis, and prognosis in lung cancer are well-established, their specific contributions to immune microenvironment modulation remain largely unexplored.

Notably, ASS1 and LMX1B were not associated with bulk shifts in common immune-cell compartments in our data. This is compatible with mechanisms that alter immune quality (function, localization, spatial exclusion) rather than quantity per se—for example, ASS1-driven metabolic/antigen-processing effects and LMX1B-linked stromal/ECM programs that can reposition or dampen antitumor immunity without large changes in overall cell proportions (54, 60). These hypotheses call for spatial and functional validation in future cohorts.

There are some limitations of this study. First, because this study was an exploratory pilot study, the number of patients enrolled was small. Additionally, there is a notable imbalance between the MPR and non-MPR groups, which may introduce bias and affect the robustness of the findings. Therefore, a larger, well-balanced randomized controlled trial is needed to further validate our findings and mitigate these limitations. Second, the biological mechanisms underlying the association between HOXC13 expression and immunotherapy outcomes in LUSC remain unclear. In particular, whether HOXC13 contributes to an immune-excluded microenvironment and reduced immunotherapy benefit requires further functional and protein-level validation in future studies. Third, although we identified a seven-gene panel associated with response, how these genes shape the LUSC immune microenvironment is not fully defined; importantly, future studies should validate their expression at the protein level and test their association with clinical efficacy.

In conclusion, this study delineates the immune microenvironment of tumor samples from patients pre- and post-NCI. The samples were stratified into MPR and non-MPR groups based on treatment efficacy. In the MPR group, the immune microenvironment was observed to transition from an immune “cold” to an immune “hot” phenotype following NCI therapy, stimulating immune activity. HOXC13 was identified as a key factor impairing immune cell infiltration and NCI efficacy in LUSC. This study identifies factors contributing to suboptimal NCI outcomes and suggests potential clinical targets.

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