Spatiotemporal single-cell analysis decodes cellular dynamics underlying different responses to immunotherapy in colorectal cancer

Immunogenomic characteristics and prognostic implications of terminally exhausted CD8+ T cells in colorectal cancers

Introduction

T-cell exhaustion is a major mechanism of immune evasion. Recently, the therapeutic and prognostic implications of progenitor exhausted T cells (Tpex) and terminally exhausted T cells (Ttex) have been explored in various cancer types. This study explored the immunogenomic characteristics and prognostic implications of Tpex and Ttex in colorectal cancers (CRCs).

Methods

We performed multiplex immunofluorescence (mIF) using antibodies against CK, CD3, CD8, TCF1, and FOXP3 to assess diverse subsets of tumor-infiltrating lymphocytes (TILs) in 517 patients with stage III or high-risk stage II CRCs. We compared the infiltration level of these TIL subsets with the genetic profiles of CRCs, including microsatellite instability (MSI), tumor mutational burden (TMB), and mutations in 40 tumor-associated genes across five biological pathways.

Results

CD8+ T cell density, the CD8/CD3 ratio, and the Ttex/CD8+ T cell ratio were elevated in microsatellite instability-high and tumor mutational burden-high tumors. Survival analysis showed that, higher CD8+ T cell density, higher regulatory T cell/CD3+ T cell ratio, and higher Ttex/CD8+ T cell ratio exhibited better 5-year relapse-free survival (RFS) rates. When tumors were categorized into CD8-high, CD8-low/Ttex-low, and CD8-low/Ttex-high groups, the CD8-high and CD8-low/Ttex-high groups showed better 5-year RFS than the CD8-low/Ttex-low group.

Discussion

Ttex infiltration is associated with MSI and TMB status and may serve as a prognostic marker of CRCs.

A single-cell atlas reveals immune heterogeneity in anti-PD-1-treated non-small cell lung cancer

Anti-PD-(L)1 treatment is standard for non-small cell lung cancer (NSCLC), but patients show variable responses to the same regimen. The tumor immune microenvironment (TIME) is associated with immunotherapy response, yet the heterogeneous underlying therapeutic outcomes remain underexplored. We applied single-cell RNA and TCR sequencing (scRNA/TCR-seq) to analyze surgical tumor samples from 234 NSCLC patients post-neoadjuvant chemo-immunotherapy. Analyses revealed five distinct TIME subtypes with varying major pathological response (MPR) rates. MPR patients had elevated levels of FGFBP2+ NK/NK-like T cells, memory B cells, or effector T cells, while non-MPR patients showed higher CCR8+ Tregs. T cell clonal expansion analyses unveiled heterogeneity in non-MPR patients, marked by varying expansions of Tex-relevant cells and CCR8+ Tregs. Precursor exhausted T cells (Texp cells) correlated with recurrence-free survival, identifying a patient subgroup with reduced recurrence risk despite lack of MPR. Our study dissects TIME heterogeneity in response to chemoimmunotherapy, offering insights for NSCLC management.

A telomere-associated molecular landscape reveals immunological, microbial, and therapeutic heterogeneity in colorectal cancer

Background

Colorectal cancer (CRC) ranks among the most prevalent malignancies of the gastrointestinal tract and remains a leading cause of cancer-related mortality worldwide. Although telomere biology has been increasingly implicated in immune modulation and tumor progression, its clinical significance in CRC remains poorly understood.

Methods

We developed a telomere score, termed TELscore, by integrating transcriptomic and intratumoral microbiome profiles from publicly available colorectal cancer (CRC) cohorts. To comprehensively characterize TELscore subgroups, we performed pathway enrichment analysis, tumor immune microenvironment (TIME) profiling, and microbiome niche assessment. Whole-slide histopathological images (WSIs) and immunohistochemical (IHC) staining were utilized to visualize immune features, including tertiary lymphoid structures (TLSs), across subgroups. Patients were stratified into high and low TELscore categories, and the predictive robustness was validated across multiple independent training and validation cohorts. Chemotherapeutic drug sensitivity was evaluated using pharmacogenomic data from the Genomics of Drug Sensitivity in Cancer (GDSC) database. Furthermore, the predictive capacity of TELscore for immunotherapy response was independently assessed in an external cohort. Finally, single-cell RNA sequencing (scRNA-seq) analysis was conducted to further dissect the cellular landscape and immunological heterogeneity within the TME.

Results

TELscore stratified patients into two biologically and clinically distinct subgroups. The high TELscore group, which exhibited significantly shorter DFS, showed marked enrichment of tumorigenic pathways such as EMT, along with a distinctly immunosuppressive TME. This was reflected by elevated ESTIMATE/TIDE scores and corroborated by CIBERSORT, which revealed increased infiltration of M0 macrophages and upregulation of immunosuppressive signatures. In contrast, the low TELscore group was enriched for cell cycle related pathways, including E2F targets and the G2/M checkpoint, and demonstrated higher infiltration of pro-inflammatory M1 macrophages. 16S rRNA sequencing further revealed a divergent intratumoral microbiome between subgroups, the high TELscore group harbored significantly greater relative abundance of Selenomonas and Lachnoclostridium, two pathogenic genera previously associated with colorectal tumorigenesis. Complementary histopathological assessment via WSI demonstrated a marked absence of intraTLSs in high TELscore tumors. From a therapeutic standpoint, high TELscore tumors exhibited reduced sensitivity to standard chemotherapeutic agents-including Fluorouracil, Irinotecan, Oxaliplatin, and Docetaxel-as reflected by elevated IC50 values. Conversely, these tumors demonstrated increased susceptibility to MAPK pathway inhibitors, such as Selumetinib and Trametinib. Notably, TELscore also served as a robust predictor of immunotherapy response, which was validated in the IMvigor210 cohort. Finally, scRNA analysis highlighted profound cellular and functional divergence between TELscore subgroups. We identified intensified intercellular communication between inflammatory macrophages and fibroblasts, reinforcing the presence of an immunosuppressive niche.

Conclusion

TELscore is a robust stratification tool that captures the interplay between tumor biology, immune characteristics, and microbial ecology in colorectal cancer. By identifying clinically relevant subtypes with distinct therapeutic vulnerabilities, TELscore offers a powerful framework to advance personalized treatment and precision oncology.

CDC34 suppresses macrophage phagocytic activity and predicts poor response to immune checkpoint inhibitor in cancers

The cell division cycle 34 (CDC34) is an E2 ubiquitin-conjugating enzyme that is required for proteasomal degradation of substrate proteins, and is able to stabilize proteins including the epidermal growth factor receptor to promote lung carcinogenesis. Here, we conducted a pan-cancer analysis of CDC34 in The Cancer Genome Atlas datasets, and found its high expression in breast cancer and negative association with patient outcomes. Analysis of single-cell RNA-sequencing data revealed a negative role of CDC34 in macrophage phagocytotic activity for cancer cells. CDC34 stabilized hypoxia-inducible factor 1α (HIF1α) and transcriptionally upregulated CD47 in cancer cells to evade phagocytosis by macrophages. Inhibition of CDC34 inhibited tumor growth and synergized with anti-PD-L1 antibody in murine models. CDC34 was positively associated with CD47 and negatively associated with CD8+ granzyme B+ T-cell infiltration in patient samples, and patients with co-overexpression of CDC34 and CD47 had markedly poorer prognosis compared to those with high expression of either marker alone. In pre-treatment tumor samples, non-responders to immunotherapy exhibited significantly higher CDC34 levels and reduced CD8+ T-cell infiltration compared to responders. These findings indicated that CDC34 is critical to immune evasion and could be a potential therapeutic target for those resistant to immune checkpoint inhibitors.

VPS9D1-AS1 antisense therapy via lipid nanoparticles reprograms cold tumors and enhances immunotherapy in colorectal cancer

Advanced colorectal cancer (CRC) is characterized by a highly suppressive immune tumor microenvironment (TME) and is insensitive to immunotherapy. The induction of cancer immunogenic cell death (ICD) has been acknowledged as a promising immunotherapeutic strategy. Here, we demonstrate that the long noncoding RNA VPS9D1-AS1 is expressed predominantly in consensus molecular subtype (CMS)-2 CRC, and that its overexpression is associated with immune checkpoint blockade (ICB) sensitivity. A lipid-nanoparticle-(LNP)-based drug delivery system loaded with antisense oligonucleotides (ASOs) was established to target VPS9D1-AS1. This LNP-based drug exhibited high efficiency in inhibiting VPS9D1-AS1 expression in both tumor cells and patient-derived-xenograft (PDX) tumors, significantly suppressing tumor growth and metastasis. Mechanistically, targeting VPS9D1-AS1 activates MLKL-induced ICD, which in turn promotes antigen exposure in tumor cells. Moreover, VPS9D1-AS1 blockade inhibits HLA-G to sensitize CRC cells to immunotherapy. Consequently, LNP-based nano-ASO drugs targeting VPS9D1-AS1 promote TME remodeling by increasing the infiltrations of CD8+ T cells and dendritic cells (DCs). In addition, targeting VPS9D1-AS1 harmonizes the crosstalk between tumor cells and DCs via the AXL/GAS6 pathway. In vivo animal studies demonstrated that the combined targeting of PD1 and VPS9D1-AS1 enhances the efficacy of ICB treatment. It is anticipated that nanodrugs targeting VPS9D1-AS1 can be applied in clinical advanced CRC therapy in the near future.

A glutamine metabolism gene signature with prognostic and predictive value for colorectal cancer survival and immunotherapy response

Background

Colorectal cancer (CRC) remains a major cause of cancer mortality, and dysregulated glutamine metabolism has emerged as a potential therapeutic target. However, the precise role of glutamine in CRC progression and treatment response remains debated.

Methods

The authors collected transcriptome and microbiome information, from multiple sources to construct the GLMscore, a prognostic signature in CRC. To comprehensively characterize the biological features of GLMscore groups, the integration of transcriptomic profiling, KEGG pathway enrichment analysis, immune infiltration analysis, tumor immune microenvironment characterization, microbiome analysis, and tissue imaging were applied. Furthermore, CRC patients were stratified into GLMscore high and GLMscore low groups. The robustness of GLMscore was validated in both training and validation cohorts, and the predictive value for immunotherapy response was assessed. Finally, single-cell RNA sequencing (scRNA-seq) analysis was conducted to delineate the differences between GLMscore high and GLMscore low groups.

Results

High GLMscore was associated with elevated expression of pathways related to tumorigenesis, epithelial-mesenchymal transition (EMT), and angiogenesis. Furthermore, high GLMscore patients exhibited an immunosuppressive TME characterized by increased infiltration of M0 and M2 macrophages, reduced overall immune infiltration (supported by ESTIMATE and TIDE scores), and increased expression of immune exclusion and suppression pathways. Analysis of pathological whole-slide images (WSIs) revealed a lack of intratumoral tertiary lymphoid structures (TLSs) in high GLMscore patients. The GLMscore also predicted resistance to common chemotherapeutic agents (using GDSC data) and, importantly, predicted poor response to immunotherapy in the IMvigor210 cohort. Analysis of 16S rRNA gene sequencing data revealed an enrichment of potentially oncogenic microbiota, including Hungatella and Selenomonas, in high GLMscore group. Single-cell analysis further confirmed the immunosuppressive TME and identified increased cell-cell communication between inflammatory macrophages and tumor cells in high GLMscore group.

Conclusion

The authors innovatively constructed GLMscore, a robust scoring system in quantifying CRC patients, exploring the distinct biological features, tumor immune microenvironment and microbiome ecology, exhibiting high validity in predicting survival prognosis and clinical treatment efficacy.

Activated platelets stimulate effector CD8+ T cells to enhance HNSCC immunotherapy efficacy

Programmed Death Receptor-1 (PD-1) is an immune checkpoint receptor expressed on the surface of T cells. Monoclonal antibodies targeting PD-1 and its ligand, PD-L1, are among the most widely utilized immune checkpoint inhibitors in cancer immunotherapy, dramatically improving the prognosis of patients with various malignancies. Traditionally, platelets, which are cytoplasmic fragments derived from megakaryocytes, have been primarily recognized for their roles in hemostasis and coagulation. However, recent studies have highlighted the emerging role of platelets in cancer biology and therapy. Platelets can modulate immune cell functions through various mechanisms, including the release of bioactive molecules and direct interactions with immune cells. A deeper understanding of the interplay between platelets and immune responses could pave the way for novel therapeutic strategies in cancer treatment. In our research, in patients with better treatment responses, there are higher levels of mature and activated CD8+ T cells in their PBMCs prior to treatment. Additionally, the activation of platelets is also more pronounced, and the proteins expressed on these platelets may modulate immune cells. After receiving immunotherapy, patients in the responsive (R) group exhibited a higher abundance of activated effector CD8+ T cells, which demonstrated stronger immune response capabilities. Furthermore, the increased levels of activated platelets in the R group may contribute to the regulation of CD8+ effector memory T cells, influencing their quantity and function. Our study suggests that the functional state of CD8+ T cells and the level of activated platelets prior to treatment may serve as predictive indicators for the efficacy of PD-1 inhibitors in head and neck cancer patients. Activated CD8+ effector T cells may contribute to the differences in immunotherapy responses, with activated platelets playing a role in promoting the maturation and activation of CD8+ effector memory T cells.These insights help better understand the interactions between platelets and immune cells, particularly emphasizing the role of CD8+ effector memory T cells in immunotherapy. Additionally, they offer potential strategies for predicting patient responses to PD-1 inhibitor treatment and optimizing the efficacy of immunotherapy.

Single-cell meta-analysis of T cells reveals clonal dynamics of response to checkpoint immunotherapy

Despite the crucial role of T cell clones in anti-tumor activity, their characterization and association with clinical outcomes following immune checkpoint inhibitors are lacking. Here, we analyzed paired single-cell RNA sequencing/T cell receptor sequencing of 767,606 T cells across 460 samples spanning 6 cancer types. We found a robust signature of response based on expanded CD8+ clones that differentiates responders from non-responders. Analysis of persistent clones showed transcriptional changes that are differentially induced by therapy in the different response groups, suggesting an improved reinvigoration capacity in responding patients. Moreover, a gene trajectory analysis revealed changes in the pseudo-temporal state of de novo clones that are associated with clinical outcomes. Lastly, we found that clones shared between tumor and blood are more abundant in non-responders and execute distinct transcriptional programs. Overall, our results highlight differences in clonal transcriptional states that are linked to patient response, offering valuable insights into the mechanisms driving effective anti-tumor immunity.

Immunosequencing identifies signatures of T cell responses for early detection of nasopharyngeal carcinoma

To identify nasopharyngeal carcinoma (NPC)-relevant T cell receptors (TCRs), we profile the repertoires of peripheral blood TCRβ chains from 228 NPC patients, 241 at-risk controls positive for serum Epstein-Barr virus (EBV) VCA-IgA antibody, and 251 seronegative controls. We develop a TCR-based signature (T-score) based on 208 NPC-enriched CDR3β sequences, which accurately diagnoses NPC in both the original and independent validation cohorts. Notably, a higher T-score, associated with a shorter time interval to NPC diagnosis, effectively identifies early-stage NPC among EBV-seropositive at-risk individuals prior to clinical diagnosis. These NPC-enriched TCRs react against not only EBV-specific antigens but also non-EBV antigens expressed by NPC cells, indicating a broad range of specificities. Moreover, the abundance of NPC-enriched CD8+ T cells in blood correlates with the infiltration of non-exhausted T cell counterparts in tumors and predicts prolonged survival, suggesting that these NPC-enriched T cells have significant potential for disease monitoring and therapeutic applications.

Pathological complete response after monotherapy with immune checkpoint inhibitors for bifocal colon cancer in a patient with lynch syndrome and situs inversus totalis: a case report

Background

Lynch syndrome is the most common hereditary colorectal cancer (CRC) syndrome, accounting for 3-5% of all CRC cases. Situs inversus totalis (SIT) is a rare congenital malformation with an incidence of 1 in 8,000 to 1 in 25,000. The co-occurrence of Lynch syndrome and SIT is extremely uncommon. Immune checkpoint inhibitors (ICIs) have demonstrated significant efficacy in treating microsatellite instability-high/deficient mismatch repair (MSI-H/dMMR) CRC. Tumors associated with Lynch syndrome frequently exhibit MSI-H, providing a theoretical basis for ICI use.

Case presentation

We report a case of bifocal colon cancer associated with Lynch syndrome and SIT. After seven cycles of sintilimab, the patient developed gastrointestinal perforation due to tumor regression, necessitating emergency surgery. The anatomical variations associated with SIT required the surgical team to adopt an alternative approach. Postoperatively, the patient continued sintilimab treatment for 2 years. In June 2024, he underwent a colostomy reversal and proximal colectomy. Pathological examination revealed a tumor regression grade (TRG) of 0, indicating complete pathological remission (pCR), with no recurrence or metastasis detected upon follow-up.

Conclusions

The anatomical variations associated with SIT increase the complexity of surgical procedures. Advanced imaging modalities such as computed tomography (CT) and magnetic resonance imaging (MRI) are essential for assessing fine anatomical details and facilitating surgery. ICIs are an effective treatment option for Lynch syndrome-associated CRC, as demonstrated in this case. Future studies should investigate the optimal timing of immunotherapy, combination treatment strategies, and methods to mitigate immune-related toxicities. Such research will help develop comprehensive and personalized treatment plans for Lynch syndrome-associated CRC.

Exploring the Role of Cellular Interactions in the Colorectal Cancer Microenvironment

Colorectal cancer (CRC) stands as one of the tumors with globally high incidence and mortality rates. In recent years, researchers have extensively explored the role of the tumor immune microenvironment (TME) in CRC, highlighting the crucial influence of immune cell populations in driving tumor progression and shaping therapeutic outcomes. The TME encompasses an array of cellular and noncellular constituents, spanning tumor cells, immune cells, myeloid cells, and tumor-associated fibroblasts, among others. However, the cellular composition within the TME is highly dynamic, evolving throughout different stages of tumor progression. These shifts in cell subpopulation proportions lead to a gradual transition in the immune response, shifting from an early antitumor growth to a late-stage environment that supports tumor survival. Therefore, it is crucial to further investigate and understand the complex interactions among the various cell populations within the TME. In this review, we explore the key cellular components of varying origins, subpopulations with shared origins, and noncellular elements within the CRC TME, examining their interconnections and critical considerations for developing personalized and precise immunotherapy strategies.

Interferon-γ-stimulated antigen-presenting cancer-associated fibroblasts hinder neoadjuvant chemoimmunotherapy efficacy in lung cancer

Conventional neoadjuvant chemotherapy provides limited benefit for patients with resectable non-small cell lung cancer (NSCLC). Recently, neoadjuvant chemoimmunotherapy (NCIT) has transformed the perioperative management of NSCLC by priming systemic anti-tumor immunity before surgery, yet it remains ineffective for at least 50% of patients. Through single-cell sequencing analysis of our NCIT cohort, we identify that antigen-presenting cancer-associated fibroblasts (apCAFs) can impede the efficacy of NCIT. Using a custom cancer-associated fibroblast biobank, we uncover that interferon (IFN)-γ stimulates apCAF expansion via the JAK1/2-STAT1-IFI6/27 pathway. Mechanistically, apCAFs significantly contribute to PD-L2 expression in the tumor microenvironment (TME), triggering the accumulation of FOXP1+regulatory T cells (Tregs) through the PD-L2-RGMB axis. Reprogramming apCAFs by inhibiting the IFN-γ pathway or blocking the PD-L2-RGMB axis substantially mitigates apCAFs-mediated FOXP1+Tregs' expansion. In summary, we reveal the role of apCAFs in compromising NCIT efficacy and propose applications for anti-PD-L2/RGMB regimens to synergize with anti-PD1 therapies by targeting apCAFs.

Tumor Metastasis: Mechanistic Insights and Therapeutic Intervention

Metastasis remains a leading cause of cancer‐related deaths, defined by a complex, multi‐step process in which tumor cells spread and form secondary growths in distant tissues. Despite substantial progress in understanding metastasis, the molecular mechanisms driving this process and the development of effective therapies remain incompletely understood. Elucidating the molecular pathways governing metastasis is essential for the discovery of innovative therapeutic targets. The rapid advancements in sequencing technologies and the expansion of biological databases have significantly deepened our understanding of the molecular drivers of metastasis and associated drug resistance. This review focuses on the molecular drivers of metastasis, particularly the roles of genetic mutations, epigenetic changes, and post‐translational modifications in metastasis progression. We also examine how the tumor microenvironment influences metastatic behavior and explore emerging therapeutic strategies, including targeted therapies and immunotherapies. Finally, we discuss future research directions, stressing the importance of novel treatment approaches and personalized strategies to overcome metastasis and improve patient outcomes. By integrating contemporary insights into the molecular basis of metastasis and therapeutic innovation, this review provides a comprehensive framework to guide future research and clinical advancements in metastatic cancer.

Predicting immunotherapy prognosis and targeted therapy sensitivity of colon cancer based on a CAF-related molecular signature

The role of cancer-associated fibroblasts (CAFs) in modulating the tumor microenvironment (TME) is gaining attention, yet their impact on prognosis and therapeutic response in colon cancer remains unclear. Here, we identified genes associated with CAF infiltration via weighted gene co-expression network analysis (WGCNA) utilizing data from The Cancer Genome Atlas (TCGA) and GSE39582 cohorts. Univariate Cox regression and least absolute shrinkage and selection operator (LASSO) regression analyses were used to construct CAF molecular signatures (CAFscore). Patients were categorized into high and low CAFscore groups to analyze clinicopathological traits, somatic mutations, immune evasion, and treatment responses. In this study, a total of 244 genes were correlated with CAF infiltration, with 11 linked to overall survival. Notably, FSTL3, CRIP2, and SLC2A3 were selected for the CAFscore. A higher CAFscore was associated with poorer prognoses, increased malignancy, and therapeutic resistance, particularly among patients with high tumor mutation burden and microsatellite instability. Furthermore, elevated FSTL3 expression was associated with reduced CD8+ T cell infiltration, indicating a suppressive TME. Mechanistically, CAFs may promote immune evasion via NAMPT ligand-receptor interactions based on single-cell RNA sequencing data. Thus, the CAFscore is crucial for personalizing treatment strategies and identifying patients who require more aggressive management.

Enhancing immunotherapy efficacy in oral cancer through AKB-9778-mediated vascular normalization

Tumor vasculature exhibit numerous abnormal features distinct from those of healthy vessels, potentially advancing tumor development by establishing an aberrant microenvironment. Therefore, vascular normalization has proven to be an effective tactic for substantially enhancing treatment efficacy across multiple tumors. However, the methods to attain vascular normalization may vary among tumor types. VE-PTP, expressed exclusively in vascular endothelial cells (ECs) and acting as a critical suppressor of vascular maturity and functionality, is upregulated in oral cancer due to hypoxia. In this study, we explored the effect and mechanism of AKB-9778, a competitive inhibitor of VE-PTP, in promoting vascular normalization of oral cancer. Initially, we showed that AKB-9778 can slow down tumor progression by fostering vascular normalization in a murine OSCC model. This was evidenced by improvements in vessel density, pericyte coverage, local hypoxia, and vascular permeability. RNA sequencing additionally indicated that the ECs of tumor vasculature exhibit abnormal alterations in adhesion molecules, and AKB-9778 treatment might facilitate vascular normalization by modulating lipid metabolism pathways, especially HSD17B7-regulated steroid biosynthesis. AKB-9778 treatment significantly up-regulated the HSD17B7 expression, thereby restoring the lipid content in tumor ECs. Moreover, this restoration of lipid metabolism mediated by HSD17B7 was associated with improved adhesion molecule expression and vascular normalization, facilitating immune cell infiltration and contributing to AKB-9778's anti-tumor effects. Finally, we verified the effects and safety of combined AKB-9778 treatment on improving the efficacy of anti-PD-1 immunotherapy. In summary, this study revealed the mechanism and potential application of AKB-9778-induced vascular normalization in patients with oral cancer.

Multi-omics analyses reveal biological and clinical insights in recurrent stage I non-small cell lung cancer

Post-operative recurrence rates of stage I non-small cell lung cancer (NSCLC) range from 20% to 40%. Nonetheless, the molecular mechanisms underlying recurrence hitherto remain largely elusive. Here, we generate genomic, epigenomic and transcriptomic profiles of paired tumors and adjacent tissues from 122 stage I NSCLC patients, among which 57 patients develop recurrence after surgery during follow-up. Integrated analyses illustrate that the presence of predominantly solid or micropapillary histological subtypes, increased genomic instability, and APOBEC-related signature are associated with recurrence. Furthermore, TP53 missense mutation in DNA-binding domain could contribute to shorter time to recurrence. DNA hypomethylation is pronounced in recurrent NSCLC, and PRAME is the significantly hypomethylated and overexpressed gene in recurrent lung adenocarcinoma (LUAD). Mechanistically, hypomethylation at TEAD1 binding site facilitates the transcriptional activation of PRAME. Inhibition of PRAME restrains the tumor metastasis via downregulation of epithelial-mesenchymal transition-related genes. We also identify that enrichment of AT2 cells with higher copy number variation burden, exhausted CD8 + T cells and Macro_SPP1, along with the reduced interaction between AT2 and immune cells, is essential for the formation of ecosystem in recurrent LUAD. Finally, multi-omics clustering could stratify the NSCLC patients into 4 subclusters with varying recurrence risk and subcluster-specific therapeutic vulnerabilities. Collectively, this study constitutes a promising resource enabling insights into the biological mechanisms and clinical management for post-operative recurrence of stage I NSCLC.

Advancements in cellular immunotherapy: overcoming resistance in lung and colorectal cancer

Immunotherapy has revolutionized cancer treatment, offering hope for patients with otherwise treatment-resistant tumors. Among the most promising approaches are cellular therapies, particularly chimeric antigen receptor T-cell (CAR-T) therapy, which has shown remarkable success in hematologic malignancies. However, the application of these therapies to solid tumors, such as lung and colorectal cancers, has faced significant challenges. Tumor resistance mechanisms-ranging from immune evasion, antigen loss, and immune checkpoint upregulation, to tumor microenvironment immunosuppression-remain major obstacles. This mini-review highlights the latest advancements in tumor immunotherapy, with a focus on cellular therapies, and addresses the resistance mechanisms that hinder their effectiveness in lung and colorectal cancers. We examine the evolution of CAR-T cell therapy, as well as the potential of engineered natural killer (NK) cells and macrophages in solid tumor treatment. The review also explores cutting-edge strategies aimed at overcoming resistance, including combination therapies, gene editing technologies, and nanotechnology for targeted drug delivery. By discussing the molecular, cellular, and microenvironmental factors contributing to resistance, we aim to provide a comprehensive overview of how these challenges can be overcome, paving the way for more effective, personalized immunotherapies in lung and colorectal cancer treatment.

The characterization of tumor immune microenvironment after neoadjuvant immunotherapy in head and neck squamous cell cancer using multiplex immunohistochemistry

OBJECTIVE

Optimizing clinical decision-making in head and neck squamous cell carcinoma (HNSCC) is challenging due to the ambiguous understanding of the immune cell dynamics and immune checkpoints regulation in the disease after the administration of neoadjuvant immunotherapy (NIT).

METHODS

HNSCC biopsy samples collected before and after the neoadjuvant treatment are classified into the pathologic response (PR) and the non-pathologic response (NPR) groups according to treatment responses and the expression of immune cells and checkpoints was labeled using multiplex immunohistochemistry (m-IHC).

RESULTS

The populations of CD4+ T cells, CD8+ T cells, regulatory T cells (Treg), PD-1, and PD-L1 were particularly higher in the PR group than the NPR group in pre-treatment tissues, with the p-values of log-transformed positive cell density <0.05. Almost all markers showed a lower expression in the PR patients after treatment, resulting lower post/pre-treatment ratios of positive cell densities in the PR patients relative to the NPR patients. Following treatment, TIM3+ T cells and LAG3+ T cells exhibited significantly diminished levels in the PR cohort relative to the NPR cohort, with post/pre-treatment expression ratios showing significant differences (P < 0.05). Tumor infiltration lymphocyte analysis revealed that the PR group exhibited a considerably higher average density of CD8+ T cells infiltrating in the tumor marginal zone.

CONCLUSION

The presence of T cells demonstrated significant predictive capability for responses to neoadjuvant immunotherapy in HNSCC patients. Furthermore, TIM3+ T cells and LAG3+ T cells were found to be remarkably lower in the partial response (PR) cohort than in the non-partial response (NPR) cohort post-treatment. This research contributes critical understanding of the physiological changes occurring in immune cell responses.

scImmOmics: a manually curated resource of single-cell multi-omics immune data

Single-cell sequencing technology has enabled the discovery and characterization of subpopulations of immune cells with unique functions, which is critical for revealing immune responses under healthy or disease conditions. Efforts have been made to collect and curate single-cell RNA sequencing (scRNA-seq) data, yet an immune-specific single-cell multi-omics atlas with harmonized metadata is still lacking. Here, we present scImmOmics (https://bio.liclab.net/scImmOmics/home), a manually curated single-cell multi-omics immune database constructed based on high-quality immune cells with known immune cell labels. Currently, scImmOmics documents >2.9 million cell-type labeled immune cells derived from seven single-cell sequencing technologies, involving 131 immune cell types, 47 tissues and 4 species. To ensure data consistency, we standardized the nomenclature of immune cell types and presented them in a hierarchical tree structure to clearly describe the lineage relationships within the immune system. scImmOmics also provides comprehensive immune regulatory information, including T-cell/B-cell receptor sequencing clonotype information, cell-specific regulatory information (e.g. gene/chromatin accessibility/protein/transcription factor states within known cell types, cell-to-cell communication and co-expression networks) and immune cell responses to cytokines. Collectively, scImmOmics is a comprehensive and valuable platform for unraveling the heterogeneity and diversity of immune cells and elucidating the specific regulatory mechanisms at the single-cell level.

Integrating scRNA-seq and Visium HD for the analysis of the tumor microenvironment in the progression of colorectal cancer

BACKGROUND

Colorectal cancer (CRC) development is a complex, multi-stage process, transitioning from normal to adenomatous tissue, and then to invasive carcinoma. Despite research, there's a knowledge gap on using high-resolution spatial omics to understand CRC's tumor microenvironment dynamics.

METHODS

We used single-cell transcriptomics to study major biological changes and cell interactions in CRC progression. Additionally, high-resolution spatial transcriptomics helped us examine the spatial distribution of cells with significant pathway changes, offering insights into the tumor microenvironment's development throughout CRC stages.

RESULTS

In the progression of CRC, plasma cells, neutrophils, and fibroblasts exhibit the most significant changes in hallmark pathways, while epithelial cells show the most pronounced alterations in metabolic pathways. We also identified a population of NOTUM + epithelial cells and IGHG1/3 + plasma cells that are concentrated at the boundary between normal tissue and adenomas. Pathway analysis further suggests that these NOTUM + cells activate numerous cancer-related pathways, despite the absence of significant pathological morphological changes. Additionally, we conducted a targeted drug prediction analysis to identify potential therapeutic agents for NOTUM-expressing epithelial cells.

CONCLUSIONS

Analyzing scRNA-seq and Visium HD data, we found that IGHG1/3 + plasma cells and tumor-associated neutrophil (TANs) may significantly affect colorectal tissue transformation from normal to adenoma and carcinoma. These cells are concentrated at the transition between normal and adenomatous tissue. We also found NOTUM-expressing cells at the edge of normal and adenomatous areas, possibly indicating a morphological transition as normal cells evolve into adenoma cells.

IDO1 inhibitor enhances the effectiveness of PD-1 blockade in microsatellite stable colorectal cancer by promoting macrophage pro-inflammatory phenotype polarization

Microsatellite stable (MSS) colorectal cancer (CRC) is a subtype of CRC that generally exhibits resistance to immunotherapy, particularly immune checkpoint inhibitors such as PD-1 blockade. This study investigates the effects and underlying mechanisms of combining PD-1 blockade with IDO1 inhibition in MSS CRC. Bioinformatics analyses of TCGA-COAD and TCGA-READ cohorts revealed significantly elevated IDO1 expression in CRC tumors, correlating with tumor mutation burden across TCGA datasets. In vivo experiments demonstrated that the combination of IDO1 inhibition and PD-1 blockade significantly reduced tumor growth and increased immune cell infiltration, particularly pro-inflammatory macrophages and CD8+ T cells. IDO1 knockdown in CRC cell lines impaired tolerance to interferon-γ and increased apoptosis in vitro, which were rescued by the application of kynurenine, the end product of IDO1. IDO1 knockdown in MSS CRC enhanced the effectiveness of PD-1 blockade therapy in vivo. IDO1 knockdown cancer cells promoted pro-inflammatory macrophage polarization and enhanced phagocytic activity in vitro, associated with the upregulation of JAK2-STAT3-IL6 signaling pathway. These findings highlight the role of IDO1 in modulating the tumor immune microenvironment in MSS CRC and suggest that combining PD-1 blockade with IDO1 inhibition could enhance therapeutic efficacy by promoting macrophage pro-inflammatory polarization and infiltration through the JAK2-STAT3-IL6 pathway.

Disrupting EDEM3-induced M2-like macrophage trafficking by glucose restriction overcomes resistance to PD-1/PD-L1 blockade

BACKGROUND

Immunotherapy is beneficial for some colorectal cancer (CRC) patients, but immunosuppressive networks limit its effectiveness. Cancer-associatedfibroblasts (CAFs) are significant in immune escape and resistance toimmunotherapy, emphasizing the urgent need for new treatment strategies.

METHODS

Flow cytometric, Western blotting, proteomics analysis, analysis of public database data, genetically modified cell line models, T cell coculture, crystal violetstaining, ELISA, metabonomic and clinical tumour samples were conducted to assess the role of EDEM3 in immune escape and itsmolecular mechanisms. We evaluated theeffects of FMD plus 2-DG on antitumour immunity using multipleximmunofluorescence, flow cytometry, cytokine profiling, TUNEL assays, xenografttumours, and in vivo studies.

RESULTS

We show thatCAFs upregulate PD-L1 glycosylation and contribute to immune evasion byglycosyltransferase EDEM3. Additionally, EDEM3 plays a role in tumour immunityduring tumour progression. However, the EDEM3-mediated upregulation of PD-L1 expression underpins PD-1/PD-L1 blockade resistance in vivo. This finding contradictsthe previous trend that positive PD-L1 expression indicates a strong responseto PD-1/PD-L1 blockade. Mechanistically, high-EDEM3 expression facilitates M2-like This finding contradictsthe previous trend that positive PD-L1 expression indicates a strong responseto PD-1/PD-L1 blockade.Mechanistically, polarizationand chemotactic migration of macrophages, which are enriched in theperipheral region of tumours compared to thecore region, precluding access of CD8+ T cells to tumourfoci. Furthermore, we EDEM3 predominantly activates the recruited M2-like macrophagesvia a glucose metabolism-dependent mechanism. Manipulationof glucose utilization by a fasting-mimicking diet(FMD) plus 2-DG treatmentsynergistically with PD-1 antibody elicits potent antitumour activity byeffectively decreasing tumour glycosylated PD-L1 expression, augmenting the CD8+effector T cell infiltration and activation while concurrently reducing the infiltration.TheCAFs-EDEM3-M2-like macrophage axis plays a critical role in promotingimmunotherapy resistance. infiltration.TheCAFs-EDEM3-M2-like macrophage axis plays a critical role in promotingimmunotherapy resistance.

CONCLUSIONS

Our study suggests that blocking EDEM3-induced M2-like macro phage trafficking by FMD plus 2-DG is a promising and effective strategy to overcomeresistance to checkpoint blockade therapy offeringhope for improved treatment outcomes.

KEY POINTS

Cancer-associated fibroblasts (CAFs) can enhance PD-L1 glycosylation through the glycosyltransferase EDEM3, contributing to immune evasion during tumour progression. EDEM3 predominantly activates the recruit M2-like macrophages via a glucose metabolism-dependent mechanism. Blocking glucose utilization antagonizes recruiting and polarizing M2-like macrophages synergistically with PD-1 antibody to improve anticancer immunity.

Navigating the immune landscape with plasma cells: A pan-cancer signature for precision immunotherapy

Immunotherapy has revolutionized cancer treatment; however, predicting patient response remains a significant challenge. Our study identified a novel plasma cell signature, Plasma cell.Sig, through a pan-cancer single-cell RNA sequencing analysis, which predicts patient outcomes to immunotherapy with remarkable accuracy. The signature was developed using rigorous machine learning algorithms and validated across multiple cohorts, demonstrating superior predictive power with an area under the curve (AUC) exceeding 0.7. Notably, the low-risk group, as classified by Plasma cell.Sig, exhibited enriched immune cell infiltration and heightened tumor immunogenicity, indicating an enhanced responsiveness to immunotherapy. Conversely, the high-risk group showed reduced immune activity and potential mechanisms of immune evasion. These findings not only enhance understanding of the intrinsic and extrinsic immune landscapes within the tumor microenvironment but also pave the way for more precise, biomarker-guided immunotherapy approaches in oncology.

Intratumoural CD8+ CXCR5+ follicular cytotoxic T cells have prognostic value and are associated with CD19+ CD38+ B cells and tertiary lymphoid structures in colorectal cancer

BACKGROUND

Colorectal cancer (CRC) is the most common digestive cancer in the world. Microsatellite stability (MSS) and microsatellite instability (MSI-high) are important molecular subtypes of CRC closely related to tumor occurrence and progression and immunotherapy efficacy. The presence of CD8+ CXCR5+ follicular cytotoxic T (TFC) cells is strongly associated with autoimmune disease and CD8+ effector function. However, the roles of TFC cells in MSI-high CRC and MSS CRC are unclear. Here, we aimed to explore the characteristics of TFC cells in CRC and compare their biological functions between MSI-high and MSS CRC.

METHODS

We explored the expression of TFC cell in tumor tissues and peripheral blood in our clinical cohort and public datasets. By combining single-cell RNA sequencing (scRNA-seq) and bulk RNA sequencing, we explored the potential function of TFC cells and developed a prediction model for CRC. We also compared the biological functions of these cells between MSS and MSI-high CRC and used flow cytometry and coculture experiments to explore their potential regulatory functions.

RESULTS

TFC cell markers are downregulated in tumor tissues and patient peripheral blood vs. controls. The prediction model for CRC performed well in the training and validation cohorts (KM plot p < 0.001). MSS CRC patients exhibit enrichment of genes related to the cell cycle (MKI67) and T cell activation (CD38 and HLA-DR) and decreased enrichment of immune checkpoint markers (PD1, TIM3, and LAG3). The expression of TFC cell-related genes is positively correlated with that of CD8+IFN-γ+-related genes and closely related to that of TLS-related genes in MSS CRC. The proportion of TFC cells is positively correlated with that of CD19+CD38+ B cells in MSS CRC.

CONCLUSIONS

The prognostic prediction model has good predictive value. In MSS CRC, TFC cells function mostly in T cell activation and the cell cycle and have low expression of immune checkpoint molecules, which may influence the effectiveness of ICB therapy. TFC cells may regulate antitumor function by regulating CD19+ CD38+ B cells and TLSs.

Navigating the Complexity of Resistance in Lung Cancer Therapy: Mechanisms, Organoid Models, and Strategies for Overcoming Treatment Failure

Background: The persistence of chemotherapy-resistant and dormant cancer cells remains a critical challenge in the treatment of lung cancer. Objectives: This review focuses on non-small cell lung cancer and small cell lung cancer, examining the complex mechanisms that drive treatment resistance. Methods: This review analyzed current studies on chemotherapy resistance in NSCLC and SCLC, focusing on tumor microenvironment, genetic mutations, cancer cell heterogeneity, and emerging therapies. Results: Conventional chemotherapy and targeted therapies, such as tyrosine kinase inhibitors, often fail due to factors including the tumor microenvironment, genetic mutations, and cancer cell heterogeneity. Dormant cancer cells, which can remain undetected in a quiescent state for extended periods, pose a significant risk of recurrence upon reactivation. These cells, along with intrinsic resistance mechanisms, greatly complicate treatment efforts. Understanding these pathways is crucial for the development of more effective therapies. Emerging strategies, including combination therapies that target multiple pathways, are under investigation to improve treatment outcomes. Innovative approaches, such as antibody-drug conjugates and targeted protein degradation, offer promising solutions by directly delivering cytotoxic agents to cancer cells or degrading proteins that are essential for cancer survival. The lung cancer organoid model shows substantial promise to advance both research and clinical applications in this field, enhancing the ability to study resistance mechanisms and develop personalized treatments. The integration of current research underscores the need for continuous innovation in treatment modalities. Conclusions: Personalized strategies that combine novel therapies with an in-depth understanding of tumor biology are essential to overcome the challenges posed by treatment-resistant and dormant cancer cells in lung cancer. A multifaceted approach has the potential to significantly improve patient outcomes.