Single-cell analyses reveal key immune cell subsets associated with response to PD-L1 blockade in triple-negative breast cancer

Deciphering immune cell heterogeneity in vascular diseases: Insights from single-cell sequencing

The complexity and diversity of vascular diseases highlight the urgent need to study their pathogenesis, particularly the key role of immune cell-mediated inflammatory responses in their development. While previous reviews have outlined the involvement of immune cells in vascular pathology, a comprehensive understanding of their dynamic changes, functional states, and intercellular interactions remains incomplete. Recent advances in single-cell sequencing (SCS) have provided unprecedented insights into immune cell heterogeneity, enabling the identification of novel subpopulations and their roles in disease progression.This review extends prior work by systematically summarizing the latest applications of SCS in vascular diseases, highlighting newly discovered immune cell subsets, their interactions, and their impact on vascular pathology. By addressing current gaps in the literature-such as the functional plasticity of immune cells and their temporal dynamics-this review offers new perspectives on immune-mediated mechanisms in vascular diseases and proposes novel therapeutic strategies for their prevention and treatment.

Effects of ER-phagy regulatory genes on the microenvironment of hepatocellular carcinoma: a comprehensive analysis

The relationships between gene regulatory functions and hepatocellular carcinoma (HCC) occurrence and progression are constantly being clarified. However, tumour microenvironment complexity has hindered the classification of the role of genes. A comprehensive analysis to further clarify gene functions could provide additional benefits to HCC patients. In the present study, we combined single-cell sequencing data, Mendelian randomization, and bioinformatics analysis for comprehensive analysis. After the study was completed we found that T cell, dendritic cell (DC), macrophage and monocyte contents and the interaction between immune cells in the HCC microenvironment differed between the microvascular invasion-positive (MVI +) and microvascular invasion-negative (MVI-) groups. Mendelian randomization analysis indicated that causal relationships between several endoplasmic reticulum autophagy (ER-phagy) genes and T cell, DC, macrophage and monocyte contents. Single-cell sequencing data were used to validate the association of these genes with immune cells in the microenvironment. Based on the above results, we preliminarily elucidated the potential role of ER autophagy in the HCC microenvironment. Furthermore, a prognostic model was constructed using these causal association genes, which could accurately predict the prognosis and survival of HCC patients.

Deciphering the Immunomodulatory Function of GSN+ Inflammatory Cancer-Associated Fibroblasts in Renal Cell Carcinoma Immunotherapy: Insights From Pan-Cancer Single-Cell Landscape and Spatial Transcriptomics Analysis

The heterogeneity of cancer-associated fibroblasts (CAFs) could affect the response to immune checkpoint inhibitor (ICI) therapy. However, limited studies have investigated the role of inflammatory CAFs (iCAFs) in ICI therapy using pan-cancer single-cell RNA sequencing (scRNA-seq) and spatial transcriptomics sequencing (ST-seq) analysis. We performed pan-cancer scRNA-seq and ST-seq analyses to identify the subtype of GSN+ iCAFs, exploring its spatial distribution characteristics in the context of ICI therapy. The pan-cancer scRNA-seq and bulk RNA-seq data are incorporated to develop the Caf.Sig model, which predicts ICI response based on CAF gene signatures and machine learning approaches. Comprehensive scRNA-seq analysis, along with in vivo and in vitro experiments, investigates the mechanisms by which GSN+ iCAFs influence ICI efficacy. The Caf.Sig model demonstrates well performances in predicting ICI therapy response in pan-cancer patients. A higher proportion of GSN+ iCAFs is observed in ICI non-responders compared to responders in the pan-cancer landscape and clear cell renal cell carcinoma (ccRCC). Using real-world immunotherapy data, the Caf.Sig model accurately predicts ICI response in pan-cancer, potentially linked to interactions between GSN+ iCAFs and CD8+ Tex cells. ST-seq analysis confirms that interactions and cellular distances between GSN+ iCAFs and CD8+ exhausted T (Tex) cells impact ICI efficacy. In a co-culture system of primary CAFs, primary tumour cells and CD8+ T cells, downregulation of GSN on CAFs drives CD8+ T cells towards a dysfunctional state in ccRCC. In a subcutaneously tumour-grafted mouse model, combining GSN overexpression with ICI treatment achieves optimal efficacy in ccRCC. Our study provides the Caf.Sig model as an outperforming approach for patient selection of ICI therapy, and advances our understanding of CAF biology and suggests potential therapeutic strategies for upregulating GSN in CAFs in cancer immunotherapy.

The impact of breast radiotherapy on the tumor genome and immune ecosystem

Radiotherapy is a pillar of breast cancer treatment; however, it remains unclear how radiotherapy modulates the tumor microenvironment. We investigated this question in a cohort of 20 patients with estrogen-receptor positive (ER+) breast tumors who received neoadjuvant radiotherapy. Tumor biopsies were collected before and 7 days postradiation. Single-cell DNA sequencing (scDNA-seq) and scRNA-seq were conducted on 8 and 11 patients, respectively, at these two time points. The scRNA data showed increased infiltration of naive-like CD4 T cells and an early, activated CD8 T cell population following radiotherapy. Radiotherapy also eliminated existing cytotoxic T cells and resulted in myeloid cell increases. In tumor cells, the scDNA-seq data showed a high genomic selection of subclones in half of the patients with high ER expression, while the remaining number had low genomic selection and an interferon response. Collectively, these data provide insight into the impact of radiotherapy in ER+ breast cancer patients.

STAT5 and STAT3 balance shapes dendritic cell function and tumour immunity

Immune checkpoint blockade (ICB) has transformed cancer therapy1,2. The efficacy of immunotherapy depends on dendritic cell-mediated tumour antigen presentation, T cell priming and activation3,4. However, the relationship between the key transcription factors in dendritic cells and ICB efficacy remains unknown. Here we found that ICB reprograms the interplay between the STAT3 and STAT5 transcriptional pathways in dendritic cells, thereby activating T cell immunity and enabling ICB efficacy. Mechanistically, STAT3 restrained the JAK2 and STAT5 transcriptional pathway, determining the fate of dendritic cell function. As STAT3 is often activated in the tumour microenvironment5, we developed two distinct PROTAC (proteolysis-targeting chimera) degraders of STAT3, SD-36 and SD-2301. STAT3 degraders effectively degraded STAT3 in dendritic cells and reprogrammed the dendritic cell-transcriptional network towards immunogenicity. Furthermore, STAT3 degrader monotherapy was efficacious in treatment of advanced tumours and ICB-resistant tumours without toxicity in mice. Thus, the crosstalk between STAT3 and STAT5 transcriptional pathways determines the dendritic cell phenotype in the tumour microenvironment and STAT3 degraders hold promise for cancer 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.

Single-cell transcriptomic analysis reveals gut microbiota-immunotherapy synergy through modulating tumor microenvironment

The gut microbiota crucially regulates the efficacy of immune checkpoint inhibitor (ICI) based immunotherapy, but the underlying mechanisms remain unclear at the single-cell resolution. Using single-cell RNA sequencing and subsequent validations, we investigate gut microbiota-ICI synergy by profiling the tumor microenvironment (TME) and elucidating critical cellular interactions in mouse models. Our findings reveal that intact gut microbiota combined with ICIs may synergistically increase the proportions of CD8+, CD4+, and γδ T cells, reduce glycolysis metabolism, and reverse exhausted CD8+ T cells into memory/effector CD8+ T cells, enhancing antitumor response. This synergistic effect also induces macrophage reprogramming from M2 protumor Spp1+ tumor-associated macrophages (TAMs) to Cd74+ TAMs, which act as antigen-presenting cells (APCs). These macrophage subtypes show a negative correlation within tumors, particularly during fecal microbiota transplantation. Depleting Spp1+ TAMs in Spp1 conditional knockout mice boosts ICI efficacy and T cell infiltration, regardless of gut microbiota status, suggesting a potential upstream role of the gut microbiota and highlighting the crucial negative impact of Spp1+ TAMs during macrophage reprogramming on immunotherapy outcomes. Mechanistically, we propose a γδ T cell-APC-CD8+ T cell axis, where gut microbiota and ICIs enhance Cd40lg expression on γδ T cells, activating Cd40 overexpressing APCs (e.g., Cd74+ TAMs) through CD40-CD40L-related NF-κB signaling and boosting CD8+ T cell responses via CD86-CD28 interactions. These findings highlight the potential importance of γδ T cells and SPP1-related macrophage reprogramming in activating CD8+ T cells, as well as the synergistic effect of gut microbiota and ICIs in immunotherapy through modulating the TME.

Emerging clinical applications of single-cell RNA sequencing in oncology

Single-cell RNA sequencing (scRNA-seq) has revolutionized our understanding of complex tissues both in health and in disease. Over the past decade, scRNA-seq has been applied to tumour samples obtained from patients with cancer in hundreds of studies, thereby advancing the view that each tumour is a complex ecosystem and uncovering the diverse states of both cancer cells and the tumour microenvironment. Such studies have primarily investigated and provided insights into the basic biology of cancer, although considerable research interest exists in leveraging these findings towards clinical applications. In this Review, we summarize the available data from scRNA-seq studies investigating samples from patients with cancer with a particular focus on findings that are of potential clinical relevance. We highlight four main research objectives of scRNA-seq studies and describe some of the most relevant findings towards such goals. We also describe the limitations of scRNA-seq, as well as future approaches in this field that are anticipated to further advance clinical applicability.

Systemic immune characteristics predicting toxicity to immune checkpoint inhibitors in patients with advanced breast cancer

BACKGROUND

Immune checkpoint inhibitors (ICIs) are among the most promising treatment options for cancer. However, frequent and sometimes life-threatening immune-related adverse events (irAEs) are associated with ICI treatment. Therefore, it is imperative to establish a model for predicting the risk of irAEs to identify high-risk groups, enable more accurate clinical risk‒benefit analysis for ICI treatment and decrease the incidence of irAEs. However, no ideal model for predicting irAEs has been applied in clinical practice. The aim of this study was to analyze the systemic immune characteristics of patients with irAEs and establish a model for predicting the risk of irAEs.

METHODS

We conducted a study to monitor irAEs in patients with advanced breast cancer undergoing immunotherapy during and following the treatment course. Peripheral blood mononuclear cells (PBMCs) were collected before and after two cycles of therapy. Mass cytometry time-of-flight (CyTOF) was employed to identify baseline and posttreatment immune cell subpopulations, and the relationships between the proportions of cells in these subpopulations and the occurrence of irAEs were explored. Additionally, we conducted subgroup analyses stratified by the anatomic location and time of onset of irAEs. Furthermore, we developed a logistic regression model to predict the risk of irAEs and validated this model using two independent validation cohorts from the Gene Expression Omnibus (GEO) database (accession numbers GSE189125 and GSE186143).

RESULTS

By analyzing 106 blood samples and samples from two independent validation cohorts (n = 16 and 60 patients), we found that high proportions of CXCR3+CCR6+CD4+ T cells and CD38+CD86+CXCR3+CCR6+CD8+ T cells and a low proportion of CXCR3lowCD56dim natural killer (NK) cells at baseline were significantly correlated with the incidence of irAEs (P = 0.0029, P < 0.001, and P = 0.0017, respectively). In the subgroup analysis, we observed consistent results in patients with immune-related pneumonitis (ir-pneumonitis) and immune-related thyroiditis (ir-thyroiditis). In the early irAE group, the baseline proportion of CXCR3+CCR6+CD4+ T cells was greater than that in the late irAE group (P = 0.011). An analysis of PBMCs before and after ICI treatment revealed thatthe dynamic changes in the proportions of naïve CD4+ T cells and CXCR3lowCD56dim NK cells were closely related to irAE occurrence. Finally, we ultimately developed a model for predicting the risk of irAEs, which yielded an area under the receiver operating characteristic curve (AUROC) of 0.79 in the training cohort and an AUROC of 0.75 in the single-cell validation cohort (GSE189125).

CONCLUSIONS

These findings indicate that different populations of immune cells are associated with different irAEs and that characterization of these cells may be used as biomarkers to predict the risk of specific toxicities. This will facilitate the management of irAEs and may lead to a reduction in the incidence of irAEs.

IL-1β+ macrophages and the control of pathogenic inflammation in cancer

While highlighting the complexity and heterogeneity of tumor immune microenvironments, the application of single-cell analyses in human cancers has identified recurrent subsets of tumor-associated macrophages (TAMs). Among these, interleukin (IL)-1β+ TAMs - cells with high levels of expression of inflammatory response and tissue repair genes, but with limited capacity to stimulate cytotoxic immunity - are emerging as key drivers of pathogenic inflammation in cancer. In this review we discuss recent literature defining the phenotypical, molecular, and functional properties of IL-1β+ TAMs, as well as their temporal dynamics and spatial organization. Elucidating the biology of these cells across tumor initiation, progression, metastasis, and therapy could inform the design and interpretation of clinical trials targeting IL-1β and/or other inflammatory factors in cancer immunotherapy.

Palbociclib stimulates CD8+ T cell response in triple-negative breast cancer via regulating phosphoglycerate dehydrogenase

CDK4/6 inhibitors are applied for the treatment of breast cancer. The purpose of this study was to explore the effects of palbociclib (PALB) on triple-negative breast cancer. An in vivo assay was applied to determine the effects of PALB on breast cancer. Gene expression was detected using immunohistochemistry. mRNA levels were detected using reverse transcription-quantitative PCR. Protein expression was detected using western blot. The expansion of CD8+ T cell subsets was detected using flow cytometry. We found that PALB treatment promoted the persistence of CD8+ T cells, manifested by the maintenance of stem-like CD8+ T cells and effector T cells. Moreover, PALB downregulated PHGDH, high levels of which predicted poor prognosis of breast cancer patients. Moreover, overexpression of PHGDH antagonized the effects of PALB and suppressed the persistence of CD8+ T cells. Additionally, PALB enhanced the effects of anti-PD1 immunotherapy and suppressed the tumor growth of breast cancer. In summary, PALB promoted the maintenance of CD8+ memory precursors in breast cancer via downregulating PHGDH.

Tumor-infiltrating mast cells as potential chemoimmunotherapy enhancer in triple-negative breast cancer

Over the past decade, combining immune checkpoint blockade with chemotherapy has reshaped the paradigm of triple-negative breast cancer (TNBC), but the cellular dynamics in the tumor immune microenvironment (TIME) that orchestrate clinical response remain elusive. In a recent issue of Cancer Cell, Zhang et al integrated murine and human single-cell sequencing data, and unveiled that tumor-infiltrating mast cells (TIMCs) could exert distinct antitumor effects by enriching and fueling various immune cell clusters, suggesting the pivotal tuning role of TIMCs in the TIME of TNBC, as well as paving promising avenues for future TIMC-targeting therapies in synergy with chemoimmunotherapy against TNBC.

Efficacy, safety and single-cell analysis of neoadjuvant immunochemotherapy in locally advanced oral squamous cell carcinoma: a phase II trial

The clinical activity of neoadjuvant immunochemotherapy (NAIC) for treating locally advanced oral squamous cell carcinoma (LA-OSCC) remains uncertain. This single-arm, phase II trial (ChiCTR2200066119) tested 2 cycles of NAIC with camrelizumab plus nab-paclitaxel and cisplatin in LA-OSCC patients. For primary endpoint, the major pathological response (MPR) rate was 69.0% (95% confidence interval (CI): 49.2%-84.7%). The treatment was well-tolerated, with only 2 patients (6.45%) having grade 3 or 4 treatment-related adverse events during neoadjuvant treatment. For secondary endpoints, the pathological complete response rate was 41.4% (95%CI: 23.5%-61.1%) and the objective response rate was 82.8% (24/29, 95%CI: 64.2%-94.2%). The 18-month overall survival and disease-free survival probabilities were 96.77% (95%CI: 79.23%-99.54%) and 85.71% (95%CI: 53.95%-96.22%), respectively. Exploratory analysis showed that patients with MPR exhibited higher density of baseline CD4_Tfh_CXCL13 cells, and increased density of tertiary lymphoid structures after NAIC. Baseline CD4_Tfh_CXCL13 cells might be potential predictive biomarker of efficacy. The interaction between CXCL13 on CD4_Tfh_CXCL13 cells and CXCR5 on B cells may play a role in treatment response. These findings suggest the potential of NAIC as a promising treatment for LA-OSCC and offer preliminary insights into responsive biomarkers.

A single-cell map of patients with non-small cell lung cancer harboring rare-driver mutations after anti-PD-1 treatment

The effects of the tumor microenvironment the therapeutic efficacy of combining chemotherapy with checkpoint inhibitors in patients with lung cancer harboring rare -driver mutations remain unclear. We utilized single-cell RNA- and T-cell receptor (TCR) -sequencing to explore the immune and stromal cell profiles of 12 tumors and five tumor-adjacent tissues in seven patients with non-small cell lung cancer (NSCLCs) with rare -driver mutations treated with anti-PD-1 agents combined with chemotherapy. A class of highly expanded T -cells, known as GZMK + CD8+ effector memory T cells (GZMK + CD8+Tem), was enriched in both responsive tumors with and without rare driver mutations, suggesting similar anti-tumor immune mechanisms in both cohorts and that high levels of GZMK + CD8+Tem might be associated with effective responses to combination therapy. Non-responsive tumors exhibited a highly immunosuppressive M2-phenotype with enriched macrophages and monocytes. In non-major pathological response tumors, tumor cells interacted with alveolar and M0 macrophages via LAMC2-(ITGA6+ITGB1), possibly leading to M2 polarization. OAS1 was specifically expressed in CHIT1+ and FABP4+ macrophages and promoted macrophage polarization. These findings suggest that combination therapy reprogramed alveolar and M0-like macrophages to a pro-tumor phenotype, creating an immunosuppressive tumor microenvironment that resisted anti-PD1 therapy. In conclusion, GZMK + CD8+Tem is crucial for effective responses, whereas myeloid cells contribute to the immunosuppressive effects in anti-PD-1 therapies for NSCLCs with rare-driver mutations.

Resistance to anti-LAG-3 plus anti-PD-1 therapy in head and neck cancer is mediated by Sox9+ tumor cells interaction with Fpr1+ neutrophils

Relatlimab and nivolumab combination therapy shows significant efficacy in treating various types of cancer. Current research on the molecular mechanisms of this treatment is abundant, but in-depth investigations into post-treatment resistance remain notably lacking. In this study, we identify significant enrichment of SRY (sex determining region Y)-box 9 (Sox9)+ tumor cells in resistant samples using single cell RNA sequencing (scRNAseq) in a head and neck squamous cell carcinoma (HNSCC) mouse model. In addition, Sox9 directly regulates the expression of annexin A1 (Anxa1), mediating apoptosis of formyl peptide receptor 1 (Fpr1)+ neutrophils through the Anxa1-Fpr1 axis, which promotes mitochondrial fission, inhibits mitophagy by downregulating BCL2/adenovirus E1B interacting protein 3 (Bnip3) expression and ultimately prevents the accumulation of neutrophils in tumor tissues. The reduction of Fpr1+ neutrophils impairs the infiltration and tumor cell-killing ability of cytotoxic Cd8 T and γδT cells within the tumor microenvironment, thereby leading to the development of resistance to the combination therapy. We further validate these findings using various transgenic mouse models. Overall, this study comprehensively explains the mechanisms underlying resistance to the anti-LAG-3 plus anti-PD-1 combination therapy and identifies potential therapeutic targets to overcome this resistance.

ICI-induced cardiovascular toxicity: mechanisms and immune reprogramming therapeutic strategies

The advent of immune checkpoint inhibitors (ICIs) has revolutionized cancer treatment, offering life-saving benefits to tumor patients. However, the utilize of ICI agents is often accompanied by immune-related adverse events (irAEs), among which cardiovascular toxicities have attracted more and more attention. ICI induced cardiovascular toxicities predominantly present as acute myocarditis and chronic atherosclerosis, both of which are driven by excessive immune activation. Reprogramming of T cells and macrophages has been demonstrated as a pivotal factor in the pathogenesis of these complications. Therapeutic strategies targeting glycolysis, fatty acid oxidation, reactive oxygen species (ROS) production and some other key signaling have shown promise in mitigating immune hyperactivation and inflammation. In this review, we explored the intricate mechanisms underlying ICI-induced cardiovascular toxicities and highlighted the protective potential of immune reprogramming. We emphasize the roles of T cell and macrophage reprogramming in the heart and vasculature, showcasing their contributions to both short-term and long-term regulation of cardiovascular health. Ultimately, a deeper understanding of these processes will not only enhance the safety of ICIs but also pave the way for innovative strategies to manage immune-related toxicities in cancers therapy.

Perturbing local steroidogenesis to improve breast cancer immunity

Breast cancer, particularly triple-negative breast cancer (TNBC), evades the body's immune defences, in part by cultivating an immunosuppressive tumour microenvironment. Here, we show that suppressing local steroidogenesis can augment anti-tumour immunity against TNBC. Through targeted metabolomics of steroids coupled with immunohistochemistry, we profiled the existence of immunosuppressive steroids in TNBC patient tumours and discerned the steroidogenic activity in immune-infiltrating regions. In mouse, genetic inhibition of immune cell steroidogenesis restricted TNBC tumour progression with a significant reduction in immunosuppressive components such as tumour associated macrophages. Steroidogenesis inhibition appears to bolster anti-tumour immune responses in dendritic and T cells by impeding glucocorticoid signalling. Undertaking metabolic modelling of the single-cell transcriptomics and targeted tumour-steroidomics, we pinpointed the predominant steroidogenic cells. Inhibiting steroidogenesis pharmacologically using a identified drug, posaconazole, curtailed tumour expansion in a humanised TNBC mouse model. This investigation paves the way for targeting steroidogenesis and its signalling pathways in breast cancer affected by immune-steroid maladaptation.

Dynamics of tertiary lymphoid structures and immune cross talk in early versus advanced colorectal cancer: potential implications for immunotherapy

BACKGROUND

Irrespective of microsatellite status, immune checkpoint inhibitor therapy shows superior efficacy in early-stage colorectal cancer (CRC) compared to advanced cases. The distinctions of the tumor microenvironment (TME) and tertiary lymphoid structure (TLS) between early- and advanced-stage CRC may represent a critical factor, yet remain incompletely elucidated.

METHODS

We comprehensively analyzed single-cell RNA sequencing data, bulk RNA transcription data and pathological tissue data to investigate the dynamic changes in the TME. The features of TLS in early- and advanced-stage tumors and their potential impact on immunotherapy were explored using three in-house cohorts.

RESULTS

We provided single-cell fine maps of the immune landscape in early and advanced CRC. Significant functional differences were identified in CD4 + Tfh and BGC cells between early and advanced CRC. We revealed CXCL13 expression on CD8 + Tex cells, along with CD40-CD40L interactions between CD4 + Tfh and BGC cells, could be key regulators of TLS functionality and subsequently affect the response to immunotherapy.

CONCLUSIONS

Our research shed light on the multilayered immune dysfunction in advanced CRC and elucidates the alterations in the TLS during the progression of CRC, providing insights for functional studies and the exploration of potential target in advanced CRC.

YTHDC2 manipulates anti-tumoral macrophage polarization and predicts favorable outcomes in triple negative breast cancer

Triple-negative breast cancer (TNBC) possesses high malignant and metastatic rates among all subtypes. Chemotherapy is a standard of care for TNBC but only a small moiety of patients achieved complete relief (CR) after chemotherapy. The recent concept of tumor ecosystem has provided new insights into solutions from an approach of enhancing anti-tumoral immunity of macrophages. We hereby observed a positive correlation of YTHDC2 abundance with anti-tumoral gene markers of macrophages. YTHDC2-high macrophages also exerted interactions with other immune cells such as T helper cells, cytotoxic T cells, and NK cells. Further investigation on the transcriptional regulatory network identified six transcriptional factors upregulated by YTHDC2, and they together influenced the expressions of TWISTNB and the oncogene MYC. Additionally, our survival analysis prompted that YTHDC2 is prognostic of higher chemo-therapeutic efficacy and better survival outcomes. We demonstrated that ample macrophage YTHDC2 indicates anti-tumoral phenotype polarization and propitious survival outcome in post-treatment TNBC patients (Clinical trial registry name: Chinese Clinical Trial Registry, Registration No.: ChiCTR2400084513, Registration Date: 2024-05-20).

The dynamic immune behavior of primary and metastatic ovarian carcinoma

Patients with high-grade serous ovarian carcinoma (HGSC) are usually diagnosed with advanced-stage disease, and the tumors often have immunosuppressive characteristics. Together, these factors are important for disease progression, drug resistance, and mortality. In this study, we used a combination of single-cell sequencing and spatial transcriptomics to identify the molecular mechanisms that lead to immunosuppression in HGSC. Primary tumors consistently showed a more active immune microenvironment than did omental tumors. In addition, we found that untreated primary tumors were mostly populated by dysfunctional CD4 and CD8 T cells in later stages of differentiation; this, in turn, was correlated with expression changes in the interferon α and γ pathways in epithelial cells, showing that cross-communication between the epithelial and immune compartments is important for immune suppression in HGSC. These findings could have implications for the design of clinical trials with immune-modulating drugs.

Asymmetric cell division of ALDH1-positive cancer stem cells generates glycolytic metabolically diverse cell populations

Metabolic heterogeneity in various cancer cells within a tumor causes resistance to medical therapies and promotes tumor recurrence and metastasis. However, the mechanisms by which tumors acquire metabolic heterogeneity are poorly understood. Here, we revealed that PKCλ-dependent asymmetric division of ALDH1-positive cancer stem cells (CSCs) led to an uneven distribution of glycolytic capacity, which is crucial for understanding metabolic heterogeneity within a tumor. The rate-limiting enzyme PFKP and the metabolic probe CDG in glycolysis codistributed with the ALDH1A3 protein during the post-cell division phase, highlighting a mechanism for acquiring metabolic diversity. PKCλ deficiency reduced the asymmetric distribution of these proteins in ALDH1high cells with high ALDH1 activity, suggesting a fundamental role for PKCλ in metabolic heterogeneity. We identified 28 distinct distribution patterns combining PFKP and CDG distributions, demonstrating the complexity of glycolytic heterogeneity. Furthermore, validation and prediction of cell distribution patterns via a probabilistic model confirmed that PKCλ deficiency diminished glycolytic diversity in individual cells within a cancer cell colony generated from an ALDH1-positive CSC. These findings suggest that PKCλ-dependent asymmetric cell division of ALDH1-positive CSCs is crucial for glycolytic heterogeneity in cancer cells within a tumor, potentially offering new therapeutic targets against tumor resistance and metastasis.

New horizons at the interface of artificial intelligence and translational cancer research

Artificial intelligence (AI) is increasingly being utilized in cancer research as a computational strategy for analyzing multiomics datasets. Advances in single-cell and spatial profiling technologies have contributed significantly to our understanding of tumor biology, and AI methodologies are now being applied to accelerate translational efforts, including target discovery, biomarker identification, patient stratification, and therapeutic response prediction. Despite these advancements, the integration of AI into clinical workflows remains limited, presenting both challenges and opportunities. This review discusses AI applications in multiomics analysis and translational oncology, emphasizing their role in advancing biological discoveries and informing clinical decision-making. Key areas of focus include cellular heterogeneity, tumor microenvironment interactions, and AI-aided diagnostics. Challenges such as reproducibility, interpretability of AI models, and clinical integration are explored, with attention to strategies for addressing these hurdles. Together, these developments underscore the potential of AI and multiomics to enhance precision oncology and contribute to advancements in cancer care.

Targeting B7-H3 inhibition-induced activation of fatty acid synthesis boosts anti-B7-H3 immunotherapy in triple-negative breast cancer

BACKGROUND

Triple-negative breast cancer (TNBC) is the most malignant breast cancer, highlighting the need for effective immunotherapeutic targets. The immune checkpoint molecule B7-H3 has recently gained attention as a promising therapeutic target due to its pivotal role in promoting tumorigenesis and cancer progression. However, the therapeutic impact of B7-H3 inhibitors (B7-H3i) remains unclear.

METHODS

Transcriptomic and metabolomic analyses were conducted to explore the underlying mechanisms of B7-H3 inhibition in TNBC. The therapeutic efficacy of the combined treatment strategy was substantiated through comprehensive phenotypic assays conducted in vitro and validated in vivo using animal models.

RESULTS

B7-H3 blockade induces a "primed for death" stress state in cancer cells, leading to distinct alterations in metabolic pathways. Specifically, B7-H3 knockdown activated the AKT signaling pathway and upregulated sterol regulatory element-binding protein 1 (SREBP1), which in turn elevated FASN expression. The simultaneous inhibition of both B7-H3 and FASN more effectively attenuated the malignant progression of TNBC.

CONCLUSIONS

Our findings propose an "immune attack-metabolic compensation" dynamic model and suggest the feasibility of a dual-targeting strategy that concurrently inhibits both B7-H3 and FASN to enhance therapeutic efficacy in TNBC patients.

Rare Subset of T Cells Form Heterotypic Clusters with Circulating Tumor Cells to Foster Cancer Metastasis

The immune ecosystem is central to maintaining effective defensive responses. However, how immune cells in the periphery blood interact with circulating tumor cells (CTCs) - seeds of metastasis - remains largely understudied. Here, our analysis of the blood specimens (N=1,529) from patients with advanced breast cancer revealed that over 75% of the CTC-positive blood specimens contained heterotypic CTC clusters with CD45 + white blood cells (WBCs). Detection of CTC-WBC clusters correlates with breast cancer subtypes (triple negative and luminal B), racial groups (Black), and decreased survival rates. Flow cytometry and ImageStream analyses revealed diverse WBC composition of heterotypic CTC-WBC clusters, including overrepresented T cells and underrepresented neutrophils. Most strikingly, a rare subset of CD4 and CD8 double positive T (DPT) cells showed an up to 140-fold enrichment in the CTC clusters versus its frequency in WBCs. DPT cells shared part of the profiles with CD4 + T cells and others with CD8 + T cells but exhibited unique features of T cell exhaustion and immune suppression with higher expression of TIM-3 and PD-1. Single-cell RNA sequencing and genetic perturbation studies further pinpointed the integrin VLA4 (α4β1) in DPT cells and its ligand VCAM1 in tumor cells as essential mediators of heterotypic WBC-CTC clusters. Neoadjuvant administration of anti-α4 (VLA4) neutralizing antibodies markedly blocked CTC-DPT cell clustering and inhibited metastasis for extended survival in preclinical mouse models in vivo . These findings uncover a pivotal role of rare DPT cells with immune suppressive features in fostering cancer dissemination through direct interactive clustering with CTCs. It lays a foundation for developing innovative biomarkers and therapeutic strategies to prevent and target cancer metastasis, ultimately benefiting cancer care.

Brief summary

Our findings uncover a fostering role of immune-suppressive T cells in contact with circulating tumor cells and identify therapeutic approaches to eliminate devastating cancer metastasis.

CD103+CD56+ ILCs Are Associated with an Altered CD8+ T-cell Profile within the Tumor Microenvironment

Immunotherapies have had unprecedented success in the treatment of multiple cancer types, albeit with variable response rates. Unraveling the complex network of immune cells within the tumor microenvironment (TME) may provide additional insights to enhance antitumor immunity and improve clinical response. Many studies have shown that NK cells or innate lymphoid cells (ILC) have regulatory capacity. Here, we identified CD103 as a marker that was found on CD56+ cells that were associated with a poor proliferative capacity of tumor-infiltrating lymphocytes in culture. We further demonstrated that CD103+CD56+ ILCs isolated directly from tumors represented a distinct ILC population that expressed unique surface markers (such as CD49a and CD101), transcription factor networks, and transcriptomic profiles compared with CD103-CD56+ NK cells. Using single-cell multiomic and spatial approaches, we found that these CD103+CD56+ ILCs were associated with CD8+ T cells with reduced expression of granzyme B. Thus, this study identifies a population of CD103+CD56+ ILCs with potentially inhibitory functions that are associated with a TME that includes CD8+ T cells with poor antitumor activity. Further studies focusing on these cells may provide additional insights into the biology of an inhibitory TME.

TREM2+ macrophages: a key role in disease development

Triggering receptors expressed on myeloid cells 2 (TREM2), an immune receptor expressed on myeloid cells, has garnered considerable attention in recent years due to its role in unique signaling pathways and diverse biological functions, including phagocytosis, lipid metabolism, cell survival, and inflammatory responses. Although TREM2 is expressed in various cell types, such as macrophages, dendritic cells (DCs), osteoclasts, and others, where it exhibits context-dependent functional characteristics, it is mainly expressed in macrophages. Notably, TREM2 is implicated in the development and progression of multiple diseases, playing dual and often opposing roles in noncancerous diseases and cancers. This review aims to highlight the pivotal role of TREM2 in macrophages and immune-related diseases, elucidate its underlying mechanisms of action, explore its potential as a clinical diagnostic and prognostic marker, and propose therapeutic strategies targeting TREM2 based on current clinical trial data, providing comprehensive guidance and references for clinical practice.

Intrinsic subtype and immunity score in identification of triple-negative breast cancer at low risk

INTRODUCTION

Triple-negative breast cancer (TNBC) is group of heterogeneity caner. Despite majority of them had the unfavorable prognosis, a subset of patients who do not receive chemotherapy exhibit a good prognosis. Biomarkers are required to recognize these group of pateints and improve the current therapeutic strategies for them.

METHODS

A retrospective analysis of 997 patients with TNBC from three datasets including 188 case of Peking Union Medical College Hospital (PUMCH) and two TNBC datasets from published cohort studies(279 case of Affy-set, 530 case of GSE set) was conducted. Intrinsic subtypes (basal-like, immune-enhanced, human epidermal growth factor receptor-2 [HER2]-enriched and luminal A/B) and tumor environmental immunity were evaluated using expression profiles of a 72-gene panel. Association of intrinsic subtype and immunity score with distant metastasis-free survival (DMFS) and overall survival (OS) was analyzed.

RESULTS

Five intrinsic subtypes were identified in the patients with TNBC, comprising 64 % basal-like, 19 % immune-enhanced, 11 % HER2-enriched, 5 % luminal A, and 2 % luminal B. In the absence of adjuvant chemotherapy (ACT), Luminal A and immune-enhanced subtypes showed better DMFS than basal-like, HER2-enriched, and luminal B subtypes(P = 0.35). Significantly good OS was observed in luminal A and immune-enhanced subtypes compared to basal-like and HER2-enriched subtypes (P < 0.05). So two subtype groups were further classified as low-risk subtypes, including luminal A and immune-enhanced, and high-risk subtypes, including basal-like, HER2-enriched, and luminal B. Except for the immune-enhanced subtype, each subtype was further sorted and grouped according to immunity score, istrong and iweak. Significant improvements in both DMFS and OS were observed in patients with istrong compared with those with iweak(P = 0.01 and 0.0051 respectively). When combining intrinsic subtype and immunity status to predict the benefit from ACT, all high-risk subtype patients demonstrated improved DMFS(P = 0.075) and OS(P < 0.0001), with istrong patients exhibiting greater benefit; low-risk subtype plus iweak patients showed marginal benefit, whereas low-risk subtype plus istrong patients demonstrated least benefit from ACT.

CONCLUSION

Intrinsic subtype and immunity score is good prognostic biomarkers for patients with TNBC in the absence of chemotherapy. Combined intrinsic subtype and immunity evaluation could identify patients with TNBC who do not benefit from chemotherapy.

Circadian Rhythm Disruption in Triple-Negative Breast Cancer: Molecular Insights and Treatment Strategies

Disruption of the circadian clock has been closely linked to the initiation, development, and progression of cancer. This study aims to explore the impact of circadian rhythm disruption (CRD) on triple-negative breast cancer (TNBC). We analyzed bulk and single-cell RNA sequencing data to assess circadian rhythm status in TNBC using multiple bioinformatic tools, alongside metabolomic profiles and tumor microenvironment evaluations to understand the influence of CRD on metabolic reprogramming and immune evasion. The results indicate that TNBC experiences profound CRD. Patients with a higher CRDscore exhibit significantly poorer relapse-free survival compared to those with a lower CRDscore. Cyclic ordering by periodic structure (CYCLOPS) identified significant changes in rhythmic gene expression patterns between TNBC and normal tissues, with TNBC showing a "rush hour" effect, where peak expression times are concentrated within specific time windows. Transcripts with disrupted circadian rhythms in TNBC were found to be involved in key pathways related to cell cycle regulation, metabolism, and immune response. Metabolomic analysis further revealed that TNBCs with high CRDscore are enriched in carbohydrate and amino acid metabolism pathways, notably showing upregulation of tryptophan metabolism. High CRDscore was also linked to an immunosuppressive tumor microenvironment, characterized by reduced immune cell infiltration, exhausted CD8+ T cells, and a diminished response to immune checkpoint blockade therapy. These findings suggest that the disrupted molecular clock in TNBC may activate tryptophan metabolism, thereby promoting immune evasion and potentially reducing the effectiveness of immunotherapy.

Tumor Microenvironment On-A-Chip and Single-Cell Analysis Reveal Synergistic Stromal-Immune Crosstalk on Breast Cancer Progression

Solid tumors develop within a complex environment called the tumor microenvironment (TME), which is sculpted by the presence of other cells, such as cancer-associated fibroblasts (CAFs) and immune cells like macrophages (Mφs). Despite the presence of immune cells, tumor cells orchestrate a tumor-supportive environment through intricate interaction with the components of the TME. However, the specific mechanism by which this intercellular dialogue is regulated is not fully understood. To that end, the development of an organotypic 3D breast TME-on-a-chip (TMEC) model, integrated with single-cell RNA sequencing analysis, is reported to mechanistically evaluate the progression of triple-negative breast cancer (TNBC) cells in the presence of patient-derived CAFs and Mφs. Extensive functional assays, including invasion and morphometric characterization, reveal the synergistic influence of CAFs and Mφs on tumor cells. Furthermore, gene expression and pathway enrichment analyses identify the involvement of the KYNU gene, suggesting a potential immune evasion mechanism through the kynurenine pathway. Lastly, the pharmacological targeting of the identified pathway is investigated.

Dendritic cell maturation in cancer

Dendritic cells (DCs) are specialized antigen-presenting cells that are present at low abundance in the circulation and tissues; they serve as crucial immune sentinels by continually sampling their environment, migrating to secondary lymphoid organs and shaping adaptive immune responses through antigen presentation. Owing to their ability to orchestrate tolerogenic or immunogenic responses to a specific antigen, DCs have a pivotal role in antitumour immunity and the response to immune checkpoint blockade and other immunotherapeutic approaches. The multifaceted functions of DCs are acquired through a complex, multistage process called maturation. Although the role of inflammatory triggers in driving DC maturation was established decades ago, less is known about DC maturation in non-inflammatory contexts, such as during homeostasis and in cancer. The advent of single-cell technologies has enabled an unbiased, high-dimensional characterization of various DC states, including mature DCs. This approach has clarified the molecular programmes associated with DC maturation and also revealed how cancers exploit these pathways to subvert immune surveillance. In this Review, we discuss the mechanisms by which cancer disrupts DC maturation and highlight emerging therapeutic opportunities to modulate DC states. These insights could inform the development of DC-centric immunotherapies, expanding the arsenal of strategies to enhance antitumour immunity.

Multi-omics in immunotherapy research for HNSCC: present situation and future perspectives

Head and neck squamous cell carcinoma (HNSCC) is the sixth most common cancer worldwide, significantly impacting patient survival and quality of life. The recent emergence of immunotherapy has provided new hope for HNSCC patients, improving survival rates; however, only 15%-20% of patients benefit, and side effects are inevitable. With advancements in omics technologies and the growing prevalence of bioinformatics research, the immune microenvironment of HNSCC has become increasingly well understood, and the molecular mechanisms underlying immunotherapy responses continue to be elucidated. In this review, we summarize commonly used omics techniques and their applications in the research of HNSCC immunotherapy, including predicting and enhancing efficacy, formulating personalized treatment plans, establishing robust preclinical research models, and identifying new immunotherapy targets. Finally, we explore future perspective in terms of sequencing samples, data integration analysis, emerging technologies, clinicopathological features, and interdisciplinary approaches.

Immunogenomic cancer evolution: A framework to understand cancer immunosuppression

The process of tumor development involves tumor cells eluding detection and suppression of immune responses, which can cause decreased tumor cell antigenicity, expression of immunosuppressive molecules, and immunosuppressive cell recruitment to the tumor microenvironment (TME). Immunologically and genomically integrated analysis (immunogenomic analysis) of patient specimens has revealed that oncogenic aberrant signaling is involved in both carcinogenesis and immune evasion. In noninflamed cancers such as epidermal growth factor receptor (EGFR)-mutated lung cancers, genetic abnormalities in cancer cells contribute to the formation of an immunosuppressive TME by recruiting immunosuppressive cells, which cannot be fully explained by the cancer immunoediting hypothesis. This review summarizes the latest findings regarding the links between cancer genetic abnormalities and immunosuppression causing clinical resistance to immunotherapy. We propose the concepts of immunogenomic cancer evolution, in which cancer cell genomic evolution shapes the immunosuppressive TME, and immunogenomic precision medicine, in which cancer immunotherapy can be combined with molecularly targeted reagents that modulate the immunosuppressive TME.

Integrated single-cell and bulk transcriptomic analysis identifies a novel macrophage subtype associated with poor prognosis in breast cancer

BACKGROUND

Tumor-associated macrophages (TAMs) are pivotal components of the breast cancer (BC) tumor microenvironment (TME), significantly influencing tumor progression and response to therapy. However, the heterogeneity and specific roles of TAM subpopulations in BC remain inadequately understood.

METHODS

We performed an integrated analysis of single-cell RNA sequencing (scRNA-seq) and bulk RNA sequencing (RNA-seq) data from BC patients to comprehensively characterize TAM heterogeneity. Utilizing the MetaTiME computational framework and consensus clustering, we identified distinct TAM subtypes and assessed their associations with clinical outcomes and treatment responses. A machine learning-based predictive model was developed to evaluate the prognostic significance of TAM-related gene expression profiles.

RESULTS

Our analysis revealed three distinct TAM subgroups. Notably, we identified a novel macrophage subtype, M_Macrophage-SPP1-C1Q, characterized by high expression of SPP1 and C1QA, representing an intermediate differentiation state with unique proliferative and oncogenic properties. High infiltration of M_Macrophage-SPP1-C1Q was significantly associated with poor overall survival (OS) and chemotherapy resistance in BC patients. We developed a Random Forest (RF)-based predictive model, Macro.RF, which accurately stratified patients based on survival outcomes and chemotherapy responses, independent of established prognostic parameters.

CONCLUSION

This study uncovers a previously unrecognized TAM subtype that drives poor prognosis in BC. The identification of M_Macrophage-SPP1-C1Q enhances our understanding of TAM heterogeneity within the TME and offers a novel prognostic biomarker. The Macro.RF model provides a robust tool for predicting clinical outcomes and guiding personalized treatment strategies in BC patients.

Redirecting cytotoxic lymphocytes to breast cancer tumors via metabolite-sensing receptors

Insufficient infiltration of cytotoxic lymphocytes to solid tumors limits the efficacy of immunotherapies and cell therapies. Here, we report a programmable mechanism to mobilize Natural Killer (NK) and T cells to breast cancer tumors by engineering these cells to express orphan and metabolite-sensing G protein-coupled receptors (GPCRs). First, in vivo and in vitro CRISPR activation screens in NK-92 cells identified GPR183, GPR84, GPR34, GPR18, FPR3, and LPAR2 as top enhancers of both tumor infiltration and chemotaxis to breast cancer. These genes equip NK and T cells with the ability to sense and migrate to chemoattracting metabolites such as 7α,25-dihydroxycholesterol and other factors released from breast cancer. Based on Perturb-seq and functional investigations, GPR183 also enhances effector functions, such that engineering NK and CAR NK cells to express GPR183 enhances their ability to migrate to, infiltrate, and control breast cancer tumors. Our study uncovered metabolite-based tumor immune recruitment mechanisms, opening avenues for spatially targeted cell therapies.

Molecular Subtypes and Mechanisms of Breast Cancer: Precision Medicine Approaches for Targeted Therapies

Breast cancer remains one of the most prevalent diseases worldwide, primarily affecting women. Its heterogeneous nature poses a significant challenge in the development of effective and targeted treatments. Molecular characterization has enabled breast cancer to be classified into four main subtypes: luminal A, luminal B, HER2-positive, and triple-negative breast cancer, based on hormone receptor expression and HER2 status. A deeper understanding of these molecular markers and their associated signaling pathways, such as MAPK and PI3K/AKT, is essential for improving prognosis and optimizing treatment strategies. Currently, several therapeutic agents are utilized in neoadjuvant and adjuvant therapies, often in combination with surgical interventions. However, emerging evidence highlights the growing challenge of drug resistance, which significantly limits the efficacy of existing treatments. Addressing this issue may require innovative approaches, including combination therapies and precision medicine strategies, tailored to the molecular profile of each patient. Therefore, a comprehensive understanding of the pathophysiologic mechanisms driving breast cancer progression and resistance is crucial for the development of advanced targeted therapies with greater precision and efficacy. This review aims to explore recent advancements in molecular research related to breast cancer subtypes and provide a critical analysis of current therapeutic approaches within the framework of precision medicine.

Genetically engineered macrophages reverse the immunosuppressive tumor microenvironment and improve immunotherapeutic efficacy in TNBC

The main challenges in current immunotherapy for triple-negative breast cancer (TNBC) lie in the immunosuppressive tumor microenvironment (TME). Considering tumor-associated macrophages (TAMs) are the most abundant immune cells in the TME, resetting TAMs is a promising strategy for ameliorating the immunosuppressive TME. Here, we developed genetically engineered macrophages (GEMs) with gene-carrying adenoviruses, to maintain the M1-like phenotype and directly deliver the immune regulators interleukin-12 and CXCL9 into local tumors, thereby reversing the immunosuppressive TME. In tumor-bearing mice, GEMs demonstrated targeted enrichment in tumors and successfully reprogramed TAMs to M1-like macrophages. Moreover, GEMs significantly enhanced the accumulation, proliferation, and activation of CD8+ T cells, mature dendritic cells, and natural killer cells within tumors, while diminishing M2-like macrophages, immunosuppressive myeloid-derived suppressor cells, and regulatory T cells. This treatment efficiently suppressed tumor growth. In addition, combination therapy with GEMs and anti-programmed cell death protein 1 further improved interferon-γ+CD8+ T cell percentages and tumor inhibition efficacy in an orthotopic murine TNBC model. Therefore, this study provides a novel strategy for reversing the immunosuppressive TME and improving immunotherapeutic efficacy through live macrophage-mediated gene delivery.

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.

CD4+ anti-TGF-β CAR T cells and CD8+ conventional CAR T cells exhibit synergistic antitumor effects

Transforming growth factor (TGF)-β1 restricts the expansion, survival, and function of CD4+ T cells. Here, we demonstrate that CD4+ but not CD8+ anti-TGF-β CAR T cells (T28zT2 T cells) can suppress tumor growth partly through secreting Granzyme B and interferon (IFN)-γ. TGF-β1-treated CD4+ T28zT2 T cells persist well in peripheral blood and tumors, maintain their mitochondrial form and function, and do not cause in vivo toxicity. They also improve the expansion and persistence of untransduced CD8+ T cells in vivo. Tumor-infiltrating CD4+ T28zT2 T cells are enriched with TCF-1+IL7R+ memory-like T cells, express NKG2D, and downregulate T cell exhaustion markers, including PD-1 and LAG3. Importantly, a combination of CD4+ T28zT2 T cells and CD8+ anti-glypican-3 (GPC3) or anti-mesothelin (MSLN) CAR T cells exhibits augmented antitumor effects in xenografts. These findings suggest that rewiring TGF-β signaling with T28zT2 in CD4+ T cells is a promising strategy for eradicating solid tumors.

Continuous replenishment of the dysfunctional CD8 T cell axis is associated with response to chemoimmunotherapy in advanced breast cancer

Chemotherapy combined with immune checkpoint blockade has shown clinical activity in breast cancer. Response, however, occurs in only a low proportion of patients. How the immune landscape of the tumor determines the immune and clinical responses to chemoimmunotherapy is not well understood. Here, using a combination of single-cell RNA sequencing (scRNA-seq) and single-cell T cell receptor sequencing (scTCR-seq), we profile 40 biopsies from 27 patients with metastatic triple-negative breast cancer (TNBC), receiving chemotherapy and anti-PD-L1 alone or in combination with anti-CD73, in a phase 2 randomized clinical trial. Our results show an enrichment of late-dysfunctional, clonally expanded CD8+ T cells in responder (R) patients. On treatment, R display an influx of newly emerging clonotypes, as well as expansion of the CD8+ precursors. Collectively, our data suggest that baseline clonal expansion could be a potential predictor of response and that both clonal reinvigoration of pre-existing tumor-reactive T cells and clonal replacement on-treatment are important for a protective response to chemoimmunotherapy.

An automatic annotation tool and reference database for T cell subtypes and states at single-cell resolution

T cells have various subtypes and states with different functions. However, a reference list and automated annotation tool for T cell subtypes and states are lacking, which is critical for analyzing and comparing T cells under various conditions. We constructed the largest human T cell reference, containing 1,348,268 T cells from 35 conditions and 16 tissues. We classified T cells into 33 subtypes and further stratified them into 68 categories according to subtype and state. Based on this reference, we developed a tool named STCAT to automatically annotate T cells from scRNA-seq data by hierarchical models and marker correction. The accuracy of STCAT was 28% higher than that of existing tools validated on six independent datasets, including cancer and healthy samples. Using STCAT, we consistently discovered that CD4+ Th17 cells were enriched in late-stage lung cancer patients in multiple datasets, whereas MAIT cells were prevalent in milder-stage COVID-19 patients. We also confirmed a decrease in Treg cytotoxicity in post-treatment ovarian cancer. Systematic landscape analyses of CD4+ and CD8+ T cell references revealed that CD4+ Treg cells were enriched in tumor samples and that CD8+ naive-related cells were abundant in healthy individuals. Finally, we deposited all the T cell references and annotations into a TCellAtlas (https://guolab.wchscu.cn/TCellAtlas) database, which allows users to browse T cell expression profiles and analyze customized scRNA-seq data by STCAT. In conclusion, comprehensive human T cell subtypes and states reference, automated annotation tool, and database will greatly facilitate research on T cell immunity and tumor immunology.

Single-cell transcriptomic analyses reveal heterogeneity and key subsets associated with survival and response to PD-1 blockade in cervical squamous cell carcinoma

BACKGROUND

Understanding the intricate tumor microenvironment (TME) is crucial for elucidating the mechanisms underlying the progression of cervical squamous cell carcinoma (CSCC) and its response to anti-PD-1 therapy.

METHODS

In this study, we characterized 50,649 cells obtained from the CSCC for single-cell RNA sequencing and integrated bulk sequencing data from The Cancer Genome Atlas (TCGA) and clinical samples to explore their cell composition, metabolic processes, signaling pathways, specific transcription factors, lineage tracking and response to immunotherapy. In vivo experiments were performed to validate the function of key cell subsets.

RESULTS

We identified ten major cell type and 35 subsets of stromal and immune cells in TME and observed distinct patterns in the metabolic processes and signaling pathways of these cells between tumor and normal tissues. Furthermore, PCNA clamp-associated factor (PCLAF)+ tumor-associated epithelial cell (TAEpis) was negatively correlated with the number of C-X-C motif chemokine ligand 13 (CXCL13)+ CD8+ T cells, overall survival, and response to anti-programmed cell death-1(PD-1) therapy in patients with CSCC. Both in vivo and in vitro experiments demonstrated that PCLAF+ TAEpis promotes the apoptosis of CD8+ T and tumor growth, while also inhibiting T cell infiltration and function.

CONCLUSION

Our findings illuminate the heterogeneity of the complex TME in CSCC and offer evidence supporting PCLAF+ TAEpis as a promising therapeutic target.

Single-cell spatial transcriptomics unravels cell states and ecosystems associated with clinical response to immunotherapy

BACKGROUND

The tumor microenvironment (TME) is a complex and dynamic ecosystem that is known to influence responses to immunotherapy. We leveraged single-cell spatial transcriptomics to systematically dissect the intricate complexity of the TME, in particular the cellular heterogeneity and spatial interactions. Their collective impact on immunotherapy efficacy was studied in the context of a homogeneous group of patients with vulvar high-grade squamous intraepithelial lesions (vHSIL) treated with an immunotherapeutic tumor-specific peptide vaccine.

METHODS

We performed single-cell spatial transcriptomics on 20 pretreatment vHSIL lesions, stratified by clinical response to immunotherapeutic vaccination into complete responders (CR), partial responders (PR) and non-responders (NR). Using a 1,000-gene panel, we mapped over 274,000 single cells in situ, identifying 18 cell clusters and 99 distinct non-epithelial cell states. Findings were validated against public single-cell transcriptomic data sets to assess their broader relevance across tumor types.

RESULTS

Profound heterogeneity within the TME was detected across the response groups. CR lesions exhibited a higher ratio of immune-supportive to immune-suppressive cells-a pattern mirrored in other solid tumors following neoadjuvant checkpoint blockade. Key immune populations enriched in CRs included CD4+CD161+ effector T cells and chemotactic CD4+ and CD8+ T cells. Conversely, PRs were characterized by increased proportions of T helper 2 cells and CCL18-expressing macrophages, which are associated with the recruitment of type 2 T cells and regulatory T cells. NRs displayed preferential infiltration with immunosuppressive fibroblasts. Distinct spatial immune ecosystems further defined response groups. Although a number of immune cells were detected in all patients, type 1 effector cells dominated interactions in CRs, type 2 cells were prominently interacting in PRs, while NRs lacked organized immune cell interactions.

CONCLUSIONS

This study underscores the dual importance of both cellular composition and spatial organization in steering clinical response to immunotherapy.

New insights into cancer immune checkpoints landscape from single-cell RNA sequencing

Immune checkpoint blockade (ICB) therapy represents a pivotal advancement in tumor immunotherapy by restoring the cytotoxic lymphocytes' anti-tumor activity through the modulation of immune checkpoint functions. Nevertheless, many patients experience suboptimal therapeutic outcomes, likely due to the immunosuppressive tumor microenvironment, drug resistance, and other factors. Single-cell RNA sequencing has assisted to precisely investigate the immune infiltration patterns before and after ICB treatment, enabling a high-resolution depiction of previously unrecognized functional interaction among immune checkpoints. This review addresses the heterogeneity between tumor microenvironments that respond to or resist ICB therapy, highlighting critical factors underlying the variation in immunotherapy efficacy and elucidating treatment failure. Furthermore, a comprehensive examination is provided of how specific ICBs modulate immune and tumor cells to achieve anti-tumor effects and generate treatment resistance, alongside a summary of emerging immune checkpoints identified as promising targets for cancer immunotherapy through single-cell RNA sequencing applications.

Therapies targeting triple-negative breast cancer: a perspective on anti-FGFR

Triple-negative breast cancer (TNBC) is one of the subtypes with the worst prognosis due to tumour heterogeneity and lack of appropriate treatment. This condition is a consequence of the distinctive tumour microenvironment (TME). The TME is associated with factors such as the promotion of proliferation, angiogenesis, inhibition of apoptosis, suppression of the immune system and drug resistance. Therefore, remodelling the TME is critical for the treatment of TNBC. A key role in the formation of the TME is played by the fibroblast growth factor/fibroblast growth factor receptor(FGF/FGFR) signalling pathway. Thus, the FGFRs may be a potential target for treating TNBC. Over-activated FGFRs promote growth, migration and drug resistance in TNBC by influencing the onset of TME events, tumour angiogenesis and immune rejection. A thorough comprehension of the FGF/FGFR signalling pathway's mechanism of action in the development of TNBC could offer valuable insights for discovering new therapeutic strategies and drug targets. Inhibiting the FGF/FGFR axis could potentially hinder the growth of TNBC and its drug resistance by disrupting crucial biological processes in the TME, such as angiogenesis and immune evasion. This review evaluates the potential of inhibiting the FGF/FGFR axis as a strategy for treating TNBC. It explores the prospects for developing related therapeutic approaches. This study explores the research and application prospects of the FGF/FGFR axis in TNBC. The aim is to provide guidance for further therapeutic research and facilitate the development of innovative approaches targeting TNBC.

Single-cell and transcriptome analyses revealed CTHRC1 a potential therapeutic target mediating invasion and tumor microenvironment in TNBC: experimental validation

Background

Investigating the pivotal role of CTHRC1 in the tumor microenvironment of triple-negative breast cancer (TNBC).

Method

The RNA transcriptomic data obtained from the Cancer Genome Atlas and single-cell sequencing data from TNBC in Gene Expression Omnibus (GEO) were acquired and subjected to analysis. A comprehensive investigation was conducted with a specific focus on characterizing CTHRC1 in TNBC and its correlation with invasive genes. Furthermore, additional analyses were performed to explore the relationship between CTHRC1, tumor immune cell infiltration, and immunotherapy in TNBC. The expression of CTHRC1 in the tumor microenvironment, cellular differentiation, and cellular communication was systematically analyzed using single-cell data from TNBC.

Result

The expression of CTHRC1 in patients with TNBC gradually increases concomitantly with the progression of tumor T-stage and N-stage. Simultaneously, there is a concurrent increase in the expression of most invasive gene sets. Furthermore, there is a significant augmentation in both infiltration abundance and activity of M2-type macrophages associated with elevated levels of CTHRC1 expression. Single-cell data reveal an upregulated expression of the invasive gene set in CTHRC1-positive cancer associated fibroblasts (CAFs), thereby modulating their interaction with M2-type macrophages. Multiple immunofluorescence analyses confirmed that CTHRC1 modulates immune cell infiltration and tumor cell invasion through the mediation of CAFs.

Conclusion

CTHRC1 was a molecule that exhibits characteristic expression in TNBC. CTHRC1 positive CAFs exert regulatory effects within the immunosuppressive microenvironment of TNBC by modulating M2-type macrophages.

Exploring the "chemo" in chemoimmunotherapy for triple-negative breast cancer

In this issue of Cancer Cell, Zhang et al. use single-cell RNA sequencing to compare immune cell dynamics in triple-negative breast cancers treated with the PD-L1 inhibitor atezolizumab plus paclitaxel or nab-paclitaxel. They identify distinct T cell activation patterns and highlight mast cells' role in immune activation exclusively in the nab-paclitaxel combination.

Distinct cellular mechanisms underlie chemotherapies and PD-L1 blockade combinations in triple-negative breast cancer

Combining immune checkpoint blockade (ICB) with chemotherapy shows promise for treating triple-negative breast cancer (TNBC), though the mechanisms remain incompletely understood. Here, we integrate published and new single-cell RNA sequencing (scRNA-seq) data to investigate the tumor immune microenvironment (TIME) in TNBC patients treated with paclitaxel (PTX), nab-paclitaxel (Nab-PTX), and their combinations with the anti-PD-L1 antibody atezolizumab (ATZ). Compared to ATZ plus PTX, ATZ plus Nab-PTX rewires TCF7+ stem-like effector memory CD8+ T cells (Tsem) and CD4+ T follicular helper (Tfh) cells. Nab-paclitaxel, unlike PTX, also reshapes the myeloid compartment, expanding mast cells and pro-inflammatory macrophages. Our analyses in human TNBC and murine models underscore the crucial role of mast cells in orchestrating anti-tumor immune responses, likely by promoting the recruitment and activation of T and B cells. In vivo experiments demonstrate that activating mast cells alongside PD-L1 blockade attenuates TNBC progression, suggesting mast cells as a promising adjunct for enhancing ICB therapy efficacy.

Immunosuppressive microenvironment of liver restrains chemotherapeutic efficacy in triple-negative breast cancer

BACKGROUND

Patients with liver metastases of triple-negative breast cancer (TNBC) show poor prognosis compared with other metastases. Chemotherapy is the primary treatment for advanced TNBC. Tumor cell diversity and the tumor microenvironment could affect therapeutic effect. However, whether liver metastases of TNBC exhibit differential chemotherapy efficacy compared with the primary tumors remains inadequately understood. The specific mechanisms that modulate chemotherapy efficacy in liver metastases need further investigation.

METHODS

Single-cell RNA sequencing data from public databases were leveraged to contrast the immune profiles of liver metastases and primary tumors in TNBC. Murine models bearing liver tumors or primary tumors of TNBC were used to evaluate chemotherapy efficacy. Techniques such as immunohistochemistry, wound healing assays, and colony formation assays were employed to account for tumor heterogeneity. Intratumoral T lymphocytes and macrophages were quantified and characterized using RNA sequencing, immunohistochemistry, and flow cytometry. Antibody-mediated depletion of CD8+T cells or macrophages in mice substantiated their impact on chemotherapy responses.

RESULTS

Single-cell RNA sequencing data showed the immune microenvironments of liver metastases and primary tumors exhibited significant differences, which may critically influence chemotherapy outcomes. Mouse models confirmed that chemotherapy was less effective against liver tumors compared with subcutaneous tumors. After excluding the influence of tumor cell heterogeneity, the weaker responsiveness in liver tumors was mediated by the impeded infiltration of CD8+T cells, attributed to the decreased activation of macrophages. Augmenting macrophage activation can improve the chemotherapeutic efficacy in liver tumors. Moreover, chemotherapy drove the immune microenvironment towards increased suppression through distinct mechanisms, with neutrophil extracellular traps (NETs) accumulating in liver tumors and impaired functionality of macrophages at the primary site. The combination of NET inhibitors or macrophage activators with chemotherapy enhanced treatment effectiveness.

CONCLUSIONS

These findings disclose the compromised chemotherapeutic efficacy in liver tumors of TNBC and elucidate the underlying immune-related mechanisms within the tumor microenvironment. Targeting the specific underpinnings of immune suppression at different tumor sites with selective drugs could optimize chemotherapeutic efficacy.

Mathematical Modeling Predicts Optimal Immune Checkpoint Inhibitor and Radiotherapy Combinations and Timing of Administration

Radiotherapy (RT) combined with immune checkpoint inhibitor (ICI) therapy has attracted substantial attention due to its potential to improve outcomes for patients with several types of cancer. However, the optimal administration timepoints and drug combinations remain unclear because the mechanisms underlying RT-induced changes in immune checkpoint molecule expression and interaction with their ligand(s) remain unclear. In this study, we demonstrated the dynamics of lymphocyte-mediated molecular interactions in tissue samples from patients with esophageal cancer throughout RT schedules. Single-cell RNA sequencing and spatial transcriptomic analyses were performed to investigate the dynamics of these interactions. The biological signal in lymphocytes transitioned from innate to adaptive immune reaction, with increases in ligand-receptor interactions, such as PD-1-PD-L1, CTLA4-CD80/86, and TIGIT-PVR interactions. A mathematical model was constructed to predict the efficacy of five types of ICIs when administered at four different timepoints. The model suggested that concurrent anti-PD-1/PD-L1 therapy or concurrent/adjuvant anti-CTLA4/TIGIT therapy would exert a maximal effect with RT. This study provides rationale for clinical trials of RT combined with defined ICI therapy, and these findings will support future studies to search for more effective targets and timing of therapy administration.

Profiling Multiple CD8+ T-cell Functional Dimensions Enhances Breast Cancer Immune Assessment

CD8+ T-cell abundance is insufficient to assess antitumor immunity and shows poor performance in predicting breast cancer prognosis and immunotherapy response, presumably owing to the complexity of CD8+ T-cell functionalities. Although single-cell RNA sequencing can dissect the multifaceted functions of CD8+ T cells for better immune assessment, its clinical application is limited. In this study, we developed bulk RNA sequencing-based FuncDimen models from integrative analysis of single-cell RNA sequencing and matched bulk RNA sequencing data to evaluate CD8+ T-cell functionalities across five dimensions: tumor reactivity, cytotoxicity, IFNγ secretion, proliferation, and apoptosis. The FuncDimen models quantifying different functional dimensions of CD8+ T cells were validated in our breast cancer cohort and external databases using immunofluorescence and imaging mass cytometry. We calculated the FuncAggre score by weighted aggregation of all five FuncDimen models to encapsulate the overall antitumor immunity. In our breast cancer cohort and external databases, the FuncAggre score demonstrated superior predictive performance for breast cancer prognosis (time-dependent AUC: 0.56-0.70) and immunotherapy response (AUC: 0.71-0.83) over other immune biomarkers, regardless of the breast cancer molecular subtype. Together, the FuncDimen models offer a refined assessment of antitumor immunity mediated by CD8+ T cells in the clinic, enhancing prognostic prediction and aiding personalized immunotherapy in breast cancer.