CXCL9:SPP1 macrophage polarity identifies a network of cellular programs that control human cancers

Pushing the boundaries of radiotherapy-immunotherapy combinations: highlights from the 7th immunorad conference

Over the last decade, the annual Immunorad Conference, held under the joint auspicies of Gustave Roussy (Villejuif, France) and the Weill Cornell Medical College (New-York, USA) has aimed at exploring the latest advancements in the fields of tumor immunology and radiotherapy-immunotherapy combinations for the treatment of cancer. Gathering medical oncologists, radiation oncologists, physicians and researchers with esteemed expertise in these fields, the Immunorad Conference bridges the gap between preclinical outcomes and clinical opportunities. Thus, it paves a promising way toward optimizing radiotherapy-immunotherapy combinations and, from a broader perspective, improving therapeutic strategies for patients with cancer. Herein, we report on the topics developed by key-opinion leaders during the 7th Immunorad Conference held in Paris-Les Cordeliers (France) from September 27th to 29th 2023, and set the stage for the 8th edition of Immunorad which will be held at Weill Cornell Medical College (New-York, USA) in October 2024.

The Identification of Novel Prognostic and Predictive Biomarkers in Breast Cancer via the Elucidation of Tumor Ecotypes Using Ecotyper

Background

Breast cancer is a highly heterogeneous disease, characterized by tumor and nontumor cells at various cell states. Ecotyper is an innovative machine learning framework that quantifies the tumor microenvironment and delineates the tumor ecosystem, demonstrating clinical significance. However, further validation is needed in breast cancer.

Methods

Ecotyper was applied to identify multiple cellular states and tumor ecotypes using large-scale breast cancer bulk sequencing data, followed by a detailed analysis of their associations with clinical classification, molecular subtypes, survival prognosis, and immunotherapy response. Identified subtypes were further characterized using single-cell and spatial data sets to reveal molecular profiles.

Results

In a comprehensive analysis of 6578 breast cancer samples from four data sets, Ecotyper identified 69 cellular states and 10 tumor ecotypes. Of these, 37 cellular states significantly correlated with overall survival. Notably, specific states within epithelial cells, macrophages/monocytes, and fibroblasts were linked to a worse prognosis. CE2 abundance was identified as the most significant marker indicating unfavorable prognosis and was further validated in an additional data set of 116 HER2-negative patients. These biomarkers also indicated the efficacy of neoadjuvant immunotherapy in breast cancer. CE2-high cancers were characterized by an abundance of basal-like epithelial cells, scant lymphocytic infiltration, and activation of hypoxia signaling. Single-cell analysis showed that CE2-high areas were rich in SPP1-positive tumor-associated macrophages(TAM), basal-like epithelial cells, and hypoxic cancer-associated fibroblasts(CAF). Spatially, these regions were often peripheral in triple-negative breast cancer, adjacent to fibrotic/necrotic zones. Multiplex immunofluorescence confirmed the enrichment of SPP1+CD68+TAM and HIF1A+SMA+CAF in hypoxic triple-negative breast cancer (TNBC) regions.

Conclusions

Ecotyper identified novel biomarkers for breast cancer prognosis and treatment prediction. The CE2-high region may represent a hypoxic immune-suppressive niche.

Interactions between cancer cells and tumor-associated macrophages in tumor microenvironment

Tumor microenvironment (TME) refers to the local environment in which various cancer cells grow, encompassing tumor cells, adjacent non-tumor cells, and associated non-cellular elements, all of which collectively promote cancer occurrence and progression. As a principal immune component in the TME, tumor-associated macrophages (TAMs) exert a considerable influence on cancer behaviors via their interactions with cancer cells. The interactive loops between cancer cells and TAMs, including secretory factors derived from both cancer cells and TAMs, are crucial for the proliferation, stemness, drug resistance, invasion, migration, metastasis, and immune escape of various cancers. Cancer cells release paracrine proteins (HMGB1, AREG etc.), cytokines (IL-6, CCL2 etc.), RNAs (miR-21-5p, circPLEKHM1, LINC01812 etc.), and metabolites (lactic acid, succinate etc.) to regulate the polarization phenotype, mediator secretion and function of TAMs. In turn, mediators (TGF-β, IL-10, IL-6 etc.) from TAMs promote cancer progression. This review summarizes recent advancements in the interactive loops between cancer cells and TAMs in TME. Inhibiting the recruitment and M2 polarization of TAMs, reprogramming TAMs from M2 to M1 phenotype, blocking TAMs-mediated immunosuppression and immune escape, and combining with existing immunotherapy can target TAMs to overcome immunotherapy resistance in various cancers. The new breakthroughs lie in identifying effective targets for drug development, improving the drug delivery system to enhance the drug delivery efficiency, and adopting combined therapy. Interventions targeting secretory factors, cell surface receptors, intracellular signaling pathways, and metabolic modulation in the interactive loops between cancer cells and TAMs are expected to suppress cancer progression and improve therapeutic effects.

TGF-β1 induces autophagy and mediates the effect on macrophages differentiation in primary liver cancer

BACKGROUND

Tumor-associated macrophages (TAMs) are closely associated with tumor development and patient outcomes due to their plasticity and polarization capacity. Several distinct TAMs have been proposed, but a complete understanding of heterogeneity and differentiation spectrum of macrophage in human primary liver cancer remains elusive.

METHODS

Deep single-cell RNA sequencing (scRNA-seq) data from 19 primary liver cancer patients were used to profile the transcriptomes of TAMs in liver cancer. Ingenuity pathway analysis (IPA) and in vitro experiments were used to explore possible mechanisms responsible for related signaling pathways altered at the transcriptional level. Finally, we analyzed the relationship between the abundance of the TAMs and the survival outcomes of the 428 patients in the Cancer Genome Atlas (TCGA).

RESULTS

Transcriptional profiles allowed us to identify four distinct TAMs cell subsets based on molecular and functional properties and to reconstruct their developmental trajectory. Specifically, TAM_c4 was preferentially enriched and potentially expanded in the advanced-stage patients or those receiving immune checkpoint blockade therapy (ICT). Gene pathway analysis revealed aberrant TGFB1 activation in TAM_c4, which was experimentally confirmed to drive TAM phenotypic transitions via autophagy signaling. High abundance of TAM_c4 is found to be related to a short survival time and low abundance of CD8+ T cells in primary liver cancers.

CONCLUSIONS

This integrated transcriptome compendium and experimental validation offer both mechanistic insights and a resource for understanding TAM heterogeneity in primary liver cancers.

CD301b+ monocyte-derived dendritic cells mediate resistance to radiotherapy

Monocytes infiltrating tumors acquire various states that distinctly impact cancer treatment. Here, we show that resistance of tumors to radiotherapy (RT) is controlled by the accumulation of monocyte-derived dendritic cells (moDCs). These moDCs are characterized by the expression of CD301b and have a superior capacity to generate regulatory T cells (Tregs). Accordingly, moDC depletion limits Treg generation and improves the therapeutic outcome of RT. Mechanistically, we demonstrate that granulocyte-macrophage colony-stimulating factor (GM-CSF) derived from radioresistant tumor cells following RT is necessary for the accumulation of moDCs. Our results unravel the immunosuppressive function of moDCs and identify GM-CSF as an immunotherapeutic target during RT.

Exploration of histone protein γ-H2AX as a prognostic factor in soft tissue sarcomas and its association with biological behavior, immune cell environment and survival in leiomyosarcoma

This study evaluates the H2AX/γ-H2AX expression in soft tissue sarcomas (STS), its implications for biological behavior and immune environment, and its potential as a prognostic biomarker. RNA-Seq data from 237 STS were obtained from The Cancer Genome Atlas project. Patients were stratified by H2AX mRNA expression using a survival-associated cutoff. Differentially expressed genes and pathways as well as immune signatures between H2AXhigh- and H2AXlow tumors were identified with DESeq2 analysis, gene set enrichment analyses (GSEA), Enrichr pathway analysis and CIBERSORTx. Tissue microarrays of a different cohort of 291 STS were generated for immunohistochemical staining to assess γ-H2AX protein expression, followed by statistical evaluation. High H2AX mRNA expression was associated with shorter overall survival (OS) in STS (p = 0.02), particularly in leiomyosarcomas (LMS) (p < 0.001), and was a negative prognostic factor in LMS (HR 11.15, p < 0.001). H2AXhigh LMS tumors showed upregulation of cell cycle-related pathways, while H2AXlow LMS exhibited increased inflammatory activity, including elevated M1 macrophage signatures and resting mast cell signatures (both p < 0.001). High γ-H2AX protein levels were an independent negative prognostic factor in the total LMS cohort (HR 12.12, p = 0.025) and in the subgroup of non-uterine LMS (HR 153.80, p = 0.013). Consistent with CIBERSORTx analysis, γ-H2AXlow LMS showed higher mast cell infiltration than γ-H2AXhigh LMS (p = 0.038). In conclusion, H2AX mRNA and γ-H2AX protein expression are associated with distinct biological behavior, differences in the immune cell environment, and might serve as useful prognostic biomarkers in LMS.

One Step Ahead: Preventing Tumor Adaptation to Immune Therapy

Immune checkpoint inhibitors are cancer therapeutics that have shown remarkable success in extending lives in many cancers, including melanoma, MSI-high cancers, and other cancers. However, these therapeutics have not shown benefit for many patients with cancer, especially those with advanced cancer diagnoses. In addition, many patients develop resistance to these therapeutics and/or life-altering adverse events that can include cardiotoxicity, pneumonitis, thyroiditis, pancreatitis, and hepatitis. Extensive efforts to improve cancer care by uncovering mechanisms of resistance to immune therapy in solid tumors have led to identification of new sources of resistance and to the development of new approaches to activate or sustain antitumor immunity. Chronic stimulation of T cells by tumors and by checkpoint inhibitors can lead to a progressive state of T-cell exhaustion. Chronic T-cell activation by the tumor microenvironment (TME) or immune therapeutics can upregulate the expression and function of alternate checkpoints, including the T-cell protein LAG-3. Persistent interferon signaling in the TME can drive epigenetic changes in cancer cells that enable tumors to counter immune activation and disrupt tumor cell elimination. In addition, immune-suppressive macrophages can flood tumors in response to signals from dying tumor cells, further preventing effective immune responses. New clinical developments and/or approvals for therapies that target alternate immune checkpoints, such as the T-cell checkpoint LAG-3; myeloid cell proteins, such as the kinase phosphoinositide 3-kinase gamma isoform; and chronic interferon signaling, such as Jak 1 inhibitors, have been approved for cancer care or shown promise in recent clinical trials.

Single-cell and spatial transcriptome analyses reveal tumor heterogeneity and immune remodeling involved in pituitary neuroendocrine tumor progression

Pituitary neuroendocrine tumors (PitNETs) can be invasive or aggressive, yet the mechanisms behind these behaviors remain poorly understood, impeding treatment advancements. Here, we integrat single-cell RNA sequencing and spatial transcriptomics, analyzing over 177,000 cells and 35,000 spots across 57 tissue samples. This comprehensive approach facilitates the identification of PitNETs tumor populations and characterizes the reconfiguration of the tumor microenvironment (TME) as PitNETs progress and invade. We trace the trajectory of TPIT-lineage PitNETs and identify an aggressive tumor cluster marked by elevated p53-mediated proliferation and a higher Trouillas classification, both associated with tumor progression. Additionally, we document the heterogeneity of immune stromal cells within PitNETs, particularly noting the enrichment of SPP1+ tumor associated macrophages (TAMs) in invasive tumors. These TAMs facilitate tumor invasion through the SPP1-ITGAV/ITGB1 signaling pathway. Our in-depth single-cell and spatial analysis of PitNETs uncovers the molecular dynamics within the TME, suggesting potential targets for therapeutic intervention.

Deciphering the cellular and molecular landscape of cervical cancer progression through single-cell and spatial transcriptomics

Cervical cancer represents a significant global health challenge, with complex cellular and molecular mechanisms driving its progression from HPV infection to invasive malignancy. This study employed an integrated approach combining single-cell RNA sequencing (scRNA-seq) and spatial transcriptomics (stRNA-seq) to comprehensively characterize the tumor microenvironment (TME) across different stages of cervical cancer development. Through analysis of samples from normal cervix, HPV-infected normal cervix, high-grade squamous intraepithelial lesions (HSIL), and invasive cervical cancer, we identified distinct cellular populations and their dynamic changes during disease progression. Our findings revealed significant heterogeneity in immune cell populations, particularly highlighting the role of SPP1+ macrophages that were substantially enriched in cervical cancer compared to precancerous and normal tissues. Cell-cell communication networks and spatial mapping demonstrated that SPP1+ macrophages interact extensively with immune cells through the SPP1-CD44 signaling axis. This interaction contributes to an immunosuppressive microenvironment through modulation of T cell function and promotion of tumor cell survival. Furthermore, high expression of SPP1 correlated with advanced tumor stages and poor overall survival in cervical cancer patients, highlighting its potential as a prognostic biomarker. Our comprehensive characterization of the cellular landscape and intercellular communication networks in cervical cancer progression provides valuable insights for the development of targeted therapeutic strategies aimed at modulating the TME, particularly through disruption of the SPP1-CD44 axis. These findings establish a foundation for more effective personalized approaches to improve clinical outcomes in cervical cancer patients.

Dual cytokine-engineered macrophages rejuvenate the tumor microenvironment and enhance anti-PD-1 therapy in renal cell carcinoma

Despite advances in PD-1 blockade therapy, the immunosuppressive tumor microenvironment (TME) limits its efficacy in renal cell carcinoma (RCC). Here, we developed dual-cytokine-engineered macrophages co-delivering IL-12 and CXCL-9 to reprogram TME and enhance anti-PD-1 responsiveness. Single-cell RNA sequencing revealed that RCC harbor abundant M2-like tumor-associated macrophages (TAMs), which correlate with T-cell exhaustion. In vitro, engineered macrophages polarized M2-like TAMs to antitumor M1 phenotypes, secreted CXCL-9 to recruit cytotoxic T cells, and released IL-12 to amplify T/NK cell activation. In vivo, intravenously administered engineered macrophages homed to tumors, reshaped the TME by increasing CD8+ T cells, dendritic cells, and NK cells while reducing immunosuppressive Tregs and MDSCs. This approach synergized with PD-1 blockade, resulting in a 2.5-fold greater tumor growth inhibition compared to anti-PD-1 monotherapy. This dual-cytokine macrophage platform offers a novel strategy to overcome resistance to checkpoint inhibitors in RCC by delivering cytokine and remodeling TME, with implications for clinical translation.

Semaglultide targets Spp1+ microglia/macrophage to attenuate neuroinflammation following perioperative stroke

Peripheral surgery evokes neuroimmune activation in the central nervous system and modulates immune cell polarization in the ischemic brain. However, the phenotypic change of microglia and myeloid cells within post-surgical ischemic brain tissue remain poorly defined. Using an integrated approach that combines single-cell RNA sequencing with comprehensive biological analysis in a perioperative ischemic stroke (PIS) model, we identified a distinct Spp1-positive macrophage/microglia (Spp1+ Mac/MG) subgroup that exhibit enriched anti-inflammatory pathways with distinct lipid metabolic reprogrammed profile. Moreover, using immunofluorescence staining, we identified the expression of Glucagon-like peptide-1 receptor (GLP1R) in Spp1+F4/80+ cells and Spp1+Iba-1+ cells. Intraperitoneal administration of semaglutide, a GLP1R agonist clinically approved for the treatment of type 2 diabetes mellitus, resulted in a significant reduction of cerebral infarct volume in PIS mice compared to that in ischemic stroke (IS) mice. Meanwhile, semaglutide treatment also increased the proportion of Spp1+Edu+Iba-1+ cells 3 days after PIS. Using high-parameter flow cytometry, immunofluorescence staining and RNA sequencing, we demonstrated that semaglutide treatment significantly attenuated the expression of neuroinflammatory markers in mice following PIS. We also found that semaglutide treatment significantly ameliorated sensorimotor dysfunction up to 3 days after PIS in mice. Our current finding reveal a novel protective Spp1+Mac/MG subset after PIS and demonstrated that it can be upregulated by semaglutide. We propose that targeting Spp1+Mac/MG subsets using semaglutide could serve as a promising strategy to attenuate the exacerbated neuroinflammation in PIS.

Blockade of CLEVER-1 restrains immune evasion and enhances anti-PD-1 immunotherapy in gastric cancer

BACKGROUND

Gastric cancer (GC) remains a major global health burden. Despite the advancements in immunotherapy for patients with GC, the heterogeneity of GC limits response rates, especially in immune "cold" subtypes, including genomically stable and epithelial-mesenchymal transition GC. Common lymphatic endothelial and vascular endothelial receptor-1 (CLEVER-1), a newly recognized immune checkpoint molecule predominantly expressed on tumor-associated macrophages (TAMs), remains poorly understood in GC. This study aims to explore the clinical significance of CLEVER-1+TAM infiltration, elucidate its role in modulating the tumor immune landscape, and investigate the therapeutic potential of CLEVER-1 blockade in enhancing immunotherapy.

METHODS

This study analyzed two independent GC cohorts and single-cell RNA sequencing data (GSE183904). CLEVER-1 expression in TAMs was assessed via multiplex immunofluorescence, flow cytometry, and RNA sequencing. The clinical relevance of CLEVER-1+TAM infiltration was evaluated in relation to tumor, node, metastases staging, molecular subtypes, prognosis, and immunochemotherapy response. Transcriptomic and pathway analyses characterized the immunophenotype of CLEVER-1+TAMs. Functional assays examined their suppression on CD8+T cells, while interventional experiments assessed the impact of CLEVER-1 blockade alone or with programmed cell death protein-1 (PD-1) inhibition.

RESULTS

CLEVER-1 was predominantly expressed on TAMs in GC and was associated with worse clinical outcomes. Transcriptomic and phenotypic analyses revealed that CLEVER-1+TAMs display a dynamic immunophenotype and critically suppress T-cell function, fostering an immunosuppressive microenvironment. High CLEVER-1+TAM infiltration was linked to poor response or adaptive resistance to PD-1 blockade therapy. CLEVER-1 blockade reprogrammed TAMs toward a pro-inflammatory phenotype, resulting in enhanced CD8+T cell cytotoxicity and proliferation. Co-targeting CLEVER-1 and PD-1 synergistically enhanced antitumor responses.

CONCLUSIONS

High infiltration of CLEVER-1+TAMs indicates immune suppression and poor prognosis in GC. The combination of CLEVER-1 and PD-1 blockade emerges as a dual-pronged strategy to boost immune-mediated tumor control and prevent treatment relapse in GC.

Unveiling the hidden dance: SPP1 + macrophages identified in ulcerative colitis reveal crosstalk with CHI3L1 + fibroblasts

BACKGROUND

Ulcerative colitis (UC) is a chronic inflammatory bowel disease characterized by persistent inflammation of the colon. The specific cause of UC is still not fully understood, but this condition is believed to arise from a combination of environmental, genetic, microbial, and immune factors. This study aimed to explore the specific roles of macrophages and fibroblasts in UC pathogenesis, focusing on their interactions and contributions to disease progression.

METHODS

We utilized single-cell RNA sequencing (scRNA-seq) to analyze macrophages and fibroblasts in peripheral blood and colon biopsy samples from UC patients. Bulk RNA sequencing and spatial transcriptomic data from the Gene Expression Omnibus (GEO) database and flow cytometry and multiplex immunohistochemistry (mIHC) data were used for validation. Statistical analyses were performed to assess the correlation between cell abundance and disease severity.

RESULTS

Macrophages and fibroblasts were identified as key communication hubs in UC; specifically, SPP1 + macrophages and CHI3L1 + fibroblasts were significantly enriched at the sites of inflammation. These cells are strongly correlated with disease severity and orchestrate inflammatory responses within the intestinal immune microenvironment, contributing to UC-associated colorectal cancer.

CONCLUSIONS

Our study identified SPP1 + macrophages and CHI3L1 + fibroblasts as key contributors to UC pathogenesis. These cells are enriched in inflammatory sites, are correlated with disease severity, and play a role in UC-associated colorectal cancer, providing new insights into UC mechanisms.

A novel NFKB1 agonist remodels tumor microenvironment and activates dendritic cells to promote anti-tumor immunity in colorectal cancer

BACKGROUND

The immunosuppressive nature of the tumor microenvironment (TME) and the existence of cancer stem cells (CSCs) present significant hurdles in tumor therapy. The identification of therapeutic agents that can target both CSCs and the TME could be a potential approach to overcome treatment resistance.

METHODS

We conducted an in vivo chemical screen to identify F1929-1458, which is capable of eliciting an organism-wide response to destroy stem cell tumors in Drosophila. We then performed functional validation using a mouse colorectal cancer graft tumor model established with the CT26 cell line characterized by its high content of CSCs. Single-cell sequencing was employed to analyze alterations in the TME. Small molecule pull-down mass spectrometry, cellular thermal shift assay, drug affinity experiment, and molecular docking were utilized to identify the target of F1929-1458. An in vitro co-culture system was applied to establish that the damage-associated molecular patterns (DAMPs) released by the tumor cells are accountable for the activation of dendritic cells (DCs).

RESULTS

We demonstrated that F1929-1458 treatment enhanced T cell infiltration and T cell mediated tumor regression, its anti-tumor effect was nullified in nude mice and was abolished after anti-CD3 neutralizing antibody treatment. We found that F1929-1458 binds NFKB1 to activate the NF-κB signaling pathway in tumor cells. The activation further elicits cellular stress, causing tumor cells to release DAMPs (HMGB1-gDNA complex, ATP, and OxLDL). These DAMPs, in turn, stimulate the cGAS-STING and NLRP3 inflammasome pathways in DCs, resulting in the generation of type I IFNs and IL-1β. These cytokines facilitate the maturation of DCs and antigen presentation, ultimately enhancing T cell-mediated anti-tumor immunity. Additionally, we showed that the combination of F1929-1458 and the anti-PD-1 antibody exhibited a synergistic anti-tumor effect.

CONCLUSION

Our study identified a novel NFKB1 agonist that promotes anti-tumor immunity by remodeling the TME and activating DCs and that may provide a new way to overcome resistance to current anti-tumor immunotherapy in colorectal cancer.

Spatial analysis identifies DC niches as predictors of pembrolizumab therapy in head and neck squamous cell cancer

Head and neck squamous cell carcinoma (HNSCC) shows variable response to anti-programmed cell death protein 1 (PD-1) therapy, which can be partially explained by a combined positive score (CPS) of tumor and immune cell expression of programmed death-ligand 1 (PD-L1) within the local tumor microenvironment (TME). To better define TME immune determinants associated with treatment efficacy, we conduct a study of n = 48 HNSCC tumors from patients prior to pembrolizumab therapy. Our investigation combines a rapid bioorthogonal multiplex staining method with computational analysis of whole-slide imaging to capture the single-cell spatial heterogeneity and complexity of the TME. Analyzing 6,316 fields of view (FOVs), we provide comprehensive PD-L1 phenotyping and cell proximity assays across the entirety of tissue sections. While none of the PD-L1 metrics adequately predict response, we find that the spatial organization of CCR7+ dendritic cells (DCs) in niches better predicts overall patient survival than CPS alone. This study highlights the importance of understanding the spatial context of immune networks for immunotherapy.

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.

Tumour and microenvironment crosstalk in NSCLC progression and response to therapy

The treatment landscape of non-small-cell lung cancer (NSCLC) is evolving rapidly, driven by advances in the development of targeted agents and immunotherapies. Despite this progress, some patients have suboptimal responses to treatment, highlighting the need for new therapeutic strategies. In the past decade, the important role of the tumour microenvironment (TME) in NSCLC progression, metastatic dissemination and response to treatment has become increasingly evident. Understanding the complexity of the TME and its interactions with NSCLC can propel efforts to improve current treatment modalities, overcome resistance and develop new treatments, which will ultimately improve the outcomes of patients. In this Review, we provide a comprehensive view of the NSCLC TME, examining its components and highlighting distinct archetypes characterized by spatial niches within and surrounding tumour nests, which form complex neighbourhoods. Next, we explore the interactions within these components, focusing on how inflammation and immunosuppression shape the dynamics of the NSCLC TME. We also address the emerging influences of patient-related factors, such as ageing, sex and health disparities, on the NSCLC-TME crosstalk. Finally, we discuss how various therapeutic strategies interact with and are influenced by the TME in NSCLC. Overall, we emphasize the interconnectedness of these elements and how they influence therapeutic outcomes and tumour progression.

PERK+ Macrophages Drive Immunotherapy Resistance in Lymph Node Metastases of Oral Squamous Cell Carcinoma

PURPOSE

Neoadjuvant anti-PD-1 immunotherapy combined with chemotherapy has shown promising pathologic responses in various cancers, including oral squamous cell carcinoma (OSCC). However, the pathologic response of lymph node (LN) metastases remains poorly understood. This study aims to systematically evaluate the pathologic response rates (pRR) of LN metastases in patients with OSCC and identify potential targets to improve therapeutic outcomes.

PATIENTS AND METHODS

We assessed the pRRs of LN metastases and matched primary tumors (PT) in patients with OSCC enrolled in a randomized, two-arm, phase II clinical trial (NCT04649476). Single-cell and spatial transcriptomics and multiplex IHC were performed to analyze the tumor microenvironment and identify potential therapeutic targets in LN metastases. A neoadjuvant orthotopic OSCC mouse model was established to evaluate the therapeutic potential of these targets.

RESULTS

We observed significant heterogeneity in pathologic regression of LN metastases, with lower pRRs compared with PTs. pRRs in LN metastases were correlated with overall and disease-free survival in patients with OSCC. We identified an abundance of macrophages in LN metastases exhibiting an unfolded protein response and activated protein kinase RNA-like endoplasmic reticulum kinase (PERK) signaling. These macrophages contributed to an extracellular matrix-enriched microenvironment through interactions with fibroblasts, which hindered T cell-mediated cytotoxicity. Pharmacologic inhibition of the PERK pathway significantly enhanced anti-PD-1 therapy in LN metastases and PTs in the mouse model.

CONCLUSIONS

Our study confirms that the pathologic response of LN metastases in patients with OSCC undergoing neoadjuvant immunotherapy or immunochemotherapy is inferior to that of PTs. It suggests that targeting the PERK pathway in macrophages could be a potential strategy to enhance treatment outcomes.

Overcoming myeloid-driven resistance to CAR T therapy by targeting SPP1

Chimeric antigen receptor CAR T cell therapy faces notable limitations in treatment of solid tumors. The suppressive tumor microenvironment TME, characterized by complex interactions among immune and stromal cells, is gaining recognition in conferring resistance to CAR T cell therapy. Despite the abundance and diversity of macrophages in the TME, their intricate involvement in modulating responses to CAR T cell therapies remains poorly understood. Here, we conducted single-cell RNA sequencing scRNA seq on tumors from 41 glioma patients undergoing IL13Ra2-targeted CAR T cell therapy, identifying elevated suppressive SPP1 signatures predominantly in macrophages from patients who were resistant to treatment. Further integrative scRNA seq analysis of high-grade gliomas as well as an interferon-signaling deficient syngeneic mouse model both resistant to CAR T therapy demonstrated the role of congruent suppressive pathways in mediating resistance to CAR T cells and a dominant role for SPP1+ macrophages. SPP1 blockade with an anti-SPP1 antibody abrogates the suppressive TME effects and substantially prolongs survival in IFN signaling-deficient and glioma syngeneic mouse models resistant to CAR T cell therapy. These findings illuminate the role of SPP1+ macrophages in fueling a suppressive TME and driving solid tumor resistance to CAR cell therapies. Targeting SPP1 may serve as a universal strategy to reprogram immune dynamics in solid tumors mitigating resistance to CAR T therapies.

Intercellular communication between FAP+ fibroblasts and SPP1+ macrophages in prostate cancer via multi-omics

Background

Prostate cancer (PCa) presents substantial heterogeneity and unpredictability in its progression. Despite therapeutic advancements, mortality from advanced PCa remains a significant challenge. Understanding the intercellular communication within the tumor microenvironment (TME) is critical for uncovering mechanisms driving tumorigenesis and identifying novel therapeutic targets.

Methods

We employed an integrative approach combining bulk RNA sequencing, single-cell RNA sequencing (scRNA-seq), and spatial transcriptomics to investigate interactions between FAP+ fibroblasts and tumor-associated macrophages in PCa. Key findings were validated using immunohistochemical and immunofluorescence staining techniques.

Results

Analysis of 23,519 scRNA-seq data from 23 prostate samples revealed a pronounced accumulation of FAP+ fibroblasts in tumor tissues. Spatial transcriptomics and bulk RNA sequencing demonstrated strong associations between FAP+ fibroblasts and SPP1+ macrophages. Notably, tumor-specific intercellular signaling pathways, such as CSF1/CSF1R and CXCL/ACKR1, were identified, highlighting their potential role in fostering an immunosuppressive TME.

Conclusion

Our findings unveil a distinct pattern of crosstalk between FAP+ fibroblasts and SPP1+ macrophages in PCa, shedding light on potential therapeutic targets for advanced PCa.

Macrophage at maternal-fetal Interface: Perspective on pregnancy and related disorders

Immune cells at the maternal-fetal interface (MFI) undergo dynamic changes to facilitate fetal growth and development during pregnancy. In contrast to the adaptive immune system, where effector T cells, Tregs, and suppressor T cells play key roles in maintaining immune tolerance toward the semi-allogeneic fetus, the innate immune system-comprising decidual nature killer (dNK) cells, macrophages, and dendritic cells (DCs)-makes up a significant portion of the decidual leukocyte population. These innate immune cells are crucial in modulating trophoblast invasion, spiral artery remodeling, and apoptotic cell phagocytosis. Dysregulation of the innate immune system has been linked to impaired uterine vessel remodeling and defective trophoblast invasion, which can lead to complications such as spontaneous abortion, preeclampsia (PE), and preterm. This review focuses on recent advancements in understanding the innate immune defenses at the maternal-fetal interface and their connections to pregnancy-related diseases, with particular emphasis on the role of macrophages.

Single-cell and spatial transcriptomics reveal correlation between RNA methylation-related miRNA risk model and immune infiltration in hepatocellular carcinoma

Introduction

Increasing evidence highlights the pivotal role of RNA methylation and miRNAs in hepatocellular carcinoma (HCC). However, the risk associated with RNA methylation-related miRNAs (RMRMs) in the HCC immune microenvironment remains largely unknown. Here, we predicted the correlation between RMRM risk and immune cell infiltration in HCC using machine learning.

Methods

MiRNA sequencing data was used to identify RMRMs. A risk score model of HCC was developed utilizing four RMRMs, including miR-551a, miR-4739, miR-326, and miR-210-3p.

Results

Patients with high-risk scores exhibited poorer prognoses. Single-cell RNA sequencing (scRNA-seq) analysis revealed the high-risk group exhibited increased infiltration levels of several immune cell subtypes, including myeloid-derived suppressor cell (MDSC), macrophage, and T cells. The data integration of scRNA-seq and bulk RNA-seq showed the decreased TIDE score in the high-risk patients and the elevated levels of Macro-secreted phosphoprotein 1 (SPP1), MDSC-meiotic nuclear divisions 1 (MND1), γδ T cells, and Macro-complement C1q C chain (C1QC) predicted adverse prognosis. ScRNA-seq and spatial transcriptomics data integration unveiled the spatial distribution of RMRMs risk scores and their correlation with immune cell subtype localization. Risk model-based clustering of HCC samples revealed that cluster 2, characterized by a higher risk score, correlated with a poorer prognosis and reduced immune and stromal scores. In vitro, the overexpression of miR-4739 in Huh-7 cells significantly induced SPP1+ macrophages, and the culture medium derived from SPP1+ macrophages further promoted the proliferation and migration of Huh-7 cells. Furthermore, miR-4739 reduced m1A methylation by inhibiting tRNA methyltransferase 61A (TRMT61A) expression.

Discussion

Our study reveals that the RMRM risk model could effectively predict the prognosis of HCC, and SPP1+ macrophages regulated by miR-4739-RNA methylation promote the proliferation and migration of HCC cells. These results highlight the potential of RMRMs in predicting the prognosis of HCC.

Mapping the genetic landscape establishing a tumor immune microenvironment favorable for anti-PD-1 response

Identifying host genetic factors modulating immune checkpoint inhibitor (ICI) efficacy is experimentally challenging. Our approach, utilizing the Collaborative Cross mouse genetic resource, fixes the tumor genomic configuration while varying host genetics. We find that response to anti-PD-1 (aPD1) immunotherapy is significantly heritable in four distinct murine tumor models (H2: 0.18-0.40). For the MC38 colorectal carcinoma system, we map four significant ICI response quantitative trait loci (QTLs) with significant epistatic interactions. The differentially expressed genes within these QTLs that define responder genetics are highly enriched for processes involving antigen processing and presentation, allograft rejection, and graft vs. host disease (all p < 1 × 10-10). Functional blockade of two top candidate immune targets, GM-CSF and IL-2RB, completely abrogates the MC38 transcriptional response to aPD1 therapy. Thus, our in vivo experimental platform is a powerful approach for discovery of host genetic factors that establish the tumor immune microenvironment propitious for ICI response.

SPP1 + macrophages cause exhaustion of tumor-specific T cells in liver metastases

Functional tumor-specific CD8+ T cells are essential for effective anti-tumor immune response and immune checkpoint inhibitor therapy. Here we show that, compared to other organ sites, primary, metastatic liver tumors in murine models contain a higher number of tumor-specific CD8+ T cells which are also dysfunctional. High-dimensional, multi-omic analysis of patient samples reveals a higher frequency of exhausted tumor-reactive CD8+ T cells and enriched interactions between these cells and SPP1+ macrophages in profibrotic, alpha-SMA rich regions specifically in the liver. Differential pseudotime trajectory inference analysis reveals that extrahepatic signaling promotes an intermediate cell (IC) population in the liver, characterized by co-expression of VISG4, CSF1R, CD163, TGF-βR, IL-6R, and SPP1. Analysis of premetastatic adenocarcinoma patient samples reveals enrichment of this population may predict liver metastasis. These findings suggest a mechanism by which extrahepatic tumors drive liver metastasis by promoting an IC population that inhibits tumor-reactive CD8+ T cell function.

Immunometabolism of tumor-associated macrophages: A therapeutic perspective

Tumor-associated macrophages (TAMs) play a pivotal role in the tumor microenvironment (TME), actively contributing to the formation of an immunosuppressive niche that fosters tumor progression. Consequently, there has been a growing interest in targeting TAMs as a promising avenue for cancer therapy. Recent advances in the field of immunometabolism have shed light on the influence of metabolic adaptations on macrophage physiology in the context of cancer. Here, we discuss the key metabolic pathways that shape the phenotypic diversity of macrophages. We place special emphasis on how metabolic reprogramming impacts the activation status of TAMs and their functions within the TME. Additionally, we explore alterations in TAM metabolism and their effects on phagocytosis, production of cytokines/chemokines and interaction with cytotoxic T and NK immune cells. Moreover, we examine the application of nanomedical approaches to target TAMs and assess the clinical significance of modulating the metabolism of TAMs as a strategy to develop new anti-cancer therapies. Taken together, in this comprehensive review article focusing on TAMs, we provide invaluable insights for the development of effective immunotherapeutic strategies and the enhancement of clinical outcomes for cancer patients.

KLF7-regulated ITGA2 as a therapeutic target for inhibiting oral cancer stem cells

Cancer stem cells (CSCs) play crucial roles in tumor metastasis, therapy resistance, and immune evasion. Identifying and understanding the factors that regulate the stemness of tumor cells presents promising opportunities for developing effective therapeutic strategies. In this study on oral squamous cell carcinoma (OSCC), we confirmed the key role of KLF7 in maintaining the stemness of OSCC. Using chromatin immunoprecipitation sequencing and dual-luciferase assays, we identified ITGA2, a membrane receptor, as a key downstream gene regulated by KLF7 in the maintenance of stemness. Tumor sphere formation assays, flow cytometry analyses, and in vivo limiting dilution tumorigenicity evaluations demonstrated that knocking down ITGA2 significantly impaired stemness. Upon binding to its extracellular matrix (ECM) ligand, type I collagen, ITGA2 activates stemness-associated signaling pathways, including PI3K-AKT, MAPK, and Hippo. TC-I 15, a small-molecule inhibitor of the ITGA2-collagen interaction, significantly sensitizes oral squamous cell carcinoma (OSCC) to cisplatin in xenograft models. In summary, we reveal that the KLF7/ITGA2 axis is a crucial modulator of stemness in OSCC. Our findings suggest that ITGA2 is a promising therapeutic target, offering a novel anti-CSC strategy.

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.

Denosumab Enhances Antitumor Immunity by Suppressing SPP1 and Boosting Cytotoxic T Cells

Denosumab, a RANK ligand inhibitor, is primarily used to prevent osteoclastogenesis in the treatment of conditions such as osteoporosis, bone metastasis, and giant cell tumor of bone (GCTB). RANK ligand also plays an important role in immunity by activating NF-κB and its target genes, including the osteopontin-coding gene SPP1 (also known as OPN), which is linked to CXCL9:SPP1 macrophage polarization and prognosis. In this study, we explored an additional role of denosumab in enhancing antitumor immunity in patients. Single-cell RNA sequencing was performed on nine human GCTB samples, including six untreated and three treated only with denosumab, to exclude confounding treatment factors linked with bone metastasis samples. We further analyzed paired samples collected before and after denosumab treatment from a cohort of nine patients with GCTB and conducted a pan-cancer analysis of 34 distinct types of cancers. Our single-cell analysis of GCTB resulted in a comprehensive cell atlas revealing an antitumor role of denosumab in inhibiting SPP1 expression and augmenting active cytotoxic T-cell abundance. Furthermore, we validated this immunomodulatory role of denosumab using the paired GCTB samples. Finally, the pan-cancer analysis supported a negative correlation between SPP1 and CD8A levels, with the CD8A:SPP1 ratio correlating with overall survival in 14 cancer types, which was superior to either CD8A or SPP1 alone. Our research provides clinical evidence that denosumab improves antitumor immunity by decreasing SPP1 expression and enhancing cytotoxic T-cell activity, serving as a milestone in the development of innovative use of denosumab and offering potential benefits to patients with elevated levels of SPP1.

Osteopontin promotes tumor microenvironment remodeling and therapy resistance

Osteopontin (OPN) is a multifunctional secretory protein which can be expressed and secreted by a variety of tumor cells and immune cells. Tumor microenvironment remodeling provides favorable conditions for tumor progression, immune escape and therapy resistance. As a bridge molecule in crosstalk between tumor cells and tumor microenvironment, OPN can not only come from tumor cells to regulate the functions of various immune cells, promoting the formation of immunosuppressive environment, but also can be secreted by immune cells to act on tumor cells, leading to tumor progression, thus constructing a positive feedback regulatory network. Here, we summarize the molecular structure, source and receptor of OPN, and clarify the mechanism of OPN on tumor-associated macrophages, dendritic cells, myeloid-derived suppressor cells, tumor progression and therapy resistance to comprehensively understand the great potential of OPN as a tumor biomarker and therapeutic target.

Osteosarcoma Cell-Derived Migrasomes Promote Macrophage M2 Polarization to Aggravate Osteosarcoma Proliferation and Metastasis

The local tumor microenvironment (TME) of osteosarcoma (OS) includes several tumor niches that control tumor growth and cell extravasation. Migrasomes are recently discovered extracellular vesicles produced during cell migration. Herein, the results show OS cell production of migrasomes in vivo and in vitro. Osteosarcoma cell-derived migrasomes (OCDMs) aggravate OS proliferation and metastasis, and impeding OCDM formation alleviates the malignant progression of OS. Further studies revealed that migrasome-associated nanoparticles (MANPs) are the functional unit of OCDMs and that OCDMs promote M2 polarization of macrophages in the TME in a MANPs-dependent manner. Moreover, milk fat globule-EGF factor 8 (MFGE8) in OCDMs is identified as a key protein that enhances phagocytosis to promote the M2 polarization of macrophages. Overall, the results reveal that OCDMs enhance the M2 polarization of macrophages in the TME to aggravate OS progression via MFGE8. These findings may guide the development of OCDM-modulating OS therapies.

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.

Single-Cell Profiling Reveals Conserved Differentiation and Partial EMT Programs Orchestrating Ecosystem-Level Antagonisms in Head and Neck Cancer

Head and neck squamous cell carcinoma (HNSC) exhibits profound intratumoral heterogeneity, driven by dynamic interactions between malignant cells and the tumour microenvironment (TME). Using consensus non-negative matrix factorisation (cNMF) on multi-site HNSC single-cell transcriptomes, we resolving conserved meta-programs define cellular ecosystems. Six major epithelial programmes emerged, including a differentiation-associated programme (Epi_Diff) correlated with SPDEF activity and favourable patient prognosis, and an invasive programme (Epi_pEMT) potentially controlled by TEAD4-mediated ECM remodelling, exhibiting partial EMT markers (VIM, TGFB1). Compartment-specific crosstalk analysis revealed Epi_pEMT cells may coordinate with mCAF1 fibroblasts and TAM(SPP1) through COL1A1-CD44 and SPP1-CD44 signalling, suggesting potential formation of a pro-invasive niche. Conversely, Epi_Diff cells may interact with NK/T cells through CEACAM5-CD8A and CCL5-ACKR2, and may contribute to inhibit immune infiltration. Multi-compartment correlation analysis revealed three ecosystem-level patterns: (1) Inverse association between Epi_Diff and Epi_pEMT (Spearman R = -0.43); (2) Negative correlation between mCAF1 abundance and cCAF frequency (R = -0.48); (3) TAM(SPP1) dominance inversely correlating with both TAM(C1Q) (R = -0.43) and NK/T infiltration (R = -0.36). These axes suggest a potential hierarchical ecology framework where lineage-specific polarisation and inter-compartment synergies may collectively govern disease progression.

Unveiling fine-scale spatial structures and amplifying gene expression signals in ultra-large ST slices with HERGAST

We propose HERGAST, a system for spatial structure identification and signal amplification in ultra-large-scale and ultra-high-resolution spatial transcriptomics data. To handle ultra-large spatial transcriptomics (ST) data, we consider the divide and conquer strategy and devise a Divide-Iterate-Conquer framework especially for spatial transcriptomics data analysis, which can also be adopted by other computational methods for extending to ultra-large-scale ST data analysis. To tackle the potential over-smoothing problem arising from data splitting, we construct a heterogeneous graph network to incorporate both local and global spatial relationships. In simulations, HERGAST consistently outperforms other methods across all settings with more than a 10% increase in average adjusted rand index (ARI). In real-world datasets, HERGAST's high-precision spatial clustering identifies SPP1+ macrophages intermingled within colorectal tumors, while the enhanced gene expression signals reveal unique spatial expression patterns of key genes in breast cancer.

Macrophage-derived exosomes in cancer: a double-edged sword with therapeutic potential

Solid cancer contains a complicated communication network between cancer cells and components in the tumor microenvironment (TME), significantly influencing the progression of cancer. Exosomes function as key carriers of signaling molecules in these communications, including the intricate signalings of tumor-associated macrophages (TAMs) on cancer cells and the TME. With their natural lipid bilayer structures and biological activity that relates to their original cell, exosomes have emerged as efficient carriers in studies on cancer therapy. Intrigued by the heterogeneity and plasticity of both macrophages and exosomes, we regard macrophage-derived exosomes in cancer as a double-edged sword. For instance, TAM-derived exosomes, educated by the TME, can promote resistance to cancer therapies, while macrophage-derived exosomes generated in vitro have shown favorable potential in cancer therapy. Here, we depict the reasons for the heterogeneity of TAM-derived exosomes, as well as the manifold roles of TAM-derived exosomes in cancer progression, metastasis, and resistance to cancer therapy. In particular, we emphasize the recent advancements of modified macrophage-derived exosomes in diverse cancer therapies, arguing that these modified exosomes are endowed with unique advantages by their macrophage origin. We outline the challenges in translating these scientific discoveries into clinical cancer therapy, aiming to provide patients with safe and effective treatments.

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).

Dual Disruption of EGFR/PI3K Signaling: IGF2BP2 Targeting Reverses Anti-EGFR Resistance in CAFs-Infiltrated Oral Squamous Cell Carcinoma

RNA-binding proteins (RBPs) critically regulate post-transcriptional gene networks, yet their roles and mechanisms in oral squamous cell carcinoma (OSCC) remain underexplored. Dysregulated RBPs were identified through integrated analysis of RNA-seq and single-cell RNA-seq. The oncogenic functions of IGF2BP2 were evaluated through tissue microarrays, CCK-8, transwell assays, mouse xenografts, and Igf2bp2-deficient mouse models of tongue SCC (TSCC). Subsequently, we utilized RNA-seq, RIP-seq, RIP/MeRIP-qPCR, and dual-luciferase reporter assays to investigate IGF2BP2-target genes. Furthermore, cell co-culture system and mouse TSCC models were used to validate the therapeutic effect of the IGF2BP2 inhibitor. IGF2BP2 was the most markedly upregulated RBP in OSCC cells and cancer-associated fibroblasts (CAFs), correlating with unfavorable prognosis. IGF2BP2 deprivation significantly impaired human OSCC proliferation and metastasis, and delayed mouse TSCC onset. Mechanistically, IGF2BP2 stabilized EGFR and PIK3R1 mRNA via m6A-dependent interactions, thereby sustaining activation of the EGFR/PI3K/AKT oncogenic axis. Pharmacological inhibition of IGF2BP2 exhibited anti-OSCC efficacy in vivo and in vitro by concurrently suppressing EGFR and PI3K/AKT pathway activity, overcoming anti-EGFR resistance resulting from cell-intrinsic PI3K/AKT hyperactivation and CAF-secreted factors. Our findings identified IGF2BP2 as a master regulator of OSCC progression and a promising therapeutic target, offering an alternative strategy for OSCC patients suffering anti-EGFR resistance.

Spatially segregated APOE+ macrophages restrict immunotherapy efficacy in clear cell renal cell carcinoma

Background: Immunotherapy has revolutionized cancer treatment and holds great potential for them, including metastatic clear cell renal cell carcinoma (ccRCC). However, immune resistance remains a major obstacle, limiting its efficacy and durability. Understanding the mechanisms of immune tolerance in the tumor microenvironment (TME) is pivotal for overcoming these challenges and enhancing therapeutic outcomes. Methods: Over 2000 samples, including a real-world cohort of 230 advanced ccRCC patients treated with immune checkpoint blockade (ICB) were analyzed. Single-cell RNA sequencing data from 13 tumor regions were categorized into ICB-exposed, ICB-resistant, and ICB-responsive groups. Multiple robust algorithms and multiplex immunofluorescence were used to explore TME composition and macrophage heterogeneity. Spatial communication dynamics were further investigated. In vitro experiments were performed to evaluate the impact of SPP1 on 786-O and 769-P cells. Co-culture experiments with THP-1-derived macrophages, followed by Western blot, flow cytometry, and functional assays, were performed to investigate SPP1-mediated macrophage polarization and its impact on tumor progression. Results: The results revealed an elevated presence of Apolipoprotein E (APOE)+ macrophages in ICB-resistant ccRCC. Notably, higher APOE+ macrophage proportion indicated shorter prognosis and worse response to ICB (P < 0.001). Elevated expression of CCAAT Enhancer Binding Protein Delta (CEBPD) was markedly linked to several immunosuppressive pathways, hindering T cell recruitment, promoting exhaustion, ultimately diminishing poorer prognosis and worse ICB efficacy. Meanwhile, upregulated Secreted Phosphoprotein 1 (SPP1) significantly enhances the proliferation, clonal formation, and migration of ccRCC cells. Tumor-derived SPP1. Additionally, SPP1 signaling from malignant cells appeared to recruit APOE+ macrophages to tumor margins, and promotes macrophage polarization into APOE+ M2-like macrophages. In the vicinity of the tumor, these APOE+ macrophages shape immunosuppressive TME by releasing abundant TGF-β signals, limiting anti-tumor effector T cells activity in ICB-resistant tumors, and contributing to tumor progression. Conclusion: This study reveals the critical role of APOE+ macrophages in promoting immune suppression and resistance to ICB therapy in ccRCC. By promoting T cell exhaustion and immunosuppressive signaling, particularly via localized TGF-β, these spatially segregated macrophages undermine treatment efficacy. Targeting APOE+ macrophages, especially in conjunction with ICB, presents a promising strategy to overcome immune resistance and enhance outcomes for ccRCC patients.

The role of hypoxia-senescence co-related molecular subtypes and prognostic characteristics in hepatocellular carcinoma

Hepatocellular carcinoma (HCC) is known for its high invasiveness, high fatality rate. Both hypoxia and senescence play crucial roles in the initiation and progression of cancer, yet their prognostic implications in HCC are yet to be fully understood. The hypoxia-senescence co-related genes (HSCRGs) were screened from public databases. Transcriptome data and clinical information were obtained from patients with HCC using the Cancer Genome Atlas, GSE76427, and International Cancer Genome Consortium (ICGC). The random forest tree algorithm was used to identify the characteristic genes of the disease, and the genes were verified by related experiments. SVM algorithm was used to classify HCC patients based on HSCRGs. The prediction model based on HSCRGs was established by LASSO, univariate and multivariate COX regression analysis. We used the ICGC for outside validation. The risk score model was analyzed from subgroup analysis, immune infiltration, and functional strength. The expression patterns of key prognostic genes in tumor microenvironment were decoded by single cell analysis. A total of 184 HSCRGs were identified. The expression pattern and functional characteristics of MLH1 gene in HCC were verified. Two HCC subtypes were identified based on HSCRGs. Then, a prediction model based on HSCRGs was established, and risk score was identified as an independent prognostic indicator of HCC. A new nomogram is constructed and shows good prediction ability. We further determined that the level of infiltration of immune cells and the expression of immune checkpoints are significantly affected by the risk score. The immune microenvironment was different between the two risk groups. The high-risk group was dominated by immunosuppressed cells, and the prognosis was poor. Single-cell analysis revealed the expression of seven key prognostic genes in the tumor microenvironment. Finally, qPCR results further verified the expression levels of seven prognostic genes. HSCRGs are of great significance in the prognosis prediction, risk stratification and targeted therapy of patients with HCC.

Single-cell and spatial transcriptomic analyses revealing tumor microenvironment remodeling after neoadjuvant chemoimmunotherapy in non-small cell lung cancer

Non-small cell lung cancer (NSCLC) represents the most common pathological type of lung cancer, and the combination of neoadjuvant immunotherapy with chemotherapy has emerged as the first-line treatment for NSCLC. Nevertheless, the efficacy of this therapeutic approach remains variable. The present study aims to examine the impact of chemoimmunotherapy in NSCLC patients, with a view to identifying key molecules, critical cell subpopulations, communication patterns and spatial distributions that potentially correlate with therapeutic sensitivity. A total of 16 lung cancer tissue samples were collected from a cohort of 12 NSCLC patients and subjected to single-cell RNA and spatial transcriptome sequencing. Our data demonstrated that the distribution of CD4 + Treg T cells and mCAFs indicated an immunosuppressive tumor microenvironment, while the accumulation of CD4 + Th17 T cells and iCAFs could act as a positive marker for the sensitivity to chemoimmunotherapy. Furthermore, a significant high level of SELENOP-macrophages was observed in tissues from positive responders, and a strong co-localization between SELENOP-macrophages and antigen-presenting cancer associated fibroblasts (CAFs) in the tumor boundaries was identified, indicating the cooperative roles of these two cell types in response to combined therapy. Moreover, SELENOP-macrophages were observed to be accumulated in tertiary lymphoid structures, which further suggested its critical role in recruiting lymphocytes. Furthermore, analysis of cell-cell communication, based on spatial transcriptomics, suggests that the interactions between SELENOP-macrophages, apCAFs, CD4 + and CD8 + T cells were significantly enhanced in responders. In addition, SELENOP-macrophages recruited CD4 + Naïve, Helper and CD8 + Naïve T cells through pathways such as the cholesterol, interleukin, chemokine and HLA when responding to combined therapy. The present study further unveils the dynamic spatial and transcriptional changes in the tumor microenvironment of non-small cell lung cancer in response to combination therapy.

Mapping immunotherapy potential: spatial transcriptomics in the unraveling of tumor-immune microenvironments in head and neck squamous cell carcinoma

Head and neck squamous cell carcinoma (HNSCC) often exhibits poor response rates to immune checkpoint inhibitor (ICI) therapies, largely owing to the intricate composition and spatial organization of immune cells within the tumor-immune microenvironment (TIME). The diversity of immune cell populations, their spatial relationships, and dynamic interactions significantly influence the immunosuppressive nature of the TIME, thereby limiting the efficacy of immunotherapy. To address these challenges and enhance the therapeutic potential of ICIs in HNSCC, a comprehensive analysis of the TIME is essential. Spatial transcriptomics (ST), a cutting-edge technology, enables high-resolution mapping of gene expression within the spatial context of the tumor, providing critical insights into the functional roles and interactions of immune cells in the TIME. This review highlights the importance of ST in uncovering the complexities of the TIME in HNSCC and proposes strategies for leveraging these insights to develop more effective immunotherapeutic approaches. By integrating spatial and molecular information, this review aims to pave the way for personalized and precision-based treatments in HNSCC, ultimately improving patient outcomes.

Identification of DNA damage and repair gene-related markers in pancreatic ductal adenocarcinoma by single-cell and bulk RNA sequencing

BACKGROUND

The DNA damage response (DDR) has a major impact on the development and progression of pancreatic ductal adenocarcinoma (PDAC). Investigating biomarkers linked to the DDR may facilitate prognostic assessment and prediction of immunological characteristics for patients with PDAC.

METHODS

The single-cell RNA sequencing (scRNA-seq) dataset GSE212966 was obtained from the GEO database, whereas the bulk RNA-seq data were sourced from The Cancer Genome Atlas (TCGA) and Genotype-Tissue Expression (GTEx) databases. Least absolute shrinkage and selection operator (LASSO) and univariate Cox regression analyses were used to select genes to construct a prognostic risk model. Finally, the correlations of the model score with drug sensitivity, immunological checkpoints, and immune infiltration were assessed.

RESULTS

We used 16 DDR marker genes to construct a predictive model. Furthermore, we established that the model had strong performance in both the training and validation cohorts. For PDAC, the model risk score served as an independent predictor of prognosis. There were notable differences in the proportions of the immune cells in the tumor microenvironment and drug sensitivity between the high and low risk score groups. The study confirmed that the risk score model is useful for predicting the immunotherapy response. Our experiments verified that knockdown of LY6D inhibits cell proliferation, promotes apoptosis and DNA damage.

CONCLUSION

Our creative integration of bulk RNA sequencing and scRNA-seq data allowed us to construct a DDR-related prognostic model. Our model can be used to predict the immunological features, treatment response and prognosis of PDAC with a relatively high degree of accuracy.

Immune-parenchymal multicellular niches are shared across distinct thyroid autoimmune diseases

Thyroid hormone, produced in the thyroid gland, regulates metabolism, development, and cardiac function. The thyroid is susceptible to autoimmune attack by both cellular and humoral immunity exemplified by Hashimoto's thyroiditis (HT) and Graves' Disease (GD), respectively. In HT, immune-mediated destruction impairs thyroid hormone production, while in GD, stimulating autoantibodies promote over-production. Here, we generated a multi-modal atlas of 604,076 human thyroid and blood cells from HT, GD, and control patients. We found that, despite markedly different clinical presentations and distinct antigenic triggers, HT and GD exhibit convergent cellular dynamics resulting in a shared continuum of immune infiltration. Along this continuum, a key feature is a thyrocyte niche containing CD8 + T cells that may segregate pathogenic T cells from regions with preserved thyroid hormone production. These findings of a shared disease continuum characterized by spatially defined immune niches provide a new framework for understanding tissue homeostasis in human autoimmune disease.

Cholangiocarcinoma PDHA1 succinylation suppresses macrophage antigen presentation via alpha-ketoglutaric acid accumulation

Gemcitabine combined with cisplatin is the first-line chemotherapy for advanced cholangiocarcinoma, but drug resistance remains a challenge, leading to unsatisfactory therapeutic effect. Here, we elucidate the possibility of chemotherapy regimens sensitized by inhibiting succinylation in patients with cholangiocarcinoma from the perspective of post-translational modification. Our omics analysis reveals that succinylation of PDHA1 lysine 83, a key enzyme in the tricarboxylic acid cycle, alters PDH enzyme activity, modulates metabolic flux, and leads to alpha-ketoglutaric acid accumulation in the tumor microenvironment. This process activates the OXGR1 receptor on macrophages, triggering MAPK signaling and inhibiting MHC-II antigen presentation, which promotes immune escape and tumor progression. Moreover, we show that inhibiting PDHA1 succinylation with CPI-613 enhances the efficacy of gemcitabine and cisplatin. Targeting PDHA1 succinylation may be a promising strategy to improve treatment outcomes in cholangiocarcinoma and warrants further clinical exploration.

Quantitative characterization of cell niches in spatially resolved omics data

Spatial omics enable the characterization of colocalized cell communities that coordinate specific functions within tissues. These communities, or niches, are shaped by interactions between neighboring cells, yet existing computational methods rarely leverage such interactions for their identification and characterization. To address this gap, here we introduce NicheCompass, a graph deep-learning method that models cellular communication to learn interpretable cell embeddings that encode signaling events, enabling the identification of niches and their underlying processes. Unlike existing methods, NicheCompass quantitatively characterizes niches based on communication pathways and consistently outperforms alternatives. We show its versatility by mapping tissue architecture during mouse embryonic development and delineating tumor niches in human cancers, including a spatial reference mapping application. Finally, we extend its capabilities to spatial multi-omics, demonstrate cross-technology integration with datasets from different sequencing platforms and construct a whole mouse brain spatial atlas comprising 8.4 million cells, highlighting NicheCompass' scalability. Overall, NicheCompass provides a scalable framework for identifying and analyzing niches through signaling events.

Decoding multicellular interaction networks-a new horizon in tumor microenvironment research

The tumor microenvironment (TME) milieu directs a plethora of tumor-modulating functions. Recent years have seen pivotal breakthroughs in our understanding of the TME's role in tumor initiation and progression, with tangible clinical applications. Individual components of the TME exert their function predominantly by cell-cell crosstalk, both in the form of physical interaction and secreted factors. Notably, different spatial niches represent exclusive signaling hubs in the TME, propagating pro- or antitumoral functions. The exploration of these interactions has been vastly facilitated by novel molecular technologies, each of which provides a different perspective on this intricate intercellular communication network. Together, these complementary methods paint a detailed, high-resolution map of the TME's interaction landscape. In this viewpoint, we explore how cellular interactions can unlock a new level of understanding of TME complexity, and discuss the promises and challenges of characterizing tumors based on their cellular interaction footprint.

Quantitative characterization of tissue states using multiomics and ecological spatial analysis

The spatial organization of cells in tissues underlies biological function, and recent advances in spatial profiling technologies have enhanced our ability to analyze such arrangements to study biological processes and disease progression. We propose MESA (multiomics and ecological spatial analysis), a framework drawing inspiration from ecological concepts to delineate functional and spatial shifts across tissue states. MESA introduces metrics to systematically quantify spatial diversity and identify hot spots, linking spatial patterns to phenotypic outcomes, including disease progression. Furthermore, MESA integrates spatial and single-cell multiomics data to facilitate an in-depth, molecular understanding of cellular neighborhoods and their spatial interactions within tissue microenvironments. Applying MESA to diverse datasets demonstrates additional insights it brings over prior methods, including newly identified spatial structures and key cell populations linked to disease states. Available as a Python package, MESA offers a versatile framework for quantitative decoding of tissue architectures in spatial omics across health and disease.

Embracing diversity: macrophage complexity in cancer

Macrophages are myeloid cells that receive, integrate, and respond to tumoral cues. Tumors evolve and are shaped by macrophages, with tumor-associated macrophage (TAM)-tumor sculpting capacities going beyond an increase in their cellular mass. Longitudinal and local heterogeneity of TAM states is now possible with the use of single-cell and spatial transcriptomics. However, understanding TAM biology and its fundamental functional programs is still challenging, probably because of the lack of models that fully integrate TAM complexity. Here, we aim to review TAM diversity not only at the level of single-cell phenotypes but also by integrating complex physiological signals that determine their complexity and plasticity in tumors.

Engineering Mice to Study Human Immunity

Humanized mice, which carry a human hematopoietic and immune system, have greatly advanced our understanding of human immune responses and immunological diseases. These mice are created via the transplantation of human hematopoietic stem and progenitor cells into immunocompromised murine hosts further engineered to support human hematopoiesis and immune cell growth. This article explores genetic modifications in mice that enhance xeno-tolerance, promote human hematopoiesis and immunity, and enable xenotransplantation of human tissues with resident immune cells. We also discuss genetic editing of the human immune system, provide examples of how humanized mice with humanized organs model diseases for mechanistic studies, and highlight the roles of these models in advancing knowledge of organ biology, immune responses to pathogens, and preclinical drugs tested for cancer treatment. The integration of multi-omics and state-of-the art approaches with humanized mouse models is crucial for bridging existing human data with causality and promises to significantly advance mechanistic studies.

The single-cell immune landscape of HIV-associated aggressive B-cell lymphoma

Background

Human immunodeficiency virus (HIV)-associated lymphomas (HAL), mainly aggressive B-cell lymphomas, pose a significant challenge in cancer research due to their multifaceted pathogenesis and aggressive clinical course. Despite the clinical importance, the genomic and immune characteristics of these lymphomas remain poorly elucidated.

Methods

We employed single-cell RNA sequencing (scRNA-seq) on lymph node samples from aggressive B-cell lymphomas, mainly including 6 cases of diffuse large B-cell lymphoma (DLBCL) and 5 cases of Burkitt lymphoma (BL) from people living with HIV (PLWH), along with 3 DLBCL cases from individuals without HIV for comparison.

Results

Malignant B cells in HAL consistently exhibited high proliferative and oxidative phosphorylation (OXPHOS)-type metabolic signatures. Moreover, these cells demonstrated loss expression of major histocompatibility complex class I (MHC-I), strategically reducing tumor immunogenicity. HAL harbors special populations of naive and atypical memory B cells that exhibited high metabolic and immune-activated transcriptional profiles. Additionally, HAL exhibited senescence-like dysfunction in T cells, characterized by the reductions in regulatory activity of Treg and cytotoxic activity of CD8+ T cells, as well as decreases expression of IL7R genes and increases expression of FOS and FOSB genes. Our immunofluorescence results showed that the cytotoxic CD8+ T cells in HAL may have a dysfunction of lytic granule polarization. Furthermore, macrophages from HAL exhibited stronger immunosuppressive transcriptional characteristics, and a robust immunosuppressive SPP1-CD44 interaction was predicted between C1QA+ macrophages and T cells.

Conclusions

Our findings clearly indicate that HAL differs significantly from non-HAL, ranging from malignant B cells to the immune microenvironment. This study provides a comprehensive single-cell atlas of HIV-associated aggressive B-cell lymphomas, offering new insights into aggressiveness and immune evasion observed in HAL.