Macrophage diversity in cancer revisited in the era of single-cell omics

Characterisation of the tumour microenvironment and PD-L1 granularity reveals the prognostic value of cancer-associated myofibroblasts in non-invasive bladder cancer

High-risk non-muscle-invasive bladder cancer (NMIBC) presents high recurrence and progression rates. Despite the use of Bacillus Calmette-Guérin gold-standard immunotherapy and the recent irruption of anti-PD-1/PD-L1 drugs, we are missing a comprehensive understanding of the tumor microenvironment (TME) that may help us find biomarkers associated to treatment outcome. Here, we prospectively analyzed TME composition and PD-L1 expression of tumor and non-tumoral tissue biopsies from 73 NMIBC patients and used scRNA-seq, transcriptomic cohorts and tissue micro-array to validate the prognostic value of cell types of interest. Compared to non-tumoral tissue, NMIBC presented microvascular alterations, increased cancer-associated fibroblast (CAF) and myofibroblast (myoCAF) presence, and varied immune cell distribution, such as increased macrophage infiltration. Heterogeneous PD-L1 expression was observed across subsets, with macrophages showing the highest expression levels, but cancer cells as the primary potential anti-PD-L1 binding targets. Unbiased analysis revealed that myoCAF and M2-like macrophages are specifically enriched in high-grade NMIBC tumors. The topological distribution of these two cell types changed as NMIBC progresses, as shown by immunofluorescence. Only myoCAFs were associated with higher rates of progression and recurrence in three independent cohorts (888 total patients), reaching prediction values comparable to transcriptomic classes, which we further validated using tissue micro-array. Our study provides a roadmap to establish the landscape of the NMIBC TME, highlighting myoCAFs as potential prognostic markers.

Cross-disease integration of single-cell RNA sequencing data from lung myeloid cells reveals TAM signature in in vitro model

Advancements in single-cell RNA sequencing (scRNA-seq) have revealed the phenotypic and functional diversity of tumor-associated macrophages (TAMs), identifying specific populations that directly impact the antitumor response. However, despite the recognition of TAMs as promising therapeutic targets for cancer treatment, research is hindered by the lack of validated human preclinical models. Here, we applied scRNA-seq to a 3D human cell-based model comprising tumor cell line-derived spheroids, cancer-associated fibroblasts and primary monocytes, a setup widely used in immuno-oncology research. Integration of our in vitro data with publicly available patient-derived datasets showed that the macrophages in this model share phenotypic characteristics with the pro-angiogenic and pro-fibrotic SPP1+ TAM population recently found across multiple cancer types and inflammatory lung diseases. This population was linked to aspects of disease progression and associated with poor prognosis in several tumor indications, highlighting the need for relevant models enabling its study as an immunotherapy target. Our research validates the use of a 3D human cell-based culture as a more in vivo-relevant model and enables the preclinical testing of novel macrophage-targeting drugs in a human disease-relevant setup.

Loss of the extracellular protease ADAMTS1 reveals an antitumorigenic program involving the action of NIDOGEN-1 on macrophage polarization

Recent research highlighted the contribution of extracellular matrix, and particularly of ADAMTS proteases, in immune regulation. Now, our work with melanoma and mammary tumor models revealed that tumor blockade induced by the lack of Adamts1 led to an increased vascular deposition of its substrate, the basement membrane glycoprotein NIDOGEN-1 (NID1). Significantly, the overexpression of NID1 in the melanoma syngeneic model also blocked tumor progression, disclosing an overlapping phenotype with the absence of Adamts1. These tumors showed important alterations in their immune infiltrates, emphasizing an enhanced presence of antitumorigenic macrophages and a global inflammatory landscape. We corroborated in vitro that full length NID1, but not its fragments, promoted an M1-like macrophage polarization, mainly mediated by the αvβ3 integrin. Significantly, the projection of RNA-seq from our tumor models to two large human melanoma datasets allowed us to discover a new gene signature associated with good prognosis and the abundance of M1-like macrophages. These results support NID1 as a novel tumor suppressor with immunomodulatory properties, and unveil the existence of key oncological drivers in the extracellular scenario.

Advances in Sampling and Analytical Techniques for Single-Cell Metabolomics: Exploring Cellular Heterogeneity

Single-cell metabolomics is an emerging and powerful technology that uncovers intercellular heterogeneity and reveals microenvironmental dynamics in both physiological and pathological conditions. This technology enables detailed observations of cellular interactions, providing valuable insights into processes such as aging, immune responses, and disease development. Despite significant advances, the need for detailed discussions on sampling and analytical methods in single-cell metabolomics continues to grow, with increasing focus on selecting the most suitable techniques for diverse research objectives. This review addresses these challenges by exploring key sampling and analytical strategies used in single-cell metabolomics. We focus on three main approaches: the capture and isolation of specific cell types, the precise aspiration of individual cells, and in situ mass spectrometry imaging. These methods are critically assessed to highlight strategies for achieving accurate metabolite detection at the single-cell level across diverse research applications.

The role of tumor microenvironment and immune cell crosstalk in triple-negative breast cancer (TNBC): Emerging therapeutic opportunities

Triple-negative breast cancer (TNBC) is an aggressive subtype characterized by its lack of estrogen, progesterone, and HER2 receptors, leading to limited treatment options and poor prognosis. This review synthesizes current research on the tumor microenvironment (TME) and immune cell crosstalk in TNBC to identify emerging therapeutic opportunities. The TME in TNBC is a complex ecosystem comprising immune cells, fibroblasts, and extracellular matrix components, which significantly influence tumor growth and metastasis. Single-cell RNA sequencing reveals T-cell heterogeneity and identifies prognostic genes. Regulatory T cells (Tregs) play a key role in immunosuppression, with thymidine kinase-1 (TK1) identified as a potential therapeutic target. MUC1-C and CXCL9 modulate the TME, impacting T-cell depletion and macrophage differentiation. Spatial analysis highlights the importance of cell-to-cell interactions in predicting recurrence. Epithelial-mesenchymal transition (EMT) and thermogenesis also influence the TME, while epigenetic modifications, such as HDAC inhibition, can induce pyroptosis and enhance immune cell recruitment. Integrating genomic information with TME analysis is crucial for developing personalized treatments, considering racial disparities in immune infiltration. Emerging therapies targeting immune checkpoints, modulating Treg activity, and inducing pyroptosis hold promise for improving TNBC patient outcomes. Future research should focus on multi-omics data, spatial transcriptomics, and patient-derived models to refine therapeutic interventions.

Characterizing chromosome instability reveals its association with lipid-associated macrophages and clonal evolution of lymph node metastasis in esophageal squamous cell carcinoma

Esophageal cancer is an aggressive cancer, and metastasis is one of the major factors contributing to treatment failure, leading to poor clinical outcomes. Chromosome instability (CIN) is frequently observed in esophageal squamous cell carcinoma (ESCC). However, the functional impact of CIN is not well studied in ESCC metastasis. We aim to study the role and underlying mechanisms of CIN in lymph node (LN) metastasis. Integrated analysis was performed using single-cell RNA sequencing data with matched whole-exome sequencing in primary ESCC, genomic sequencing in ESCC organoids and clinical specimens, and spatial protein profiling to characterize CIN and relevant tumor immune microenvironment (TIME) associated with LN metastasis. CIN in primary ESCC is significantly associated with LN metastasis at diagnosis, particularly in those patients with homologous recombination deficiency and use of alternative end joining (alt-EJ). Primary CIN ESCC exhibited increased epithelial-mesenchymal transition (EMT), hypoxia, angiogenesis, RNA metabolism, and heat stress, associated with a strong metastatic potential. Although CIN ESCC has elevated neoantigen loads, its TIME was enriched for immunosuppressive lipid-associated tumor-associated macrophages (LA-TAMs). Secreted phosphoprotein 1 (SPP1) plays a key role in mediating the communications of CIN ESCC cells and LA-TAMs. In LN metastases, structural CIN (sCIN) with retrotransposon insertion and reactivation is important for ESCC clonal evolution and cell proliferation, associated with increased LA-TAMs infiltration and poor overall patient survival. ESCC with high CIN has a strong metastatic potential. Our findings reveal a novel link between error-prone DSB repair pathways and LA-TAMs through CIN in LN metastasis.

BRAF/MEK inhibition induces cell state transitions boosting immune checkpoint sensitivity in BRAFV600E-mutant glioma

Resistance to v-raf murine sarcoma viral oncogene homolog B1 (BRAF) plus mitogen-activated protein kinase kinase (MEK) inhibition (BRAFi+MEKi) in BRAFV600E-mutant gliomas drives rebound, progression, and high mortality, yet it remains poorly understood. This study addresses the urgent need to develop treatments for BRAFi+MEKi-resistant glioma using preclinical mouse models and patient-derived materials. BRAFi+MEKi reveals glioma plasticity by heightening cell state transitions along glial differentiation trajectories, giving rise to astrocyte- and immunomodulatory oligodendrocyte (OL)-like states. PD-L1 upregulation in OL-like cells links cell state transitions to immune evasion, possibly orchestrated by Galectin-3. BRAFi+MEKi induces interferon response signatures, tumor infiltration, and suppression of T cells. Combining BRAFi+MEKi with immune checkpoint inhibition enhances survival in a T cell-dependent manner, reinvigorates T cells, and outperforms individual or sequential therapies in mice. Elevated PD-L1 expression in BRAF-mutant versus BRAF-wild-type glioblastoma supports the rationale for PD-1 inhibition in patients. These findings underscore the potential of targeting glioma plasticity and highlight combination strategies to overcome therapy resistance in BRAFV600E-mutant high-grade glioma.

Epithelial-to-mesenchymal transition (EMT) and cancer metastasis: the status quo of methods and experimental models 2025

Epithelial-to-mesenchymal transition (EMT) is a crucial cellular process for embryogenesis, wound healing, and cancer progression. It involves a shift in cell interactions, leading to the detachment of epithelial cells and activation of gene programs promoting a mesenchymal state. EMT plays a significant role in cancer metastasis triggering tumor initiation and stemness, and activates metastatic cascades resulting in resistance to therapy. Moreover, reversal of EMT contributes to the formation of metastatic lesions. Metastasis still needs to be better understood functionally in its major but complex steps of migration, invasion, intravasation, dissemination, which contributes to the establishment of minimal residual disease (MRD), extravasation, and successful seeding and growth of metastatic lesions at microenvironmentally heterogeneous sites. Therefore, the current review article intends to present, and discuss comprehensively, the status quo of experimental models able to investigate EMT and metastasis in vitro and in vivo, for researchers planning to enter the field. We emphasize various methods to understand EMT function and the major steps of metastasis, including diverse migration, invasion and matrix degradation assays, microfluidics, 3D co-culture models, spheroids, organoids, or latest spatial and imaging methods to analyze complex compartments. In vivo models such as the chorionallantoic membrane (CAM) assay, cell line-derived and patient-derived xenografts, syngeneic, genetically modified, and humanized mice, are presented as a promising arsenal of tools to analyze intravasation, site specific metastasis, and treatment response. Furthermore, we give a brief overview on methods detecting dissemination and MRD in carcinomas, highlighting its significance in tracking the course of disease and response to treatment. Enhanced lineage tracking tools, dynamic in vivo imaging, and therapeutically useful in vivo models as powerful preclinical tools may still better reveal functional interdependencies between metastasis and EMT. Future directions are discussed in light of emerging views on the biology, diagnosis, and treatment of EMT and metastasis.

Distinct TAM subset with cross-dressing capability determines the bifurcation of tumor immunity

Tumor-associated macrophage (TAM) heterogeneity significantly influences the tumor microenvironment, positioning TAM inhibition as a promising anticancer strategy. Although several TAM subsets have been described, their functional roles remain unclear. In this study, we identified a distinct subset of CD9hiCD63hiCD206+Class IIlo hypoxic TAMs, located near tumors. These TAMs engage in trogocytosis, acquiring tumor membrane fragments, and cross-dress major histocompatibility complex (MHC)/tumor antigen epitopes. These processes facilitate their recognition by cytotoxic T lymphocytes, enhancing antitumor immune responses. We further found CH25H as a key regulator of TAM cross-dressing, with its inhibition associated with the activity of HIF1-α and VHL. These findings highlight the potential of modulating TAMs as an innovative immunotherapy strategy.

Lung tumor immunity: redirecting macrophages through infection-induced inflammation

Macrophages play a central role in maintaining tissue homeostasis and in surveillance against pathogens and disease. In the lung, they can adopt either proinflammatory or anti-inflammatory states depending on the nature of the stimulus. As the predominant immune cells in both the lung tumor microenvironment and in sites of lung infection, the functional plasticity of macrophages makes them key players in determining disease outcome. Accurately defining their inflammatory profiles offers an opportunity to reprogram infection-associated macrophages towards enhanced tumor-killing phenotypes. This review explores how acute inflammation can drive macrophage-mediated antitumor immunity and highlights key molecules and signaling pathways that may be leveraged to therapeutically modulate macrophage function.

Emerging therapeutics targeting tumor-associated macrophages for the treatment of solid organ cancers

INTRODUCTION

Over the last decade, immune checkpoint inhibitors (ICIs) like PD-1/PD-L1 or CTLA-4, which reinvigorate T cells for tumor control have become standard-of-care treatment options. In response to the increasingly recognized mechanisms of resistance to T cell activation in immunologically cold tumors, immuno-oncology drug development has started to shift beyond T cell approaches. These include tumor-associated macrophages (TAMs), a major pro-tumor immune cell population in the tumor microenvironment known to silence immune responses.

AREAS COVERED

Here we outline anti-TAM therapies in current development, either as monotherapy or in combination with other treatment modalities. We describe emerging drugs targeting TAMs under investigation in phase II and III testing with a focus on their distinguishing mechanism of action which include (1) reprogramming of TAMs toward anti-tumor function and immune surveillance, (2) blockade of recruitment, and (3) reduction and ablation of TAMs.

EXPERT OPINION

Several new immuno-oncology agents are under investigation to harness anti-tumor functions of TAMs. While robust anti-tumor efficacy of anti-TAM therapies across advanced solid organ cancers remains elusive to-date, TAM reprogramming therapies have yielded benefits in select cancers. The inherent heterogeneity of the diverse TAM population will require enhanced investments into biomarker-driven approaches to fully leverage its therapeutic potential.

Elucidating the tumor microenvironment interactions in breast, cervical, and ovarian cancer through single-cell RNA sequencing

This study aimed to identify the key cell types and their interactions in gynecological oncology of breast cancer, cervical cancer, and ovarian cancer. Single-cell RNA sequencing was performed on tumor samples of gynecological oncology from the GEO database. Cell types were identified using SingleR and cell composition was analyzed to understand the tumor microenvironment (TME). CellChat was used to analyze cell interactions, and pseudotemporal analysis was conducted on cancer-associated fibroblasts (CAFs) and tumor-associated macrophages (TAMs) to understand their differentiation status. Four CAF subtypes were identified: iCAF, myCAF, proCAF, and matCAF. The iCAF subpopulation secreted COL1A1 and promoted tumor cell migration, while myCAF was involved in angiogenesis. The matCAF subpopulation was present throughout tumor development. TAMs were found to promote angiogenesis through the VEGFA_VEGFR2 signaling pathway. CAFs and TAMs play pivotal roles in tumor progression through their interactions and signaling pathways.

Histone methyltransferase ASH1L primes metastases and metabolic reprogramming of macrophages in the bone niche

Bone metastasis is a major cause of cancer death; however, the epigenetic determinants driving this process remain elusive. Here, we report that histone methyltransferase ASH1L is genetically amplified and is required for bone metastasis in men with prostate cancer. ASH1L rewires histone methylations and cooperates with HIF-1α to induce pro-metastatic transcriptome in invading cancer cells, resulting in monocyte differentiation into lipid-associated macrophage (LA-TAM) and enhancing their pro-tumoral phenotype in the metastatic bone niche. We identified IGF-2 as a direct target of ASH1L/HIF-1α and mediates LA-TAMs' differentiation and phenotypic changes by reprogramming oxidative phosphorylation. Pharmacologic inhibition of the ASH1L-HIF-1α-macrophages axis elicits robust anti-metastasis responses in preclinical models. Our study demonstrates epigenetic alterations in cancer cells reprogram metabolism and features of myeloid components, facilitating metastatic outgrowth. It establishes ASH1L as an epigenetic driver priming metastasis and macrophage plasticity in the bone niche, providing a bona fide therapeutic target in metastatic malignancies.

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.

Phenotypic heterogeneity and plasticity in colorectal cancer metastasis

Phenotypic heterogeneity and plasticity in colorectal cancer (CRC) has a crucial role in tumor progression, metastasis, and therapy resistance. However, the regulatory factors and the extrinsic signals driving phenotypic heterogeneity remain unknown. Using a combination of single-cell multiomics and spatial transcriptomics data from primary and metastatic CRC patients, we reveal cancer cell states with regenerative and inflammatory phenotypes that closely resemble metastasis-initiating cells in mouse models. We identify an intermediate population with a hybrid regenerative and stem phenotype. We reveal the transcription factors AP-1 and nuclear factor κB (NF-κB) as their key regulators and show localization of these states in an immunosuppressive niche both at the invasive edge in primary CRC and in liver metastasis. We uncover ligand-receptor interactions predicted to activate the regenerative and inflammatory phenotype in cancer cells. Together, our findings reveal regulatory and signaling factors that mediate distinct cancer cell states and can serve as potential targets to impair metastasis.

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.

Macrophage sensitivity to bexmarilimab-induced reprogramming is shaped by the tumor microenvironment

BACKGROUND

Tumor-associated macrophages (TAMs) adapt to the tumor microenvironment (TME), either aiding cancer eradication or promoting tumor growth and immune evasion. To manipulate TAMs therapeutically, a deep understanding of their interaction with the TME is essential. This study explores the responsiveness of TMEs to bexmarilimab, a macrophage reprogramming therapy showing clinical benefit in various solid tumors.

METHODS

We exploited a breast cancer patient-derived explant culture (PDEC) model to characterize bexmarilimab responses in both tumor and adjacent cancer-free tissues by RNA sequencing and multiplex cytokine profiling. Using single-cell RNA sequencing, spatial transcriptomics, and conditioned media treatment, we further investigated the effects of Clever-1+ macrophages and TME features on bexmarilimab sensitivity.

RESULTS

The PDEC model captured key aspects of bexmarilimab's mode of action and validated a gene signature for determining treatment sensitivity. We identified three distinct responses to bexmarilimab in tumors and adjacent cancer-free tissues, shaped by the local microenvironment and macrophage phenotype, origin, and localization. The inflammatory state of the TME emerged as the primary determinant of response. Immune activation occurred in immunologically cold TMEs lacking late-stage activated TAMs, whereas interferon-regulated TMEs exhibited suppressed inflammation. In cancer-free breast tissue, bexmarilimab activated B cell responses independent of treatment sensitivity in the adjacent tumor.

CONCLUSIONS

These findings reveal the complexity of TAM targeting in cancer and emphasize the need for patient selection to maximize bexmarilimab's efficacy.

Extracellular PKM2 modulates cancer immunity by regulating macrophage polarity

Tumor controls its immunity by educating its microenvironment, including regulating polarity of tumor associated macrophages. It is well documented that cancer cells release PKM2 to facilitate tumor progression. We report here that the extracellular PKM2 (EcPKM2) modulates tumor immunity by facilitating M2 macrophage polarization in tumors. EcPKM2 interacts with integrin αvβ3 on macrophage to activate integrin-FAK-PI3K signal axis. Activation of FAK-PI3K by EcPKM2 suppresses PTEN expression, which subsequently upregulates arginase1 (Arg1) expression and activity in macrophage to facilitate M2 polarity. Our studies uncover a novel and important mechanism for modulation of tumor immunity. More importantly, an antibody against PKM2 that disrupts the interaction between EcPKM2 and integrin αvβ3 is effective in converting M2 macrophages to M1 macrophages in tumors, suggesting a new therapeutic strategy and target for cancer therapies. Combination of the anti-PKM2 antibody with checkpoint blockades provides enhanced treatment effects.

Translating genetics into tissue: inflammatory cytokine-producing TAMs and PD-L1 tumor expression as poor prognosis factors in cutaneous melanoma

Myeloid cells within tumor microenvironments exhibit significant heterogeneity and play a critical role in influencing clinical outcomes. In this study, we investigated the infiltration of various myeloid cell subtypes in a cohort of cutaneous melanomas, revealing no significant correlation between myeloid cell densities and the occurrence of distant metastasis. We further examined the phenotypic characteristics of primary melanoma tumor-associated macrophages (TAMs) utilizing the seven-phenotype classification recently proposed by Ma et al., derived from extensive pan-cancer single-cell RNA-sequencing studies. First, we analyzed the transcriptomic profile of TAMs isolated from stage IV metastasizing primary melanomas, alongside melanoma-conditioned monocytes cultured in vitro, both supporting the inflammatory cytokine-producing macrophage phenotype. Next, we employed multicolor fluorescence confocal microscopy, to assess the expression of TAM phenotype markers at the protein level in a cohort of primary melanoma samples. Notably, markers indicative of the inflammatory TAM phenotype, quantified at single-cell level, were significantly enriched in metastasizing tumors, demonstrating an independent correlation with shorter disease-free and overall survival (log-rank test, p< 0.0002). Additionally, our screening of phenotype markers expression revealed that PD-L1 positivity in tumor cells, rather than in TAMs, was associated with poor prognosis, highlighting a novel aspect of the immune landscape in cutaneous melanoma.

Macrophage polarization in cancer and beyond: from inflammatory signaling pathways to potential therapeutic strategies

Macrophages are innate immune cells distributed throughout the body that play vital roles in organ development, tissue homeostasis, and immune surveillance. Macrophages acquire a binary M1/M2 polarized phenotype through signaling cascades upon sensing different signaling molecules in the environment, thereby playing a core role in a series of immune tasks, rendering precise regulation essential. M1/M2 macrophage phenotypes regulate inflammatory responses, while controlled activation of inflammatory signaling pathways is involved in regulating macrophage polarization. Among the relevant signaling pathways, we focus on the six well-characterized NF-κB, MAPK, JAK-STAT, PI3K/AKT, inflammasome, and cGAS-STING inflammatory pathways, and elucidate their roles and crosstalk in macrophage polarization. Furthermore, the effects of many environmental signals that influence macrophage polarization are investigated by modulating these pathways in vivo and in vitro. We thus detail the physiological and pathophysiological status of these six inflammatory signaling pathways and involvement in regulating macrophage polarization in cancer and beyond, as well as describe potential therapeutic approaches targeting these signaling pathways. In this review, the latest research advances in inflammatory signaling pathways regulating macrophage polarization are reviewed, as targeting these inflammatory signaling pathways provides suitable strategies to intervene in macrophage polarization and various tumor and non-tumor diseases.

Astragalus polysaccharides inhibits tumor proliferation and enhances cisplatin sensitivity in bladder cancer by regulating the PI3K/AKT/FoxO1 axis

Cisplatin (DDP) resistance presents a major challenge in bladder cancer (BLCA) treatment. Recent evidence suggests that Astragalus polysaccharide (APS), extracted from Astragalus membranaceus, may sensitize tumors to DDP. However, the precise mechanisms by which APS modulates DDP sensitivity in BLCA are not fully elucidated. The study employed computational biology, bioinformatics, and both in vitro and in vivo experiments to explore the role of APS in BLCA. The results demonstrate that APS inhibits BLCA cell proliferation, induces apoptosis in vitro, and suppresses tumor growth in vivo. Additionally, APS induces G0/G1 cell cycle arrest in BLCA cells by downregulating CCND1 expression. Moreover, APS further enhances DDP-induced apoptosis by downregulating PI3K-p110β and p-AKT expression, while upregulating FoxO1 expression. Bioinformatics analysis indicates that APS may remodel the tumor microenvironment (TME) and influence cell-cell interactions, specifically through modulation of macrophage M2 polarization and CD8+ T cell exhaustion, thereby overcoming DDP resistance. In conclusion, APS potentiates DDP-induced apoptosis in BLCA cells via the PI3K/AKT/FoxO1 axis and may act as an immunomodulator to remodel the TME, offering a potential strategy to combat DDP resistance in BLCA.

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.

GPR65 Inactivation in Tumor Cells Drives Antigen-Independent CAR T-cell Resistance via Macrophage Remodeling

SIGNIFICANCE

The study identifies GPR65 as an important determinant of B-cell acute lymphoblastic leukemia response to CAR T-cell therapy. Notably, GPR65 absence signals CAR T resistance. By emphasizing the therapeutic potential of targeting VEGFA or host macrophages, our study identifies routes to optimize CAR T-cell therapy outcomes in hematologic malignancies via tumor microenvironment manipulation.

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.

Understanding the Dual Role of Macrophages in Tumor Growth and Therapy: A Mechanistic Review

Macrophages are heterogeneous cells that are the mediators of tissue homeostasis. These immune cells originated from monocytes and are classified into two basic categories, M1 and M2 macrophages. M1 macrophages exhibit anti-tumorous inflammatory reactions due to the behavior of phagocytosis. M2 macrophages or tumor-associated macrophages (TAMs) are the most abundant immune cells in the tumor microenvironment (TME) and have a basic role in tumor progression by interacting with other immune cells in TME. By the expression of various cytokines, chemokines, and growth factors, TAMs lead to strengthening tumor cell proliferation, angiogenesis, and suppression of the immune system which further support invasion and metastasis. This review discusses recent and updated mechanisms regarding tumor progression by M2 macrophages. Moreover, the current therapeutic approaches targeting TAMs, their advantages, and limitations are also summarized, and further treatment approaches are outlined along with an elaboration of the tumor regression role of macrophages. This comprehensive review article possibly helps to understand the mechanisms underlying the tumor progression and regression role of macrophages in a comparative way from a basic level to the advanced one.

Advances in Spatial Omics Technologies

Rapidly developing spatial omics technologies provide us with new approaches to deeply understanding the diversity and functions of cell types within organisms. Unlike traditional approaches, spatial omics technologies enable researchers to dissect the complex relationships between tissue structure and function at the cellular or even subcellular level. The application of spatial omics technologies provides new perspectives on key biological processes such as nervous system development, organ development, and tumor microenvironment. This review focuses on the advancements and strategies of spatial omics technologies, summarizes their applications in biomedical research, and highlights the power of spatial omics technologies in advancing the understanding of life sciences related to development and disease.

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.

CAR macrophages with built-In CD47 blocker combat tumor antigen heterogeneity and activate T cells via cross-presentation

Macrophage-based cancer cellular therapy has gained substantial interest. However, the capability of engineered macrophages to target cancer heterogeneity and modulate adaptive immunity remains unclear. Here, exploiting the myeloid antibody-dependent cellular phagocytosis biology and phagocytosis checkpoint blockade, we report the enhanced synthetic phagocytosis receptor (eSPR) that integrate FcRγ-driven phagocytic chimeric antigen receptors (CAR) with built-in secreted CD47 blockers. The eSPR engineering empowers macrophages to combat tumor antigen heterogeneity. Transduced by adenoviral vectors, eSPR macrophages are intrinsically pro-inflammatory imprinted and resist tumoral polarization. Transcriptomically and phenotypically, eSPR macrophages elicit a more favorable tumor immune landscape. Mechanistically, eSPR macrophages in situ stimulate CD8 T cells via phagocytosis-dependent antigen cross-presentation. We also validate the functionality of the eSPR system in human primary macrophages.

The clinical significance and potential therapeutic target of tumor-associated macrophage in non-small cell lung cancer

One of the leading causes of cancer-related mortality globally is non-small cell lung cancer (NSCLC). It has become a significant public health concern due to its rising incidence rate and fatality. Tumor-associated macrophage (TAM) is important in the tumor microenvironment (TME) of NSCLC because they have an impact on the development, metastasis, and incidence of tumors. As a crucial element of the TME, TAM contributes to tumor immune evasion, facilitates tumor proliferation and metastasis, and modulates tumor angiogenesis, immunosuppression, and treatment resistance through the secretion of diverse cytokines, chemokines, and growth factors. Consequently, TAM assumes a multifaceted and intricate function in the onset, progression, and therapeutic response of NSCLC, serving as a crucial focal point for comprehending the tumor microenvironment and formulating novel therapeutic methods. The study aims to review the biological properties and potential processes of TAM in NSCLC, investigate its involvement in the clinical of NSCLC patients, and discuss its potential as a therapeutic target.

Mesothelial and immune cells interplay in the tumor microenvironment

Mesothelial cells (MCs) constitute a dynamic mesothelium in which their numerous crucial functions synergistically interact with other cells to maintain serosal integrity and homeostasis. Previous studies have confirmed the crucial role of interactions between MCs and tumor cells in tumorigenesis and progression in the tumor microenvironment (TME). However, recent research has found that MCs can induce an immunosuppressive microenvironment by secreting various cytokines, chemokines, and exosomes which recruit immunosuppressive cells or interact with immune cells, thus contributing to tumor progression. This review primarily examines the immunoregulatory role of MCs in the TME of mesothelioma and metastatic pleural and peritoneal carcinomas. It also explores the potential mechanisms by which these interactions induce immunosuppression and their impact on tumor growth and therapy.

Targeting VSIG4+ tissue-resident macrophages enhances T cell cytotoxicity and immunotherapy efficacy in cancer

Tissue-resident macrophage (TRM) is crucial for organ development and homeostasis. However, the role of TRM-derived tumor-associated macrophage (TAM) subpopulations in cancer remains unclear. Using single-cell RNA sequencing and lineage tracing, we reported a TRM-derived TAM subpopulation, characterized by VSIG4 overexpression in testicular cancer. Macroscopically, such subpopulation was also found in tumors such as hepatocellular carcinoma, lung cancer, and glioblastoma. It was associated with poor prognosis and the suppression of CD8+ T-cell-dependent immunity via VSIG4. Notably, VSIG4 promoted immunosuppressive effects through direct or indirect modes, including interacting with receptors on CD8+ T cells or inducing transcription of IL-11 in TAMs. More importantly, MEF2C was identified as a key transcription factor that maintained VSIG4 expression and determined the biological behaviors of VSIG4+ TAMs. In preclinical models, targeting VSIG4+ TAMs via VSIG4 or MEF2C demonstrated a favorable effect of enhancing the efficacy of immune checkpoint inhibitors.

Regulating the fate of tumor-associated macrophages

Tumor-associated macrophages (TAMs) are key players in tumor progression, yet their role in this process remains only partially understood. In this issue of Cancer Cell, Sheban et al. demonstrate that zinc finger E-box-binding homeobox 2 (ZEB2) acts as a master regulator that reprograms TAMs toward a pro-tumor phenotype and that therapeutic targeting of ZEB2 exhibits anti-tumor activity.

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.

Single-cell RNA sequencing dissects the immunosuppressive signatures in Helicobacter pylori-infected human gastric ecosystem

Helicobacter pylori (H. pylori) manipulates the host immune system to establish a persistent colonization, posing a serious threat to human health, but the mechanisms remain poorly understood. Here we integrate single-cell RNA sequencing and TCR profiling for analyzing 187,192 cells from 11 H. pylori-negative and 12 H. pylori-positive individuals to describe the human gastric ecosystem reprogrammed by H. pylori infection, as manifested by impaired antigen presentation and phagocytosis function. We further delineate a monocyte-to-C1QC+ macrophage differentiation trajectory driven by H. pylori infection, while T cell responses exhibit broad functional impairment and hyporesponsiveness with restricted clonal expansion capacity. We also identify an HLA-DRs- and CTLA4-expressing T cell population residing in H. pylori-inhabited stomach that potentially contribute to immune evasion. Together, our findings provide single-cell resolution information into the immunosuppressive microenvironment shaped by H. pylori infection, offering critical insights for developing novel therapeutic approaches to eliminate this globally prevalent pathogen.

Myeloid-lineage-specific membrane protein LRRC25 suppresses immunity in solid tumor and is a potential cancer immunotherapy checkpoint target

Leucine-rich repeat containing 25 (LRRC25), a type I membrane protein, is specifically expressed in myeloid cells including neutrophils and macrophages. The anti-inflammatory role of LRRC25 was suggested in a few pathogenic models. However, its role in cancer immunity has not been interrogated. Here, we demonstrate that LRRC25 is robustly expressed in tumor-associated macrophages (TAMs). Lrrc25 deficiency in the tumor microenvironment (TME) suppresses growth of multiple murine tumor models by reprogramming TAMs toward an anti-tumor phenotype and thereby enhancing infiltration and activation of CD8+ T cells. The Nox2-ROS-Nlrp3-Il1β pathway is elevated in Lrrc25-deficient TAMs. Furthermore, a human myeloid cell line or mice with loss of Lrrc25 appear normal, indicating that LRRC25 is a safe immune target. Our results suggest that as an unappreciated immune checkpoint for tumor immunotherapy, the myeloid-specific membrane protein LRRC25 orchestrates the activity of TAMs via the canonical Nlrp3-IL1β inflammatory pathway and influences CD8+ T cell chemotaxis to the TME.

Spatial mapping of transcriptomic plasticity in metastatic pancreatic cancer

Patients with treatment-refractory pancreatic cancer often succumb to systemic metastases1-3; however, the transcriptomic heterogeneity that underlies therapeutic recalcitrance remains understudied, particularly in a spatial context. Here we construct high-resolution maps of lineage states, clonal architecture and the tumour microenvironment (TME) using spatially resolved transcriptomics from 55 samples of primary tumour and metastases (liver, lung and peritoneum) collected from rapid autopsies of 13 people. We observe discernible transcriptomic shifts in cancer-cell lineage states as tumours transition from primary sites to organ-specific metastases, with the most pronounced intra-patient distinctions between liver and lung. Phylogenetic trees constructed from inferred copy number variations in primary and metastatic loci in each patient highlight diverse patient-specific evolutionary trajectories and clonal dissemination. We show that multiple tumour lineage states co-exist in each tissue, including concurrent metastatic foci in the same organ. Agnostic to tissue site, lineage states correlate with distinct TME features, such as the spatial proximity of TGFB1-expressing myofibroblastic cancer-associated fibroblasts (myCAFs) to aggressive 'basal-like' cancer cells, but not to cells in the 'classical' or 'intermediate' states. These findings were validated through orthogonal and cross-species analyses using mouse tissues and patient-derived organoids. Notably, basal-like cancer cells aligned with myCAFs correlate with plasma-cell exclusion from the tumour milieu, and neighbouring cell analyses suggest that CXCR4-CXCL12 signalling is the underlying basis for observed immune exclusion. Collectively, our findings underscore the profound transcriptomic heterogeneity and microenvironmental dynamics that characterize treatment-refractory pancreatic cancer.

Peritoneal resident macrophages constitute an immunosuppressive environment in peritoneal metastasized colorectal cancer

Patients with peritoneal metastasized colorectal cancer (PM-CRC) have a dismal prognosis. We hypothesized that an immunosuppressive environment in the peritoneal cavity underlies poor prognosis. We define the composition of the human peritoneal immune system (PerIS) using single-cell technologies in 18 patients with- and without PM-CRC, as well as in matched peritoneal metastases (n = 8). Here we show that the PerIS contains abundant immunosuppressive C1Q+VSIG4+ and SPP1+VSIG4+ peritoneal-resident macrophages (PRMs), as well as monocyte-like cavity macrophages (mono-CMs), which share features with tumor-associated macrophages, even in homeostasis. In PM-CRC, expression of immunosuppressive cytokines IL10 and VEGF increases, while simultaneously expression of antigen-presenting molecules decreases in PRMs. These intratumoral suppressive PRMs originate from the PerIS, and intraperitoneal depletion of PRMs in vivo using anti-CSF1R combined with anti-PD1 significantly reduces tumor burden and improves survival. Thus, PRMs define a metastatic site-specific immunosuppressive niche, and targeting PRMs is a promising treatment strategy for PM-CRC.

Zn‐DHM Nanozymes Enhance Muscle Regeneration Through ROS Scavenging and Macrophage Polarization in Volumetric Muscle Loss Revealed by Single‐Cell Profiling

Volumetric muscle loss (VML) is a severe condition in which the loss of skeletal muscle surpasses the body's intrinsic repair capabilities, leading to irreversible functional deficits and potential disability, with persistent inflammation and impaired myogenic differentiation. To address these challenges, a novel zinc‐dihydromyricetin (Zn‐DHM) nanozyme with superoxide dismutase (SOD)‐like activity is developed, designed to neutralize excessive reactive oxygen species (ROS) and restore oxidative balance. Zn‐DHM mitigates oxidative stress and promotes polarization of macrophages from the proinflammatory M1 phenotype to the anti‐inflammatory M2 phenotype, thereby reducing chronic inflammation and creating a conducive environment for muscle repair. Further, Zn‐DHM significantly enhances the myogenic differentiation of C2C12 cells, accelerating wound healing processes. These studies confirm the biosafety and low toxicity of Zn‐DHM. As per a murine tibialis anterior VML model, Zn‐DHM effectively suppresses inflammation and markedly improves skeletal muscle repair outcomes. Single‐cell RNA sequencing reveals that Zn‐DHM treatment increases the expression of M2 macrophage markers and enhances the proliferation and differentiation capacity of muscle stem cells (MuSCs). In addition, intercellular communication analysis reveals interactions between MuSCs and macrophages in the Zn‐DHM treatment group, suggesting that these interactions may drive tissue regeneration through the activation of the GAS and Notch signaling pathways.

Modulation of M1 and M2 macrophage polarization by metformin: Implications for inflammatory diseases and malignant tumors

Macrophages perform an essential role in the body's defense mechanisms and tissue homeostasis. These cells exhibit plasticity and are categorized into two phenotypes, including classically activated/M1 pro-inflammatory and alternatively activated/M2 anti-inflammatory phenotypes. Functional deviation in macrophage polarization occurs in different pathological conditions that need correction. In addition to antidiabetic impacts, metformin also possesses multiple biological activities, including immunomodulatory, anti-inflammatory, anti-tumorigenic, anti-aging, cardioprotective, hepatoprotective, and tissue-regenerative properties. Metformin can influence the polarization of macrophages toward M1 and M2 phenotypes. The ability of metformin to support M2 polarization and suppress M1 polarization could enhance its anti-inflammatory properties and potentiate its protective effects in conditions such as chronic inflammatory diseases, atherosclerosis, and obesity. However, in metformin-treated tumors, the proportion of M2 macrophages is decreased, while the frequency ratio of M1 macrophages is increased, indicating that metformin can modulate macrophage polarization from a pro-tumoral M2 state to an anti-tumoral M1 phenotype in malignancies. Metformin affects macrophage polarization through AMPK-dependent and independent pathways involving factors, such as NF-κB, mTOR, ATF, AKT/AS160, SIRT1, STAT3, HO-1, PGC-1α/PPAR-γ, and NLRP3 inflammasome. By modulating cellular metabolism and apoptosis, metformin can also influence macrophage polarization. This review provides comprehensive evidence regarding metformin's effects on macrophage polarization and the underlying mechanisms. The polarization-inducing capabilities of metformin may provide significant therapeutic applications in various inflammatory diseases and malignant tumors.

Transmembrane Serine Protease TMPRSS11B promotes an acidified tumor microenvironment and immune suppression in lung squamous cell carcinoma

Lung cancer is the leading cause of cancer-related deaths worldwide. Existing therapeutic options have limited efficacy, particularly for lung squamous cell carcinoma (LUSC), underscoring the critical need for the identification of new therapeutic targets. We previously demonstrated that the Transmembrane Serine Protease TMPRSS11B promotes transformation of human bronchial epithelial cells and enhances lactate export from LUSC cells. To determine the impact of TMPRSS11B activity on the host immune system and the tumor microenvironment (TME), we evaluated the effect of Tmprss11b depletion in a syngeneic mouse model. Tmprss11b depletion significantly reduced tumor burden in immunocompetent mice and triggered an infiltration of immune cells. RNA FISH analysis and spatial transcriptomics in the autochthonous Rosa26-Sox2-Ires-Gfp LSL/LSL ; Nkx2-1 fl/fl ; Lkb 1 fl/fl (SNL) model revealed an enrichment of Tmprss11b expression in LUSC tumors, specifically in Krt13 + hillock-like cells. Ultra-pH sensitive nanoparticle imaging and metabolite analysis identified regions of acidification, elevated lactate, and enrichment of M2-like macrophages in LUSC tumors. These results demonstrate that TMPRSS11B promotes an acidified and immunosuppressive TME and nominate this enzyme as a therapeutic target in LUSC.

Single-Cell Profiling and Proteomics-Based Insights Into mTORC1-Mediated Angio+TAMs Polarization in Recurrent IDH-Mutant Gliomas

BACKGROUND

IDH mutant gliomas often exhibit recurrence and progression, with the mTORC1 pathway and tumor-associated macrophages potentially contributing to these processes. However, the precise mechanisms are not fully understood. This study seeks to investigate these relationships using proteomic, phosphoproteomic, and multi-dimensional transcriptomic approaches.

METHODS

This study established a matched transcriptomic, proteomic, and phosphoproteomic cohort of IDH-mutant gliomas with recurrence and progression, incorporating multiple glioma-related datasets. We first identified the genomic landscape of recurrent IDH-mutant gliomas through multi-dimensional differential enrichment, GSVA, and deconvolution analyses. Next, we explored tumor-associated macrophage subpopulations using single-cell sequencing in mouse models of IDH-mutant and wild-type gliomas, analyzing transcriptional changes via AddmodelScore and pseudotime analysis. We then identified these subpopulations in matched primary and recurrent IDH-mutant datasets, investigating their interactions with the tumor microenvironment and performing deconvolution to explore their contribution to glioma progression. Finally, spatial transcriptomics was used to map these subpopulations to glioma tissue sections, revealing spatial co-localization with mTORC1 and angiogenesis-related pathways.

RESULTS

Multi-dimensional differential enrichment, GSVA, and deconvolution analyses indicated that the mTORC1 pathway and the proportion of M2 macrophages are upregulated during the recurrence and progression of IDH-mutant gliomas. CGGA database analysis showed that mTORC1 activity is significantly higher in recurrent IDH-mutant gliomas compared to IDH-wildtype, with a correlation to M2 macrophage infiltration. KSEA revealed that AURKA is enriched during progression, and its inhibition reduces mTORC1 pathway activity. Single-cell sequencing in mouse models identified a distinct glioma subpopulation with upregulated mTORC1, exhibiting both M2 macrophage and angiogenesis transcriptional features, which increased after implantation of IDH-mutant tumor cells. Similarly, human glioma single-cell data revealed the same subpopulation, with cell-cell communication analysis showing active VEGF signaling. Finally, spatial transcriptomics deconvolution confirmed the co-localization of this subpopulation with mTORC1 and VEGFA in high-grade IDH-mutant gliomas.

CONCLUSIONS

Our findings suggest mTORC1 activation and Angio-TAMs play key roles in the recurrence and progression of IDH-mutant gliomas.

Immune evasion mechanisms in early-stage I high-grade serous ovarian carcinoma: insights into regulatory T cell dynamics

The mechanisms driving immune evasion in early-stage I high-grade serous ovarian carcinoma (HGSOC) remain poorly understood. To investigate this, we performed single-cell RNA-sequencing analysis. Our findings revealed a highly immunosuppressive HGSOC microenvironment, characterized by abundant infiltration of regulatory T cells (Tregs). Trajectory analysis uncovered differentiation pathways of naïve Tregs, which underwent either activation and proliferation or transcriptional instability. The predicted Treg-cell interaction network, including crosstalk within tumor cells, facilitates Treg mobility and maturation while reinforcing their immunosuppressive function and persistence in the tumor. Moreover, their interactions with immune cells likely inhibit CD8 T cells and antigen-presenting cells, supporting tumor immune escape. Additionally, more immunogenic tumor conditions, marked by IFNγ production, may contribute to Treg destabilization. Our findings underscore the pivotal role of Tregs in early immune evasion of HGSOC and provide insights into potential therapeutic strategies targeting their activity and differentiation fate.

The maternal-fetal interface at single-cell resolution: uncovering the cellular anatomy of the placenta and decidua

The maternal-fetal interface represents a critical site of immunological interactions that can greatly influence pregnancy outcomes. The unique cellular composition and cell-cell interactions taking place within these tissues has spurred substantial research efforts focused on the maternal-fetal interface. With the recent advent of single-cell technologies, multiple investigators have applied such methods to gain an unprecedented level of insight into maternal-fetal communication. Here, we provide an overview of the dynamic cellular composition and cell-cell communications at the maternal-fetal interface as reported by single-cell investigations. By primarily focusing on data from pregnancies in the second and third trimesters, we aim to showcase how single-cell technologies have bolstered the foundational understanding of each cell's contribution to physiologic gestation. Indeed, single-cell technologies have enabled the examination of classical placental cells, such as the trophoblast, as well as uncovered new roles for structural cells now recognized as active participants in pregnancy and parturition, such as decidual and fetal stromal cells, which are reviewed herein. Furthermore, single-cell data investigating the ontogeny, function, differentiation, and interactions among immune cells present at the maternal-fetal interface, namely macrophages, T cells, dendritic cells, neutrophils, mast cells, innate lymphoid cells, natural killer cells, and B cells are discussed in this review. Moreover, a key output of single-cell investigations is the inference of cell-cell interactions, which has been leveraged to not only dissect the intercellular communications within specific tissues but also between compartments such as the decidua basalis and placental villi. Collectively, this review emphasizes the ways by which single-cell technologies have expanded the understanding of cell composition and cellular processes underlying pregnancy in mid-to-late gestation at the maternal-fetal interface, which can prompt their continued application to reveal new pathways and targets for the treatment of obstetrical disease.

Unraveling the immune-activated tumor microenvironment correlated with clinical response to atezolizumab plus bevacizumab in advanced HCC

Background & Aims

Despite atezolizumab plus bevacizumab being a standard treatment for advanced hepatocellular carcinoma (HCC), a significant proportion of patients do not achieve durable benefit. This study aimed to identify predictive biomarkers for this therapy by investigating the role of immune activation within the tumor microenvironment (TME).

Methods

We characterized the intratumoral TME of patients with advanced HCC treated with atezolizumab plus bevacizumab using single cell transcriptomics on pretreatment tumor biopsies from 12 patients. To complement and support these findings, we integrated our single cell data with publicly available bulk RNA-sequencing data from independent clinical trial cohorts.

Results

Patients who responded to combination therapy with atezolizumab plus bevacizumab demonstrated an immune-activated TME, marked by enhanced cytotoxicity and a tumor-specific T cell response. These patients also exhibited an increased proportion of inflammatory cytokine-enriched tumor-associated macrophage clusters with stronger interactions with T cells, an increased population of conventional dendritic cells, and activated antigen-presenting function in tumor endothelial cells. When publicly available bulk RNA-sequencing data from independent clinical trial cohorts were analyzed, these immune activation features were associated with improved progression-free survival (median 10.8 months, 95% CI: 7.3-not reached versus 5.5 months, 95% CI: 4.0-6.7; p <0.001).

Conclusions

These findings suggest that the existence of an activated immune TME before treatment is crucial for a favorable clinical response in patients with HCC treated with atezolizumab plus bevacizumab.

Impact and implications

Only a subset of patients with HCC benefit from combination therapy with atezolizumab plus bevacizumab, limiting its clinical utility. In this study, we used single cell RNA analysis to identify TME features associated with a clinical response to this therapy. Our findings suggest that a pre-existing immune-activated TME is crucial for predicting the response to atezolizumab plus bevacizumab. Specifically, features such as enhanced T cell cytotoxicity, inflammatory cytokine-enriched macrophage clusters, active antigen presentation in endothelial cells, and an increased presence of dendritic cells may aid patient selection and inform therapeutic strategies.

Histone acetylation modulators in breast cancer

Breast cancer is the most prevalent cancer in women worldwide. Aberrant epigenetic reprogramming such as dysregulation of histone acetylation has been associated with the development of breast cancer. Histone acetylation modulators have been targeted as potential treatments for breast cancer. This review comprehensively discusses the roles of these modulators and the effects of their inhibitors on breast cancer. In addition, epigenetic reprogramming not only affects breast cancer cells but also the immunosuppressive myeloid cells, which can facilitate breast cancer progression. Therefore, the review also highlights the roles of these immunosuppressive myeloid cells and summarizes how histone acetylation modulators affect their functions and phenotypes. This review provides insights into histone acetylation modulators as potential therapeutic targets for breast cancer.

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.

SIMVI disentangles intrinsic and spatial-induced cellular states in spatial omics data

Spatial omics technologies enable analysis of gene expression and interaction dynamics in relation to tissue structure and function. However, existing computational methods may not properly distinguish cellular intrinsic variability and intercellular interactions, and may thus fail to reliably capture spatial regulations. Here, we present Spatial Interaction Modeling using Variational Inference (SIMVI), an annotation-free deep learning framework that disentangles cell intrinsic and spatial-induced latent variables in spatial omics data with rigorous theoretical support. By this disentanglement, SIMVI enables estimation of spatial effects at a single-cell resolution, and empowers various downstream analyses. We demonstrate the superior performance of SIMVI across datasets from diverse platforms and tissues. SIMVI illuminates the cyclical spatial dynamics of germinal center B cells in human tonsil. Applying SIMVI to multiome melanoma data reveals potential tumor epigenetic reprogramming states. On our newly-collected cohort-level CosMx melanoma data, SIMVI uncovers space-and-outcome-dependent macrophage states and cellular communication machinery in tumor microenvironments.

Characterizing macrophage diversity in colorectal malignancies through single-cell genomics

Colorectal cancer (CRC) is one of the most common malignant tumors of the digestive tract, with increasing incidence and mortality rates, posing a significant burden on human health. Its progression relies on various mechanisms, among which the tumor microenvironment and tumor-associated macrophages (TAMs) have garnered increasing attention. Macrophage infiltration in various solid tumors is associated with poor prognosis and is linked to chemotherapy resistance in many cancers. These significant biological behaviors depend on the heterogeneity of macrophages. Tumor-promoting TAMs comprise subpopulations characterized by distinct markers and unique transcriptional profiles, rendering them potential targets for anticancer therapies through either depletion or reprogramming from a pro-tumoral to an anti-tumoral state. Single-cell RNA sequencing technology has significantly enhanced our research resolution, breaking the traditional simplistic definitions of macrophage subtypes and deepening our understanding of the diversity within TAMs. However, a unified elucidation of the nomenclature and molecular characteristics associated with this diversity remains lacking. In this review, we assess the application of conventional macrophage polarization subtypes in colorectal malignancies and explore several unique subtypes defined from a single-cell omics perspective in recent years, categorizing them based on their potential functions.

HTLV-1-infected cells drive the differentiation of monocytes into macrophages in vitro

BACKGROUND

The human T-cell lymphotropic virus type 1 (HTLV-1) is a retrovirus that causes HTLV-1-associated myelopathy/tropical spastic paraparesis (HAM/TSP). HAM/TSP is a chronic inflammatory neurodegenerative disease characterized by leukocyte infiltration in the spinal cord. T-lymphocytes are the most important targets of HTLV-1 infection, but monocytes are also infected. Monocytes from HTLV-1-infected individuals exhibit important functional differences compared to cells from uninfected donors. Here, we investigated the effects of cell-cell physical contact and/or secreted factors of HTLV-1-infected cells in monocyte activation and differentiation.

METHODS

The THP-1 human monocytic cell line was co-cultured with a human cell line transformed by HTLV-1 (MT-2) for 6 days. To determine the effects of co-culturing HTLV-1-infected cells in THP-1 monocytes cells were characterized by flow cytometry, immunofluorescence microscopy, and real-time PCR. Computational analysis of published transcriptomic datasets was realized to compare molecular profiles of macrophages and mononuclear cells from HTLV-1 carriers.

RESULTS

Co-culture of monocytes with HTLV-1-infected cells induced macrophage differentiation and upregulation of typical macrophages-associated molecules (HLA-DR, CD80, and CD86), increased cytokine (TNFα, IL-6, and IL-1β) levels and their coding genes expression. Consistently, published transcriptomic datasets showed changes in important genes associated with inflammation during HAM/TSP in patients. The presence of HTLV-1-infected cells in the culture also induced significant upregulation of Interferon Stimulated Genes (ISG), indicating viral infection. Monocyte activation and differentiation into pro-inflammatory macrophages occurred in a cell-to-cell contact-independent manner, suggesting the role of factors secreted by infected cells.

CONCLUSIONS

Together, our results indicated that HTLV-1-infected cells induced monocyte differentiation into macrophages inflammatory, predominantly.

Emodin Decreases Tumor-Associated Macrophages Accumulation and Suppresses Bladder Cancer Development by Inhibiting CXCL1 Secretion from Cancer-Associated Fibroblasts

Tumor-associated macrophages (TAMs) and cancer-associated fibroblasts (CAFs) are the most abundant stromal cells in the bladder cancer (BC) microenvironment (TME). However, the detailed mechanisms underlying TAM-CAF communication and their contributions to BC progression remain incompletely understood. Emerging evidence shows that Emodin exerts anti-tumor effect on several tumor models by targeting TME. To date, the impact of Emodin on BC has not been previously reported. Our study firstly demonstrated that Emodin significantly inhibited tumor growth and reduced TAM accumulation in a murine BC model. Emodin markedly decreased serum levels of multiple chemokines in tumor-bearing mice, with CXCL1 showing the most pronounced reduction. Strikingly, Emodin selectively suppressed CXCL1 secretion in CAFs but not in TAMs or tumor cells. Furthermore, the decrease in TAM migration induced by Emodin was dependent on CAF-derived CXCL1. Using a subcutaneous tumor model, we found that Emodin failed to inhibit tumor growth when CXCL1-deficient CAFs were co-injected with tumor cells, underscoring the critical role of CXCL1 in this process. Bioinformatics analysis further revealed that elevated CXCL1 levels correlated negatively with invasive/metastatic potential and overall survival in BC patients. In conclusion, our findings establish that Emodin delays BC progression by disrupting CXCL1-mediated crosstalk between CAFs and TAMs.