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

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.

Dendritic cell maturation in cancer

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

The dual role of CXCL9/SPP1 polarized tumor-associated macrophages in modulating anti-tumor immunity in hepatocellular carcinoma

Introduction

The main challenge for cancer therapy lies in immuno-suppressive tumor micro-environment. Reprogramming tumor-associated macrophages (TAMs) into an anti-tumor phenotype is a promising strategy.

Methods

A comprehensive analysis by combing multi-regional single-cell, bulk and spatial transcriptome profiling with radiomics characterization was conducted to dissect the heterogeneity of TAMs and resolve the landscape of the CXCL9:SPP1 (CS) macrophage polarity in HCC.

Results

TAMs were particularly increased in HCC. SPP1+ TAMs and CXCL9+ TAMs were identified as the dominant subtypes with different evolutionary trajectories. SPP1+ TAMs, located in the tumor core, co-localized with cancer-associated fibroblasts to promote tumor growth and further contributed to worse prognosis. In contrast, CXCL9+ TAMs, located in the peritumoral region, synergized with CD8+ T cells to create an immunostimulatory micro-environment. For the first time, we explored the applicability of CS polarity in HCC tumors and revealed several key transcription factors involved in shaping this polarity. Moreover, CS polarity could serve as a potential indicator of prognostic and micro-environmental status for HCC patients. Based on medical imaging data, we developed a radiomics tool, RCSP (Radiogenomics-based CXCL9/SPP1 Polarity), to assist in non-invasively predicting the CS polarity in HCC patients.

Conclusion

Our research sheds light on the regulatory roles of SPP1+ TAMs and CXCL9+ TAMs in the micro-environment and provides new therapeutic targets or insights for the reprogramming of targeted macrophages in HCC.

Interleukin-1 receptor antagonist is a conserved early factor for exacerbating tuberculosis susceptibility

Mycobacterium tuberculosis (Mtb) causes 1.25 million deaths a year. However, tuberculosis (TB) pathogenesis remains poorly understood and is not fully recapitulated in standard mouse models. Here we find that gene signatures from three different Mtb-susceptible mouse models predict active TB disease in humans significantly better than a signature from resistant C57BL/6 (B6) mice. Conserved among susceptible mice, non-human primates, and humans, but largely absent from B6 mice, was Mtb-induced differentiation of macrophages into an Spp1 + differentiation state. Spp1 + macrophages expressed high levels of immunosuppressive molecules including IL-1 receptor antagonist (IL-1Ra). IL-1Ra was previously reported to cause Mtb susceptibility in one mouse model, but whether IL-1Ra is broadly important remains uncertain. Here we report that enhancement of IL-1 signaling via deletion of IL-Ra promoted bacterial control across three susceptible mouse models. We found IL-1 signaling amplified production of multiple cytokines by lymphoid and stromal cells, providing a multifactorial mechanism for how IL-1 promotes Mtb control. Our results indicate that myeloid cell expression of immunosuppressive molecules, in particular IL-1 receptor antagonist, is a conserved early mechanism limiting Mtb control in mice, non-human primates, and humans.

Immunogenomic cancer evolution: A framework to understand cancer immunosuppression

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

Integrated single-cell and spatial analysis identifies context-dependent myeloid-T cell interactions in head and neck cancer immune checkpoint blockade response

Background

Approximately 15-20% of head and neck cancer squamous cell carcinoma (HNSCC) patients respond favorably to immune checkpoint blockade (ICB). Previous single-cell RNA-Seq (scRNA-Seq) studies identified immune features, including macrophage subset ratios and T-cell subtypes, in HNSCC ICB response. However, the spatial features of HNSCC-infiltrated immune cells in response to ICB treatment need to be better characterized.

Methods

Here, we perform a systematic evaluation of cell interactions between immune cell types within the tumor microenvironment using spatial omics data using complementary techniques from both 10X Visium spot-based spatial transcriptomics and Nanostring CosMx single-cell spatial omics with RNA gene panel including 435 ligands and receptors. In this study, we used integrated bioinformatics analyses to identify cellular neighborhoods of co-localizing cell types in single-cell spatial transcriptomics and proteomics data. In addition, we used both publicly available scRNA-Seq and in-house spatial RNA-Seq data to identify spatially constrained Ligand-Receptor interactions in Responder patients.

Results

With 522,399 single cells profiled with both RNA and protein from 26 patients, in addition to spot-resolved spatial RNA-Seq from 8 patients treated with ICB together with bioinformatics analysis of publicly available single-cell and bulk RNA-Seq, we have identified a spatial and cell-type specific context-dependency of myeloid and T cell interaction difference between Responders and Non-Responders. We defined further cellular neighborhood and the sources of chemokine CXCL9/10-CXCR3 interactions in Responders, emerging targets in ICB, as well as CXCL16-CXCR6, CCL4/5-CCR5, and other underappreciated and potential markers and targets for ICB response in HNSCC. In addition, we have contributed a rich data resource of cell-cell Ligand Receptor interactions for the immunotherapy and HNSCC research community.

Discussion

Our work provides a comprehensive single-cell and spatial atlas of immune cell interactions that correlate with response to ICB in HNSCC. We showcase how integrating multiple technologies and bioinformatics approaches can provide new insights into potential immune-based biomarkers of ICB response. Our results suggested refining future studies using preclinical animal models in a more context-specific manner to elucidate potential underlying mechanisms that lead to improved ICB responses.

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

BACKGROUND

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

METHODS

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

RESULTS

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

CONCLUSION

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

Myeloid cell path to malignancy: insights into liver cancer

Clinically approved treatments for advanced liver cancer often lack potency because of the heterogeneous characteristics of hepatocellular carcinoma (HCC). This complexity is largely driven by context-dependent inflammatory responses brought on by diverse etiologies, such as metabolic dysfunction-associated steatohepatitis (MASH), the genetic makeup of cancer cells, and the versatile adaptability of immune cells, such as myeloid cells. In this review, we discuss the evolutionary dynamics of the immune landscape, particularly that of liver-resident Kupffer cells (KCs), TREM2+, and SPP1+ macrophages with an active role during liver disease progression, which eventually fuels hepatocarcinogenesis. We highlight exploitable immunomodulatory avenues amenable to mitigate both the inherent pathological characteristics of liver cancers and the associated external factors that favor malignancy, paving a roadmap toward improving the management and therapeutic outcome for patients with HCC.

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.

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

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

Oropharyngeal carcinomas induce circulating monocytes to express a TAM-like pro-tumor expression profile that suppresses T-cell proliferation

Introduction

Tumor-associated macrophages (TAMs) recruited from circulating monocytes drive tumor-growth and establish an immunosuppressive tumor microenvironment (TME). Initial events in transition from resting monocytes to TAMs are poorly understood. Here, we report that monocytes from oropharyngeal cancer (OPC) patients and control monocytes treated with OPC-conditioned media (CM) express a repertoire of pro-tumor mediators that is characteristic of TAMs.

Methods

Monocytes were stimulated with OPC cell line CM, analyzed by single-cell RNAseq. Results of select genes were confirmed by qPCR with monocytes and analyzed in OPC tumors vs. clinically normal tissue. OPC spheroids containing control monocytes and T-cells were established, TAM phenotype characterized by flow analysis and qPCR, and T-cell proliferation assessed by flow.

Results

OPC-conditioned media induced multiple pro-tumor genes including CXCL1, CXCL5, CXCL8, SPP1, IL1B, GPNMB, and FABP5. Patient monocytes had higher baseline levels or achieved higher levels after stimulation than control monocytes. A subset of patient monocytes had high baseline levels of CXCL9/-10/-11 expression that resisted downregulation in response to stimulation, a potential sign of a more favorable TME. CXCL9/-10/-11 expression in OPC tumor biopsies compared to clinically normal tissue correlated with patient outcome. Spheroid TAMs derived from control monocytes maintained the pro-tumor repertoire seen with monocytes stimulated by tumor line conditioned media. These TAMs suppress T-cell proliferation. Inhibition of COX-2 or IL1 signaling during differentiation into TAMs partially blocked the suppression of T-cell proliferation.

Conclusion

Targeting the early transition of monocytes into pro-tumor TAMs could be used to develop new therapies for OPC.

The IFN-high phenotype: A biomarker-driven breakthrough in colorectal cancer treatment

Patient stratification is crucial for improving immunotherapy effectiveness. Acha-Sagredo et al. identified an interferon (IFN)-high immunophenotype and CD74 overexpression as predictors for immunotherapy response in colorectal cancer (CRC). This signature, involving cytotoxic T cells and antigen-presenting macrophages, was found in both mismatch repair-deficient and -proficient CRCs. CD74 overexpression could serve as a biomarker, enabling personalized CRC treatment.

Epigenetic therapy sensitizes anti-PD-1 refractory head and neck cancers to immunotherapy rechallenge

BACKGROUNDImmune checkpoint blockade (ICB) is an effective treatment in a subset of patients diagnosed with head and neck squamous cell carcinoma (HNSCC); however, the majority of patients are refractory.METHODSIn a nonrandomized, open-label Phase 1b clinical trial, participants with recurrent and/or metastatic (R/M) HNSCC were treated with low-dose 5-azacytidine (5-aza) daily for either 5 or 10 days in combination with durvalumab and tremelimumab after progression on ICB. The primary objective was to assess the biologically effective dose of 5-aza as determined by molecular changes in paired baseline and on-treatment tumor biopsies; the secondary objective was safety.RESULTSThirty-eight percent (3 of 8) of participants with evaluable paired tissue samples had a greater-than 2-fold increase from baseline in IFN-γ signature and CD274 (programmed cell death protein 1 ligand, PD-L1) expression within the tumor microenvironment (TME), which was associated with increased CD8+ T cell infiltration and decreased infiltration of CD4+ T regulatory cells. The mean neutrophil-to-lymphocyte ratio (NLR) decreased by greater than 50%, from 14.2 (SD 22.6) to 6.9 (SD 5.2). Median overall survival (OS) was 16.3 months (95% CI 1.9, NA), 2-year OS rate was 24.7% (95% CI: 4.5%, 53.2%), and 58% (7 of 12) of treated participants demonstrated prolonged OS of greater than 12 months.CONCLUSIONOur findings suggest that low-dose 5-aza can reprogram systemic host immune responses and the local TME to increase IFN-γ and PD-L1 expression. The increased expression of these established biomarkers correlated with prolonged OS upon ICB rechallenge.TRIAL REGISTRATIONClinicalTrials.gov NCT03019003.FUNDINGNIH/NCI P01 CA240239.

Targeting HIF-2α in glioblastoma reshapes the immune infiltrate and enhances response to immune checkpoint blockade

Glioblastoma (GBM) is an aggressive primary brain tumor with dismal clinical prognosis and resistance to current therapies. GBM progression is facilitated by the tumor microenvironment (TME), with an immune infiltrate dominated by tumor-associated microglia/macrophages (TAMs) and regulatory T cells (Tregs). The TME is also characterized by hypoxia and the expression of hypoxia-inducible factors (HIFs), with HIF-2α emerging as a potential regulator of tumor progression. However, its role in GBM immunosuppression remains unknown. Here, we investigate HIF-2α and the use of the HIF-2α inhibitor PT2385 to modulate the TME in the immunocompetent GL261 mouse GBM model. PT2385 administration in vivo decreased tumor volume and prolonged survival of tumor-bearing mice, without affecting GL261 viability in vitro. Notably, HIF-2α inhibition alleviated the immunosuppressive TME and synergized with immune checkpoint blockade (ICB) using αPD-1 and αTIM-3 antibodies to promote long-term survival. Comprehensive analysis of the immune infiltrate through single-cell RNA sequencing and flow cytometry revealed that combining PT2385 with ICB reduced numbers of pro-tumoral macrophages and Tregs while increasing numbers of microglia, with a corresponding transcriptional modulation towards an anti-tumoral profile of these TAMs. In vitro, deletion of HIF-2α in microglia impeded their polarization towards a pro-tumoral M2-like profile, and its inhibition impaired Treg migration. Our results show that targeting HIF-2α can switch an immunosuppressive TME towards one that favors a robust and sustained response to ICB based immunotherapy. These findings establish that clinically relevant HIF-2α inhibitors should be explored not only in malignancies with defects in the HIF-2α axis, but also in those exhibiting an immunosuppressive TME that limits immunotherapy responsiveness.

SPP1 macrophages across diseases: A call for reclassification?

SPP1+ macrophages, characterized by elevated expression of the osteopontin gene (secreted phosphoprotein 1, SPP1), have emerged as key players in various pathological contexts, including aging, chronic inflammatory diseases, and cancer. While frequently classified as a subclass of tumor-associated macrophages in oncological settings, their presence in noncancer conditions, such as aging-related disorders and muscular diseases, suggests a broader role beyond tumors. These macrophages share conserved traits, including fibrosis promotion, extracellular matrix remodeling, and immune modulation, often linked to poor clinical outcomes. This perspective explores the multifaceted roles of SPP1+ macrophages across diseases and advocates for their reclassification as a distinct macrophage subtype associated with chronic or prolonged inflammation. Recognizing their cross-disease relevance could reshape macrophage biology and inform targeted therapeutic strategies.

A single fluorescent probe for dual-color imaging and polarity precise analysis in lipid droplets and endoplasmic reticulum

BACKGROUND

Elaborating the subcellular polarity is pivotal for pathophysiological research and early disease diagnosis. Despite its significance, achieving simultaneous two-color fluorescence imaging and quantitative analysis of polarity across multiple organelles remains challenging. This limitation primarily stems from the lack of single fluorescent (SF) probes capable of such precise and multifaceted functionality.

RESULTS

We introduce a novel SF probe LE-TPA, designed for concurrent dual-color imaging and precise polarity determination in lipid droplets (LDs) and the endoplasmic reticulum (ER) under a single excitation. LE-TPA adopts a D-π-A-π-D configuration, which demonstrates highly selective and sensitive fluorescence response to polarity variations in Oleic acid-THF or THF-water mixtures, accompanied with an exceptional linearity (R2 > 0.99) between the max λem and polarity parameter Δf, paving the way for quantitative polarity analysis in live samples. Furthermore, LE-TPA enables simultaneous, real-time imaging of these organelles due to their different water contents, and provides compelling evidence for supporting the hypothesis that LDs derive from the ER. Importantly, LE-TPA effectively identifies polarity differences between healthy and cancerous cells at the subcellular level and allows precise polarity mapping of non-alcoholic fatty liver disease (NAFLD) tissues at different pathological stages.

SIGNIFICANCE

These findings highlight the versatility of probe LE-TPA as a powerful tool for subcellular polarity studies and related disease diagnosis.

NLRP4 unlocks an NK/macrophages-centered ecosystem to suppress non-small cell lung cancer

BACKGROUND

Tumor immune evasion extends beyond T cells, affecting innate immune elements like natural killer cells (NK) and macrophages within the tumor-immune microenvironment (TIME). Nevertheless, translational strategies to trigger collaboration of NK cells and macrophages to initiate sufficient anti-tumor cytoxicity remain scarce and are urgently needed.

METHODS

In this study, TCGA datasets was used to confirm the prognosis value of the expression level of NLR family pyrin domain containing 4 (NLRP4) in NSCLC and the tumor tissues microarray was used to further check its clinical-relevance at protein-level. Subsequently, a tumor cell line with stable NLRP4 overexpression was established and subcutaneous tumor models in C57BL/6J mice were used to validate the anti-tumor characteristics of NLRP4. After analyzing the tumor microenvironment using flow cytometry and multiplex immunofluorescence, we further validated our findings through co-culture transwell assays and TCGA analysis. Utilizing bulk-RNA sequencing, proteomics, and mass spectrometry of mouse tumor tissues, we innovatively identified the downstream pathways of NLRP4 and verified them through co-immunoprecipitation (co-IP) and Western blot (WB) experiments.

RESULTS

NLRP4 could trigger a distinct anti-tumor ecosystem organized by TIGIT+TNFA+ NK and iNOS+ M1 in lung cancer, discovered in TCGA analysis and verified in murine model. NLRP4-eco exerted tumor-suppression capacity through chemokine reprogramming including CCL5 and CXCL2. Meanwhile, the cytoxicity of NK could be facilitated by iNOS+M1. Mechanistically, NLRP4 stimulated PI3K/Akt-NF-kB axis through suppression of the activity of PP2A. Besides, knockdown of CCL5 and blockade of CXCL2-CXCR2 axis abolished chemotaxis of TIGIT+TNFA+ NK and iNOS+ M1 respectively, as well as for LB-100, a PP2A inhibitor.

CONCLUSION

Altogether, we delineated NLRP4's unexplored facets and discovered an NLRP4-driven anti-tumor ecosystem composed of TIGIT+TNFA+ NK and iNOS+ M1. Finally, targeting PP2A by its inhibitor successfully mimicked the anti-tumor capacity of the overexpression of NLRP4.

Blocking ITGA5 potentiates the efficacy of anti-PD-1 therapy on glioblastoma by remodeling tumor-associated macrophages

BACKGROUND

Glioblastoma (GBM) is largely refractory to antibodies against programmed cell death 1 (anti-PD-1) therapy. Fully understanding the cellular heterogeneity and immune adaptations in response to anti-PD-1 therapy is necessary to design more effective immunotherapies for GBM. This study aimed to dissect the molecular mechanisms of specific immunosuppressive subpopulations to drive anti-PD-1 resistance in GBM.

METHODS

We systematically analysed single-cell RNA sequencing and spatial transcriptomics data from GBM tissues receiving anti-PD-1 therapy to characterize the microenvironment alterations. The biological functions of a novel circular RNA (circRNA) were validated both in vitro and in vivo. Mechanically, co-immunoprecipitation, RNA immunoprecipitation and pull-down assays were conducted.

RESULTS

Mesenchymal GBM (MES-GBM) cells, which were associated with a poor prognosis, and secreted phosphoprotein 1 (SPP1)+ myeloid-derived macrophages (SPP1+ MDMs), a unique subpopulation of MDMs with complex functions, preferentially accumulated in non-responders to anti-PD-1 therapy, indicating that MES-GBM cells and SPP1+ MDMs were the main anti-PD-1-resistant cell subpopulations. Functionally, we determined that circular RNA succinate dehydrogenase complex assembly factor 2 (circSDHAF2), which was positively associated with the abundance of these two anti-PD-1-resistant cell subpopulations, facilitated the formation of a regional MES-GBM and SPP1+ MDM cell interaction loop, resulting in a spatially specific adaptive immunosuppressive microenvironment. Mechanically, we found that circSDHAF2 promoted MES-GBM cell formation by stabilizing the integrin alpha 5 (ITGA5) protein through N-glycosylation. Meanwhile, the N-glycosylation of the ITGA5 protein facilitated its translocation into exosomes and subsequent delivery to MDMs to induce the formation of SPP1+ MDMs, which in turn maintained the MES-GBM cell status and induced T-cell dysfunction via the SPP1-ITGA5 pathway, ultimately promoting GBM immune escape. Importantly, our findings demonstrated that antibody-mediated ITGA5 blockade enhanced anti-PD-1-mediated antitumor immunity.

CONCLUSIONS

This work elucidated the potential tissue adaptation mechanism of intratumoral dynamic interactions between MES-GBM cells, MDMs and T cells in anti-PD-1 non-responders and identified the therapeutic potential of targeting ITGA5 to reduce anti-PD-1 resistance in GBM.

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

BACKGROUND

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

METHODS

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

RESULTS

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

CONCLUSIONS

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

Multi-omics and machine learning-driven CD8+ T cell heterogeneity score for head and neck squamous cell carcinoma

The heterogeneity of head and neck squamous cell carcinoma (HNSCC) poses a significant challenge to treatment, underscoring the urgent need for more precise and personalized therapeutic approaches. CD8+ T cells, integral components of the tumor immune microenvironment, have emerged as key targets for immunotherapy. Our research has established a correlation between a decrease in CD8+ T cell score and a poor clinical prognosis, highlighting the prognostic value of this biomarker. By analyzing the gene expression related to CD8+ T cells, we have differentiated HNSCC into cold and hot tumor subtypes, uncovering disparities in clinical prognosis and responses to immunotherapy. Utilizing eight machine learning methods, we identified the key gene OLR1. Single-cell analysis of HNSCC tissues and peripheral blood, along with spatial transcriptome analysis, revealed that OLR1 predominantly functions in macrophages, modulating the immune microenvironment of HNSCC. The expression level of OLR1 may serve as a predictive marker for immunotherapy responses. Moreover, drug sensitivity analysis and molecular docking studies have indicated that simvastatin and pazopanib are potential inhibitors of OLR1. These findings suggest that simvastatin and pazopanib could open up innovative potential therapeutic avenues for individuals with HNSCC.

Targeted nanoparticle delivery system for tumor-associated macrophage reprogramming to enhance TNBC therapy

Triple-negative breast cancer (TNBC) poses as a daunting and intricate manifestation of breast cancer, highlighted by few treatment options and a poor outlook. The crucial element in fostering tumor growth and immune resistance is the polarization of tumor-associated macrophages (TAMs) into the M2 state within the tumor microenvironment (TME). To address this, we developed M2 targeting peptide-chitosan-curcumin nanoparticles (M2pep-Cs-Cur NPs), a targeted delivery system utilizing chitosan (Cs) as a carrier, curcumin (Cur) as a therapeutic agent, and targeting peptides for specificity. These NPs effectively inhibited TNBC cell proliferation (~ 70%) and invasion (~ 70%), while increasing the responsiveness of tumors to anti-PD-L1 treatment (~ 50% survival enhancement) in vitro and in vivo. Bioinformatics analysis suggested that Cur modulates TAM polarization by influencing key genes such as COX-2, offering insights into its underlying mechanisms. This study highlights the potential of M2pep-Cs-Cur NPs to reverse M2 polarization in TAMs, providing a promising targeted therapeutic strategy to overcome immunotherapy resistance and improve TNBC outcomes.

Cxcl9-deficiency attenuates the progression of post-traumatic osteoarthritis in mice

OBJECTIVE

Osteoarthritis (OA) is one of the leading causes of disability in the aging population. While about 10% of the adult population is affected by OA, there is to date no curative treatment and joint replacement surgery remains the only option for treating end-stage OA. Previous studies found elevated levels of the chemokine C-X-C motif ligand 9 (CXCL9) in the synovial fluid of OA knees. However, the exact role of CXCL9 in OA progression is still unknown.

METHODS

Female wild-type and Cxcl9-deficient mice were challenged with a unilateral anterior cruciate ligament transection (ACLT). Joint destruction in early and late stages of experimental OA was assessed using micro-CT scanning, histological scoring, histomorphometry, and gene expression analysis.

RESULTS

Inactivation of Cxcl9 protected from cartilage destruction and osteophyte formation in post-traumatic OA in mice. Similarly, indices of joint inflammation including synovitis and expression of pro-inflammatory interleukin-1beta were reduced in OA knees of Cxcl9-deficient mice. However, bone erosion and pathophysiological changes in the subchondral bone compartment remained unaffected in Cxcl9-deficient mice with experimental OA.

CONCLUSION

Our results point towards a pro-inflammatory role of CXCL9 in OA and identify a potential new target for the pharmacological treatment of OA.

A highly resolved integrated single-cell atlas of HPV-negative head and neck cancer

Head and Neck Squamous Cell Carcinomas (HNSCC) are the seventh most prevalent form of cancer and are associated with human papilloma virus infection (HPV-positive) or with tobacco and alcohol use (HPV-negative). HPV-negative HNSCCs have a high recurrence rate, and individual patients' responses to treatment vary greatly due to the high level of cellular heterogeneity of the tumor and its microenvironment. Here, we describe a HNSCC single cell atlas, which we created by integrating six publicly available datasets encompassing over 230,000 cells across 54 patients. We contextualized the relationships between existing signatures and cell populations, identified new subpopulations, and show the power of this large-scale resource to robustly identify associations between transcriptional signatures and clinical phenotypes that would not be possible to discover using fewer patients. We reveal a previously undefined myeloid population, sex-associated changes in cell type proportions, and novel interactions between CXCL8-positive fibroblasts and vascular endothelial cells. Beyond our findings, the atlas will serve as a public resource for the high-resolution characterization of tumor heterogeneity of HPV-negative HNSCC.

Innate Immunity and Asthma Exacerbations: Insights From Human Models

Asthma is a common chronic respiratory disease characterized by the presence of airway inflammation, airway hyperresponsiveness, and mucus hypersecretion. Repeated asthma exacerbations can lead to progressive airway remodeling and irreversible airflow obstruction. Thus, understanding and preventing asthma exacerbations are of paramount importance. Although multiple endotypes exist, asthma is most often driven by type 2 airway inflammation. New therapies that target specific type 2 mediators have been shown to reduce the frequency of asthma exacerbations but are incompletely effective in a significant number of asthmatics. Furthermore, it remains unknown whether current treatments lead to sustained changes in the airway or if targeting additional pathways may be necessary to achieve asthma remission. Activation of innate immunity is the initial event in the inflammatory sequence that occurs during an asthma exacerbation. However, there continue to be critical gaps in our understanding of the innate immune response to asthma exacerbating factors. In this review, we summarize the current understanding of the role of innate immunity in asthma exacerbations and the methods used to study them. We also identify potential novel therapeutic targets for asthma and future areas for investigation.

Profiling immune cell tissue niches in the spatial -omics era

Immune responses require complex, spatially coordinated interactions between immune cells and their tissue environment. For decades, we have imaged tissue sections to visualize a limited number of immune-related macromolecules in situ, functioning as surrogates for cell types or processes of interest. However, this inevitably provides a limited snapshot of the tissue's immune landscape. Recent developments in high-throughput spatial -omics technologies, particularly spatial transcriptomics, and its application to human samples has facilitated a more comprehensive understanding of tissue immunity by mapping fine-grained immune cell states to their precise tissue location while providing contextual information about their immediate cellular and tissue environment. These data provide opportunities to investigate mechanisms underlying the spatial distribution of immune cells and its functional implications, including the identification of immune niches, although the criteria used to define this term have been inconsistent. Here, we review recent technological and analytic advances in multiparameter spatial profiling, focusing on how these methods have generated new insights in translational immunology. We propose a 3-step framework for the definition and characterization of immune niches, which is powerfully facilitated by new spatial profiling methodologies. Finally, we summarize current approaches to analyze adaptive immune repertoires and lymphocyte clonal expansion in a spatially resolved manner.

Tumor and blood B-cell abundance outperforms established immune checkpoint blockade response prediction signatures in head and neck cancer

BACKGROUND

Immunotherapy has improved the outcomes for some patients with head and neck squamous-cell carcinoma (HNSCC). However, the low and variable response rates observed highlight the need for robust response biomarkers to select patients for treatment.

PATIENTS AND METHODS

We assembled and analyzed a large HNSCC dataset, encompassing 11 clinical cohorts including 1232 patient samples, spanning a variety of disease subtypes and immune checkpoint blockade (ICB) treatment types, tissue sources, data modalities, and timing of measurements. We conducted a comprehensive evaluation of the predictive power of various cell types, traditional biomarkers, and emerging predictors in both blood and tumor tissues of HNSCC patients.

RESULTS

Tumor B-cell infiltration emerged as a strong and robust predictor of both patient survival and ICB response. It outperformed all other established biomarkers of response to ICB, including the tertiary lymphoid structure signature and numerous T-cell-based signatures. B-cell infiltration was associated with a 'hot' antitumor microenvironment that promotes tumor eradication. Furthermore, B-cell levels in peripheral blood mononuclear cells (PBMCs) correlated strongly with tumor B-cell levels and demonstrated high predictive value for ICB response, with high odds ratios (≥7.8) in two independent clinical cohorts.

CONCLUSION

B-cell abundance, whether assessed in PBMCs or tumor tissues, is one of the strongest predictors of ICB response in HNSCC. For translation to patient care, measuring B-cell abundance in PBMCs via cytometry offers a practical and accessible tool for clinical decision making.

Lymphocytes-Associated Extracellular Vesicles Activate Natural Killer Cells in HNSCC

Small extracellular vesicles (sEVs) facilitate intercellular communication and play a pivotal role in tumor progression. Accumulated evidence has indicated the diversity of sEVs but with limited results revealing the landscape of heterogeneity of sEVs. The heterogeneity of cargo RNA in sEVs presents the different cell origins and indicates different functions. Here, we analyzed the heterogeneity of sEVs at droplet levels from single-cell RNA sequencing results of head and neck squamous cell carcinoma (HNSCC) with the previously reported algorithm SEVtras. With the sEVs secretion activity calculated by SEVtras, we also found that the T cells held the major role of sEVs secretion. In addition, we found these sEVs secreted by T cells increased the cytotoxic ability of natural killer cells (NK cells), which illustrated an indirect manner for the anti-tumor function of T cells. These results revealed the heterogeneity of cargo RNA of sEVs in HNSCC and underlined a sEVs-dependent manner in which T cells act on NK cells and anti-tumor immunity.

Primary and Acquired Resistance to Immunotherapy with Checkpoint Inhibitors in NSCLC: From Bedside to Bench and Back

Immunotherapy with checkpoint inhibitors has become the cornerstone of systemic treatment for non-oncogene addicted non-small-cell lung cancer. Despite its pivotal role, a significant proportion of patients-approximately 70-85%-either exhibit primary resistance to PD-1 blockade or develop acquired resistance following an initial benefit, even in combination with chemotherapy and/or anti-CTLA-4 agents. The phenomenon of primary and acquired resistance to immunotherapy represents a critical clinical challenge, largely based on our incomplete understanding of the mechanisms of action of immunotherapy, and the resulting lack of accurate predictive biomarkers. Here, we review the definitions and explore the proposed mechanisms of primary and acquired resistance, including those related to the tumor microenvironment, systemic factors, and intrinsic tumor characteristics. We also discuss translational data on adaptive changes within tumor cells and the immune infiltrate following exposure to checkpoint inhibitors. Lastly, we offer a comprehensive overview of current and emerging therapeutic strategies designed to prevent primary resistance and counteract acquired resistance.

High-dimensional deconstruction of HNSC reveals clinically distinct cellular states and ecosystems that are associated with prognosis and therapy response

BACKGROUND

Characterizing the variety of cell types in the tumor microenvironment (TME) and their organization into cellular communities is vital for elucidating the biological diversity of cancer and informing therapeutic strategies.

METHODS

Here, we employed a machine learning-based algorithm framework, EcoTyper, to analyze single-cell transcriptomes from 139 patients with head and neck squamous cell carcinoma (HNSC)and gene expression profiles from 983 additional HNSC patients, aiming to delineate the fundamental cell states and ecosystems integral to HNSC.

RESULTS

A diverse landscape of 66 cell states and 9 ecosystems within the HNSC microenvironment was identified, revealing classical cell types while also expanding upon previous immune classifications. Survival analysis revealed that specific cell states and ecotypes (ecosystems) are associated with patient prognosis, underscoring their potential as indicators of clinical outcomes. Moreover, distinct cell states and ecotypes exhibited varying responses to immunotherapy and chemotherapy, with several showing promise as predictive biomarkers for treatment efficacy.

CONCLUSION

Our large-scale integrative transcriptome analysis provides high-resolution insights into the cellular states and ecosystems of HNSC, facilitating the discovery of novel biomarkers and supporting the development of precision therapies.

Ligand-receptor interactions combined with histopathology for improved prognostic modeling in HPV-negative head and neck squamous cell carcinoma

Head and neck squamous cell carcinoma (HNSC) is a prevalent malignancy, with HPV-negative tumors exhibiting aggressive behavior and poor prognosis. Understanding the intricate interactions within the tumor microenvironment (TME) is crucial for improving prognostic models and identifying therapeutic targets. Using BulkSignalR, we identified ligand-receptor interactions in HPV-negative TCGA-HNSC cohort (n = 395). A prognostic model incorporating 14 ligand-receptor pairs was developed using random forest survival analysis and LASSO-penalized Cox regression based on overall survival and progression-free interval of HPV-negative tumors from TCGA-HNSC. Multi-omics analysis revealed distinct molecular features between risk groups, including differences in extracellular matrix remodeling, angiogenesis, immune infiltration, and APOBEC enzyme activity. Deep learning-based tissue morphology analysis on HE-stained whole slide images further improved risk stratification, with region selection via Silicon enhancing accuracy. The integration of routine histopathology with deep learning and multi-omics data offers a clinically accessible tool for precise risk stratification, facilitating personalized treatment strategies in HPV-negative HNSC.

Spatial transcriptomic analysis of tumor microenvironment in esophageal squamous cell carcinoma with HIV infection

BACKGROUND

Human Immunodeficiency Virus (HIV) is one of the most prevalent viruses, causing significant immune depletion in affected individuals. Current treatments can control HIV and prolong patients' lives, but new challenges have emerged. Increasing incidence of cancers occur in HIV patients. Esophageal squamous cell carcinoma (ESCC) is one of the most common cancers observed in HIV patients. However, the spatial cellular characteristics of HIV-related ESCC have not been explored, and the differences between HIV-ESCC and typical ESCC remain unclear.

METHODS

We performed spatial transcriptome sequencing on HIV-ESCC samples to depict the microenvironment and employed cell communication analysis and multiplex immunofluorescence to investigate the molecular mechanism in HIV-ESCC.

RESULTS

We found that HIV-ESCC exhibited a unique cellular composition, with fibroblasts and epithelial cells intermixed throughout the tumor tissue, lacking obvious spatial separation, while other cell types were sparse. Besides, HIV-ESCC exhibited an immune desert phenotype, characterized by a low degree of immune cell infiltration, with only a few SPP1+ macrophages showing immune resistance functions. Cell communication analysis and multiplex immunofluorescence staining revealed that tumor fibroblasts in HIV-ESCC interact with CD44+ epithelial cells via COL1A2, promoting the expression of PIK3R1 in epithelial cells. This interaction activates the PI3K-AKT signaling pathway, which contributes to the progression of HIV-ESCC.

CONCLUSIONS

Our findings depict the spatial microenvironment of HIV-ESCC and elucidate a molecular mechanism in the progression of HIV-ESCC. This will provide us insights into the molecular basis of HIV-ESCC and potential treatment strategies.

Integrated analysis of single-cell and bulk transcriptomics reveals cellular subtypes and molecular features associated with osteosarcoma prognosis

BACKGROUND

Osteosarcoma (OS) is the most common primary bone malignancy with variable molecular biology and prognosis. However, our understanding of the association between cell types and OS progression remains poor.

METHODS

We generated a human OS cell atlas by integrating over 110,000 single cells from 17 samples. Multiple machine learning algorithms were applied to develop tumor purity prediction models based on transcriptomic profile of OS. The Scissor algorithm and gene enrichment analyses were conducted to delve into cell-intrinsic molecular characteristics linked to OS prognosis. Moreover, the study investigated the impact of ATF6α in OS aggressiveness through genetic and pharmacological loss of function analyses. Lastly, the CellChat algorithm was employed to investigate cell-cell communications.

RESULTS

Utilizing the high-quality human OS cell atlas, we identified tumor purity as a prognostic indicator and developed a robust tumor purity prediction model. We respectively delineated cancer cell- and immune cell-intrinsic molecular characteristics associated with OS prognosis at single-cell resolution. Interestingly, tumor cells with activated unfolded protein response (UPR) pathway were significantly associated with disease aggressiveness. Notably, ATF6α emerged as the top-activated transcription factor for this tumor subcluster. Subsequently, we confirmed that ATF6α was markedly associated with OS progression, while both genetic and pharmacological inhibition of ATF6α impaired the survival of HOS cells. Lastly, we depicted the landscape of signal crosstalk between the UPR-related subcluster and other cell types within the tumor microenvironment.

CONCLUSION

In summary, our work provides novel insights into the molecular biology of OS, and offers valuable resource for OS biomarker discovery and treatment strategy development.

Optimizing a 5-factor cocktail to prepare reparative macrophages for wound healing

The treatment of nonhealing wounds, such as diabetic ulcers, remains a critical clinical challenge. Recent breakthroughs in cell therapy have shown great promise, with one primary focus on preparing cells with comprehensive reparative functions and foreseeable safety. In our previous study, we recapitulated the proregenerative and immunosuppressive functions of tumor-associated macrophages in non-tumor-derived macrophages, endowing the latter with characteristics for promoting diabetic wound healing-termed tumor-associated macrophage-educated macrophages. To eliminate the use of tumor-derived sources and devise a more controllable method to prepare tumor-associated macrophage-educated macrophage-like cells, in this study, we identify a cocktail comprising 5 recombinant proteins as an essential condition to induce nonpolarized macrophages into therapeutic cells with prohealing functions. The screened 5 factors are osteopontin, macrophage inflammatory protein 2, chemokine (C-C motif) ligand 8, vascular endothelial growth factor B, and macrophage colony-stimulating factor. We demonstrate the rationale for screening these factors and the phenotype of the 5 factor-induced tumor-associated macrophage-educated macrophage-like macrophages prepared from murine bone marrow-derived macrophages, which exhibit angiogenic and immunomodulatory effects in vitro. Then, we induce primary human monocytes from periphery blood into the 5 factor-induced tumor-associated macrophage-educated macrophage-like macrophages, which show prohealing effects in a human primary cell-based ex vivo model (T-Skin™). Our study demonstrates a simple, effective, and controllable approach to induce primary macrophages to possess repairing activities, which may provide insights for developing cell-based therapeutics for nonhealing wounds clinically.

STAT3-controlled CHI3L1/SPP1 positive feedback loop demonstrates the spatial heterogeneity and immune characteristics of glioblastoma

Proneural-mesenchymal transition (PMT) is a phenotypic alteration and contributes to the malignant progression of glioblastoma (GBM). Macrophages, as a main infiltrating component of the tumor immune microenvironment (TIM), control the biological processes of PMT; however, the mechanisms driving this process remain largely unknown. Here, the overall landscape of tumor and nontumor cells was described by scMulti-omics technology. Then, we demonstrated that chitinase-3-like protein 1 (CHI3L1) played a critical role in maintaining mesenchymal (MES) status and reprogramming macrophage phenotype using C57BL/6 and NSG mice models derived from PN20 cells. Mechanistically, osteopontin (OPN)/ITGB1 maintained the activation of nuclear factor κB (NF-κB) and signal transducer and activator of transcription 3 (STAT3) pathways by establishing a positive feedback loop with the CHI3L1-STAT3 axis, resulting in PMT. CHI3L1 enhanced the phosphorylation, nuclear localization, and transcriptional activity of STAT3 via directly binding its coiled-coil domain (CCD). Importantly, we screened and validated that hygromycin B (HB), an inhibitor of the STAT3-CCD domain, disrupted the CHI3L1-STAT3 interaction, thereby reducing the tumor burden in vitro and in vivo.

VSIG4+ tumor-associated macrophages mediate neutrophil infiltration and impair antigen-specific immunity in aggressive cancers through epigenetic regulation of SPP1

V-set and immunoglobulin domain-containing 4 (VSIG4) positive tumor-associated macrophage (VSIG4+ TAM) is an immunosuppressive subpopulation newly identified in aggressive cancers. However, the mechanism how VSIG4+ TAMs mediate immune evasion in aggressive cancers have not been fully elucidated. In our study, we found targeting VSIG4+ TAMs by VSIG4 deficiency or blockade remarkably limited tumor growth and metastasis, especially those derived from anaplastic thyroid cancer (ATC) and pancreatic cancer, two extremely aggressive types. Moreover, the combination of VSIG4 blockade with a BRAF inhibitor synergistically enhanced anti-tumor activity in ATC-tumor bearing mice. VSIG4 deficiency recovered the antigen presentation (B2m, H2-k1, H2-d1) of TAMs and activated antigen-specific CD8+ T cells by promoting their in vivo proliferation and intratumoral infiltration. Notably, loss of VSIG4 in TAMs significantly reduced the production of lactate and histone H3 lysine 18 lactylation, resulting the decreased transcription of SPP1 mediated by STAT3, which collectively disrupted the cell-cell interactions between TAMs and neutrophils. Further combination of VSIG4 with SPP1 blockade synergistically boosted anti-tumor activity. Overall, our studies demonstrate the epigenetic regulation function of VSIG4 confers on TAMs an alternative pattern, beyond the checkpoint role of VSIG4, to shape the immunosuppressive tumor microenvironment and impair antigen-specific immunity against aggressive cancers.

CAF-macrophage crosstalk in tumour microenvironments governs the response to immune checkpoint blockade in gastric cancer peritoneal metastases

BACKGROUND

Peritoneal metastasis is the most common metastasis pattern of gastric cancer. Patients with gastric cancer peritoneal metastasis (GCPM) have a poor prognosis and respond poorly to conventional treatments. Recently, immune checkpoint blockade (ICB) has demonstrated favourable efficacy in the treatment of GCPM. Stratification of best responders and elucidation of resistance mechanisms of ICB therapies are highly important and remain major clinical challenges.

DESIGN

We performed a phase II trial involving patients with GCPM treated with ICB (sintilimab) combined with chemotherapy. The samples of primary tumours, GCPMs and peripheral blood from patients were collected for single-cell sequencing to comprehensively interpret the tumour microenvironment of GCPM and its impacts on immunotherapy efficacy.

RESULTS

The GCPM ecosystem coordinates a unique immunosuppressive pattern distinct from that of primary GC, which is dominated by a stroma-myeloid niche composed of SPP1+tumour-associated macrophages (TAMs) and Thrombospondin 2 (THBS2)+matrix cancer-associated fibroblasts (mCAFs). Consequently, this stroma-myeloid crosstalk is the major mediator of ICB resistance in patients with GCPM. Mechanistically, the accumulated THBS2+mCAFs facilitate the recruitment of peritoneum-specific tissue-resident macrophages and their transformation into SPP1+TAMs via the complement C3 and its receptor C3a receptor 1 (C3AR1), thereby forming a protumoral stroma-myeloid niche. Blocking the C3-C3AR1 axis disrupts the stroma-myeloid crosstalk and thereby significantly improves the benefits of ICB in in vivo models.

CONCLUSION

Our findings provide a new molecular portrait of cell compositions associated with ICB resistance in patients with GCPM and aid in the prioritisation of therapeutic candidates to potentiate immunotherapy.

Identification and validation of SPP1 as a potential biomarker for COPD through comprehensive bioinformatics analysis

BACKGROUND

Chronic Obstructive Pulmonary Disease (COPD) is a challenging respiratory condition characterized by persistent airflow limitation and progressive lung function decline. The identification of robust biomarkers is crucial for early diagnosis, monitoring disease progression, and guiding therapeutic strategies.

METHODS

In this study, we employed a comprehensive bioinformatics approach utilizing multiple Gene Expression Omnibus (GEO) datasets to identify potential COPD biomarkers. Differentially expressed genes (DEGs) were identified from GSE38974 and GSE76925, and Weighted Gene Co-expression Network Analysis (WGCNA) on GSE76925 revealed significant gene modules associated with COPD traits.

RESULTS

Integrative analysis highlighted five candidate genes, with Secreted Phosphoprotein 1 (SPP1) emerging as a promising biomarker. SPP1 exhibited consistent negative correlations with lung function parameters in human datasets (GSE103174) and significant upregulation in COPD-relevant animal models (GSE36174 and GSE52509). Moreover, SPP1 levels were elevated across various respiratory samples, including alveolar epithelium, alveolar macrophages, sputum, and lung tissue, from COPD patients.

CONCLUSION

These findings highlight the potential of SPP1 as a diagnostic and prognostic biomarker for COPD, emphasizing the need for further investigation into its role in COPD pathogenesis and its effectiveness in clinical applications.

Single-Cell and Spatial Transcriptomics Delineate the Microstructure and Immune Landscape of Intrahepatic Cholangiocarcinoma in the Leading-Edge Area

Intrahepatic cholangiocarcinoma (ICC) tumor cells and their interactions with the immune microenvironment, particularly at the leading-edge area, have been underexplored. This study employs single-cell RNA sequencing (scRNA-seq) and spatial transcriptome (ST) analysis on samples from the tumor core, adjacent non-tumorous tissue, and the leading-edge area of nine ICC patients. These findings indicate that tumor cells at the leading-edge area demonstrate enhanced proliferation and are tightly associated with the stroma, including endothelial cells and POSTN+ FAP+ fibroblasts. Notably, CD8+ T cells in this region exhibit a naive phenotype with low cytotoxicity and signs of exhaustion, likely due to compromised antigen presentation by antigen-presenting cells (APCs). The predominant CD8+ T cell subset, mucosal-associated invariant T (MAIT) cells, recruits SPP1+ macrophages within the stroma. This interaction, along with the presence of POSTN+ cancer-associated fibroblasts (CAFs) and endothelial cells, forms a unique "triad structure" that fosters tumor growth and ICC progression. The research highlights the intricate characteristics and interactions of ICC tumor cells in the leading-edge area, offering insights into potential therapeutic targets for intervention.

Large-scale transcript variants dictate neoepitopes for cancer immunotherapy

Precise neoepitope discovery is crucial for effective cancer therapeutic vaccines. Conventional approaches struggle to build a repertoire with sufficient immunogenic epitopes. We developed a workflow leveraging full-length ribosome-nascent chain complex-bound mRNA sequencing (FL-RNC seq) and artificial intelligence-based predictive models to accurately identify the neoepitope landscape, especially large-scale transcript variants (LSTVs) missed by short-read sequencing. In the MC38 mouse model, we identified 22 LSTV-derived neoepitopes encoded by a synthesized mRNA lipid nanoparticle vaccine. As a standalone therapy and combined with anti-PD-1 immunotherapy, the vaccine curbed tumor progression, induced robust T cell-specific immunity, and modulated the tumor microenvironment. This underscores the multifaceted potentials of LSTV-derived vaccines. Our approach expands the neoepitope source repertoire, offering a method for discovering personalized cancer vaccines applicable to a broader tumor range. The results highlight the importance of comprehensive neoepitope identification and the promise of LSTV-based vaccines for cancer immunotherapy.

Genetic variation in IL-4 activated tissue resident macrophages determines strain-specific synergistic responses to LPS epigenetically

How macrophages in the tissue environment integrate multiple stimuli depends on the genetic background of the host, but this is still poorly understood. We investigate IL-4 activation of male C57BL/6 and BALB/c strain specific in vivo tissue-resident macrophages (TRMs) from the peritoneal cavity. C57BL/6 TRMs are more transcriptionally responsive to IL-4 stimulation, with induced genes associated with more super enhancers, induced enhancers, and topologically associating domains (TAD) boundaries. IL-4-directed epigenomic remodeling reveals C57BL/6 specific enrichment of NF-κB, IRF, and STAT motifs. Additionally, IL-4-activated C57BL/6 TRMs demonstrate an augmented synergistic response upon in vitro lipopolysaccharide (LPS) exposure, despite naïve BALB/c TRMs displaying a more robust transcriptional response to LPS. Single-cell RNA sequencing (scRNA-seq) analysis of mixed bone marrow chimeras indicates that transcriptional differences and synergy are cell intrinsic within the same tissue environment. Hence, genetic variation alters IL-4-induced cell intrinsic epigenetic reprogramming resulting in strain specific synergistic responses to LPS exposure.

Mitochondrial respiratory complex III sustains IL-10 production in activated macrophages and promotes tumor-mediated immune evasion

The cytokine interleukin-10 (IL-10) limits the immune response and promotes resolution of acute inflammation. Because of its immunosuppressive effects, IL-10 up-regulation is a common feature of tumor progression and metastasis. Recently, IL-10 regulation has been shown to depend on mitochondria and redox-sensitive signals. We have found that Suppressor of site IIIQo Electron Leak 1.2 (S3QEL 1.2), a specific inhibitor of reactive oxygen species (ROS) production from mitochondrial complex III, and myxothiazol, a complex III inhibitor, decrease IL-10 in lipopolysaccharide (LPS)-activated macrophages. IL-10 down-regulation is likely to be mediated by suppression of c-Fos, which is a subunit of activator protein 1 (AP1), a transcription factor required for IL-10 gene expression. S3QEL 1.2 impairs IL-10 production in vivo after LPS challenge and promotes the survival of mice bearing B16F10 melanoma by lowering tumor growth. Our data identify a link between complex III-dependent ROS generation and IL-10 production in macrophages, the targeting of which could have potential in boosting antitumor immunity.

Genetically Defined Organoid Models Reveal Mechanisms Driving Squamous Cell Neoplastic Evolution and Identify Potential Therapeutic Vulnerabilities

Upper aerodigestive squamous cell carcinoma (UASCC) is an aggressive and lethal neoplasm, with its early neoplastic transformation mechanisms remaining poorly understood. Here, we characterize over 25 genetically-defined organoid models derived from murine and human oral/esophageal tissues harboring key driver mutations. Double knockout of TP53 and CDKN2A induced morphological dysplasia, hyperproliferation, loss of squamous differentiation, and tumorigenicity, which were further exacerbated by additional driver mutations (e.g., PIK3CA, NOTCH1, KMT2C). Single-cell analysis revealed an expansion of quiescent basal cells and proliferative squamous cells, alongside a loss of differentiated squamous cells during malignant transformation. A distinct senescence program, regulated by ANXA1, was markedly diminished during early neoplastic evolution. Mechanistically, the ANXA1-SMAD3-p27KIP1 pathway was identified as a critical regulator of this senescence program, acting to suppress neoplastic features in organoid models. Lastly, our high-throughput, single-organoid-resolution drug screens unexpectedly revealed PIK3CA-driven organoids exhibited sensitivity to Mitomycin C and Onalespib. This study provides novel mechanistic insights into early neoplastic evolution and underscores the value of genetically-defined organoid models for investigating cancer biology and identifying targeted therapies.

TREM2 promotes the formation of a tumor-supportive microenvironment in hepatocellular carcinoma

BACKGROUND

Triggering receptor expressed on myeloid cells 2 (TREM2), a surface receptor predominantly expressed on myeloid cells, is a major hub gene in pathology-induced immune signaling. However, its function in hepatocellular carcinoma (HCC) remains controversial. This study aimed to evaluate the role of TREM2 in the tumor microenvironment in the context of HCC progression.

METHODS

HCC was experimentally induced in wild-type (WT) and Trem2-deficient (Trem2-/-) mice, and clinical sample analysis and in vitro studies on macrophages were conducted. HCC cells were treated with conditioned medium from WT or Trem2-/- macrophages, and their malignant phenotypes and underlying mechanisms were analyzed.

RESULTS

TREM2 deficiency reduced liver tumor burden in orthotopic and subcutaneous HCC models by altering CD8+ T cell infiltration. Trem2-deficient macrophages presented increased chemokine secretion. TGF-β1 was found to be positively correlated with TREM2 expression in HCC, and TGF-β blockade reversed TREM2 induction. On the other hand, TREM2+ macrophages were found to be associated with glycolysis and PKM2 expression in HCC cells; this association may be related to the secretion of IL-1β, which enhances the malignant phenotypes of HCC cells.

CONCLUSIONS

These results reveal that TREM2+ macrophages play a driving role in HCC progression by suppressing CD8+ T cell infiltration and promoting tumor cell glycolysis, providing a new therapeutic target for HCC.

HPV integration in head and neck cancer: downstream splicing events and expression ratios linked with poor outcomes

HPV integration (HPVint) is associated with carcinogenesis and tumor progression in HPV-associated cancers, including head and neck squamous cell carcinomas (HNSCC). While its impact on human DNA has been well characterized, its relationship with clinical outcomes remains unconfirmed. Here we investigate the consequences of HPVint both with respect to human and HPV characteristics by analyzing 261 HPV-associated HNSCC bulk and single-cell RNA-seq samples from five cohorts, and DNA HPVint events from 102 HPV+ participants in two of the cohorts. By leveraging this large meta-cohort, we first reveal an oncogenic network based on the recurrent HPV integration locations in HNSCC. We then classify HPVint-positive (HPVint(+)) participants by HPV RNA features, specifically based on spliced HPV-human fusion transcripts and ratios of HPV gene transcripts, showing that subsets of participants have worse clinical outcomes. Our analyses, focused mainly on RNA instead of DNA, expand our understanding of the carcinogenic mechanisms of HPVint, partially addressing the conflicting findings of whether HPVint is associated with aggressive phenotypes and worse clinical consequences, and provide potential biomarkers to advance precision oncology in HPV-associated HNSCC.

Deciphering SPP1-related macrophage signaling in the pathogenesis of intervertebral disc degeneration

This study delved into the molecular mechanisms underlying mechanical stress-induced intervertebral disc degeneration (msi-IDD) through single-cell and high-throughput transcriptome sequencing in mouse models and patient samples. Results exhibited an upsurge in macrophage presence in msi-IDD intervertebral disc (IVD) tissues, with secreted phosphoprotein 1 (SPP1) identified as a pivotal driver exacerbating degeneration via the protein kinase RNA-like endoplasmic reticulum kinase/ activating transcription factor 4/ interleukin-10 (PERK/ATF4/IL-10) signaling axis. Inhibition of SPP1 demonstrated promising outcomes in mitigating msi-IDD progression in both in vitro and in vivo models. These findings underscore the therapeutic promise associated with the modulation of the PERK signaling pathway in IDD, shedding light on the pathogenesis of msi-IDD and proposing a promising avenue for intervention strategies.

An activin receptor-like kinase 1-governed monocytic lineage shapes an immunosuppressive landscape in breast cancer metastases

The biology centered around the TGF-β type I receptor activin receptor-like kinase (ALK) 1 (encoded by ACVRL1) has been almost exclusively based on its reported endothelial expression pattern since its first functional characterization more than 2 decades ago. Here, in efforts to better define the therapeutic context in which to use ALK1 inhibitors, we uncover a population of tumor-associated macrophages (TAMs) that, by virtue of their unanticipated Acvrl1 expression, are effector targets for adjuvant antiangiogenic immunotherapy in mouse models of metastatic breast cancer. The combinatorial benefit depended on ALK1-mediated modulation of the differentiation potential of bone marrow-derived granulocyte-macrophage progenitors, the release of CD14+ monocytes into circulation, and their eventual extravasation. Notably, ACVRL1+ TAMs coincided with an immunosuppressive phenotype and were overrepresented in human cancers progressing on therapy. Accordingly, breast cancer patients with a prominent ACVRL1hi TAM signature exhibited a significantly shorter survival. In conclusion, we shed light on an unexpected multimodal regulation of tumorigenic phenotypes by ALK1 and demonstrate its utility as a target for antiangiogenic immunotherapy.

Molecular Insights on Signaling Cascades in Breast Cancer: A Comprehensive Review

The complex signaling network within the breast tumor microenvironment is crucial for its growth, metastasis, angiogenesis, therapy escape, stem cell maintenance, and immunomodulation. An array of secretory factors and their receptors activate downstream signaling cascades regulating breast cancer progression and metastasis. Among various signaling pathways, the EGFR, ER, Notch, and Hedgehog signaling pathways have recently been identified as crucial in terms of breast cancer proliferation, survival, differentiation, maintenance of CSCs, and therapy failure. These receptors mediate various downstream signaling pathways such as MAPK, including MEK/ERK signaling pathways that promote common pro-oncogenic signaling, whereas dysregulation of PI3K/Akt, Wnt/β-catenin, and JAK/STAT activates key oncogenic events such as drug resistance, CSC enrichment, and metabolic reprogramming. Additionally, these cascades orchestrate an intricate interplay between stromal cells, immune cells, and tumor cells. Metabolic reprogramming and adaptations contribute to aggressive breast cancer and are unresponsive to therapy. Herein, recent insights into the novel signaling pathways operating within the breast TME that aid in their advancement are emphasized and current developments in practices targeting the breast TME to enhance treatment efficacy are reviewed.

Macrophage heterogeneity and oncogenic mechanisms in lung adenocarcinoma: insights from scRNA-seq analysis and predictive modeling

Background

Macrophages play a dual role in the tumor microenvironment(TME), capable of secreting pro-inflammatory factors to combat tumors while also promoting tumor growth through angiogenesis and immune suppression. This study aims to explore the characteristics of macrophages in lung adenocarcinoma (LUAD) and establish a prognostic model based on macrophage-related genes.

Method

We performed scRNA-seq analysis to investigate macrophage heterogeneity and their potential pseudotime evolutionary processes. Specifically, we used scRNA-seq data processing, intercellular communication analysis, pseudotime trajectory analysis, and transcription factor regulatory analysis to reveal the complexity of macrophage subpopulations. Data from The Cancer Genome Atlas (TCGA) was used to assess the impact of various macrophage subtypes on LUAD prognosis. Univariate Cox regression was applied to select prognostic-related genes from macrophage markers. We constructed a prognostic model using Lasso regression and multivariate Cox regression, categorizing LUAD patients into high and low-risk groups based on the median risk score. The model's performance was validated across multiple external datasets. We also examined differences between high and low-risk groups in terms of pathway enrichment, mutation information, tumor microenvironment(TME), and immunotherapy efficacy. Finally, RT-PCR confirmed the expression of model genes in LUAD, and cellular experiments explored the carcinogenic mechanism of COL5A1.

Results

We found that signals such as SPP1 and MIF were more active in tumor tissues, indicating potential oncogenic roles of macrophages. Using macrophage marker genes, we developed a robust prognostic model for LUAD that effectively predicts prognosis and immunotherapy efficacy. A nomogram was constructed to predict LUAD prognosis based on the model's risk score and other clinical features. Differences between high and low-risk groups in terms of TME, enrichment analysis, mutational landscape, and immunotherapy efficacy were systematically analyzed. RT-PCR and cellular experiments supported the oncogenic role of COL5A1.

Conclusion

Our study identified potential oncogenic mechanisms of macrophages and their impact on LUAD prognosis. We developed a prognostic model based on macrophage marker genes, demonstrating strong performance in predicting prognosis and immunotherapy efficacy. Finally, cellular experiments suggested COL5A1 as a potential therapeutic target for LUAD.

Multi‑omics identification of a novel signature for serous ovarian carcinoma in the context of 3P medicine and based on twelve programmed cell death patterns: a multi-cohort machine learning study

BACKGROUND

Predictive, preventive, and personalized medicine (PPPM/3PM) is a strategy aimed at improving the prognosis of cancer, and programmed cell death (PCD) is increasingly recognized as a potential target in cancer therapy and prognosis. However, a PCD-based predictive model for serous ovarian carcinoma (SOC) is lacking. In the present study, we aimed to establish a cell death index (CDI)-based model using PCD-related genes.

METHODS

We included 1254 genes from 12 PCD patterns in our analysis. Differentially expressed genes (DEGs) from the Cancer Genome Atlas (TCGA) and Genotype-Tissue Expression (GTEx) were screened. Subsequently, 14 PCD-related genes were included in the PCD-gene-based CDI model. Genomics, single-cell transcriptomes, bulk transcriptomes, spatial transcriptomes, and clinical information from TCGA-OV, GSE26193, GSE63885, and GSE140082 were collected and analyzed to verify the prediction model.

RESULTS

The CDI was recognized as an independent prognostic risk factor for patients with SOC. Patients with SOC and a high CDI had lower survival rates and poorer prognoses than those with a low CDI. Specific clinical parameters and the CDI were combined to establish a nomogram that accurately assessed patient survival. We used the PCD-genes model to observe differences between high and low CDI groups. The results showed that patients with SOC and a high CDI showed immunosuppression and hardly benefited from immunotherapy; therefore, trametinib_1372 and BMS-754807 may be potential therapeutic agents for these patients.

CONCLUSIONS

The CDI-based model, which was established using 14 PCD-related genes, accurately predicted the tumor microenvironment, immunotherapy response, and drug sensitivity of patients with SOC. Thus this model may help improve the diagnostic and therapeutic efficacy of PPPM.

Targeting CD206+ macrophages disrupts the establishment of a key antitumor immune axis

CD206 is a common marker of a putative immunosuppressive "M2" state in tumor-associated macrophages (TAMs). We made a novel conditional CD206 (Mrc1) knock-in mouse to specifically visualize and/or deplete CD206+ TAMs. Early depletion of CD206+ macrophages and monocytes (Mono/Macs) led to the indirect loss of conventional type I dendritic cells (cDC1), CD8 T cells, and NK cells in tumors. CD206+ TAMs robustly expressed CXCL9, contrasting with stress-responsive Spp1-expressing TAMs and immature monocytes, which became prominent with early depletion. CD206+ TAMs differentially attracted activated CD8 T cells, and the NK and CD8 T cells in CD206-depleted tumors were deficient in Cxcr3 and cDC1-supportive Xcl1 and Flt3l expressions. Disrupting this key antitumor axis decreased tumor control by antigen-specific T cells in mice. In human cancers, a CD206Replete, but not a CD206Depleted Mono/Mac gene signature correlated robustly with CD8 T cell, cDC1, and NK signatures and was associated with better survival. These findings negate the unqualified classification of CD206+ "M2-like" macrophages as immunosuppressive.