Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy

IL-32-producing CD8+ memory T cells define immunoregulatory niches in human cutaneous leishmaniasis

Human cutaneous leishmaniasis (CL) is characterized by chronic skin pathology. Experimental and clinical data suggest that immune checkpoints (ICs) play a crucial role in disease outcome, but the cellular and molecular niches that facilitate IC molecule expression during leishmaniasis are ill defined. In Sri Lankan patients with CL, indoleamine 2,3-dioxygenase 1 (IDO1) and programmed death-ligand 1 (PD-L1) were enriched in skin lesions, and reduced PD-L1 expression early after treatment initiation was predictive of a cure rate following antimonial therapy. Here, we used spatial cell interaction mapping to identify IL-32-expressing CD8+ memory T cells and Tregs as key components of the IDO1/PD-L1 niche in Sri Lankan patients with CL and in patients with distinct forms of dermal leishmaniasis in Brazil and India. Furthermore, the abundance of IL-32+ cells and IL-32+CD8+ T cells at treatment initiation was negatively correlated with the rate of cure in Sri Lankan patients. This study provides insights into the spatial mechanisms underpinning IC expression during CL and offers a strategy for identifying additional biomarkers of treatment response.

Deciphering the immunomodulatory mechanisms of Bojungikki-tang via systematic transcriptomic and immune cell interaction network analysis

Bojungikki-tang (BJIKT), a traditional herbal formula with immunomodulatory properties, has synergistic effects with immune checkpoint inhibitors. However, the detailed molecular mechanisms underlying its effects on various immune cell types remain largely unexplored. Therefore, in this study, we aimed to propose a framework for understanding how herbal medicine modulates immunity through a systematic analysis of the drug-induced transcriptome and immune cell interaction networks. We obtained large-scale RNA-seq data for distinct five immune cell types (T cells, natural killer cells, B cells, macrophages, and dendritic cells) treated with BJIKT and its four major constituent herbs, totaling 180 sequenced samples. Transcriptomic analysis indicated that BJIKT significantly upregulated interferon-γ, TNF-α, and inflammatory pathways in B cells, macrophages, and dendritic cells. Although BJIKT did not directly activate T cells, it indirectly modulated their function through immune cell-cell interactions. The reconstructed network and cytokine assays identified IL-1β, IL-6, IL-8, MIP-1β, CXCL9, CXCL10, and TNF-α as critical cytokines influenced by BJIKT, playing pivotal roles in activating and recruiting various immune cells. Our findings provide insights into the immunomodulatory mechanisms of BJIKT and the unique actions of its constituent herbs. We highlight the potential for combining traditional herbal medicine with omics technologies to explore the therapeutic mechanisms of natural products as complementary therapies for advancing cancer immunotherapy.

Development of DPP-4-resistant CXCL9-Fc and CXCL10-Fc chemokines for effective cancer immunotherapy

CXCR3 is a chemokine receptor for three ligands: CXCL9, CXCL10, and CXCL11. Accumulating evidence, including data presented here, suggests that the interaction between CXCL9/CXCL10 and CXCR3 not only attracts CXCR3+ T cells but also promotes the induction of IFNγ-high effector/cytotoxic CD4+ and CD8+ T cells, establishing a CXCL9/10-CXCR3-IFNγ self-amplifying cycle that promotes efficient cancer cell killing. One of the homeostatic mechanisms that may limit this cycle is the cleavage of the two N-terminal amino acids of these chemokines by Dipeptidyl Peptidase IV (DPP-4). The modified chemokines retain their ability to bind CXCR3 but no longer activate it, becoming competitive antagonists to native CXCL9/CXCL10. To develop a DPP-4-resistant variant, we combined biochemical analysis with computational modeling, demonstrating that the addition of N-terminal glutamine (Q) to CXCL9-Fc and CXCL10-Fc rendered them fully active CXCR3 agonists, yet resistant to DPP-4 cleavage. Preclinical evaluations imply that they offer significant therapeutic potential in cancer immunotherapy.

Quantitatively defined stromal B cell aggregates are associated with response to checkpoint inhibitors in unresectable melanoma

Multiplex immunofluorescence (mIF) is a promising tool for immunotherapy biomarker discovery in melanoma and other solid tumors. mIF captures detailed phenotypic information of immune cells in the tumor microenvironment, as well as spatial data that can reveal biologically relevant interactions among cell types. Given the complexity of mIF data, the development of automated analysis pipelines is crucial for advancing biomarker discovery. In pre-treatment melanoma samples from 50 patients treated with immune checkpoint inhibitors (ICIs), a higher stromal B cell percentage is associated with the clinical benefit of ICI therapy. The automatic detection of B cell aggregates with DBSCAN, a novel application of a computer-aided machine learning algorithm, demonstrates the potential for enhanced accuracy compared to pathologist assessment of lymphoid aggregates. TCF1+ and LAG3- T cell subpopulations are enriched near stromal B cells, suggesting potential functional interactions. These analyses provide a roadmap for the further development of spatial immunotherapy biomarkers in melanoma and other diseases.

Enhancing melanoma therapy with hydrogel microneedles

Melanoma is highly invasive and resistant to conventional treatments, accounting for nearly 75% of skin cancer-related deaths globally. Traditional therapies, such as chemotherapy and immunotherapy, often exhibit limited efficacy and are associated with significant side effects due to systemic drug exposure. Microneedles (MNs), as an emerging drug delivery system, offer multiple advantages, including safety, painlessness, minimal invasiveness, and controlled drug release. Among these, hydrogel microneedles (HMNs) stand out due to their extracellular matrix-like structure and swelling-induced continuous hydrogel channels, which enable the direct delivery of therapeutic agents into the tumor microenvironment (TME). This approach enhances drug bioavailability while reducing systemic toxicity, establishing HMNs as a promising platform for melanoma treatment. This review highlights recent advancements in HMNs for melanoma therapy, focusing on their applications in biomarker extraction for early diagnosis and their role in supporting multimodal treatment strategies, such as chemotherapy, immunotherapy, phototherapy, targeted therapy, and combination therapy. Furthermore, the current matrix materials and fabrication techniques for HMNs are discussed. Finally, the limitations of HMNs in melanoma treatment are critically analyzed, and recommendations for future research and development are provided.

From surfing to diving into the tumor microenvironment through multiparametric imaging mass cytometry

The tumor microenvironment (TME) is a complex ecosystem where malignant and non-malignant cells cooperate and interact determining cancer progression. Cell abundance, phenotype and localization within the TME vary over tumor development and in response to therapeutic interventions. Therefore, increasing our knowledge of the spatiotemporal changes in the tumor ecosystem architecture is of importance to better understand the etiologic development of the neoplastic diseases. Imaging Mass Cytometry (IMC) represents the elective multiplexed imaging technology enabling the in-situ analysis of up to 43 different protein markers for in-depth phenotypic and spatial investigation of cells in their preserved microenvironment. IMC is currently applied in cancer research to define the composition of the cellular landscape and to identify biomarkers of predictive and prognostic significance with relevance in mechanisms of drug resistance. Herein, we describe the general principles and experimental workflow of IMC raising the informative potential in preclinical and clinical cancer research.

Cancer Cell-Intrinsic Type I Interferon Signaling Promotes Antitumor Immunity in Head and Neck Squamous Cell Carcinoma

Background: The cyclic GMP-AMP synthase (cGAS)-type I interferon (IFN-I) pathway detects cytoplasmic DNA and triggers immune responses. Cancer cells often suppress this pathway to evade immune surveillance; however, its therapeutic potential remains unclear. Methods: Mouse oral squamous cell carcinoma models, representing a prominent subtype of head and neck squamous cell carcinoma (HNSCC), were employed in this study. Flow cytometry, Western blot, ELISA, and PCR were used for analysis. Results: We found that immune-unresponsive MOC2 tumors exhibited a deficiency of antigen-presenting cells and cytotoxic T lymphocytes, along with a significant suppression of the cGAS-IFN-I pathway, compared to immune-responsive MOC1 tumors. An MOC2-conditioned medium impaired the differentiation of bone marrow-derived cells into dendritic cells (DCs), reducing the expression of DC markers as well as class I and II major histocompatibility complex (MHC) molecules. The activation of the cGAS-IFN-I pathway in MOC2 cells, either through exogenous DNA or direct IFN-I expression, enhanced class I MHC expression and antigen presentation on MOC2 cells. Furthermore, IFNB1 expression in MOC2 cells induced apoptosis and upregulated chemokines, such as CXCL9 and CXCL10, which recruit immune cells. In immunocompetent mice, IFNB1 expression suppressed MOC2 tumor growth by attracting DCs and T cells, an effect amplified by co-expressing the granulocyte-macrophage colony-stimulating factor. Conclusions: These findings highlight the potential of enhancing cancer cell-intrinsic cGAS-IFN-I signaling to improve tumor immune surveillance and control the progression of immune-cold HNSCC tumors.

Advancements in Nanomaterials and Molecular Probes for Spatial Omics

Spatial omics is emerging as a focus of life sciences because of its applications in investigating the molecular mechanisms of cancer, mapping cellular distributions, and revealing specific cellular ecological niches. Notably, the in-depth acquisition of spatial omics information relies on highly sensitive, high-resolution, and high-throughput biological analysis tools and techniques. However, conventional methods of omics data acquisition still suffer from some drawbacks such as limited-resolution and low-throughput and are difficult to adapt directly to the collection of high-quality spatial omics data. Recently, an increasing number of advanced nanomaterials and molecular probes are employed in spatial omics due to their excellent optoelectronic properties, biocompatibility, and multifunction. These well-designed innovative nanoscaffolds successfully enhance the key parameters of spatial omics and, thus, increase the spatial resolution, detection sensitivity, and detection throughput. This review summarizes the design and application of functional nanoscaffolds for spatial omics in recent years, with a particular emphasis on nanomaterials and molecular probes. We believe that the present review can inspire and motivate researchers in designing and selecting appropriate materials and probes for high-quality spatial omics, thus promoting the development of spatial omics and life sciences.

Molecular Mechanisms Governing CD8 T Cell Differentiation and Checkpoint Inhibitor Response in Cancer

CD8 T cells play a critical role in antitumor immunity. However, over time, they often become dysfunctional or exhausted and ultimately fail to control tumor growth. To effectively harness CD8 T cells for cancer immunotherapy, a detailed understanding of the mechanisms that govern their differentiation and function is crucial. This review summarizes our current knowledge of the molecular pathways that regulate CD8 T cell heterogeneity and function in chronic infection and cancer and outlines how T cells respond to therapeutic checkpoint blockade. We explore how T cell-intrinsic and -extrinsic factors influence CD8 T cell differentiation, fate choices, and functional states and ultimately dictate their response to therapy. Identifying cells that orchestrate long-term antitumor immunity and understanding the mechanisms that govern their development and persistence are critical steps toward improving cancer immunotherapy.

Integrated workflow for analysis of immune enriched spatial proteomic data with IMmuneCite

Spatial proteomics enable detailed analysis of tissue at single cell resolution. However, creating reliable segmentation masks and assigning accurate cell phenotypes to discrete cellular phenotypes can be challenging. We introduce IMmuneCite, a computational framework for comprehensive image pre-processing and single-cell dataset creation, focused on defining complex immune landscapes when using spatial proteomics platforms. We demonstrate that IMmuneCite facilitates the identification of 32 discrete immune cell phenotypes using data from human liver samples while substantially reducing nonbiological cell clusters arising from co-localization of markers for different cell lineages. We established its versatility and ability to accommodate any antibody panel and different species by applying IMmuneCite to data from murine liver tissue. This approach enabled deep characterization of different functional states in each immune compartment, uncovering key features of the immune microenvironment in clinical liver transplantation and murine hepatocellular carcinoma. In conclusion, we demonstrated that IMmuneCite is a user-friendly, integrated computational platform that facilitates investigation of the immune microenvironment across species, while ensuring the creation of an immune focused, spatially resolved single-cell proteomic dataset to provide high fidelity, biologically relevant analyses.

The fibroinflammatory response in cancer

Fibroinflammation refers to the highly integrated fibrogenic and inflammatory responses mediated by the concerted function of fibroblasts and innate immune cells in response to tissue perturbation. This process underlies the desmoplastic remodelling of the tumour microenvironment and thus plays an important role in tumour initiation, growth and metastasis. More specifically, fibroinflammation alters the biochemical and biomechanical signalling in malignant cells to promote their proliferation and survival and further supports an immunosuppressive microenvironment by polarizing the immune status of tumours. Additionally, the presence of fibroinflammation is often associated with therapeutic resistance. As such, there is increasing interest in targeting this process to normalize the tumour microenvironment and thus enhance the treatment of solid tumours. Herein, we review advances made in unravelling the complexity of cancer-associated fibroinflammation that can inform the rational design of therapies targeting this.

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.

tRNA methyltransferase DNMT2 promotes hepatocellular carcinoma progression and enhances Bortezomib resistance through inhibiting TNFSF10

The tRNA methyltransferase DNMT2 (TRDMT1) plays a crucial role in various biological functions; however, its role in cancer, particularly in liver cancer, remains incompletely understood. In this study, we demonstrate that high DNMT2 expression is negatively correlated with prognosis in clinical liver cancer patients. A series of in vitro and in vivo experiments showed that DNMT2 promotes the proliferation, colony formation, and metastasis of hepatocellular carcinoma cells. We identified the pro-apoptotic gene TNFSF10 (TRAIL) as a downstream target of DNMT2, regulated by the N6-methyladenosine (m6A) demethylase FTO. Epigenetically, DNMT2 deletion increased FTO expression, leading to a reduction in m6A methylation levels. FTO upregulated TNFSF10 expression, significantly reducing the proliferation and metastasis of DNMT2-deficient hepatocellular carcinoma cells. Furthermore, DNMT2 deletion was shown to significantly upregulate chemokine expression in tumors. Finally, we demonstrated that the NF-κB inhibitor Bortezomib further enhances DNMT2 deletion-induced apoptosis in hepatocellular carcinoma cells. This study reveals DNMT2's role in liver cancer and presents a new therapeutic target for future treatments.

Prognostic stratification of gastric cancer patients by intratumoral microbiota-mediated tumor immune microenvironment

Gastric cancer (GC) is a leading cause of cancer-related deaths worldwide, and therapeutic options for advanced GC are limited. Here, we observe that intratumoral microbiota controls chemokine expression, which in turn recruits immune cells into the tumor, and that immune infiltration is strongly associated with patient survival and disease attributes. Furthermore, microbiota regulation of chemokines is differentiated in GC patients with different survival risks. As seen in gastric tumors, in high-survival-risk patients, Pseudomonas regulates CCL4, CXCL9, CXCL10, and CXCL11 accumulation to recruit immune cells such as CD4+ T cells, CD8+ T cells, and M1 macrophages. In low-survival-risk patients, Leptospira regulates CCL4, CCL5, CXCL9, and CXCL10 accumulation to recruit multiple types of immune cells. An independent single-cell dataset of GC verified the relationship between chemokines and immune cells. What's more, chemokines, including CCL4, CCL5, CXCL9, CXCL10, and CXCL11, strongly influence the sensitivity of GC patients to potential drug candidates. This study demonstrates that intratumoral microbiota closely influences the gastric immune microenvironment and that this molding has prognostic heterogeneity, opening avenues for cancer prevention and therapy.

Identifying perturbations that boost T-cell infiltration into tumours via counterfactual learning of their spatial proteomic profiles

Cancer progression can be slowed down or halted via the activation of either endogenous or engineered T cells and their infiltration of the tumour microenvironment. Here we describe a deep-learning model that uses large-scale spatial proteomic profiles of tumours to generate minimal tumour perturbations that boost T-cell infiltration. The model integrates a counterfactual optimization strategy for the generation of the perturbations with the prediction of T-cell infiltration as a self-supervised machine learning problem. We applied the model to 368 samples of metastatic melanoma and colorectal cancer assayed using 40-plex imaging mass cytometry, and discovered cohort-dependent combinatorial perturbations (CXCL9, CXCL10, CCL22 and CCL18 for melanoma, and CXCR4, PD-1, PD-L1 and CYR61 for colorectal cancer) that support T-cell infiltration across patient cohorts, as confirmed via in vitro experiments. Leveraging counterfactual-based predictions of spatial omics data may aid the design of cancer therapeutics.

One-carbon metabolism is distinct metabolic signature for proliferative intermediate exhausted T cells of ICB-resistant cancer patients

One-carbon metabolism (1CM) has been reported to promote cancer progression across various malignancies. While 1CM is critical for cell proliferation by enhancing nucleotide synthesis, its physiological roles within different cell types in the tumor immune microenvironment (TIME) still remain unclear. In this study, we analyzed bulk-RNA sequencing and single-cell RNA sequencing (scRNA-seq) data from lung adenocarcinoma (LUAD) patients to elucidate the functional roles of 1CM within the TIME. Moreover, we examined scRNA-seq data from patients treated with immunotherapy across various cancers, including LUAD, glioblastoma, renal cell carcinoma, colorectal cancer, and triple-negative breast cancer. Compared to other cell types, 1CM gene profiles are significantly enriched in a specific subset of T cells. Intriguingly, these high-1CM T cells are identified as proliferative intermediate exhausted T cells (Texint). Furthermore, these proliferative Texint received the most robust CD137 signaling. Consistently, analysis of scRNA-seq data from LUAD patients undergoing anti-PD1 immunotherapy demonstrated that proliferative Texint exhibited higher 1CM scores and increased CD137 signaling. This observation was particularly pronounced in non-responders to immunotherapy, where the Texint population was significantly expanded. We further established that 1CM is a prominent signaling pathway in proliferative Texint in patients resistant to immunotherapy across multiple cancer types. Collectively, we identify CD137 signaling as a distinctive pathway in proliferative Texint of LUAD patients who do not respond to immunotherapy. These findings propose that targeting 1CM may represent a novel therapeutic strategy to enhance the efficacy of immunotherapy by mitigating Texint proliferation in diverse cancers.

Fibroblastic reticular cells generate protective intratumoral T cell environments in lung cancer

Stringent control of T cell activity in the tumor microenvironment is essential for the generation of protective antitumor immunity. However, the identity, differentiation, and functions of the cells that create critical fibroblastic niches promoting tumor-infiltrating T cells remain elusive. Here, we show that CCL19-expressing fibroblastic reticular cells (FRCs) generate interconnected T cell environments (TEs) in human non-small cell lung cancer, including tertiary lymphoid structures and T cell tracks. Analysis of the FRC-T cell interactome in TEs indicated molecular networks regulating niche-specific differentiation of CCL19-expressing fibroblasts and T cell activation pathways. Single-cell transcriptomics and cell fate-mapping analyses in mice confirmed that FRCs in TEs originate from mural and adventitial progenitors. Ablation of intratumoral FRC precursors decreased antitumor T cell activity, resulting in reduced tumor control during coronavirus vector-based immunotherapy. In summary, specialized FRC niches in the tumor microenvironment govern the quality and extent of antitumor T cell immunity.

A Phase II Open-Label, Randomized Clinical Trial of Atezolizumab with or without Human Recombinant IL-7 (CYT107) in Advanced Urothelial Cancer

PURPOSE

Advanced urothelial cancer generally has high mortality despite modern anti-PD-1/L1 antibody-based combinations. Augmenting checkpoint inhibitor-mediated immune responses with lymphocyte growth factors may improve outcomes. We conducted a randomized phase II study (Cancer Immunotherapy Trials Network-14) in 47 patients to explore whether human recombinant IL-7 (CYT107) could be safely combined with PD-L1 inhibition to enhance responses.

PATIENTS AND METHODS

Patients with urothelial cancer after platinum chemotherapy were randomized to atezolizumab alone or with CYT107 weekly for four doses. The primary objective was clinical efficacy by the objective response rate (ORR). Secondary objectives included safety, toxicity, and other clinical outcomes. Correlative endpoints included peripheral immunophenotyping and quantification of cytokines.

RESULTS

CYT107 plus atezolizumab was well-tolerated, without dose-limiting toxicities and lower grade 3 to 4 treatment-related adverse events compared with atezolizumab monotherapy. The ORR was 26.3% for the combination therapy versus 23.8% for atezolizumab alone (P = 0.428). The complete response rate was 10.5% for the combination therapy versus 4.8% for monotherapy. Three patients on combination therapy had responses >21 months versus one with monotherapy. CD4+ and CD8+ T-lymphocyte expansion occurred in patients with response to combination therapy, with the greatest effect in T memory stem cells. Patients who responded to treatment exhibited elevated baseline levels of CCL4 and reduced levels of VEGFA and TNF.

CONCLUSIONS

Combining CYT107 with atezolizumab was safe and resulted in lymphocyte expansion, a doubling of the complete response rate, and durable responses exceeding 2 years. However, the ORR was similar to atezolizumab alone. Increased and sustained doses of CYT107 coupled with patient selection strategies should be further investigated.

Cancer-Associated Lymphoid Aggregates in Histology Images: Manual and Deep Learning-Based Quantification Approaches

Quantification of lymphoid aggregates including tertiary lymphoid structures (TLS) with germinal centers in histology images of cancer is a promising approach for developing prognostic and predictive tissue biomarkers. In this article, we provide recommendations for identifying lymphoid aggregates in tissue sections from routine pathology workflows such as hematoxylin and eosin staining. To overcome the intrinsic variability associated with manual image analysis (such as subjective decision-making, attention span), we recently developed a deep learning-based algorithm called HookNet-TLS to detect lymphoid aggregates and germinal centers in various tissues. Here, we additionally provide a guideline for using manually annotated images for training and implementing HookNet-TLS for automated and objective quantification of lymphoid aggregates in various cancer types.

Single-cell transcriptomic and spatial analysis reveal the immunosuppressive microenvironment in relapsed/refractory angioimmunoblastic T-cell lymphoma

Angioimmunoblastic T-cell lymphoma (AITL) is a kind of aggressive T-cell lymphoma with significant enrichment of non-malignant tumor microenvironment (TME) cells. However, the complexity of TME in AITL progression is poorly understood. We performed single-cell RNA-Seq (scRNA-seq) and imaging mass cytometry (IMC) analysis to compare the cellular composition and spatial architecture between relapsed/refractory AITL (RR-AITL) and newly diagnosed AITL (ND-AITL). Our results showed that the malignant T follicular helper (Tfh) cells showed significantly increased proliferation driven by transcriptional activation of YY1 in RR-AITL, which is markedly associated with the poor prognosis of AITL patients. The CD8+ T cell proportion and cytotoxicity decreased in RR-AITL TME, resulting from elevated expression of the inhibitory checkpoints such as PD-1, TIGIT, and CTLA4. Notably, the transcriptional pattern of B cells in RR-AITL showed an intermediate state of malignant transformation to B-cell-lymphoma, and contributed to immune evasion by highly expressing CD47 and PD-L1. Besides, compared to ND-AITL samples, myeloid-cells-centered spatial communities were more prevalent but showed reduced phagocytic activity and impaired antigen processing and presentation in RR-AITL TME. Furthermore, specific inhibitory ligand-receptor interactions, such as CLEC2D-KLRB1, CTLA4-CD86, and MIF-CD74, were exclusively identified in the RR-AITL TME. Our study provides a high-resolution characterization of the immunosuppression ecosystem and reveals the potential therapeutic targets for RR-AITL patients.

Spatial patterns and MRI-based radiomic prediction of high peritumoral tertiary lymphoid structure density in hepatocellular carcinoma: a multicenter study

BACKGROUND

Tertiary lymphoid structures (TLS) within the tumor microenvironment have been associated with cancer prognosis and therapeutic response. However, the immunological pattern of a high peritumoral TLS (pTLS) density and its clinical potential in hepatocellular carcinoma (HCC) remain poor. This study aimed to elucidate biological differences related to pTLS density and develop a radiomic classifier for predicting pTLS density in HCC, offering new insights for clinical diagnosis and treatment.

METHODS

Spatial transcriptomics (n=4) and RNA sequencing data (n=952) were used to identify critical regulators of pTLS density and evaluate their prognostic significance in HCC. Baseline MRI images from 660 patients with HCC who had undergone surgery treatment between October 2015 and January 2023 were retrospectively recruited for model development and validation. This included training (n=307) and temporal validation (n=76) cohorts from Xiangya Hospital, and external validation cohorts from three independent hospitals (n=277). Radiomic features were extracted from intratumoral and peritumoral regions of interest and analyzed using machine learning algorithms to develop a predictive classifier. The classifier's performance was evaluated using the area under the curve (AUC), with prognostic and predictive value assessed across four independent cohorts and in a dual-center outcome cohort of 41 patients who received immunotherapy.

RESULTS

Patients with HCC and a high pTLS density experienced prolonged median overall survival (p<0.05) and favorable immunotherapy response (p=0.03). Moreover, immune infiltration by mature B cells was observed in the high pTLS density region. Spatial pseudotime analysis and immunohistochemistry staining revealed that expansion of pTLS in HCC was associated with elevated CXCL9 and CXCL10 co-expression. We developed an optimal radiomic-based classifier with excellent discrimination for predicting pTLS density, achieving an AUC of 0.91 (95% CI 0.87, 0.94) in the external validation cohort. This classifier also exhibited promising stratification ability in terms of overall survival (p<0.01), relapse-free survival (p<0.05), and immunotherapy response (p<0.05).

CONCLUSION

We identified key regulators of pTLS density in patients with HCC and proposed a non-invasive radiomic classifier capable of assisting in stratification for prognosis and treatment.

Huang-Jin-Shuang-Shen Decoction promotes CD8+ T-cell-mediated anti-tumor immunity by regulating chemokine CXCL10 in gastric cancer

BACKGROUND

Research on immunotherapy for gastric cancer is currently receiving significant attention, with particular emphasis on the role of CD8+ T cells in anti-tumor immune responses. In recent years, the importance of the chemokine CXCL10 in promoting anti-tumor immunity has been increasingly recognized because it plays a crucial role in recruiting CD8+ T cells to the tumor microenvironment. The Huang-Jin-Shuang-Shen (HJSS) Decoction, a Chinese medicine, has been used as an adjuvant drug for gastric cancer chemotherapy. Its mechanism of action may be related to the activation of anti-tumor immunity.

PURPOSE

To assess the role of the HJSS Decoction in regulating the immune microenvironment of gastric cancer and elucidate its mechanism.

STUDY DESIGN/METHODS

Ultra-high performance liquid chromatography Q Exactive-mass spectrometry was used to analyze the main components of the HJSS Decoction and evaluate the therapeutic effect of the HJSS Decoction synergized with 5-fluorouracil (5-FU) on gastric cancer. The proportions of CD8+ T cells and killing markers were determined using flow cytometry. Mechanisms of action and targets were screened using network pharmacology. The level of CXCL10 was detected using enzyme-linked immunosorbent assay and western blot, and nuclear factor kappa-light-chain-enhancer of activated B cells (NFκB) related signaling pathway was detected in vitro. The target function was validated by siRNA transfection.

RESULTS

The combination of HJSS Decoction and 5-FU demonstrated a synergistic effect in impeding the progression of subcutaneous gastric cancer. This was achieved through the facilitation of apoptosis and suppression of proliferation. Furthermore, HJSS Decoction exhibited the ability to enhance the population of CD8+ T cells and augment their cytotoxic capabilities, both in laboratory settings and in living organisms. Notably, HJSS Decoction upregulated the expression of CXCL10, and mechanistically, it activated the NFκB-related signaling pathway to initiate subsequent transcription of chemokines.

CONCLUSION

The present study aimed to investigate the pharmacological mechanism of the HJSS Decoction and its potential clinical application in inhibiting gastric cancer in mice. HJSS Decoction can cooperate with 5-FU to inhibit gastric cancer, and the optimal dose is medium. HJSS Decoction exerts anti-tumor immunity by activating the NFκB-related signaling pathway and promoting the expression of CXCL10, which in turn recruits CD8+ T cells into the tumor immune microenvironment. Overall, these findings provide valuable evidence for the potential clinical application of HJSS Decoction.

Powerful microscopy technologies decode spatially organized cellular networks that drive response to immunotherapy in humans

In tumors, immune cells organize into networks of different sizes and composition, including complex tertiary lymphoid structures and recently identified networks centered around the chemokines CXCL9/10/11 and CCL19. New commercially available highly multiplexed microscopy using cyclical RNA in situ hybridization and antibody-based approaches have the potential to establish the organization of the immune response in human tissue and serve as a foundation for future immunology research.

Revisiting the CXCL13/CXCR5 axis in the tumor microenvironment in the era of single-cell omics: Implications for immunotherapy

As one of the important members of the family of chemokines and their receptors, the CXCL13/CXCR5 axis is involved in follicle formation in normal lymphoid tissues and the establishment of somatic cavity immunity under physiological conditions, as well as being associated with a wide range of infectious, autoimmune, and tumoral diseases. Here in this review, we focus on its role in tumors. Traditional studies have found the axis to be both pro- and anti-tumorigenic, involving a variety of immune cells, including the tumor cells themselves and those in the tumor microenvironment (TME), and the prognostic significance of this axis is clinical context-dependent. With the development of techniques at the single-cell level, we were able to explain in detail the status of the CXCL13/CXCR5 axis in the TME based on real clinical samples and found that it involves a range of crucial intrinsic anti-tumor immune processes in the TME and is therefore important in tumor immunotherapy. We summarize the cellular subsets, physiological functions, and prognostic significance associated with this axis in the most promising immune checkpoint inhibitor (ICI) therapies of the day and summarize possible therapeutic ideas based on this axis. As with any TME study, the most important takeaway is that the complexity of the CXCL13/CXCR5 axis in TME suggests the importance of personalized therapy in tumor therapy.

YAP1 Inhibition Induces Phenotype Switching of Cancer-Associated Fibroblasts to Tumor Suppressive in Prostate Cancer

Prostate cancer rarely responds to immune-checkpoint blockade (ICB) therapies. Cancer-associated fibroblasts (CAF) are critical components of the immunologically "cold" tumor microenvironment and are considered a promising target to enhance the immunotherapy response. In this study, we aimed to reveal the mechanisms regulating CAF plasticity to identify potential strategies to switch CAFs from protumorigenic to antitumor phenotypes and to enhance ICB efficacy in prostate cancer. Integration of four prostate cancer single-cell RNA sequencing datasets defined protumorigenic and antitumor CAFs, and RNA-seq, flow cytometry, and a prostate cancer organoid model demonstrated the functions of two CAF subtypes. Extracellular matrix-associated CAFs (ECM-CAF) promoted collagen deposition and cancer cell progression, and lymphocyte-associated CAFs (Lym-CAF) exhibited an antitumor phenotype and induced the infiltration and activation of CD8+ T cells. YAP1 activity regulated the ECM-CAF phenotype, and YAP1 silencing promoted switching to Lym-CAFs. NF-κB p65 was the core transcription factor in the Lym-CAF subset, and YAP1 inhibited nuclear translocation of p65. Selective depletion of YAP1 in ECM-CAFs in vivo promoted CD8+ T-cell infiltration and activation and enhanced the therapeutic effects of anti-PD-1 treatment on prostate cancer. Overall, this study revealed a mechanism regulating CAF identity in prostate cancer and highlighted a therapeutic strategy for altering the CAF subtype to suppress tumor growth and increase sensitivity to ICB. Significance: YAP1 regulates cancer-associated fibroblast phenotypes and can be targeted to switch cancer-associated fibroblasts from a protumorigenic subtype that promotes extracellular matrix deposition to a tumor-suppressive subtype that stimulates antitumor immunity and immunotherapy efficacy.

Decoding Spatial Tissue Architecture: A Scalable Bayesian Topic Model for Multiplexed Imaging Analysis

Recent progress in multiplexed tissue imaging is advancing the study of tumor microenvironments to enhance our understanding of treatment response and disease progression. Cellular neighborhood analysis is a popular computational approach for these complex image data. Despite its popularity, there are significant challenges, including high computational demands that limit feasibility for large-scale applications and the lack of a principled strategy for integrative analysis across images. This absence hampers the precise and consistent identification of spatial features and tracking of their dynamics over disease progression. To overcome these challenges, we introduce SpatialTopic, a spatial topic model designed to decode high-level spatial architecture across multiplexed tissue images. SpatialTopic integrates both cell type and spatial information within a topic modelling framework, originally developed for natural language processing and adapted for computer vision. Spatial information is incorporated into the flexible design of documents, representing densely overlapping regions in images. We employ an efficient collapsed Gibbs sampling algorithm for model inference. We benchmarked the performance against five state-of-the-art algorithms through various case studies using different single-cell spatial transcriptomic and proteomic imaging platforms across different tissue types. We show that SpatialTopic is highly scalable on large-scale image datasets with millions of cells, along with high precision and interpretability. Our findings demonstrate that SpatialTopic consistently identifies biologically and clinically significant spatial "topics" such as tertiary lymphoid structures (TLSs) and tracks dynamic changes in spatial features over disease progression. Its computational efficiency and broad applicability across various molecular imaging platforms will enhance the analysis of large-scale tissue imaging datasets.

Activated HLA-DR+CD38+ Effector Th1/17 Cells Distinguish Crohn's Disease-associated Perianal Fistulas from Cryptoglandular Fistulas

BACKGROUND

Perianal fistulas are a debilitating complication of Crohn's disease (CD). Due to unknown reasons, CD-associated fistulas are in general more difficult to treat than cryptoglandular fistulas (non-CD-associated). Understanding the immune cell landscape is a first step towards the development of more effective therapies for CD-associated fistulas. In this work, we characterized the composition and spatial localization of disease-associated immune cells in both types of perianal fistulas by high-dimensional analyses.

METHODS

We applied single-cell mass cytometry (scMC), spectral flow cytometry (SFC), and imaging mass cytometry (IMC) to profile the immune compartment in CD-associated perianal fistulas and cryptoglandular fistulas. An exploratory cohort (CD fistula, n = 10; non-CD fistula, n = 5) was analyzed by scMC to unravel disease-associated immune cell types. SFC was performed on a second fistula cohort (CD, n = 10; non-CD, n = 11) to comprehensively phenotype disease-associated T helper (Th) cells. IMC was used on a third cohort (CD, n = 5) to investigate the spatial distribution/interaction of relevant immune cell subsets.

RESULTS

Our analyses revealed that activated HLA-DR+CD38+ effector CD4+ T cells with a Th1/17 phenotype were significantly enriched in CD-associated compared with cryptoglandular fistulas. These cells, displaying features of proliferation, regulation, and differentiation, were also present in blood, and colocalized with other CD4+ T cells, CCR6+ B cells, and macrophages in the fistula tracts.

CONCLUSIONS

Overall, proliferating activated HLA-DR+CD38+ effector Th1/17 cells distinguish CD-associated from cryptoglandular perianal fistulas and are a promising biomarker in blood to discriminate between these 2 fistula types. Targeting HLA-DR and CD38-expressing CD4+ T cells may offer a potential new therapeutic strategy for CD-related fistulas.

Phenotypic, transcriptomic, and spatial characterization of CD45RB+ naïve mature B cells: Implications in Sjögren's disease

The conventional classification of mature B cells overlooks the diversity within IgD+ CD27- naïve B cells. Here, to identify distinct mature naïve B cells, we categorized CD45RBMEM55- B cells (NA RB-) and CD45RBMEM55+ B cells (NA RB+) and explore their function and localization in circulation and tissues under physiological and pathological conditions. NA RB+ B cells, found in secondary lymphoid organs, differentiate into plasmablasts and secrete IgM. In Sjögren's disease, their numbers decrease, and they show over-activation and abnormal migration, suggesting an adaptive disease response. NA RB+ B cells also appear in inflamed salivary glands, indicating involvement in local immune responses. These findings highlight the distinct roles of NA RB+ B cells in health and Sjögren's disease.

The Effect of Radiation Treatment of Solid Tumors on Neutrophil Infiltration and Function: A Systematic Review

Radiation therapy (RT) initiates a local and systemic immune response which can induce antitumor immunity and improve immunotherapy efficacy. Neutrophils are among the first immune cells that infiltrate tumors after RT and are suggested to be essential for the initial antitumor immune response. However, neutrophils in tumors are associated with poor outcomes and RT-induced neutrophil infiltration could also change the composition of the tumor microenvironment (TME) in favor of tumor progression. To improve RT efficacy for patients with cancer it is important to understand the interplay between RT and neutrophils. Here, we review the literature on how RT affects the infiltration and function of neutrophils in the TME of solid tumors, using both patients studies and preclinical murine in vivo models. In general, it was found that neutrophil levels increase and reach maximal levels in the first days after RT and can remain elevated up to 3 weeks. Most studies report an immunosuppressive role of neutrophils in the TME after RT, caused by upregulated expression of neutrophil indoleamine 2,3-dioxygenase 1 and arginase 1, as well as neutrophil extracellular trap formation. RT was also associated with increased reactive oxygen species production by neutrophils, which can both improve and inhibit antitumor immunity. In addition, multiple murine models showed improved RT efficacy when depleting neutrophils, suggesting that neutrophils have a protumor phenotype after RT. We conclude that the role of neutrophils should not be overlooked when developing RT strategies and requires further investigation in specific tumor types. In addition, neutrophils can possibly be exploited to enhance RT efficacy by combining RT with neutrophil-targeting therapies.

Spatial dynamics of CD39+CD8+ exhausted T cell reveal tertiary lymphoid structures-mediated response to PD-1 blockade in esophageal cancer

Despite the success of immune checkpoint blockade (ICB) therapy for esophageal squamous cell cancer, the key immune cell populations that affect ICB efficacy remain unclear. Here, imaging mass cytometry of tumor tissues from ICB-treated patients identifies a distinct cell population of CD39+PD-1+CD8+ T cells, specifically the TCF1+ subset, precursor exhausted T (CD39+ Tpex) cells, which positively correlate with ICB benefit. CD39+ Tpex cells are predominantly in the stroma, while differentiated CD39+ exhausted T cells are abundantly and proximally within the parenchyma. Notably, CD39+ Tpex cells are concentrated within and around tertiary lymphoid structure (TLS). Accordingly, tumors harboring TLSs have more of these cells in tumor areas than tumors lacking TLSs, suggesting Tpex cell recruitment from TLSs to tumors. In addition, circulating CD39+ Tpex cells are also increased in responders following ICB therapy. Our findings show that this unique subpopulation of CD39+PD-1+CD8+ T cells is crucial for ICB benefit, and suggest a key role in TLS-mediated immune responses against tumors.

Lymphocyte activation gene 3 served as a potential prognostic and immunological biomarker across various cancer types: a clinical and pan-cancer analysis

Objectives

Lymphocyte activation gene 3 (LAG3), an inhibitory receptor in T-cell activation, is a negative prognostic factor. However, its impact on tumours has yet to be comprehensively elucidated on a pan-cancer scale. Thus, we aim to reveal its role at the pan-cancer level.

Methods

We performed IHC staining on a retrospective cohort of 370 patients. Then we assessed the prognostic effect of LAG3 using Kaplan-Meier survival analysis and multivariate Cox regression analysis. In pan-cancer analysis, we constructed competing endogenous RNA and protein-protein interaction networks, conducted gene set enrichment analysis and identified correlations between LAG3 gene expression and various factors, including clinical characteristics, tumour purity, mutations, tumour immunity and drug sensitivity across 33 cancer types.

Results

LAG3 was expressed higher in normal kidney tissues than in tumours. A high level of LAG3 gene expression was an independent prognostic factor for OS (HR = 6.60, 95% CI = 2.43-17.90, P < 0.001) and PFS (HR = 3.44, 95% CI = 1.68-7.10, P < 0.001). In pan-cancer analysis, LAG3 exhibited robust correlations with survival and tumour stages in various cancers. Moreover, LAG3 was strongly associated with immune-related genes, proteins and signalling pathways. LAG3 gene expression was positively associated with increased infiltration of activated immune cells and decreased infiltration of several resting cells. LAG3 gene expression was associated with tumour mutation burden and microsatellite instability in multiple cancers.

Conclusion

High LAG3 gene expression was an independent risk factor in kidney neoplasms. It also functioned as a biomarker for prognosis, TIME and immunotherapy efficacy in the pan-cancer dimension.

DC-derived CXCL10 promotes CTL activation to suppress ovarian cancer

This study investigates the role of dendritic cells (DCs), with a focus on their CXCL10 marker gene, in the activation of cytotoxic T lymphocytes (CTLs) within the ovarian cancer microenvironment and its impact on disease progression. Utilizing scRNA-seq data and immune infiltration analysis, we identified a diminished DC presence in ovarian cancer. Gene analysis pinpointed CXCL10 as a key regulator in OV progression via its influence on DCs and CTLs. Prognostic analysis and in vitro experiments substantiated this role. Our findings reveal that DC-derived CXCL10 significantly affects CTL activation and proliferation. Reduced CXCL10 levels hinder CTL cytotoxicity, promoting ovarian cancer cell migration and invasion. Experimental studies using animal models have provided further evidence that the capacity of CTLs to suppress tumor development is significantly diminished when treated with DCs that have low expression of CXCL10. Dendritic cell-derived CXCL10 emerges as a pivotal factor in restraining ovarian cancer growth and metastasis through the activation of cytotoxic T lymphocytes. This study sheds light on the crucial interplay within the ovarian cancer microenvironment, offering potential therapeutic targets for ovarian cancer treatment.

Computational immune synapse analysis reveals T-cell interactions in distinct tumor microenvironments

The tumor microenvironment (TME) and the cellular interactions within it can be critical to tumor progression and treatment response. Although technologies to generate multiplex images of the TME are advancing, the many ways in which TME imaging data can be mined to elucidate cellular interactions are only beginning to be realized. Here, we present a novel approach for multipronged computational immune synapse analysis (CISA) that reveals T-cell synaptic interactions from multiplex images. CISA enables automated discovery and quantification of immune synapse interactions based on the localization of proteins on cell membranes. We first demonstrate the ability of CISA to detect T-cell:APC (antigen presenting cell) synaptic interactions in two independent human melanoma imaging mass cytometry (IMC) tissue microarray datasets. We then verify CISA's applicability across data modalities with melanoma histocytometry whole slide images, revealing that T-cell:macrophage synapse formation correlates with T-cell proliferation. We next show the generality of CISA by extending it to breast cancer IMC images, finding that CISA quantifications of T-cell:B-cell synapses are predictive of improved patient survival. Our work demonstrates the biological and clinical significance of spatially resolving cell-cell synaptic interactions in the TME and provides a robust method to do so across imaging modalities and cancer types.

Spatial proteomic profiling elucidates immune determinants of neoadjuvant chemo-immunotherapy in esophageal squamous cell carcinoma

Esophageal squamous cell carcinoma (ESCC) presents significant clinical and therapeutic challenges due to its aggressive nature and generally poor prognosis. We initiated a Phase II clinical trial (ChiCTR1900027160) to assess the efficacy of a pioneering neoadjuvant chemo-immunotherapy regimen comprising programmed death-1 (PD-1) blockade (Toripalimab), nanoparticle albumin-bound paclitaxel (nab-paclitaxel), and the oral fluoropyrimidine derivative S-1, in patients with locally advanced ESCC. This study uniquely integrates clinical outcomes with advanced spatial proteomic profiling using Imaging Mass Cytometry (IMC) to elucidate the dynamics within the tumor microenvironment (TME), focusing on the mechanistic interplay of resistance and response. Sixty patients participated, receiving the combination therapy prior to surgical resection. Our findings demonstrated a major pathological response (MPR) in 62% of patients and a pathological complete response (pCR) in 29%. The IMC analysis provided a detailed regional assessment, revealing that the spatial arrangement of immune cells, particularly CD8+ T cells and B cells within tertiary lymphoid structures (TLS), and S100A9+ inflammatory macrophages in fibrotic regions are predictive of therapeutic outcomes. Employing machine learning approaches, such as support vector machine (SVM) and random forest (RF) analysis, we identified critical spatial features linked to drug resistance and developed predictive models for drug response, achieving an area under the curve (AUC) of 97%. These insights underscore the vital role of integrating spatial proteomics into clinical trials to dissect TME dynamics thoroughly, paving the way for personalized and precise cancer treatment strategies in ESCC. This holistic approach not only enhances our understanding of the mechanistic basis behind drug resistance but also sets a robust foundation for optimizing therapeutic interventions in ESCC.

Recycled melanoma-secreted melanosomes regulate tumor-associated macrophage diversification

Extracellular vesicles (EVs) are important mediators of communication between cells. Here, we reveal a new mode of intercellular communication by melanosomes, large EVs secreted by melanocytes for melanin transport. Unlike small EVs, which are disintegrated within the receiver cell, melanosomes stay intact within them, gain a unique protein signature, and can then be further transferred to another cell as "second-hand" EVs. We show that melanoma-secreted melanosomes passaged through epidermal keratinocytes or dermal fibroblasts can be further engulfed by resident macrophages. This process leads to macrophage polarization into pro-tumor or pro-immune cell infiltration phenotypes. Melanosomes that are transferred through fibroblasts can carry AKT1, which induces VEGF secretion from macrophages in an mTOR-dependent manner, promoting angiogenesis and metastasis in vivo. In melanoma patients, macrophages that are co-localized with AKT1 are correlated with disease aggressiveness, and immunotherapy non-responders are enriched in macrophages containing melanosome markers. Our findings suggest that interactions mediated by second-hand extracellular vesicles contribute to the formation of the metastatic niche, and that blocking the melanosome cues of macrophage diversification could be helpful in halting melanoma progression.

Differential alterations of CXCR3, CXCR5 and CX3CR1 in patients with immune thrombocytopenia

As a versatile element for maintaining homeostasis, the chemokine system has been reported to be implicated in the pathogenesis of immune thrombocytopenia (ITP). However, research pertaining to chemokine receptors and related ligands in adult ITP is still limited. The states of several typical chemokine receptors and cognate ligands in the circulation were comparatively assessed through various methodologies. Multiple variable analyses of correlation matrixes were conducted to characterize the correlation signatures of various chemokine receptors or candidate ligands with platelet counts. Our data illustrated a significant decrease in relative CXCR3 expression and elevated plasma levels of CXCL4, 9-11, 13, and CCL3 chemokines in ITP patients with varied platelet counts. Flow cytometry assays revealed eminently diminished CXCR3 levels on T and B lymphocytes and increased CXCR5 on cytotoxic T cell (Tc) subsets in ITP patients with certain platelet counts. Meanwhile, circulating CX3CR1 levels were markedly higher on T cells with a concomitant increase in plasma CX3CL1 level in ITP patients, highlighting the importance of aberrant alterations of the CX3CR1-CX3CL1 axis in ITP pathogenesis. Spearman's correlation analyses revealed a strong positive association of peripheral CXCL4 mRNA level, and negative correlations of plasma CXCL4 concentration and certain chemokine receptors with platelet counts, which might serve as a potential biomarker of platelet destruction in ITP development. Overall, these results indicate that the differential expression patterns and distinct activation states of peripheral chemokine network, and the subsequent expansion of circulating CXCR5+ Tc cells and CX3CR1+ T cells, may be a hallmark during ITP progression, which ultimately contributes to thrombocytopenia in ITP patients.

Spatial immunophenotyping of FFPE tissues by imaging mass cytometry

The immune compartment of a tissue is dynamic, changing to respond to infections, tumors, or therapeutic interventions. Within tissues, local microenvironments provide interaction partners and cytokines that can gear immune cells into distinct functional states. Thus, it is not just the immune composition of a tissue, but also the relative localization of immune cells that determines the outcome of a response. Conventional techniques like immunohistochemistry (IHC) have been used to describe infiltration of immune cells and their relative position within tissues. However, these technologies are limited on the number of targets that can be simultaneously imaged. Here, we describe a simple protocol using imaging mass cytometry (IMC) for immunophenotyping formalin-fixed, paraffin-embedded (FFPE) tissues. IMC has a 1-μm resolution and allows simultaneous detection of up to 40 targets, overcoming limitations of traditional methods. In this protocol, we detail the staining procedure, offer an example of a murine FFPE antibody panel for immunophenotyping, and additionally provide suggestions for initial image analysis. The herein presented workflow facilitates the characterization of immune niches and can be used to assess their alterations throughout immune responses or therapeutic interventions. With minimal alterations, this approach can be used on clinically relevant samples or animal models to investigate specific immune responses and better understand disease progression or treatment dynamics.

Stem-like CD8+ T cells in cancer

Stem-like CD8+ T cells (TSL) are a subset of immune cells with superior persistence and antitumor immunity. They are TCF1+ PD-1+ and important for the expansion of tumor specific CD8+ T cells in response to checkpoint blockade immunotherapy. In acute infections, naïve CD8+ T cells differentiate into effector and memory CD8+ T cells; in cancer and chronic infections, persistent antigen stimulation can lead to T cell exhaustion. Recent studies have highlighted the dichotomy between late dysfunctional (or exhausted) T cells (TLD) that are TCF1- PD-1+ and self-renewing TCF1+ PD-1+ TSL from which they derive. TCF1+ TSL cells are considered to have stem cell-like properties akin to memory T cell populations and can give rise to cytotoxic effector and transitory T cell phenotypes (TTE) which mediate tumor control. In this review, we will discuss recent advances made in research on the formation and expansion of TSL, as well as distinct niches required for their differentiation and maintenance in the setting of cancer. We will also discuss potential strategies to generate these cells, with clinical implications for stemness enhancement in vaccine design, immune checkpoint blockade (ICB), and adoptive T cell therapies.

Inhibition of insulin-like growth factors increases production of CXCL9/10 by macrophages and fibroblasts and facilitates CD8+ cytotoxic T cell recruitment to pancreatic tumours

Pancreatic ductal adenocarcinoma (PDAC) is a highly lethal malignancy with an urgent unmet clinical need for new therapies. Using a combination of in vitro assays and in vivo preclinical models we demonstrate that therapeutic inhibition of the IGF signalling axis promotes the accumulation of CD8+ cytotoxic T cells within the tumour microenvironment of PDAC tumours. Mechanistically, we show that IGF blockade promotes macrophage and fibroblast production of the chemokines CXCL9 and CXCL10 to facilitate CD8+ T cell recruitment and trafficking towards the PDAC tumour. Exploring this pathway further, we show that IGF inhibition leads to increased STAT1 transcriptional activity, correlating with a downregulation of the AKT/STAT3 signalling axis, in turn promoting Cxcl9 and Cxcl10 gene transcription. Using patient derived tumour explants, we also demonstrate that our findings translate into the human setting. PDAC tumours are frequently described as "immunologically cold", therefore bolstering CD8+ T cell recruitment to PDAC tumours through IGF inhibition may serve to improve the efficacy of immune checkpoint inhibitors which rely on the presence of CD8+ T cells in tumours.

Cancer organoids 2.0: modelling the complexity of the tumour immune microenvironment

The development of neoplasia involves a complex and continuous interplay between malignantly transformed cells and the tumour microenvironment (TME). Cancer immunotherapies targeting the immune TME have been increasingly validated in clinical trials but response rates vary substantially between tumour histologies and are often transient, idiosyncratic and confounded by resistance. Faithful experimental models of the patient-specific tumour immune microenvironment, capable of recapitulating tumour biology and immunotherapy effects, would greatly improve patient selection, target identification and definition of resistance mechanisms for immuno-oncology therapeutics. In this Review, we discuss currently available and rapidly evolving 3D tumour organoid models that capture important immune features of the TME. We highlight diverse opportunities for organoid-based investigations of tumour immunity, drug development and precision medicine.

Distinct Localization, Transcriptional Profiles, and Functionality in Early Life Tonsil Regulatory T Cells

CD4+ regulatory T cells (Tregs) are key orchestrators of the immune system, fostering the establishment of protective immunity while preventing deleterious responses. Infancy and childhood are crucial periods of rapid immunologic development, but how Tregs mediate immune responses at these earliest timepoints of human life is poorly understood. In this study, we compare blood and tissue (tonsil) Tregs across pediatric and adult subjects to investigate age-related differences in Treg biology. We observed increased FOXP3 expression and proportions of Tregs in tonsil compared with paired blood samples in children. Within tonsil, early life Tregs accumulated in extrafollicular regions with cellular interactions biased toward CD8+ T cells. Tonsil Tregs in both children and adults expressed transcriptional profiles enriched for lineage defining signatures and canonical functionality compared with blood, suggesting tissue as the primary site of Treg activity. Early life tonsil Tregs transcriptional profiles were further defined by pathways associated with activation, proliferation, and polyfunctionality. Observed differences in pediatric tonsil Treg transcriptional signatures were associated with phenotypic differences, high proliferative capacity, and robust production of IL-10 compared with adult Tregs. These results identify tissue as a major driver of Treg identity, provide new insights into developmental differences in Treg biology across the human lifespan, and demonstrate unique functional properties of early life Tregs.

Mapping the single cell spatial immune landscapes of the melanoma microenvironment

Melanoma is a highly immunogenic malignancy with an elevated mutational burden, diffuse lymphocytic infiltration, and one of the highest response rates to immune checkpoint inhibitors (ICIs). However, over half of all late-stage patients treated with ICIs will either not respond or develop progressive disease. Spatial imaging technologies are being increasingly used to study the melanoma tumor microenvironment (TME). The goal of such studies is to understand the complex interplay between the stroma, melanoma cells, and immune cell-types as well as their association with treatment response. Investigators seeking a better understanding of the role of cell location within the TME and the importance of spatial expression of biomarkers are increasingly turning to highly multiplexed imaging approaches to more accurately measure immune infiltration as well as to quantify receptor-ligand interactions (such as PD-1 and PD-L1) and cell-cell contacts. CyTOF-IMC (Cytometry by Time of Flight - Imaging Mass Cytometry) has enabled high-dimensional profiling of melanomas, allowing researchers to identify complex cellular subpopulations and immune cell interactions with unprecedented resolution. Other spatial imaging technologies, such as multiplexed immunofluorescence and spatial transcriptomics, have revealed distinct patterns of immune cell infiltration, highlighting the importance of spatial relationships, and their impact in modulating immunotherapy responses. Overall, spatial imaging technologies are just beginning to transform our understanding of melanoma biology, providing new avenues for biomarker discovery and therapeutic development. These technologies hold great promise for advancing personalized medicine to improve patient outcomes in melanoma and other solid malignancies.

Defining the niche for stem-like CD8+ T cell formation and function

TCF-1+ CD8+ T cell populations have emerged as critical determinants for long-lived immunological memory. This cell population has stem-like properties and is implicated in improved disease outcomes by driving sustained killing of infected cells and maintaining the immune-cancer equilibrium. During an immune response, several factors, including antigen deposition and affinity, the inflammatory milieu, and T cell priming dynamics, aggregate to skew CD8+ T cell differentiation. Although these mechanisms are altered between acute and chronic disease settings, phenotypically similar stem-like TCF-1+ CD8+ T cell states are formed in each of these settings. Here, we characterize the specialized microenvironments within lymph nodes and the tumor microenvironment, which foster the generation or re-activation of stem-like TCF-1+ CD8+ T cell populations. We highlight the potential for targeting the stem-like CD8+ T cell niche to enhance vaccination and cancer immunotherapy and to track the trajectory of stem-like CD8+ T cells as biomarkers of therapeutic efficacy.

Computational methods and biomarker discovery strategies for spatial proteomics: a review in immuno-oncology

Advancements in imaging technologies have revolutionized our ability to deeply profile pathological tissue architectures, generating large volumes of imaging data with unparalleled spatial resolution. This type of data collection, namely, spatial proteomics, offers invaluable insights into various human diseases. Simultaneously, computational algorithms have evolved to manage the increasing dimensionality of spatial proteomics inherent in this progress. Numerous imaging-based computational frameworks, such as computational pathology, have been proposed for research and clinical applications. However, the development of these fields demands diverse domain expertise, creating barriers to their integration and further application. This review seeks to bridge this divide by presenting a comprehensive guideline. We consolidate prevailing computational methods and outline a roadmap from image processing to data-driven, statistics-informed biomarker discovery. Additionally, we explore future perspectives as the field moves toward interfacing with other quantitative domains, holding significant promise for precision care in immuno-oncology.

Single-cell mass cytometry in immunological skin diseases

Immune-related skin diseases represent a collective of dermatological disorders intricately linked to dysfunctional immune system processes. These conditions are primarily characterized by an immoderate activation of the immune system or deviant immune responses, involving diverse immune components including immune cells, antibodies, and inflammatory mediators. However, the precise molecular dysregulation underlying numerous individual cases of these diseases and unique subsets respond under disease conditions remains elusive. Comprehending the mechanisms and determinants governing the homeostasis and functionality of diseases could offer potential therapeutic opportunities for intervention. Mass cytometry enables precise and high-throughput quantitative measurement of proteins within individual cells by utilizing antibodies labeled with rare heavy metal isotopes. Imaging mass cytometry employs mass spectrometry to obtain spatial information on cell-to-cell interactions within tissue sections, simultaneously utilizing more than 40 markers. The application of single-cell mass cytometry presents a unique opportunity to conduct highly multiplexed analysis at the single-cell level, thereby revolutionizing our understanding of cell population heterogeneity and hierarchy, cellular states, multiplexed signaling pathways, proteolysis products, and mRNA transcripts specifically in the context of many autoimmune diseases. This information holds the potential to offer novel approaches for the diagnosis, prognostic assessment, and monitoring responses to treatment, thereby enriching our strategies in managing the respective conditions. This review summarizes the present-day utilization of single-cell mass cytometry in studying immune-related skin diseases, highlighting its advantages and limitations. This technique will become increasingly prevalent in conducting extensive investigations into these disorders, ultimately yielding significant contributions to their accurate diagnosis and efficacious therapeutic interventions.

IMmuneCite: an integrated workflow for analysis of immune enriched spatial proteomic data

Spatial proteomics enable detailed analysis of tissue at single cell resolution. However, creating reliable segmentation masks and assigning accurate cell phenotypes to discrete cellular phenotypes can be challenging. We introduce IMmuneCite, a computational framework for comprehensive image pre-processing and single-cell dataset creation, focused on defining complex immune landscapes when using spatial proteomics platforms. We demonstrate that IMmuneCite facilitates the identification of 32 discrete immune cell phenotypes using data from human liver samples while substantially reducing nonbiological cell clusters arising from co-localization of markers for different cell lineages. We established its versatility and ability to accommodate any antibody panel and different species by applying IMmuneCite to data from murine liver tissue. This approach enabled deep characterization of different functional states in each immune compartment, uncovering key features of the immune microenvironment in clinical liver transplantation and murine hepatocellular carcinoma. In conclusion, we demonstrated that IMmuneCite is a user-friendly, integrated computational platform that facilitates investigation of the immune microenvironment across species, while ensuring the creation of an immune focused, spatially resolved single-cell proteomic dataset to provide high fidelity, biologically relevant analyses.

Spatial Dissection of the Immune Landscape of Solid Tumors to Advance Precision Medicine

Chemotherapeutics, radiation, targeted therapeutics, and immunotherapeutics each demonstrate clinical benefits for a small subset of patients with solid malignancies. Immune cells infiltrating the tumor and the surrounding stroma play a critical role in shaping cancer progression and modulating therapy response. They do this by interacting with the other cellular and molecular components of the tumor microenvironment. Spatial multi-omics technologies are rapidly evolving. Currently, such technologies allow high-throughput RNA and protein profiling and retain geographical information about the tumor microenvironment cellular architecture and the functional phenotype of tumor, immune, and stromal cells. An in-depth spatial characterization of the heterogeneous tumor immune landscape can improve not only the prognosis but also the prediction of therapy response, directing cancer patients to more tailored and efficacious treatments. This review highlights recent advancements in spatial transcriptomics and proteomics profiling technologies and the ways these technologies are being applied for the dissection of the immune cell composition in solid malignancies in order to further both basic research in oncology and the implementation of precision treatments in the clinic.

The balance of STING signaling orchestrates immunity in cancer

Over the past decade, it has become clear that the stimulator of interferon genes (STING) pathway is critical for a variety of immune responses. This endoplasmic reticulum-anchored adaptor protein has regulatory functions in host immunity across a spectrum of conditions, including infectious diseases, autoimmunity, neurobiology and cancer. In this Review, we outline the central importance of STING in immunological processes driven by expression of type I and III interferons, as well as inflammatory cytokines, and we look at therapeutic options for targeting STING. We also examine evidence that challenges the prevailing notion that STING activation is predominantly beneficial in combating cancer. Further exploration is imperative to discern whether STING activation in the tumor microenvironment confers true benefits or has detrimental effects. Research in this field is at a crossroads, as a clearer understanding of the nuanced functions of STING activation in cancer is required for the development of next-generation therapies.

Opposing tumor-cell-intrinsic and -extrinsic roles of the IRF1 transcription factor in antitumor immunity

Type I interferon (IFN-I) and IFN-γ foster antitumor immunity by facilitating T cell responses. Paradoxically, IFNs may promote T cell exhaustion by activating immune checkpoints. The downstream regulators of these disparate responses are incompletely understood. Here, we describe how interferon regulatory factor 1 (IRF1) orchestrates these opposing effects of IFNs. IRF1 expression in tumor cells blocks Toll-like receptor- and IFN-I-dependent host antitumor immunity by preventing interferon-stimulated gene (ISG) and effector programs in immune cells. In contrast, expression of IRF1 in the host is required for antitumor immunity. Mechanistically, IRF1 binds distinctly or together with STAT1 at promoters of immunosuppressive but not immunostimulatory ISGs in tumor cells. Overexpression of programmed cell death ligand 1 (PD-L1) in Irf1-/- tumors only partially restores tumor growth, suggesting multifactorial effects of IRF1 on antitumor immunity. Thus, we identify that IRF1 expression in tumor cells opposes host IFN-I- and IRF1-dependent antitumor immunity to facilitate immune escape and tumor growth.