Immune Interactions Research Articles

Hidden allies: how extracellular vesicles drive biofilm formation, stress adaptation, and host–immune interactions in human fungal pathogens

ABSTRACT Pathogenic fungi pose a significant threat to human health, especially given the rising incidence of invasive fungal infections and the emergence of drug-resistant strains. This requires the development of vaccines and the advancement of antifungal strategies. Recent studies have focused on the roles of fungal extracellular vesicles (EVs) in intercellular communication and host-pathogen interactions. EVs are nanosized, lipid membrane-bound particles that facilitate the transfer of proteins, lipids, and nucleic acids. Here, we review the multifaceted functions of EVs produced by different human fungal pathogens, highlighting their importance in the response of fungal cells to different environmental cues and their interactions with host immune cells. We summarize the current state of research on EVs and how leveraging this knowledge can lead to innovative approaches in vaccine development and antifungal treatment.

Abstract C028: Decreased heterogeneity in immune interactions in oral cavity squamous cell carcinoma patients with recurrence

Abstract There have been improvements in clinical risk stratifications for oral cavity squamous cell carcinoma (OSCC) with the AJCC 8th edition staging system. Other studies suggest the addition of a metric of specific immune interactions in and around the tumor may be helpful to further stratify patients, with mixed findings. The advent of spatial imaging has allowed a global view for assessing tumor features in the context of all surrounding cell interactions. We hypothesize that the lack of architectural information could contribute to varied clinical outcomes in previous studies, such as tumor recurrence. This highlights how spatial technologies could aid in understanding the role of tissue architecture and its influence on biology and medicine. To study tissue remodeling spatially, we focused on multiplexed-ion beam imaging (MIBI), a spatial proteomics platform to visualize 40 immuno-onco proteins simultaneously. Our banked patient cohort consists of 20 recurrent and 49 non-recurrent OSCC primary surgery samples. Clinical metadata capturing pathologic stage, alcohol use, smoking history, survival data, and more were also collected. With our pathologist, we curated 290 field-of-views (FOVs) of matched primary tumors, uninvolved lymph nodes, and metastatic lymph nodes (if any). Downstream computational analysis using existing MIBI codebases augmented with in-house spatial analytics has revealed a robust spatial dataset. After using machine-learning algorithms to cell segment our images, we validated these assigned cells and marker staining to further annotate cell populations. When we analyzed direct cell interactions, there was a decrease in heterogeneity in immune interactions within recurrent patients compared to non-recurrent patients. To ascertain how the loss of these interactions affected recurrence prognosis, we investigated their prevalence within the tumor border vicinity. We hypothesize that the proximity and cell-cell interactions near the border will promote a tumor-suppressive environment. Utilizing centroid-to-centroid distance measurements, we distilled the top 30 cell-cell interactions within a 100-micron distance from the tumor border. Cell pairs involving macrophage tissue-resident memory cells and CD8 T memory resident cells were more abundant in recurrent patients, while pairs involving CD4 T regulatory and CD8 cells were found in non-recurrent patients. Reassuringly, cell pairings involving myeloid cells were upregulated in the recurrent cohort as expected. Interestingly, cancer-associated fibroblast cell pairings were upregulated indiscriminately in both patient sub- cohorts. This suggests that the impact of certain known immunosuppressive changes may contribute in varying amounts to disease control. Our data demonstrates differences in the architecture of tumors with known divergent outcomes, which suggests global tissue-level changes could be a predictive factor. Clinically, interrogating these interactions of interest could guide treatment escalation or de-escalation in the future. Citation Format: Connie J. Zhou, Jane Lee, Rebecca Jaszczak, Steven R. Long, Patrick K. Ha, Matthew H. Spitzer. Decreased heterogeneity in immune interactions in oral cavity squamous cell carcinoma patients with recurrence [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Tumor-body Interactions: The Roles of Micro- and Macroenvironment in Cancer; 2024 Nov 17-20; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2024;84(22_Suppl):Abstract nr C028.

Abstract B016: Utilizing gene expression profiles (GEP) to assess tumor microenvironment (TME) and response to immunotherapy

Abstract Background: Despite the success of anti-PD-1/PD-L1 immunotherapies, outcomes for lung cancer patients remain suboptimal. There is a critical need to incorporate multi-omics data focused on the tumor microenvironment (TME) to enhance patient selection and treatment individualization. This study aimed to identify predictive and prognostic biomarkers of immunotherapy response by characterizing transcriptional profiles of lung adenocarcinoma patients who underwent genomic profiling at diagnosis. Methods: RNA sequencing data were obtained from 68 lung adenocarcinoma patients who underwent next-generation sequencing with CARIS at our institution. We analyzed gene expression profiles (GEP) comprising 18 inflammatory genes associated with antigen presentation, chemokine expression, cytolytic activity, and adaptive immune resistance, identified as potential biomarkers for immune checkpoint inhibitor (ICI) response (Cristescu et al., 2018). The genes included were CCL5, CD27, CD274 (PD-L1), CD276 (B7-H3), CD8A, CMKLR1, CXCL9, CXCR6, HLA-DQA1, HLA-DRB1, HLA-E, IDO1, LAG3, NKG7, PDCD1LG2 (PD-L2), PSMB10, STAT1, and TIGIT. GEP scores were calculated, and hierarchical clustering identified tumor subsets with similar GEPs. Gene set variation analysis was conducted to assess enrichment of cell-cell interaction activities of specific ligand-receptor pairs of immune checkpoint genes, partially overlapping with the 18 GEP genes. Results: Hierarchical clustering identified four distinct GEP clusters: "T cell-inflamed GEP," "T cell-non-inflamed GEP high," "T cell-non-inflamed GEP medium," and "T cell-non-inflamed low GEP," with average scores of 0.18 (N=9, 13%), 0.11 (N=29, 43%), 0.08 (N=19, 28%), and 0.04 (N=11, 16%), respectively. The gene scores among these clusters showed significant differences (P = 3.3e-09). Additionally, analysis of specific ligand-receptor pairs of immune checkpoint genes (PD1/PD-L1, PD-L2; CTLA4/CD28, CD80, CD86; ICOS/ICOSLG; TIM3/GAL9; SIRP1/CD47) showed consistent positive enrichment in the “T cell-inflamed” cluster, with no or negative enrichment in the “T cell-non-inflamed” clusters. This suggests active immune checkpoint interactions in clusters with high GEP scores. Conclusion: We identified four different clusters among tissues from patients with NSCLC based on GEP scoring highlighting differences in immune activation and TME makeup, which may play a role in predicting response to immunotherapies. Our results suggest that GEP may provide information on identifying optimal immunotherapeutic approaches based on TME. Our findings underscore the importance of using biomarker-guided strategies to improve patient selection for precision immunotherapy approaches in lung cancer. Citation Format: Changde Cheng, Doug Welsch, Kayla F. Goliwas, Jessy Deshane, Sameer Deshmukh, Sanad Ahlushki, Yanis Boumber, Darshan Shimoga Chandrashekar, Alexander C. Mackinnon, Aakash Desai. Utilizing gene expression profiles (GEP) to assess tumor microenvironment (TME) and response to immunotherapy [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Tumor-body Interactions: The Roles of Micro- and Macroenvironment in Cancer; 2024 Nov 17-20; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2024;84(22_Suppl):Abstract nr B016.

Crosstalk Between Fibroblasts and Immune Cells in keloids.

Our comment on Min et al.’s study, “Novel therapeutic strategy for intractable keloids: Suppression of intracellular mechanotransduction and actin polymerisation via Rho-kinase pathway inhibition” highlights the importance of immune cell interactions with mechanical forces in keloid pathogenesis. While the authors effectively demonstrate the potential of inhibiting mechanotransduction in fibroblasts, we underscore the critical role of immune cells, particularly their response to ECM stiffness, in modulating fibrosis and suggest this crosstalk may reveal additional therapeutic targets.

Whole-blood model reveals granulocytes as key sites of dengue virus propagation, expanding understanding of disease pathogenesis.

Dengue virus (DENV) infection poses a significant global health threat, yet our understanding of its immunopathogenesis remains incomplete due to limitations of existing models. Here, we establish an in vitro whole-blood model using hirudin, an anticoagulant that preserves complement activity and cellular interactions, to study DENV infection. Our model reveals the susceptibility of all major leukocyte populations to DENV infection, with monocytes and granulocytes demonstrating high permissiveness and production of infectious virus progeny. Notably, granulocytes emerge as previously unrecognized targets of DENV infection, highlighting the importance of studying viral tropism within a physiologically relevant context. We also observed efficient DENV binding to B cells, but limited production of infectious virus, suggesting a potential role in viral sequestration or immune dysregulation. Interestingly, both NK and T cells, while less permissive, were also found to be susceptible to DENV infection. Our ex vivo analysis of whole blood from DENV-infected patients confirms the susceptibility of granulocytes, monocytes, B cells, natural killer cells, and T cells to infection, further validating the clinical relevance of our model. Additionally, we observed dynamic changes in circulating blood cell populations during acute dengue, potentially reflecting both direct virus-mediated effects and immune responses. This whole-blood model offers a valuable tool for investigating the complex interplay between DENV and host factors, facilitating a deeper understanding of dengue pathogenesis and ultimately contributing to the development of novel therapeutic strategies.IMPORTANCEDengue virus (DENV) infection is a significant global health threat, with increasing incidence in endemic regions and expanding geographic range due to factors like global warming. Current models for studying DENV pathogenesis often lack the complexity of the human immune system, hindering the development of effective therapies and vaccines. To address this, we have established the first in vitro whole-blood model using hirudin, preserving critical immune components and cellular interactions. This model reveals granulocytes as previously unrecognized targets of productive DENV infection, challenging existing paradigms of viral tropism. Our ex vivo analysis of patient blood samples confirms the clinical relevance of this finding and validates our model's utility. This unique model offers a powerful platform for future studies to dissect the complex interactions between DENV and the host immune system, including the roles of different leukocyte populations, ultimately informing the development of novel therapeutic strategies to combat this devastating disease.

Label-free biosensor assay decodes the dynamics of Toll-like receptor signaling.

The discovery of Toll-like receptors (TLRs) represented a significant breakthrough that paved the way for the study of host-pathogen interactions in innate immunity. However, there are still major gaps in understanding TLR function, especially regarding the early dynamics of downstream TLR pathways. Here, we present a label-free optical biosensor-based assay as a method for detecting TLR activation in a native and label-free environment and defining the dynamics of TLR pathway activation. This technology is sufficiently sensitive to detect TLR signaling and readily discriminates between different TLR signaling pathways. We define pharmacological modulators of cell surface and endosomal TLRs and downstream signaling molecules and uncover TLR signaling signatures, including potential biased receptor signaling. These findings highlight that optical biosensor assays complement traditional assays that use a single endpoint and have the potential to facilitate the future design of selective drugs targeting TLRs and their downstream effector cascades.

Abstract 4132752: The immune checkpoint landscape in human atherosclerosis: influence of lipid lowering and type 2 diabetes

Immune checkpoint inhibitor (ICI) therapies substantially increase the risk of atherosclerotic cardiovascular events in cancer survivors. Here, we mapped the expression of immune checkpoints (ICs) within human atherosclerotic plaques, unraveling an intricate local network of immune cell-cell interactions in the context of relevant comorbidities like dyslipidemia and diabetes. Our findings identified a population of mature, regulatory CCR7 + FSCN1 + dendritic cells as pivotal orchestrators of IC-mediated signaling within human and murine plaques, a function akin to their role in tumor environments. In clinical cohorts, type 2 diabetes diminished CCR7 + FSCN1 + dendritic cells within atherosclerotic plaques and dampened interactions steered by PD-1 or CTLA4 consistently across immune cell subpopulations. This effect was also present and further decreased by lipid lowering in the circulation, where CD86–CTLA4 was among the most prominent IC pairs signaling between regulatory T cells and myeloid populations including CCR7 + FSCN1 + dendritic cells. These findings underline the vulnerability of atherosclerotic plaques to cancer immunotherapies and underscore the critical impact of cardiometabolic disease and lipid-lowering strategies on the atherosclerotic IC landscape, offering a framework toward the reshaping of clinical approaches.

IMMU-66. PHYSIOLOGICALLY RELEVANT MURINE GLIOMA MODELS THAT REPRESENT GBM HETEROGENEITY AND ENABLE THE NEXT GENERATION OF DISCOVERY AND THERAPY EFFICACY STUDIES

Abstract To transform cancer drug development pipelines and gain a deeper mechanistic understanding of cancer: immune interactions, we desperately need better experimental models that faithfully recapitulate the cellular heterogeneity, complex and dynamic cell:cell interactions, and therapy responses in humans. To address this need, we developed and characterized a cohort of five new mouse glioma models in the C57BL6/j background. These transplantable tumorsphere models were derived from spontaneous gliomas that formed in genetically engineered mouse models with different oncogenic drivers, including EGFRviii, PDGFA, PTEN, p53, and NF1 mutations. They show a range of responses to standard of care (TMZ+IR) similar to GBM patients and all are resistant, to immune checkpoint inhibitors, anti-PD1+CTLA4, treatment, unlike the GL261 model and similar to GBM patients. We deeply characterized each model, including immune phenotyping and single-cell RNA-sequencing analyses. We also performed a cross-species comparison of human and mouse GBM and stromal cell phenotypes at the single-cell level. Our results show that new mouse models recapitulate the heterogeneity of glioma cell states observed in individual patients and, importantly, also the complex and immune suppressive TME. We demonstrate at the single-cell level that glioma-associated T and myeloid cell types are molecularly similar and conserved across species. Leveraging these data sets and experimental models, we are testing now novel immunotherapy targets for GBM.

TMIC-48. THREE DIMENSIONAL CANCER CELL-MONOCYTE CO-CULTURE SPHEROIDS RECAPITULATE IMMUNOSUPPRESSIVE AND PRO-TUMORIGENIC MICROENVIRONMENTS IN BRAIN METASTATIC BREAST CANCER

Abstract Brain metastasis occurs in 15 % of breast cancer patients and is one of the major causes of breast cancer related morbidity. Brain metastatic breast cancer (BMBC) microenvironment is a heterogeneous niche of cellular and acellular components of which the innate immune cells, microglia, and macrophages, comprise the major fraction. However, the role of these innate immune cells in the tumor microenvironment (TME) in mediating cancer progression and response to therapy is not well understood. To address this need, herein, we developed three dimensional (3D) co-culture spheroids using brain metastatic triple negative breast cancer (TNBC) cell line MDA-MB-231Br or patient derived brain metastatic TNBC cell line F2-7 with THP1 monocytes. Under co-culture conditions MDA-MB-231Br co-culture spheroids assumed highly protrusive morphology with enhanced mesenchymal and proliferative characteristics. Additionally, phenotypic determination of cocultured macrophages revealed elevated levels of markers associated with alternatively activated macrophages i.e. CD163, CD206, and c-Myc. Furthermore, we found that under coculture conditions immunosuppressive and evasive markers PD1, PDL1, CD47 and CD24 were significantly upregulated. Similarly, F2-7 and monocyte cocultures also led to an immunosuppressive environment with elevated levels of M2 type markers and associated anti-inflammatory cytokines. We further found that the presence of M2 type macrophages in the microenvironment of BMBC spheroids led to acquired resistance against Paclitaxel, a clinically relevant chemotherapeutic drug against BMBC. In sum, in our coculture conditions, brain metastatic TNBC cells polarized monocytes into immunosuppressive and pro-tumorigenic tumor associated macrophages leading to a pro-tumoral microenvironment. Thus, 3D co-culture spheroids of BMBC cells and monocytes can serve as robust platform for studying cancer cell and innate immune cell interactions occurring in the BMBC environment.

IMMU-23. NEOADJUVANT ANTI-PD-1 AND ANTI-CTLA-4 COMBINATION THERAPY INDUCED INTRATUMORAL IMMUNOLOGIC ALTERATIONS IN RECURRENT GBM PATIENTS

Abstract Glioblastoma (GBM) is a highly aggressive brain tumor that responds poorly to checkpoint blockade inhibitors (ICIs), such as anti-PD-1. We previously reported that neoadjuvant anti-PD-1 therapy activated and recruited T cells into recurrent GBM (rGBM) tumors, but also increased immune checkpoint interactions between T cells and myeloid cells. To overcome this resistance mechanism, we are currently conducting a phase 1B clinical trial of neoadjuvant anti-PD-1 (Nivolumab, BMS) +/- anti-CTLA-4 (Ipilimumab, BMS) combination therapy for rGBM patients (NCT04606316). To evaluate the local tumor microenvironment effects of these checkpoint inhibitors, we used multiplex immunofluorescence (mIF), bulk RNA sequencing, and T cell receptor sequencing to analyze the intratumoral immune profile of tumors. Using mIF, we are able to determine the density of key immune cell phenotypes within the section of tumor sample as well as the proximity between phenotypes to better understand their interactions. Patients who received the combination therapy (n=15) trended to have a higher median density of cytotoxic T cells (CD45+CD8+; median density of 27.13 cells/mm2 for combination therapy and 13.78 cells/mm2 for anti-PD-1), helper T cells (CD45+CD4+; median density of 33.73 cells/mm2 for combination therapy and 9.82 cells/mm2 for anti-PD-1), monocytes (CD14+), and HLA-DR+ macrophages (CD45+CD14+HLA-DR+) while patients treated with anti-PD-1 alone (n=16) trended to have densities similar to placebo treated patients (n=6). Patients treated with combination therapy are also trending to have a higher density of macrophages in close proximity (≤20μm) to T cells, particularly HLA-DR+ macrophages, suggesting a higher frequency of interactions within their tumor microenvironments. This data set is currently incomplete, but the final data set will be completed by the meeting. Nonetheless, these preliminary results, as well as the bulk RNA sequencing and T cell receptor sequencing, suggest distinct immunologic effects of monotherapy vs. combination neoadjuvant anti-PD-1 and anti-CTLA-4 therapy in the tumor microenvironment of rGBM patients.

Development of Streptococcus pyogenes pneumnonia and pleural empyema post-chickenpox infection in a 5-year-old child: A case report

Background: The introduction of the varicella vaccine has led to a significant decrease in pediatric varicella-induced invasive Streptococcus pyogenes (group A streptococcal [GAS]) infections. However, the development of a pleural empyema following a chickenpox infection is a rare complication in pediatric patients. Case presentation: In this report, we present a 5-year-old male patient who presented to the emergency department with a deteriorating course two days after a chickenpox infection. The patient complained of high-grade documented fever, a congested throat, abdominal pain, shortness of breath, and most importantly, decreased air entry on the right side of the chest, along with the presence of crepitations. Such a deteriorated clinical picture suggested the presence of an infectious cause. The patient’s physical examination and radiological imaging provided evidence for the presence of lower right-sided lobar pneumonia. On the second day of hospitalization, the patient showed worsening respiratory distress, prompting further investigations that confirmed the development of a right-sided pleural empyema through radiological imaging. Pediatric surgery consultation was requested, and 500 cc of pus was drained following the insertion of a chest tube, which was later sent for analysis. The patient’s clinical picture improved significantly following this intervention. Due to the severity of his condition, the patient was transferred to the pediatric intensive care unit (PICU) for close monitoring. After one night in the PICU, during which his condition stabilized and oxygen therapy was gradually weaned off, the patient continued to improve on the general ward. Daily assessments and laboratory tests showed decreasing inflammatory markers and resolution of symptoms. Following three days of admission and confirmation of no underlying immunologic deficiency, the patient was discharged home with appropriate antibiotic therapy and follow-up instructions. Discussion: Similar cases have been sporadically documented in pediatric literature, with notable examples involving older patients. The pathophysiology involves complex immune interactions and virulence factors of GAS, contributing to severe outcomes such as pleural effusion. Conclusion: In this case, the 5-year-old patient experienced a severe progression from chickenpox to pleural empyema but ultimately improved following prompt medical intervention and chest tube drainage. The patient was discharged after a successful recovery, highlighting the efficacy of early recognition and treatment in managing such complications.

Cuproptosis-related lncRNA JPX regulates malignant cell behavior and epithelial-immune interaction in head and neck squamous cell carcinoma via miR-193b-3p/PLAU axis

The development, progression, and curative efficacy of head and neck squamous cell carcinoma (HNSCC) are influenced by complex interactions between epithelial and immune cells. Nevertheless, the specific changes in the nature of these interactions and their underlying molecular mechanisms in HNSCC are not yet fully understood. Cuproptosis, a form of programmed cell death that is dependent on copper, has been implicated in cancer pathogenesis. However, the understanding of cuproptosis in the context of HNSCC remains limited. In this study, we have discovered that cuproptosis-related long non-coding RNAs (CRLs) known as JPX play a role in promoting the expression of the oncogene urokinase-type plasminogen activator (PLAU) by competitively binding to miR-193b-3p in HNSCC. The increased activity of the JPX/miR-193b-3p/PLAU axis in malignant epithelial cells leads to enhanced cell proliferation, migration, and invasion in HNSCC. Moreover, the overexpression of PLAU in tumor epithelial cells facilitates its interaction with the receptor PLAUR, predominantly expressed on macrophages, thereby influencing the abnormal epithelial–immune interactome in HNSCC. Notably, the JPX inhibitor Axitinib and the PLAU inhibitor Palbociclib may not only exert their effects on the JPX/miR-193b-3p/PLAU axis that impacts the malignant tumor behaviors and the epithelial–immune cell interactions but also exhibit synergistic effects in terms of suppressing tumor cell growth and arresting cell cycle by targeting epidermal growth factor receptor (EGFR) and cyclin-dependent kinase (CDK4/6) for the treatment of HNSCC.

Immune system activation and cognitive impairment in arterial hypertension.

Chronic arterial hypertension disrupts the integrity of the cerebral microvasculature, doubling the risk of age-related dementia. Despite sufficient antihypertensive therapy, in still a significant proportion of individuals blood pressure lowering alone does not preserve cognitive health. Accumulating evidence highlights the role of inflammatory mechanisms in the pathogenesis of hypertension. In this review, we introduce a temporal framework to explore how early immune system activation and interactions at neurovascular-immune interfaces pave the way to cognitive impairment. The overall paradigm suggests that pro-hypertensive stimuli induce mechanical stress and systemic inflammatory responses that shift peripheral and meningeal immune effector mechanisms towards a pro-inflammatory state. Neurovascular-immune interfaces in the brain include a dysfunctional blood-brain barrier, crossed by peripheral immune cells; the perivascular space, in which macrophages respond to cerebrospinal fluid- and blood-derived immune regulators; and the meningeal immune reservoir, particularly T cells. Immune responses at these interfaces bridge peripheral and neurovascular unit inflammation, directly contributing to impaired brain perfusion, clearance of toxic metabolites and synaptic function. We propose that deep immunophenotyping in biofluids together with advanced neuroimaging could aid in the translational determination of sequential immune and brain endotypes specific to arterial hypertension. This could close knowledge gaps on how and when immune system activation transits into neurovascular dysfunction and cognitive impairment. In the future, targeting specific immune mechanisms could prevent and halt hypertension disease progression before clinical symptoms arise, addressing the need for new interventions against one of the leading threats to cognitive health.

Spatial Transcriptomic Signatures of Early Acute T Cell-mediated Rejection in Kidney Transplants.

Kidney transplantation significantly improves the quality of life for those with end-stage renal failure, yet allograft rejection resulting from immune cell interactions remains a persistent challenge. Although T cell-directed immunosuppressive drugs effectively contain graft rejection in most patients, a notable proportion still experiences acute T cell-mediated rejection (TCMR). Despite an emphasis on suppressing T cell-mediated immune responses, successful control over TCMR is not always achieved, suggesting the potential involvement of factors beyond T cells. Biopsy samples from suspicious (borderline) for acute TCMR (borderline TCMR) and non-TCMR patients were obtained 9 d postsurgery, and spatial transcriptomics profiling was conducted using the GeoMx Digital Spatial Profiler platform. Regions of interest in the glomerulus and interstitium were selected on the basis of immunohistochemistry staining anti-CD3 to identify areas with T-lymphocyte infiltration. Differential gene expression analysis was performed using unpaired t tests. Unbiased clustering of transcriptional profiles across all regions of interest showed distinct transcriptional profiles between glomeruli and interstitium in non-TCMR samples, whereas borderline TCMR samples displayed no distinct transcriptional profiles between these regions. Contrary to the prevailing T cell-centric view, we observed pathways and genes associated with innate immunity-related inflammatory conditions expressed in glomerular regions of borderline TCMR biopsies. Immunofluorescence staining for CD68 confirmed the presence of macrophages in the glomeruli of the post-TCMR sample in a validation cohort, indicating macrophage involvement in the glomerular response after TCMR. Activation of the innate immune response in borderline TCMR appears to impact not only the interstitium but also the glomerulus. Glomerulus-specific immune signatures suggest the role of the innate immune system in rejection. This nuanced understanding proposes the necessity for tailored therapeutic interventions targeting both innate and adaptive immune pathways to enhance transplant outcomes.

A Novel Gene Signature Based on Immune Cell Infiltration Landscape Predicts Prognosis in Lung Adenocarcinoma Patients.

The tumor microenvironment (TME) is created by the tumor and dominated by tumor-induced interactions. Long-term survival of lung adenocarcinoma (LUAD) patients is strongly influenced by immune cell infiltration in TME. The current article intends to construct a gene signature from LUAD ICI for predicting patient outcomes. For the initial phase of the study, the TCGA-LUAD dataset was chosen as the training group for dataset selection. We found two datasets named GSE72094 and GSE68465 in the Gene Expression Omnibus (GEO) database for model validation. Unsupervised clustering was performed on the training cohort patients using the ICI profiles. We employed Kaplan-Meier estimators and univariate Cox proportional-hazard models to identify prognostic differentially expressed genes in immune cell infiltration (ICI) clusters. These prognostic genes are then used to develop a LASSO Cox model that generates a prognostic gene signature. Validation was performed using Kaplan-Meier estimation, Cox, and ROC analysis. Our signature and vital immune-relevant signatures were analyzed. Finally, we performed gene set enrichment analysis (GSEA) and immune infiltration analysis on our finding gene signature to further examine the functional mechanisms and immune cellular interactions. Our study found a sixteen-gene signature (EREG, HPGDS, TSPAN32, ACSM5, SFTPD, SCN7A, CCR2, S100P, KLK12, MS4A1, INHA, HOXB9, CYP4B1, SPOCK1, STAP1, and ACAP1) to be prognostic based on data from the training cohort. This prognostic signature was certified by Kaplan-Meier, Cox proportional-hazards, and ROC curves. 11/15 immune-relevant signatures were related to our signature. The GSEA results indicated our gene signature strongly correlates with immune-related pathways. Based on the immune infiltration analysis findings, it can be deduced that a significant portion of the prognostic significance of the signature can be attributed to resting mast cells. We used bioinformatics to determine a new, robust sixteen-gene signature. We also found that this signature's prognostic ability was closely related to the resting mast cell infiltration of LUAD patients.

A Pump-Free Microfluidic Co-Culture System for Investigating NK Cell-Tumor Spheroid Interactions in Flow Conditions.

Natural killer (NK) cells are pivotal in immunotherapy due to their potent tumor-targeting capabilities. However, accessible in vitro 3D dynamic models for evaluating Tumor Infiltrating Natural Killer Cells (TINKs) remain scarce. This study addresses this gap by developing a novel pump-free microfluidic chip to investigate the interactions between NK-92 cells and prostate DU 145 tumor spheroids. The platform facilitates the separation of free NKs and TINKs for subtype characterization. The design integrates multiple planes with a multi-layer paper scaffold to accommodate tumor spheroids, allowing NK-92 cells to traverse Matrigel-coated barriers that mimic the extracellular matrix. The dual-channel pump-free device enables unidirectional circulation of NK-92 cells, allowing analysis of tumor spheroid movement and NK-92 cell interactions under flow conditions. Results demonstrate continuous fluid circulation in the dual-channel device by rocking the platform at tilt angles of 21° and 15°. Tumor spheroids showed enhanced migration under flow conditions compared to static culture. Although spheroids did not recruit significantly more NK-92 cells under flow conditions, CD56 and CD16 receptor expression on IL-2-activated free NK-92 cells and tumor-infiltrating NK-92 cells matched in vivo patterns in dynamic cultures. These findings suggest that tumor cells and fluid dynamics significantly influence NK cell subtypes. This pump-free microfluidic platform is a functional tool for simulating and studying immune cell-tumor interactions, providing valuable insights into NK cell dynamics with tumor spheroids in physiologically relevant environments.

Markov field network model of multi-modal data predicts effects of immune system perturbations on intravenous BCG vaccination in macaques.

Analysis of multi-modal datasets can identify multi-scale interactions underlying biological systems but can be beset by spurious connections due to indirect impacts propagating through an unmapped biological network. For example, studies in macaques have shown that Bacillus Calmette-Guerin (BCG) vaccination by an intravenous route protects against tuberculosis, correlating with changes across various immune data modes. To eliminate spurious correlations and identify critical immune interactions in a public multi-modal dataset (systems serology, cytokines, and cytometry) of vaccinated macaques, we applied Markov fields (MFs), a data-driven approach that explains vaccine efficacy and immune correlations via multivariate network paths, without requiring large numbers of samples (i.e., macaques) relative to multivariate features. We find that integrating multiple data modes with MFs helps remove spurious connections. Finally, we used the MF to predict outcomes of perturbations at various immune nodes, including an experimentally validated B cell depletion that induced network-wide shifts without reducing vaccine protection.

Deciphering the Tumor Microenvironment in Prostate Cancer: A Focus on the Stromal Component.

Prostate cancer progression is significantly affected by its tumor microenvironment, in which mesenchymal cells play a crucial role. Stromal cells are modified by cancer mutations, response to androgens, and lineage plasticity, and in turn, engage with epithelial tumor cells via a complex array of signaling pathways and ligand-receptor interactions, ultimately affecting tumor growth, immune interaction, and response to therapy. The metabolic rewiring and interplay in the microenvironment play an additional role in affecting the growth and progression of prostate cancer. Finally, therapeutic strategies and novel clinical trials with agents that target the stromal microenvironment or disrupt the interaction between cellular compartments are described. This review underscores cancer-associated fibroblasts as essential contributors to prostate cancer biology, emphasizing their potential as prognostic indicators and therapeutic targets.

Analysis and validation of diagnostic biomarkers and immune cell infiltration characteristics in Crohn’s disease by integrating bioinformatics and machine learning

Crohn’s disease (CD) presents significant diagnostic and therapeutic challenges due to its unclear etiology, frequent relapses, and limited treatment options. Traditional monitoring often relies on invasive and costly gastrointestinal procedures. This study aimed to identify specific diagnostic markers for CD using advanced computational approaches. Four gene expression datasets from the Gene Expression Omnibus (GEO) were analyzed, identifying differentially expressed genes (DEGs) through gene set enrichment analysis in R. Key biomarkers were selected using machine learning algorithms, including LASSO logistic regression, SVM‑RFE, and Random Forest, and their accuracy was assessed using receiver operating characteristic (ROC) curves and nomogram models. Immune cell infiltration was analyzed using the CIBERSORT algorithm, which helped reveal associations between diagnostic markers and immune cell patterns in CD. From a training set of 605 CD samples and 82 normal controls, we identified eight significant biomarkers: LCN2, FOLH1, CXCL1, FPR1, S100P, IGFBP5, CHP2, and AQP9. The diagnostic model showed high predictive power (AUC=0.954) and performed well in external validation (AUC = 1). Immune cell infiltration analysis highlighted various immune cells involved in CD, with all diagnostic markers strongly linked to immune cell interactions. Our findings propose candidate hub genes and present a nomogram for CD diagnosis, providing potential diagnostic biomarkers for clinical applications in CD.

NAT10 functions as a pivotal regulator in gastric cancer metastasis and tumor immunity.

Gastric cancer (GC) presents a significant global health burden, with metastasis being the leading cause of treatment failure and mortality. NAT10, a regulatory protein involved in mRNA acetylation, has been implicated in various cancers. However, its role in GC, especially concerning metastasis and immune interactions, remains unclear. Utilizing multi-omics data from gastric cancer samples, we conducted comprehensive analyses to investigate NAT10 expression, its correlation with clinical parameters and immune relevance. Bioinformatics analysis and digital image processing were employed for this purpose. Furthermore, in vitro and in vivo experiments were conducted to elucidate the functional role of NAT10 in gastric cancer progression, aiming to provide deeper biological insights. Our findings reveal a significant association between NAT10 expression and various aspects of transcriptional, protein, as well as tumor immunity in GC patients. Additionally, we demonstrated that NAT10 promotes gastric cancer cell proliferation and migration, both in cellular models and in animal studies, suggesting its involvement in early tumor microvascular metastasis. NAT10 emerges as a promising molecular target, offering potential avenues for further research into molecular mechanisms and therapeutic strategies for GC.