Immune Cell Infiltration Research Articles

The potential of ESCO2 as a prognostic and immunotherapeutic marker of pan-cancer and its role in anti-PD1 treatment of bladder cancer.

Background Establishment of sister chromatid cohesion N-acetyltransferase 2 (ESCO2), a member of the EFO2 family, is implicated in the pathogenesis and progression of various cancers. However, there has been limited comprehensive pan-cancer analysis conducted on ESCO2 thus far. Methods Publicly available databases, such as the UCSC Xena database, were utilized to examine differential expression patterns across various cancer types. In addition, variations in expression levels were investigated across distinct clinical stages. Univariate Cox regression and Kaplan-Meier survival analyses were conducted to evaluate the impact on overall survival (OS), disease-specific survival (DSS), disease-free interval (DFI), and progression-free interval (PFI) at a pan-cancer level. The correlation between ESCO2 expression and immune cell infiltration was examined to gain insight into the tumor microenvironment in different cancers. The results of the bioinformatic analysis were validated using immunotherapy clinical trials and pathological specimens. CCK-8 and transwell assay experiments were performed to investigate the biological function of ESCO2. Results ESCO2 expression was found to be up-regulated in most cancers, with a correlation to TNM stages. Prognostic analysis indicated that overexpression of ESCO2 was associated with poor prognosis in various cancers. Furthermore, the correlation between ESCO2 expression and immune cell infiltration suggested its potential as a predictor for immunotherapy efficacy. Notably, ESCO2 expression showed positive associations with immunoinhibitor, immnostimulator, MHC molecule, chemokine receptor, tumor mutation burden (TMB) and microsatellite instability (MSI) levels in bladder cancer (BLCA). The validation cohort for immunotherapy corroborated these findings and substantiated that ESCO2 could function as an autonomous prognostic biomarker and a promising target for cancer treatment via immunotherapy. In addition, in vitro experiments confirmed the role of ESCO2 in influcing the proliferation, invasion and migration of BLCA cells. Conclusion ESCO2 participates in regulating the immune infiltration and affecting the prognosis of patients in many cancers, especially in BLCA. ESCO2 may serve as a prognostic and immunotherapy biomarker in future treatment of human cancer.

BIOM-65. ELEVATED MMP9 EXPRESSION IN ADHERENT AND LARGE VESTIBULAR SCHWANNOMAS: A PROMISING THERAPEUTIC TARGET

Abstract Vestibular schwannoma (VS) is the most common tumor of the cerebellopontine angle affecting up to 1 in 2000 adults and presents significant treatment challenges, especially when the tumor is adherent to the brainstem and cranial nerves. These tumors often require complex surgeries with high risks of complications such as hearing loss, facial paralysis, and incomplete tumor resection. Previous studies have linked immune cell infiltration and protease activation to aggressive VS. MMP9, a protease involved in extracellular matrix (ECM) remodeling, is associated with cancer invasion and progression, suggesting its potential as a biomarker and therapeutic target. This study explores whether MMP9 can classify VS and improve surgical outcomes. METHODS Fresh tumors were collected from patients undergoing surgery to establish primary VS cultures. Transcriptomic profiling was performed to examine expression of genes related to ECM remodeling, protease activation, and immune cell infiltration. MMP9 expression during schwannoma progression was validated using immunofluorescence staining and ELISA. Transwell invasion assays were performed to evaluate the role of MMP9 in schwannoma invasion. The efficacy of small molecule inhibitors against eIF4F (a transcription factor that binds to 5’ UTR of MMP9) and against MMP9 was tested in a mouse model of schwannoma. RESULTS MMP9 was the most abundantly expressed protease in VS. MMP9 expression increased with tumor size, and was higher in adherent than non-adherent VS (49.7 vs. 13.8 ng/mL, p=0.014). MMP9 expression was abundant in perivascular regions in adherent VS. Inhibition of eIF4F reduced schwannoma cell invasion mediated by MMP9.MMP9 inhibition in vivo- reduced tumor burden by 50% in mice. CONCLUSIONS MMP9 is a highly active protease in VS growth and adherent VS. Developing MMP9-targeted therapies could be a breakthrough in managing these challenging tumors.

TMIC-73. SEX DIFFERENCES IN INTERFERON-GAMMA RESPONSES IN GLIOMA MICROENVIRONMENT

Abstract IFNγ is a cytokine with both pro- and anti-tumorigenic effects and its role in glioma immunotherapy resistance is not well understood. In the tumor microenvironment, T and NK cells produce IFNγ, which affects cellular phenotypes in most of the cancer and stromal cells since IFNγ receptor is ubiquitously expressed. IFNγ induces expression of molecules that confer resistance to immunotherapies, such as PDL1, PDL2, IDO1, and iNOS. The goal of this study is to elucidate cell type-specific responses to IFNγ in immune competent glioma models we developed that are resistant to immunotherapy. We intracranially injected male and female murine glioma cells into B6 and Ifng-/- honst mice to measure overall survival and perform immune phenotyping and single cell RNA-sequencing analyses. Ifnγ-/- hosts exhibited a shorter survival, and the proportion of GBM cells is higher in Ifng-/- hosts compared to wild type, indicating that the net effect of IFNγ signaling in glioma is anti-tumorigenic. In a recent study, we published that IFNγ-response pathway is enriched in the mesenchymal-like (MES-like) subtype of human GBM cells, compared to neutral-progenitor-like (NPC-like) and oligodendrocyte-progenitor-like (OPC-like) cells (Abdelfattah et al., 2022). To test our hypothesis that IFNγ signaling induces MES transition in glioma cells in vivo, we compared fractions of glioma cell subtypes in wildtype and Ifng-/- male and female hosts. In female Ifng-/- mice, MES-like GBM cell fraction was reduced while OPC-like fraction was increased, supporting our hypothesis. However, there was no difference in male hosts. Furthermore, gliomas grown in female B6 hosts showed higher infiltration of immune cells (CD45+), lymphocytes (CD3+) and fewer resident microglia cells (CD11b+CD45int), compared with Ifng-/- female hosts. In contrast, no significant difference in immune cell infiltration was observed between B6 vs Ifng-/- males. These results suggest an unanticipated and complex context-dependent role of IFNγ signaling in GBM, which include sex differences in its role in immune cell recruitment and MES transition in glioma cells.

EXTH-75. IMMUNOVIROTHERAPY WITH PP2A AND PD-1 INHIBITION IN PEDIATRIC HIGH-GRADE GLIOMA

Abstract Pediatric high-grade gliomas (HGGs) represent a significant clinical challenge with poor survival rates. Engineered oncolytic herpes simplex virus (oHSV) has shown potential in several clinical trials at targeting HGGs through their direct lytic effect and induction of an immune response. We have learned from our clinical trial experience (NCT02457845) that a critical barrier to more durable response is augmenting and sustaining the anti-tumor immune response generated by oHSV. LB-100, a protein phosphatase 2A (PP2A) inhibitor, is known to enhance T-cell activity. We hypothesized that LB-100 with anti-PD-1 therapy would overcome the immunosuppressive barriers, enhancing the immunotherapeutic effects of oHSV and improve survival in an immunocompetent murine model. We investigated the therapeutic impact of clinically available, next-generation oHSV, M002, which expresses murine interleukin-12, combined with LB-100 and PD-1 inhibition compared to M002 with LB-100 or anti-PD-1 antibody, each therapy alone, or control by measuring median survival and changes in the tumor immune microenvironment. The triple combination of M002, LB-100, and anti-PD-1 antibody significantly extended median survival compared to control (45 days vs 22.5 days, P=0.001) or each treatment alone, and compared to M002 and LB-100 (44 days vs 28 days, P=0.017) or M002 and anti-PD-1 (45.5 days vs 41 days, P=0.023). This increase in survival was correlated with a robust increase in CD45+ immune cell infiltration and a reduction in T-regulatory cells. We will further investigate the changes in the tumor microenvironment to better understand the specific contributions of different immune cell populations. These data support the hypothesis that LB-100 enhances the efficacy of oHSV by amplifying T-cell-mediated immune responses against tumor cells. This combination therapy demonstrates a promising strategy that warrants further exploration and potential clinical application, emphasizing the critical role of targeting multiple aspects of immune regulation to enhance the efficacy of oncolytic virotherapy in pediatric tumors.

TMIC-75. ICAM-1 PROMOTES AN IMMUNOSUPPRESSIVE LANDSCAPE IN GLIOBLASTOMAS BY REGULATING THE PHENOTYPIC POLARIZATION STATE OF TUMOR ASSOCIATED MACROPHAGES

Abstract Glioblastoma (GBM) is a fatal adult CNS tumor, with a median overall survival of 12-15 months. Intercellular adhesion molecule 1 (ICAM-1) is a cell adhesion molecule whose expression is significantly greater in the mesenchymal transcriptional subtype of GBMs, whereby it is prognostic. We have previously shown that when ICAM-1 is knocked out in the tumor microenvironment (TME) of immune-competent GBM-bearing mice, these mice showed prolonged overall survival and reduced tumor volume. It is yet to be determined how ICAM-1 expression affects infiltration and functional polarization of tumor-associated macrophages (TAMs) and other immune cells in GBM, and if we can suppress the infiltration of M2-like TAMs into the TME by inhibiting ICAM-1. We used a mouse glioma model with and without knockout (KO) of the ICAM-1 gene and intracranially injected GL261 cells. ICAM-1 KO mice survived longer and had reduced tumor volume relative to wildtype, with survival and volume differences being rescued upon ICAM-1 bone marrow reconstitution. Upon endpoint, we performed cytometry by time-of-flight, and found that ICAM-1 KO tumors harbored a reduction in helper T cells, Tregs, and cytotoxic T cells, but an increased proportion in double-negative T cells relative to ICAM-1 WT tumors. ICAM-1 KO tumors also demonstrated an increased proportion of M1-like TAMs relative to M2-like. These results were validated upon administration of ISIS-3082 to tumor models, an antisense oligonucleotide for which a human-specific form has been fast-track approved for other diseases, that targets ICAM-1 transiently in peripheral immune cells prior to TME infiltration. These findings suggest that ICAM-1 expression influences immune cell infiltration, potentially modulates the functional state of TAMs towards a M1-like state, and that ICAM-1 may be targeted in TAMs to ‘reeducate’ them before entering the TME. This may be translated into clinical practice and combined with standards-of-care to render GBMs more sensitive to treatment.

TMIC-66. A NEW MOUSE MODEL THAT COMBINES DRIVER MUTATIONS TO ACCURATELY RECAPITULATE THE DIVERSE PHENOTYPES OF HUMAN GLIOBLASTOMA

Abstract To effectively beat glioblastoma, new pre-clinical models are needed: to dissect the biology of processes like migration and therapy resistance; to understand immune suppression and immunotherapy; and to use as a model for testing in therapeutic development. We have developed a new panel of glioblastoma mouse models, which engineer well-characterised glioblastoma driver mutations into an immortalised eGFP murine astrocyte-like cell. These “GEM-CLeM” are Genetically Engineered Mouse Cell Line Models. When transplanted intra-cranially into immunocompetent mice, these lines formed tumors with the key characteristics of glioblastoma – migratory and invasive, with rapid proliferation and infiltration of suppressive immune cells. The eGFP expression allowed detection of glioblastoma cells in situ and ex vivo, and the ability to readily distinguish tumor and stromal components of the tumors. Importantly, different combinations of driver mutations led to diverse tumor phenotypes. Loss of Pten with over-expression of mutant RAS generated tumors with 100% efficiency and the same time to tumor onset as the commonly used GL261 cell line. However, unlike GL261 tumors the Pten-RASV12 tumors had a highly invasive edge and extensive migration, and were full of pro-tumorigenic macrophages and monocytes, with very few T-cells or dendritic cells. Together, this recapitulated the phenotype of human wildtype IDH1 glioblastoma. In contrast, the very common EGFRvIII mutant did not drive tumor formation in combination with Pten loss. We also modelled mutant IDH glioblastoma by combining loss of p53 with overexpression of IDH1R132H. These were slow growing, densely packed tumors with extensive microglial involvement in addition to pro-tumorigenic macrophages. This GEM-CLeM system combines the benefits of the traditional genetically engineered mouse models with accessible, rapid, reproducible tumor formation. The GEM-CLeM lines are amenable to further genetic manipulation, so cells can be customised with other mutations to ask important biological questions in the presence of an intact tumor immune microenvironment.

TMIC-16. SPECIFIC TARGETING OF THE MRNA EXPRESSION OF TGFB2 LIGAND TO POTENTIALLY ENHANCE IMMUNE THERAPIES IN LOW-GRADE GLIOMAS

Abstract Low-grade glioma (LGG) tumors are characterized by a low infiltration of immune cells, requiring therapies augmenting the immune response in the tumor microenvironment (TME). The Transforming Growth Factor beta (TGFB) pathway contributes to an immunosuppressive environment. We propose targeting the specific inhibition of Transforming Growth Factor Beta 2, TGFB2 mRNA, as an attractive therapeutic strategy using antisense oligonucleotides. We conducted a bioinformatic-led investigation highlighting the ratio of TGFB2:TGFB1 mRNA expression levels in the cohort of 513 TCGA patients, revealing the TGFB2 ratio as a negative prognostic indicator through utilizing a multivariate Cox proportional hazards model that included the TGFB2 ratio and age at diagnosis as linear covariates to predict overall survival (OS). The model showed a 1.8-fold higher TGFB2 ratio relative to TGFB1 mRNA expression correlated to worse OS. Furthermore, the impact of the TGFB2 ratio was significantly affected by the age at diagnosis, in which older patients exhibited worse OS at increased TGFB2 ratios. Increasing the ratio of TGFB2 relative to TGFB1, TGFB3, TGFBR1, or TGFBR2 in LGG patients led to significant increases in multivariate Cox model determined hazards ratios, HR (HR (95% CI range)) of 1.372 (1.224-1.539), 1.434 (1.288-1.560), 1.327 (1.195-1.473), and 1.381 (1.233-1.547) respectively (P<0.0001 for all comparisons). Correlation of TGFB2:TGFB1/TGFB3/TGFBR1/TGFBR2 ratio across 1330 Reactome pathways using Gene Set Enrichment Analysis showed the most positively correlated genes were members of TME pathways including PD-1 signaling, Syndecan interactions, Non-integrin membrane-ECM interactions, EPH-Ephrin signaling, and Collagen biosynthesis and modifying enzymes. These results suggest that the specific targeting TGFB2 in LGG can remodel the TME for immune therapies to improve OS outcomes.

TMIC-12. LITT RESULTS IN ROBUST T CELL INFILTRATION WITHIN THE TUMOR MICROENVIRONMENT IN A BRAIN METASTASIS MURINE MODEL

Abstract INTRODUCTION Laser interstitial thermal therapy (LITT) is a novel minimally invasive neurosurgical technique used to ablate intra-axial brain tumors with real-time thermometry. The impact of LITT on the brain metastatic tumor microenvironment (TME) is unknown in patients due to limitations of tumor tissue collection post-LITT. The primary objective of this study was to describe the kinetics of immunologic infiltration within the TME in a melanoma brain metastasis model. METHOD: C57BL6 mice underwent intra-cranial implantation of B16F10-OVA tumor cells and treated with LITT using a custom-made murine LITT system developed in our laboratory. The tumors were treated to 42°C (near infra-red 1064 nm DPSS laser system) 7 days post-surgery. Tumors were collected 2 days and 10 days post-LITT for immune-phenotyping using flow cytometry. Blood was collected 6 h and 48 h post-LITT to perform the ELISA for IFN-g and TNF-a. RESULTS LITT treatment triggered a cascade of local infiltration of immune cells at different time points. 2-days post-LITT resulted in increased CD8 T cells (p<0.05), macrophage (p<0.05) and microglia infiltration (p<0.01) within the TME compared to control and sham surgery animals. By 10 days after LITT, significant infiltration by CD8 T cells (p<0.0001) and M1 macrophages (p<0.0001) was observed. The CD8 T cells were T central memory (TCM) and T effector memory (TEM). Moreover, comparison between 2 days and 10 days after LITT revealed significant increase of TEM (p<0.0001) and TCM (p<0.001) 10 days post-LITT. In an ELISA assay, non-significant differences were observed in IFN-g and TNF-a level at 48 h. CONCLUSIONS LITT enhances the recruitment of cytotoxic CD8 T cells within TME in a time-dependent manner. The ability of LITT to recruit TCM and TEM to the TME strongly support its potential therapeutic benefit, especially in the context of immunotherapy.

M5C related-regulator-mediated methylation modification patterns and prognostic significance in breast cancer

5-Methylcytosine (m5C) is closely associated with cancer. However, the role of m5C in breast cancer(BC)remains unclear. This study combined single-cell RNA sequencing (scRNA-Seq) and transcriptomics datasets to screen m5C regulators associated with BC progression and analyze their clinical values. Firstly, This study elucidates the mechanisms of the m5C landscape and the specific roles of m5C regulators in BC patients. we found that the dysregulation of m5C regulators with m5Cscore play the essential role of the carcinogenesis and progression in epithelial cells and myeloid cells of BC at single cell level. External validation was conducted using an independent scRNA-Seq datasets. Then, three distinct m5C modification patterns were identified by transcriptomics datasets. Based on the m5C differentially expressed regulators, the m5Cscore was constructed, and used to divide patients with BC into high and low m5Cscore groups. Patients with a high m5Cscore had more abundant immune cell infiltration, stronger antitumor immunity, and better prognoses. Finally, Quantitative real-time (PCR) and immunohistochemistry were used for the in vitro experimental validation, which had extensive prognostic value. In this study, we aimed to assess the expression of m5C regulators involved in BC and investigate their correlation with the tumor microenvironment, clinicopathological characteristics, and prognosis of BC. The m5C regulators could be used to effectively assess the cell specific regulation prognosis of patients with BC and develop more effective immunotherapy strategies.

CTIM-34. EFFECTS OF NEOADJUVANT IMMUNE CHECKPOINT INHIBITION ON PEDIATRIC AND ADULT HIGH-GRADE GLIOMAS

Abstract High-grade gliomas (HGG) are lethal tumors with few long-term survivors affecting adult and pediatric patients. Studies investigating immune checkpoint inhibition (ICI) suggest administration of neoadjuvant anti-PD1 blockade (neo-aPD1) enhances local and systemic anti-tumor responses. This data is supported by increased T cell density in the tumor and proportion of cytotoxic T cells in peripheral blood. In a previous randomized clinical trial, neo-aPD1 improved survival in adult with recurrent glioblastoma. In this study, we utilized multiplex immunofluorescence (mIF), and single-cell RNA sequencing (scRNA-seq) to investigate the effects of neoadjuvant ICI on the TME and compare between pediatric and adult populations. Tissue samples from adult patients with recurrent GBM treated with neo-aPD1 (n=22) or adjuvant only therapy (n=5) were obtained from our UCLA off-label neo-PD1 study. Tissue samples were also obtained from pediatric patients with recurrent/progressive HGG treated with neoadjuvant ICI from the ongoing Pediatric Neuro-Oncology Consortium study PNOC19. Samples included diagnostic tissue from two patients and on study surgery tissue from four patients. All tissue samples were subjected to mIF and underwent imaging analysis to assess immune cell infiltration by quantifying lymphoid and myeloid cell densities across the two treatment groups. Our preliminary findings elucidated a trend of higher T cell infiltration in adult neoadjuvant compared to adjuvant-only treated patients (median density 58.11 vs 15.15 T-cells/mm2). Compared to their adult counterparts, neoadjuvant ICI treated pediatric patients had even more robust total T cell infiltration (median density 268.10 vs 58.11 T-cell/mm2, pediatric vs adult respectively). scRNA-seq analysis revealed a greater enrichment of monocytic macrophages in the pediatric population compared to tissue resident microglia in the adults. This early data requires analysis of additional samples to better understand differences in the anti-tumor immune response between adult and pediatric recurrent/progressive HGG patients.

EXTH-78. A NOVEL BISPECIFIC S100A4/TFR ANTIBODY TO REPROGRAM THE GLIOMA TUMOR MICROENVIRONMENT AND TARGET GLIOMA STEM CELLS

Abstract GBM (glioblastoma) is the most common and aggressive primary brain tumor in adults. While immunotherapy is a promising treatment modality for GBM, most clinical trials have thus far only provided a modest benefit to GBM patients. We propose that enhancing the efficacy of immunotherapy for GBM requires approaches that increase T cell infiltration and reprogram the myeloid cells to a more pro-inflammatory state. S100A4 is a major regulator of stemness, epithelial-mesenchymal transition, and a critical regulator of immune suppressive myeloid and T cell phenotypes in GBM. Targeting S100A4 in either glioma or stromal cells is sufficient to reprogram the tumor immune landscape and extend survival of glioma bearing mice, indicating that S100A4 is a promising immunotherapy target. We recently developed a S100A4 blocking monoclonal antibody; however, this antibody does not cross the blood brain barrier (BBB) efficiently to confer significant therapeutic benefit, limiting its efficacy in treating GBM. To overcome this challenge, we generated a bispecific S100A4-TfR antibody (BsA) that allows robust BBB penetration, and tested this in a pre-clinical syngeneic, orthotopic mouse model of GBM. Using ELISA, confocal immunofluorescent microscopy, flow cytometry, and bulk RNA sequencing, we report that systemic administration of the S100A4-TfR BsA results in increased immune cell infiltration with a preferential increase in CD4 T cell infiltration, and potent immune remodeling of the tumor microenvironment to a more pro-inflammatory state. Furthermore, the BsA is taken up by glioma cells intracellularly, which is correlated with depletion of intracellular S100A4 and decreased nuclear SOX2 localization, which would reduce stemness of glioma cells. Functionally, in vitro BsA treatment of primary glioma cell cultures shows decreased S100A4 expression, proliferation, and self-renewal. Our results suggest that S100A4-TfR BsA is a novel dual activity inhibitor to simultaneously reprogram the GBM immune landscape and reduce glioma stemness.

Discovery of key molecular signatures for diagnosis and therapies of glioblastoma by combining supervised and unsupervised learning approaches.

Glioblastoma (GBM) is the most malignant brain cancer and one of the leading causes of cancer-related death globally. So, identifying potential molecular signatures and associated drug molecules are crucial for diagnosis and therapies of GBM. This study suggested GBM-causing ten key genes (ASPM, CCNB2, CDK1, AURKA, TOP2A, CHEK1, CDCA8, SMC4, MCM10, and RAD51AP1) from nine transcriptomics datasets by combining supervised and unsupervised learning results. Differential expression patterns of key genes (KGs) between GBM and control samples were verified by different independent databases. Gene regulatory network (GRN) detected some important transcriptional and post-transcriptional regulators for KGs. The KGs-set enrichment analysis unveiled some crucial GBM-causing molecular functions, biological processes, cellular components, and pathways. The DNA methylation analysis detected some hypo-methylated CpG sites that might stimulate the GBM development. From the immune infiltration analysis, we found that almost all KGs are associated with different immune cell infiltration levels. Finally, we recommended KGs-guided four repurposable drug molecules (Fluoxetine, Vatalanib, TGX221 and RO3306) against GBM through molecular docking, drug likeness, ADMET analyses and molecular dynamics simulation studies. Thus, the discoveries of this study could serve as valuable resources for wet-lab experiments in order to take a proper treatment plan against GBM.

Silver nanoparticle induced immunogenic cell death can improve immunotherapy

Cancer immunotherapy is often hindered by an immunosuppressive tumor microenvironment (TME). Various strategies are being evaluated to shift the TME from an immunologically ‘cold’ to ‘hot’ tumor and hereby improve current immune checkpoint blockades (ICB). One particular hot topic is the use of combination therapies. Here, we set out to screen a variety of metallic nanoparticles and explored their in vitro toxicity against a series of tumor and non-tumor cell lines. For silver nanoparticles, we also explored the effects of core size and surface chemistry on cytotoxicity. Ag-citrate-5 nm nanoparticles were found to induce high cytotoxicity in Renca cells through excessive generation of reactive oxygen species (ROS) and significantly increased cytokine production. The induced toxicity resulted in a shift of the immunogenic cell death (ICD) marker calreticulin to the cell surface in vitro and in vivo. Subcutaneous Renca tumors were treated with anti-PD1 or in combination with Ag-citrate-5 nm. The combination group resulted in significant reduction in tumor size, increased necrosis, and immune cell infiltration at the tumor site. Inhibition of cytotoxic CD8 + T cells confirmed the involvement of these cells in the observed therapeutic effects. Our results suggest that Ag-citrate-5 nm is able to promote immune cell influx and increase tumor responsiveness to ICB therapies.

Exploring the mechanisms of chronic obstructive pulmonary disease and Crohn’s disease: a bioinformatics-based study

This study explored the comorbid mechanisms between Crohn’s disease (CD) and chronic obstructive pulmonary disease (COPD) using bioinformatics analysis. From the Gene Expression Omnibus (GEO) microarray dataset, 349 common differentially expressed genes (coDEGs) were identified, and 8 shared hub genes were found: CCL2, CXCL1, TLR2, ICAM1, PTPRC, ITGAX, PTGS2, and MMP9, which were vital for immune function and regulation of inflammatory responses. In addition, the study also analyzed the association between coDEGs and immune cell infiltration using the single-sample gene set enrichment algorithm (ssGSEA). Potential drugs related to these genes were identified using the connectivity map (CMap). These findings provided new perspectives for understanding the interaction between CD and COPD.

Bifunctional Metal–Organic Framework Synergistically Enhances Radiotherapy and Activates STING for Potent Cancer Radio‐Immunotherapy

AbstractThe activation of the stimulator of interferon genes (STING) protein by cyclic dinucleotide metabolites plays a critical role in antitumor immunity. However, synthetic STING agonists like 4‐(5,6‐dimethoxybenzo[b]thiophen‐2‐yl)‐4‐oxobutanoic acid (MSA‐2) exhibit suboptimal pharmacokinetics and fail to sustain STING activation in tumors for effective antitumor responses. Here, we report the design of MOF/MSA‐2, a bifunctional MSA‐2 conjugated nanoscale metal–organic framework (MOF) based on Hf6 secondary building units (SBUs) and hexakis(4′‐carboxy[1,1′‐biphenyl]‐4‐yl)benzene bridging ligands, for potent cancer radio‐immunotherapy. By leveraging the high‐Z properties of the Hf6 SBUs, the MOF enhances the therapeutic effect of X‐ray radiation and elicits potent immune stimulation in the tumor microenvironment. MOF/MSA‐2 further enhances radiotherapeutic effects of X‐rays by enabling sustained STING activation and promoting the infiltration and activation of immune cells in the tumors. MOF/MSA‐2 plus low‐dose X‐ray irradiation elicits strong STING activation and potent tumor regression, and when combined with an immune checkpoint inhibitor, effectively suppresses both primary and distant tumors through systemic immune activation.

Prognostic characteristics and drug sensitivity analysis of hepatocellular carcinoma based on histone modification-related genes: a multi-omics integrated study revealing potential therapeutic targets and individualized treatment strategies

BackgroundHepatocellular carcinoma (HCC) ranks among the most prevalent and lethal malignancies worldwide. Histone modifications (HMs) play a pivotal role in the initiation and progression of HCC. However, our understanding of HMs in HCC remains limited due to the disease’s heterogeneity and the complexity of HMs.MethodsWe integrated multi-omics data from multiple cohorts, including single-cell RNA sequencing, bulk RNA sequencing, and clinical information. Weighted gene co-expression network analysis (WGCNA) and consensus clustering were employed to identify histone-related genes. We developed a histone modification-related signature (HMRS) using 117 machine learning methods. Comprehensive analyses of molecular characteristics, immune landscape, and drug sensitivity associated with the HMRS were performed.ResultsThrough integrative analysis, we defined 110 histone-related genes and identified 45 HCC-HM-related genes (HCC-HMRgenes). The HMRS demonstrated robust prognostic value across multiple cohorts. Patients with high HMRS scores exhibited distinct genomic alterations, including higher tumor heterogeneity and TP53 mutations. The high-risk group showed enrichment in cell cycle, DNA repair, and metabolic pathways. Immune landscape analysis revealed significant differences in immune cell infiltration and pathway activities between high- and low-risk groups. Drug sensitivity prediction suggested potential therapeutic strategies for different risk groups.ConclusionOur study provides a comprehensive understanding of HMs in HCC and establishes a robust prognostic signature. The HMRS not only stratifies patients into distinct risk groups but also offers insights into underlying molecular mechanisms, immune characteristics, and potential therapeutic strategies, paving the way for personalized medicine in HCC.

Multi-omics analysis of Prolyl 3-hydroxylase 1 as a prognostic biomarker for immune infiltration in ccRCC

The formation of human collagen requires the presence of Prolyl 3-hydroxylase 1 (P3H1), but the regulatory mechanism of P3H1 remained insufficiently understood. Our study aimed to identify the role of P3H1 in clear cell renal cell carcinoma (ccRCC). P3H1 expression in ccRCC was validated using multiple databases and in vitro experiments. We performed a correlation analysis of P3H1 with drug sensitivity, immune checkpoints, and immune cell infiltration using transcriptome and single-cell sequencing. Drawing upon the Encyclopedia of RNA Interactomes database, we selected P3H1 as the focal point of our investigation, meticulously uncovering the intricate network of microRNAs and lncRNAs that potentially orchestrate ceRNA mechanisms. This study employs a multidimensional approach integrating vitro assays and multi-omics bioinformatics analyses to investigate P3H1’s impact on ccRCC prognosis, immune modulation, immune checkpoints, ceRNA regulatory network, drug sensitivity, and therapeutic responses, aiming to uncover new insights into its therapeutic potential and inform future clinical strategies.

Overexpression of CDCA8 predicts poor prognosis and drug insensitivity in lung adenocarcinoma

BackgroundLung adenocarcinoma (LUAD) accounts for the highest proportion of lung cancers; however, specific biomarkers are lacking for diagnosis, treatment, and prognostic assessment. Cell division cycle-associated 8 (CDCA8) is a cell cycle regulator with elevated expression in various cancers. However, the association between CDCA8 expression and LUAD prognosis remains unclear.MethodsThe association between CDCA8 and LUAD prognosis was evaluated based on the The Cancer Genome Atlas (TCGA) dataset, and CDCA8 related functions were determined using gene enrichment and gene ontology analyses. We also analyzed the association between CDCA8 expression and immune cell infiltration. Immunohistochemistry was used to determine the differential expression of CDCA8 in tumors and controls. Finally, we evaluated the differences in the sensitivity of different levels of CDCA8 to different anticancer drugs in LUAD.ResultsCDCA8 expression was significantly higher in primary LUAD tumors than in normal tissues (P < 0.001). Moreover, Kaplan–Meier survival analysis demonstrated that high CDCA8 expression predicted poor survival in patients with LUAD (P = 0.006). The receiver operating characteristic (ROC) curves indicated that CDCA8 was an effective guide for the diagnosis of LUAD. Functional annotation indicated that CDCA8 might be involved in functions such as p53 stabilization, nucleotide metabolism, RNA-mediated gene silencing, and the G2/M phase checkpoint. Immune infiltration results suggested that CDCA8 was positively correlated with Th2 cells and Tgd and negatively correlated with Eosinophils and Mast cells (P < 0.01). In addition, elevated expression of CDCA8 may increase the sensitivity of patients to certain anticancer drugs.ConclusionsCDCA8 upregulation is significantly associated with poor survival and immune infiltration in patients with LUAD. Our study suggests that CDCA8 can be used as a biomarker for LUAD prognosis and a reference for personalized medication.Graphical

M6A-related genes and their role in Parkinson's disease: Insights from machine learning and consensus clustering.

Parkinson disease (PD) is a chronic neurological disorder primarily characterized by a deficiency of dopamine in the brain. In recent years, numerous studies have highlighted the substantial influence of RNA N6-methyladenosine (m6A) regulators on various biological processes. Nevertheless, the specific contribution of m6A-related genes to the development and progression of PD remains uncertain. In this study, we performed a differential analysis of the GSE8397 dataset in the Gene Expression Omnibus database and selected important m6A-related genes. Candidate m6A-related genes were then screened using a random forest model to predict the risk of PD. A nomogram model was built based on the candidate m6A-related genes. By employing a consensus clustering method, PD was divided into different m6A clusters based on the selected significant m6A-related genes. Finally, we performed immune cell infiltration analysis to explore the immune infiltration between different clusters. We performed a differential analysis of the GSE8397 dataset in the Gene Expression Omnibus database and selected 11 important m6A-related genes. Four candidate m6A-related genes (YTH Domain Containing 2, heterogeneous nuclear ribonucleoprotein C, leucine-rich pentatricopeptide repeat motif containing protein and insulin-like growth factor binding protein-3) were then screened using a random forest model to predict the risk of PD. A nomogram model was built based on the 4 candidate m6A-related genes. The decision curve analysis indicated that patients can benefit from the nomogram model. By employing a consensus clustering method, PD was divided into 2 m6A clusters (cluster A and cluster B) based on the selected significant m6A-related genes. The immune cell infiltration analysis revealed that cluster A and cluster B exhibit distinct immune phenotypes. In conclusion, m6A-related genes play a significant role in the development of PD and our study on m6A clustering may potentially guide personalized treatment strategies for PD in the future.

SNAP25 as a prognostic marker in transcriptome analysis of meningioma.

Meningiomas are the most common intracranial tumors and their diagnosis relies mostly on neuroimaging and histology. However, the histology grades cannot predict the outcome exactly and some meningiomas tend to recur after resection of even benign tumors. Therefore, it is necessary to explore prognostic and diagnostic molecular targets. Differential expression analysis between meningiomas and meninges was performed based on the merged data of GSE43290 and GSE84263. Next, we performed gene set enrichment analysis (GSEA), immune cell infiltration analysis, protein-protein interaction analysis, and survival analysis using public data. The expression level of Synaptosome-associated-protein-25kDa (SNAP25) was verified by reverse transcription quantitative real-time polymerase chain reaction (RT-qPCR) and Western blotting in meningioma tissues. There were 263 upregulated and 592 downregulated genes identified in meningiomas by differential expression analysis. GSEA results revealed that meningiomas were negatively related to the pathway of soluble N-ethylmaleimide sensitive factor attachment protein receptor interactions in vascular transport and chemokine signaling. SNAP25 was characterized as a hub gene and downregulated in meningiomas. The Kaplan-Meier plot indicated that high expression of SNAP25 is a favorable factor. SNAP25 was downregulated and identified as a potential prognostic marker in meningioma.