CDKN1A is a target for phagocytosis-mediated cellular immunotherapy in acute leukemia

CDKN1A as a potential target for Eltrombopag treatment in ITP and its regulation of the communication between macrophages and transitional B cells in ITP

This study aimed to identify novel biomarkers associated with Eltrombopag response in patients with immune thrombocytopenia (ITP) and to investigate the role of macrophage and transitional B cells in ITP pathogenesis. Differentially expressed genes were identified using the GSE112278 dataset, followed by weighted gene co-expression network analysis (WGCNA) to screen hub genes. Single-cell RNA-seq data from GSE196676 were analyzed using the Seurat package to assess immune cell composition, gene expression, and cell-cell communication. CDKN1A expression was experimentally modulated in RAW264.7 macrophages via siRNA knockdown or plasmid overexpression. Phagocytic function was assessed using CFDA-labeled mouse platelets and F4/80 immunofluorescence staining. Molecular docking was conducted to evaluate the interaction between Eltrombopag and CDKN1A. Through intersection analysis, we identified CDKN1A as a key gene influencing the response of ITP patients to Eltrombopag treatment. Single-cell data analysis revealed a significant increase in the proportion of macrophages in ITP patients, accompanied by downregulation of CDKN1A expression in these macrophages, which was closely associated with macrophage activation and enhanced phagocytic capacity. Functional experiments confirmed that CDKN1A knockdown promoted, while overexpression inhibited, macrophage phagocytosis of platelets. Additionally, cell communication analysis demonstrated that macrophages in ITP patients interact with transitional B cells via the TGFβ signaling pathway. Further analysis revealed that a subset of macrophages performs effector functions by differentiating into specialized subtypes that function independently, without direct interaction with other immune cells. Our study identified CDKN1A as a key regulator of Eltrombopag's effectiveness in treating ITP. CDKN1A expression was reduced in macrophages of ITP patients and that it interacted with transitional B cells through the TGFβ signaling pathway to promote disease progression. These findings offer new insights into the pathogenic mechanisms of ITP and suggest CDKN1A as a potential therapeutic target for future interventions.

Polarized Macrophages Show Diverse Pro-Angiogenic Characteristics Under Normo- and Hyperglycemic Conditions

Angiogenesis plays a crucial role in solid tumor growth. Ischemia and inflammation induce various angiogenic mediators, and patient metabolic conditions importantly influence this process. Macrophages closely interact with the vascular system and regulate angiogenesis through pro/anti-angiogenic factors. Traditionally, pro-angiogenic activity has been attributed to M2-like macrophages. We question this, as recent evidence suggests that also M1-like macrophages can be pro-angiogenic. Therefore, the aim is to identify the pro/anti-angiogenic gene expression profiles of human polarized macrophages unbiasedly. We also examine the effect of hyperglycemia on angiogenic gene expression, reflecting its role in diabetes and other metabolic conditions. Bioinformatic analysis was performed on the angiogenesis-related gene expression profiles of CD14+ monocyte-derived M1(IFN-γ)- and M2(IL-4)-polarized macrophages. The top differentially expressed genes were selected for validation. Macrophages were generated in vitro and polarized to M1(IFN-γ) and M2(IL-4/IL-6) cells under standard/hyperglycemic conditions. After immunophenotypic confirmation, selected gene expression was quantified using qPCR. IL-4 and IL-6 induce distinct M2-like phenotypes with mixed pro/anti-angiogenic gene expression. Remarkably, IFN-γ stimulation also increases several pro-angiogenic genes. Hyperglycemia affects the angiogenic expression profile in both M1- and M2-like macrophages, although distinctive identities remain intact. The pro-angiogenic phenotype is not limited to M2-polarized macrophages. Both M1- and M2-like macrophages express complex pro/anti-angiogenic gene profiles, which are only mildly influenced by hyperglycemia.

Molecular features and diagnostic modeling of synovium- and IPFP-derived OA macrophages in the inflammatory microenvironment via scRNA-seq and machine learning

BACKGROUND

Osteoarthritis (OA) is the leading cause of degenerative joint disease, with total joint replacement as the only definitive cure. However, no disease-modifying therapy is currently available. Inflammation and fibrosis in the infrapatellar fat pad (IPFP) contribute to OA onset and progression. However, the cellular composition and molecular mechanisms in the IPFP microenvironment remain unclear. This study investigates the functions of OA-macrophages and their clinical significance.

METHODS

We analyzed single-cell RNA sequencing (scRNA-seq) data from normal and OA patients. Enrichment analysis revealed differences in biological pathways across cell types. Pseudotime and cell-cell communication analyses revealed the developmental trajectory and interactions of OA-macrophages with other cell types. Machine learning (ML) algorithms identified feature genes of OA-macrophages. An OAMGS diagnostic score was developed, and CIBERSORT was used to analyze immune infiltration and its association with immune cells. Rat OA and normal models were established, and feature gene expression was validated using immunofluorescence (IF) staining and quantitative reverse transcription PCR (RT-qPCR).

RESULTS

OA-macrophages play a central role in inflammation and fibrosis, enhancing leukocyte recruitment, chondrocyte apoptosis, and angiogenesis. They interact with chondrocytes, endothelial cells, and fibroblasts via CXCL and NF-κB signaling. High-dimensional weighted gene co-expression network analysis (hdWGCNA) identified 352 module genes linked to OA-macrophages. Machine learning developed a four-gene-based OAMGS score that accurately identifies OA-macrophages, with an AUC of 1 in the discovery cohort and 0.990 in an external cohort. Gene expression was validated in the OA model using RT-qPCR and IF.

CONCLUSION

This study identifies a macrophage subcluster elevated in OA patients. OA-macrophages play an immunoregulatory role and may serve as diagnostic markers. The OAMGS score, based on four genes, provides an accurate diagnostic tool and potential therapeutic target for OA.

Identification of key therapeutic targets in nicotine-induced intracranial aneurysm through integrated bioinformatics and machine learning approaches

BACKGROUND

Intracranial aneurysm (IA) is a critical cerebrovascular condition, and nicotine exposure is a known risk factor. This study delves into the toxicological mechanisms of nicotine in IA, aiming to identify key biomarkers and therapeutic targets.

METHODS

Gene Set Variation Analysis (GSVA), Weighted Gene Co-Expression Network Analysis (WGCNA), and enrichment analyses were conducted on differentially expressed genes (DEGs) from the GSE122897 dataset. Additionally, nicotine-related targets were identified using CTD, SwissTargetPrediction, and Super-PRED databases. Integrative machine learning approaches, such as Random Forest (RF) and Support Vector Machine (SVM), were employed to pinpoint key toxicity targets. Molecular docking and immune cell infiltration analyses were also performed.

RESULTS

DEGs in IA showed significant alterations in metabolic, secretory, signaling, and homeostatic pathways. Several immune and metabolic response pathways were notably disrupted. WGCNA identified 1127 DEGs with 37 overlapping toxic targets between IA and nicotine. ssGSEA revealed substantial upregulation in immune response and inflammation-related processes. Integrative analyses highlighted TGFB1, MCL1, and CDKN1A as core toxicity targets, confirmed via molecular docking studies. Immune cell infiltration analysis indicated significant correlations between these core targets and various immune cell populations.

CONCLUSION

This study uncovers significant disruptions in metabolic and immune pathways in IA under nicotine influence, identifying TGFB1, MCL1, and CDKN1A as critical biomarkers. These findings offer a deeper understanding of IA's molecular mechanisms and potential therapeutic targets for nicotine-related toxicity.

The anti-melanoma roles and mechanisms of tricholoma isoflavone derivative CA028

As a form of skin cancer, melanoma's incidence rate is continuing to rise globally. Therefore, there is an urgent need to find new agents to improve survival in melanoma patients. Isoflavones, a class of phytoestrogens, are primarily found in soy and other legumes. Cumulating evidence demonstrates that isoflavones exhibits significant anti-tumor properties and is beneficial for the prevention and treatment of melanoma. In the present study, we aim to investigate the anti-melanoma role of tricholoma isoflavone derivative CA028. By using in vitro melanoma cell line models, A375 and A2058 and in vivo xenograft mouse model, our results indicate that melanoma proliferation, migration, and invasion are attenuated following CA028 treatment. In addition, the treatment of CA028 induced cell apoptosis of melanoma. Finally, we addressed the mechanism of CA028 against melanoma by comparative transcriptomic analysis. The results of gene ontology highlighted the involvement of CA028's targets in the cell proliferation, cell apoptosis, and migration ability of melanoma cells. Furthermore, Ingenuity Pathway Analysis constructed the network involved in the apoptotic roles of CA028 through targeting p53 signaling and death receptor signaling. For the first time, our data suggested the possible use of modified isoflavone for therapeutic applications against melanoma.

Blockade of the CD47/SIRPα checkpoint axis potentiates the macrophage-mediated antitumor efficacy of tafasitamab

Macrophages are one of the key mediators of the therapeutic effects exerted by monoclonal antibodies, such as the anti-CD19 antibody tafasitamab, approved in combination with lenalidomide for the treatment of relapsed or refractory diffuse large B-cell lymphoma (DLBCL). However, antibody-dependent cellular phagocytosis (ADCP) in the tumor microenvironment can be counteracted by increased expression of the inhibitory receptor SIRPα on macrophages and its ligand, the immune checkpoint molecule CD47, on tumor cells. The aim of this study was to investigate the impact of the CD47-SIRPα axis on tafasitamab- mediated phagocytosis and explore the potential of anti-CD47 blockade to enhance its antitumor activity. Elevated expression of both SIRPα and CD47 was observed in DLBCL patient-derived lymph node biopsies compared to healthy control lymph nodes. CRISPR-mediated CD47 overexpression affected tafasitamab-mediated ADCP in vitro and increased expression of SIRPα on macrophages correlated with decreased ADCP activity of tafasitamab against DLBCL cell lines. A combination of tafasitamab and an anti-CD47 blocking antibody enhanced ADCP activity of in vitro-generated macrophages. Importantly, tafasitamab-mediated phagocytosis was elevated in combination with CD47 blockade using primary DLBCL cells and patient-derived lymphoma-associated macrophages in an autologous setting. Furthermore, lymphoma cells with low CD19 expression were efficiently eliminated by the combination treatment. Finally, combined treatment of tafasitamab and an anti-CD47 antibody resulted in enhanced tumor volume reduction and survival benefit in lymphoma xenograft mouse models. These findings provide evidence that CD47 blockade can enhance the phagocytic potential of tumor-targeting immunotherapies such as tafasitamab and suggest that there is value in exploring the combination in the clinic.

The Zeb1-Cxcl1 axis impairs the antitumor immune response by inducing M2 macrophage polarization in breast cancer

Zeb1, a key epithelial-mesenchymal transition (EMT) regulator, has recently been found to be involved in M2 macrophage polarization in the tumor immune microenvironment, thereby promoting tumor development. However, the underlying mechanism of Zeb1-induced M2 macrophage polarization remains largely unexplored. To identify the potential role of Zeb1 in remodeling the tumor immune microenvironment in breast cancer, we crossed the floxed Zeb1 allele homozygously into PyMT mice to generate PyMT;Zeb1cKO (MMTV-Cre;PyMT;Zeb1fl/fl ) mice. We found that the recruitment of M2-type tumor-associated macrophages (TAMs) was significantly reduced in tumors from PyMT;Zeb1cKO mice, and their tumor suppressive effects were weakened. Mechanistically, Zeb1 played a crucial role in transcriptionally promoting the production of Cxcl1 in tumor cells. In turn, Cxcl1 activated the Cxcr2-Jak-Stat3 pathway to induce M2 polarization of TAMs in a paracrine manner, which eventually led to T-cell inactivation and impaired the antitumor immune response in breast cancer. Our results collectively revealed an important role of Zeb1 in remodeling the tumor microenvironment, suggesting a novel therapeutic intervention for the treatment of advanced breast cancer.

T-cell acute lymphoblastic leukemia progression is supported by inflammatory molecules including hepatocyte growth factor

T-cell acute lymphoblastic leukemia (T-ALL) is a malignant hematological disorder characterized by an increased proliferation of immature T lymphocytes precursors. T-ALL treatment includes chemotherapy with strong side effects, and patients that undergo relapse display poor prognosis. Although cell-intrinsic oncogenic pathways are well-studied, the tumor microenvironment, like inflammatory cellular and molecular components is less explored in T-ALL. We sought to determine the composition of the inflammatory microenvironment induced by T-ALL, and its role in T-ALL progression. We show in two mouse T-ALL cell models that T-ALLs enhance blood neutrophils and resident monocytes, accompanied with a plasmatic acute secretion of inflammatory molecules. Depleting neutrophils using anti-Ly6G treatment or resident monocytes by clodronate liposomes treatment does not modulate plasmatic inflammatory molecule secretion and mice survival. However, inhibiting the secretion of inflammatory molecules by microenvironment with NECA, an agonist of adenosine receptors, diminishes T-ALL progression enhancing mouse survival. We uncovered Hepatocyte Growth Factor (HGF), T-ALL-driven and the most decreased molecule with NECA, as a potential therapeutic target in T-ALL. Altogether, we identified a signature of inflammatory molecules that can potentially be involved in T-ALL evolution and uncovered HGF/cMET pathway as important to target for limiting T-ALL progression.

The purinergic receptor P2X7 and the NLRP3 inflammasome are druggable host factors required for SARS-CoV-2 infection

Purinergic receptors and NOD-like receptor protein 3 (NLRP3) inflammasome regulate inflammation and viral infection, but their effects on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection remain poorly understood. Here, we report that the purinergic receptor P2X7 and NLRP3 inflammasome are cellular host factors required for SARS-CoV-2 infection. Lung autopsies from patients with severe coronavirus disease 2019 (COVID-19) reveal that NLRP3 expression is increased in host cellular targets of SARS-CoV-2 including alveolar macrophages, type II pneumocytes and syncytia arising from the fusion of infected macrophages, thus suggesting a potential role of NLRP3 and associated signaling pathways to both inflammation and viral replication. In vitro studies demonstrate that NLRP3-dependent inflammasome activation is detected upon macrophage abortive infection. More importantly, a weak activation of NLRP3 inflammasome is also detected during the early steps of SARS-CoV-2 infection of epithelial cells and promotes the viral replication in these cells. Interestingly, the purinergic receptor P2X7, which is known to control NLRP3 inflammasome activation, also favors the replication of D614G and alpha SARS-CoV-2 variants. Altogether, our results reveal an unexpected relationship between the purinergic receptor P2X7, the NLRP3 inflammasome and the permissiveness to SARS-CoV-2 infection that offers novel opportunities for COVID-19 treatment.

Role of anoikis-related gene PLK1 in kidney renal papillary cell carcinoma: a bioinformatics analysis and preliminary verification on promoting proliferation and migration

Background: Kidney renal papillary cell carcinoma (KIRP) is a rare malignancy with a very poor prognosis. Anoikis is a specific form of apoptosis involved in carcinogenesis, but the role of anoikis in KIRP has not been explored. Methods: Anoikis-related genes (ARGs) were obtained from the GeneCards database and Harmonizome database and were used to identify different subtypes of KIRP and construct a prognostic model of KIRP. In addition, we also explored the immune microenvironment and enrichment pathways among different subtypes by consensus clustering into different subtypes. Drug sensitivity analysis was used to screen for potential drugs. Finally, we verified the mRNA and protein expression of the independent prognostic gene PLK1 in patient tissues and various cells and further verified the changes in relevant prognostic functions after constructing a PLK1 stable knockdown model using ShRNA. Results: We identified 99 differentially expressed anoikis-related genes (DEGs) associated with KIRP survival, and selected 3 genes from them to construct a prognostic model, which can well predict the prognosis of KIRP patients. Consensus clustering divided KIRP into two subtypes, and there was a significant difference in survival rates between the two subtypes. Immune profiling revealed differing immune statuses between the two subtypes, and functional analysis reveals the differential activity of different functions in different subtypes. Drug sensitivity analysis screened out 15 highly sensitive drugs in the high-risk group and 11 highly sensitive drugs in the low-risk group. Univariate and multivariate Cox regression analysis confirmed that PLK1 was an independent prognostic factor in KIRP, and its mRNA and protein expression levels were consistent with gene differential expression levels, both of which were highly expressed in KIRP. Functional verification of PLK1 in KIRP revealed significant results. Specifically, silencing PLK1 inhibited cell proliferation, clonogenicity, and migration, which indicated that PLK1 plays an important role in the proliferation and migration of KIRP. Conclusion: The prognosis model constructed by ARGs in this study can accurately predict the prognosis of KIRP patients. ARGs, especially PLK1, play an important role in the development of KIRP. This research can help doctors provide individualized treatment plans for KIRP patients and provide researchers with new research ideas.