Degree Of Immune Cell Infiltration Research Articles

Identification of a Gene Expression Signature to Predict the Risk of Early Recurrence and the Degree of Immune Cell Infiltration in Triple-negative Breast Cancer.

Patients with triple-negative breast cancer (TNBC) have a high rate of recurrence within 3 years of diagnosis and a high rate of death within 5 years compared to other subtypes. The number of clinical trials investigating various new agents and combination therapies has recently increased; however, current strategies benefit only a minority of patients. This study aimed to identify specific genes that predict patients at high risk of recurrence and the immune status of the tumor microenvironment at an early stage, thereby providing insight into potential therapeutic targets to improve clinical outcomes in TNBC patients. We evaluated the prognostic significance of microarray mRNA expression of 20,603 genes in 233 TNBC patients from the METABRIC dataset and further validated the results using RNA-seq mRNA expression data in 143 TNBC patients from the GSE96058 dataset. Eighteen differentially expressed genes (AKNA, ARHGAP30, CA9, CD3D, CD3G, CD6, CXCR6, CYSLTR1, DOCK10, ENO1, FLT3LG, IFNG, IL2RB, LPXN, PRKCB, PVRIG, RASSF5, and STAT4) identified in both datasets were found to be reliable biomarkers for predicting TNBC recurrence and progression. Notably, the genes whose low expression was associated with increased risk of recurrence and death were immune-related genes, with significant differences in levels of immune cell infiltration in the tumor microenvironment between high- and low- expression groups. Genes reported herein may be effective biomarkers to identify TNBC patients who will and will not benefit from immunotherapy and may be particularly important genes for developing future treatment strategies, including immunotherapy.

Comprehensive pan-cancer analysis reveals prognostic implications of TMEM92 in the tumor immune microenvironment.

Transmembrane protein 92 (TMEM92) has been implicated in the facilitation of tumor progression. Nevertheless, comprehensive analyses concerning the prognostic significance of TMEM92, as well as its role in immunological responses across diverse cancer types, remain to be elucidated. In this study, data was sourced from a range of publicly accessible online platforms and databases, including TCGA, GTEx, UCSC Xena, CCLE, cBioPortal, HPA, TIMER2.0, GEPIA, CancerSEA, GDSC, exoRBase, and ImmuCellAI. We systematically analyzed the expression patterns of TMEM92 at both mRNA and protein levels across diverse human organs, tissues, extracellular vesicles (EVs), and cell lines associated with multiple cancer types. Subsequently, analyses were conducted to determine the relationship between TMEM92 and various parameters such as prognosis, DNA methylation, copy number variation (CNV), the tumor microenvironment (TME), immune cell infiltration, genes with immunological relevance, tumor mutational burden (TMB), microsatellite instability (MSI), mismatch repair (MMR), and half-maximal inhibitory concentration (IC50) values. In the present study, we observed a pronounced overexpression of TMEM92 across a majority of cancer types, which was concomitantly associated with a less favorable prognosis. A notable association emerged between TMEM92 expression and both DNA methylation and CNV. Furthermore, a pronounced relationship was discerned between TMEM92 expression, the TME, and the degree of immune cell infiltration. Intriguingly, while TMEM92 expression displayed a positive correlation with macrophage presence, it inversely correlated with the infiltration level of CD8 + T cells. Concurrently, significant associations were identified between TMEM92 and the major histocompatibility complex, TMB, MSI, and MMR. Results derived from Gene Set Enrichment Analysis and Gene Set Variation Analysis further substantiated the nexus of TMEM92 with both immune and metabolic pathways within the oncogenic context. These findings expanded the understanding of the roles of TMEM92 in tumorigenesis and progression and suggest that TMEM92 may have an immunoregulatory role in several malignancies.

Construction of a ferroptosis and hypoxia-related gene signature in cervical cancer to assess tumour immune microenvironment and predict prognosis

Background This study aimed to investigate the potential role of ferroptosis/hypoxia-related genes in cervical cancer to improve early management and treatment of cervical cancer. Methods All data were downloaded from public databases. Ferroptosis/hypoxia-related genes associated with cervical cancer prognosis were selected to construct a risk score model. The relationship between risk score and clinical features, immune microenvironment and prognosis were analysed. Results Risk score model was constructed based on eight signature genes. Drug prediction analysis showed that bevacizumab and cisplatin were related to vascular endothelial growth factor A. Risk score, as an independent prognostic factor of cervical cancer, had a good survival prediction effect. The two groups differed significantly in degree of immune cell infiltration, gene expression, tumour mutation burden and somatic variation. Conclusions We developed a novel prognostic gene signature combining ferroptosis/hypoxia-related genes, which provides new ideas for individual treatment of cervical cancer.

Magnetic resonance imaging-based radiomics was used to evaluate the level of prognosis-related immune cell infiltration in breast cancer tumor microenvironment.

The tumor immune microenvironment is a valuable source of information for predicting prognosis in breast cancer (BRCA) patients. To identify immune cells associated with BRCA patient prognosis from the Cancer Genetic Atlas (TCGA), we established an MRI-based radiomics model for evaluating the degree of immune cell infiltration in breast cancer patients. CIBERSORT was utilized to evaluate the degree of infiltration of 22 immune cell types in breast cancer patients from the TCGA database, and both univariate and multivariate Cox regressions were employed to determine the prognostic significance of immune cell infiltration levels in BRCA patients. We identified independent prognostic factors for BRCA patients. Additionally, we obtained imaging features from the Cancer Imaging Archive (TCIA) database for 73 patients who underwent preoperative MRI procedures, and used the Least Absolute Shrinkage and Selection Operator (LASSO) to select the best imaging features for constructing an MRI-based radiomics model for evaluating immune cell infiltration levels in breast cancer patients. According to the results of Cox regression analysis, M2 macrophages were identified as an independent prognostic factor for BRCA patients (HR = 32.288, 95% CI: 3.100-357.478). A total of nine significant features were selected to calculate the radiomics-based score. We established an intratumoral model with AUCs (95% CI) of 0.662 (0.495-0.802) and 0.678 (0.438-0.901) in the training and testing cohorts, respectively. Additionally, a peritumoral model was created with AUCs (95% CI) of 0.826 (0.710-0.924) and 0.752 (0.525-0.957), and a combined model was established with AUCs (95% CI) of 0.843 (0.723-0.938) and 0.744 (0.491-0.965). The peritumoral model demonstrated the highest diagnostic efficacy, with an accuracy, sensitivity, and specificity of 0.773, 0.727, and 0.818, respectively, in its testing cohort. The MRI-based radiomics model has the potential to evaluate the degree of immune cell infiltration in breast cancer patients, offering a non-invasive imaging biomarker for assessing the tumor microenvironment in this disease.

Construction and validation of a prognostic signature for mucinous colonic adenocarcinoma based on N7-methylguanosine-related long non-coding RNAs.

Mucinous colonic adenocarcinoma remains a challenging disease due to its high propensity for metastasis and recurrence. N7-methylguanosine (m7G) and long non-coding RNA (lncRNA) are closely associated with the occurrence and progression of tumors. However, research on m7G-related lncRNA in mucinous colonic adenocarcinoma is lacking. Therefore, we sought to explore the prognostic impact of m7G-related lncRNAs in mucinous adenocarcinoma (MC) patients. In this study, Pearson analysis was used to identify m7G-related lncRNAs from transcriptome data in The Cancer Genome Atlas (TCGA). Univariate Cox regression analysis and least absolute shrinkage and selection operator (LASSO) regression were used to further screen m7G-related lncRNAs and incorporate them into a prognostic signature. Based on the risk model, patients were divided into low- and high-risk groups and randomly assigned to the training set and test sets in a 6:4 ratio. Kaplan-Meier, receiver operating characteristic (ROC) curve, multivariate regression, and nomogram analyses were used to confirm the accuracy of the signature. The CIBERSORT algorithm was used to calculate the degree of immune cell infiltration (ICI). Finally, the correlation of the prognostic signature with tumor mutational burden (TMB) and immunophenotype score (IPS) was evaluated. A total of 432 m7G-related lncRNAs were identified by Pearson analysis. Univariate Cox regression, LASSO regression and survival analysis were performed to further select six m7G-related lncRNAs (P<0.05): AC254629.1, LINC01133, LINC01134, MHENCR, SMIM2-AS1, and XACT. Based on the risk model, heat maps, Kaplan-Meier curves, and ROC curves were constructed, and the results showed that there were significant differences in expression levels and survival status between the two risk groups. The area under the ROC curve (AUC) values for 3-, 5-, and 10-year survival in the training set were 0.944, 0.957, and 1.000, respectively. And in the test set were 0.964, 1.000, and 1.000, respectively. Subsequently, univariate and multivariate regression analyses of clinical characteristics and risk score were performed. The results of risk score were [hazard ratio (HR): 6.458, 95% confidence interval (CI): 2.708-15.403, P<0.001; HR: 7.280, 95% CI: 2.500-21.203, P<0.001], respectively. Using the risk score as an independent prognostic factor, the AUC of it over 3, 5, and 10 years was 0.911, 0.955, and 0.961, respectively. Calibration plots for the nomogram show that the model calibration line is very close to the ideal calibration line, indicating good calibration. The level of ICI was significantly different in the different risk groups. Survival analysis showed that, regardless of TMB risk, patients with MC and a high-risk score consistently had a poor overall survival (OS). The m7G-related lncRNA prognostic signature has potential value for the prognosis of mucinous colonic adenocarcinoma.

Vaccine-associated respiratory pathology correlates with viral clearance and protective immunity after immunization with self-amplifying RNA expressing the spike (S) protein of SARS-CoV-2 in mouse models

In this study, we evaluated the immunogenicity and protective immunity of in vitro transcribed Venezuelan equine encephalitis virus (VEEV TC-83 strain) self-amplifying RNA (saRNA) encoding the SARS-CoV-2 spike (S) protein in wild type (S-WT) and stabilized pre-fusion conformations (S-PP). Immunization with S-WT and S-PP saRNA induced specific neutralizing antibody responses in both K18-Tg hACE2 (K18) and BALB/c mice, as assessed using SARS-CoV-2 pseudotyped viruses.Protective immunity was assessed in challenge experiments. Two immunizations with S-WT and S-PP induced protective immunity, evidenced by lower mortality, lower weight loss and more than one log10 lower subgenomic virus RNA titers in the upper and lower respiratory tracts in both K18 and BALB/c mice. Histopathologic examination of lungs post-challenge showed that immunization with S-WT and S-PP resulted in a higher degree of immune cell infiltration and inflammatory changes, compared with control mice, characterized by high levels of T- and B-cell infiltration. No substantial differences were found in the presence and localization of eosinophils, macrophages, neutrophils, and natural killer cells. CD4 and CD8 T-cell depletion post immunization resulted in reduced lung inflammation post challenge but also prolonged virus clearance. These data indicate that immunization with saRNA encoding the SARS-CoV-2 S protein induces immune responses that are protective following challenge, that virus clearance is associated with pulmonary changes caused by T-cell and B-cell infiltration in the lungs, but that this T and B-cell infiltration plays an important role in viral clearance.

Identification of differentially expressed genes, signaling pathways and immune infiltration in postmenopausal osteoporosis by integrated bioinformatics analysis

BackgroundPostmenopausal osteoporosis is a systemic metabolic disorder typified by an imbalance in bone turnover, where bone resorption supersedes bone formation. This imbalance primarily arises from a decline in bone mass induced by estrogen deficiency, and an elevated risk of fractures resulting from degradation of bone microstructure. Despite recognizing these changes, the precise causative factors and potential molecular pathways remain elusive. In this study, we aimed to identify differentially expressed genes (DEGs), associated pathways, and the role of immune infiltration in osteoporosis, leveraging an integrated bioinformatics approach to shed light on potential underlying molecular mechanisms. MethodsWe retrieved the expression profiles of GSE230665 from the Gene Expression Omnibus database, comprising 15 femur samples, including 12 postmenopausal osteoporosis samples and 3 normal controls. From the aggregated microarray datasets, we derived differentially expressed genes (DEGs) for further bioinformatics analysis. We used WGCNA, analyzed DEGs, PPI, and conducted GO analysis to identify pivotal genes. We then used the CIBERSORT method to explore the degree of immune cell infiltration within femur specimens affected by postmenopausal osteoporosis. To probe into the relationship between pivotal genes and infiltrating immune cells, we conducted correlation analysis. ResultsWe identified a total of 12,204 DEGs. Among these, 12,157 were up-regulated, and 47 were down-regulated. GO and KEGG pathway analyses indicated that these DEGs predominantly targeted cellular protein localization activity and associated signaling pathways. The protein-protein interaction network highlighted four central hub-genes: RPL31, RPL34, EEF1G, and BPTF. Principal component analysis indicated a positive correlation between the expression of these genes and resting NK cells (as per CIBERSORT). In contrast, the expression of RPL31, RPL34, and EEF1G showed a negative correlation with T cells (gamma delta per CIBERSORT). ConclusionsImmune infiltration plays a role in the development of osteoporosis.

THEM6 is a prognostic biomarker for breast cancer and is associated with immune infiltration

To characterize the implications of lipid metabolism-related gene thioesterase superfamily member 6 (THEM6) in breast cancer. Several databases including The Cancer Genome Atlas (TCGA) were utilized for our meticulous bioinformatics analysis. We further performed qRT-PCR, immunoblotting and IHC assays to validate the expression of THEM6 in various breast cancer cells and tissues. In addition, we have carried out relevant functional experiments to explore the regulatory role of THEM6 in vitro. Lipid metabolism-related genes are independent factors for overall survival. According to several databases, THEM6 was significantly more expressed in cancerous tissues of breast invasive carcinoma (BRCA) compared to its paracancerous tissues. Furthermore, THEM6 overexpression was correlated with poorer overall survival of BRCA patients, serving as a separate prognostic factor for BRCA. Biological functional analyses revealed that THEM6 was associated with tumor progression and pathogenesis. Finally, we discovered that in BRCA, THEM6 expression was linked to multiple immune cell types. qRT-PCR and Western blotting experiments demonstrated a general upregulation of THEM6 expression in breast carcinoma cells. IHC showed that THEM6 was expressed in both breast cancer tissues and para-cancer tissues, but its expression level was significantly higher in carcinoma tissues. In vitro studies indicated that THEM6 increased proliferation, invasion, and inhibited apoptosis of breast carcinoma cells, while also affecting the cell cycle and promoting cancer progression. Furthermore, THEM6 may influence macrophage recruitment and polarization in the tumor microenvironment by regulating CCL2 secretion, which in turn affects macrophage recruitment in the tumor microenvironment. Our findings indicate that the overexpression of THEM6, which is linked to the development of breast cancer, is a predictor of a poor prognosis and has an impact on the degree of immune cell infiltration. Therefore, THEM6 has the potential to be a valuable target for BRCA.

Identification of immunological characterization and Anoikis-related molecular clusters in rheumatoid arthritis.

Objective: To investigate the potential association between Anoikis-related genes, which are responsible for preventing abnormal cellular proliferation, and rheumatoid arthritis (RA). Methods: Datasets GSE89408, GSE198520, and GSE97165 were obtained from the GEO with 282 RA patients and 28 healthy controls. We performed differential analysis of all genes and HLA genes. We performed a protein-protein interaction network analysis and identified hub genes based on STRING and cytoscape. Consistent clustering was performed with subgrouping of the disease. SsGSEA were used to calculate immune cell infiltration. Spearman's correlation analysis was employed to identify correlations. Enrichment scores of the GO and KEGG were calculated with the ssGSEA algorithm. The WGCNA and the DGIdb database were used to mine hub genes' interactions with drugs. Results: There were 26 differentially expressed Anoikis-related genes (FDR = 0.05, log2FC = 1) and HLA genes exhibited differential expression (P < 0.05) between the disease and control groups. Protein-protein interaction was observed among differentially expressed genes, and the correlation between PIM2 and RAC2 was found to be the highest; There were significant differences in the degree of immune cell infiltration between most of the immune cell types in the disease group and normal controls (P < 0.05). Anoikis-related genes were highly correlated with HLA genes. Based on the expression of Anoikis-related genes, RA patients were divided into two disease subtypes (cluster1 and cluster2). There were 59 differentially expressed Anoikis-related genes found, which exhibited significant differences in functional enrichment, immune cell infiltration degree, and HLA gene expression (P < 0.05). Cluster2 had significantly higher levels in all aspects than cluster1 did. The co-expression network analysis showed that cluster1 had 51 hub differentially expressed genes and cluster2 had 72 hub differentially expressed genes. Among them, three hub genes of cluster1 were interconnected with 187 drugs, and five hub genes of cluster2 were interconnected with 57 drugs. Conclusion: Our study identified a link between Anoikis-related genes and RA, and two distinct subtypes of RA were determined based on Anoikis-related gene expression. Notably, cluster2 may represent a more severe state of RA.

Development and validation of a combined hypoxia- and metabolism-related prognostic signature to predict clinical prognosis and immunotherapy responses in clear cell renal cell carcinoma.

Hypoxia and metabolism are closely correlated with the progression of cancer. We aimed to construct a combined hypoxia- and metabolism-related genes (HMRGs) prognostic signature to predict survival and immunotherapy responses in patients with clear cell renal cell carcinoma (ccRCC). The RNA-seq profiles and clinical data of ccRCC were acquired from the TCGA and the ArrayExpress (E-MTAB-1980) databases. Least absolute shrinkage and selection operator (LASSO) and univariate and multivariate Cox regression analyses were applied to establish a prognostic signature. The E-MTAB-1980 cohort was selected for validation. The effectiveness and reliability of the signature were further evaluated by Kaplan-Meier (K-M) survival and time-dependent receiver operating characteristic (ROC) curves. Further analyses, including functional enrichment, ssGSEA algorithm, CIBERSORT algorithm, and expression of immune checkpoints, were explored to investigate immune status and immunotherapy responses. We constructed a prognostic eight-gene signature with IRF6, TEK, PLCB2, ABCB1, TGFA, COL4A5, PLOD2, and TUBB6. Patients were divided into high-risk and low-risk groups based on the medium-risk score. The K-M analysis revealed that patients in the high-risk group had an apparently poor prognosis compared to those in the low-risk group in the TCGA (p < 0.001) and E-MTAB-1980 (p < 0.005). The area under ROC curve (AUC) of the prognostic signature was 0.8 at 1 year, 0.77 at 3 years, and 0.78 at 5 years in the TCGA, respectively, and was 0.82 at 1 year, 0.74 at 3 years, and 0.75 at 5 years in the E-MTAB-1980, respectively. Independent prognostic analysis confirmed the risk score as a separate prognostic factor in ccRCC patients (p < 0.001). The results of ssGSEA showed not only a high degree of immune cell infiltration but also high scores of immune-related functions in the high-risk group. The CIBERSORT analysis further confirmed that the abundance of immune cells was apparently different between the two risk groups. The risk score was significantly correlated with the expression of cytotoxic T lymphocyte-associated antigen-4 (CTLA4), lymphocyte-activation gene 3 (LAG3), and programmed cell death protein 1 (PD-1). The HMRGs signature could be used to predict clinical prognosis, evaluate the efficacy of immunotherapy, and guide personalized immunotherapy in ccRCC patients.

Analysis of Nucleoporin 107 Overexpression and Its Association with Prognosis and Immune Infiltration in Lung Adenocarcinoma by Bioinformatics Methods.

Lung adenocarcinoma (LUAD) has high morbidity and mortality. Current studies indicate nucleoporin 107 (NUP107) is involved in the construction of nuclear pore complex, and NUP107 overexpression contributes to the growth and development in most types of cancers, but its effect in LUAD has not been elucidated. Differences in NUP107 expression were investigated using the Cancer Genome Atlas (TCGA) and multiple Gene Expression Omnibus (GEO) data sets. Enrichment analysis were implemented to probe the NUP107 function. The association of NUP107 with the degree of immune cell infiltration was investigated by the TIMER database, single-sample gene set enrichment analysis (ssGSEA), and ESTIMATE. The association of NUP107 expression with tumor mutation burden (TMB), TP53, and immune checkpoint was analyzed. Single-cell RNA sequencing data were used to detect NUP107 expression in different cell clusters. Finally, we performed real-time quantitative polymerase chain reaction (RT-qPCR) and immunohistochemistry (IHC) to prove the difference of NUP107 expression. NUP107 was overexpressed in LUAD and mainly expressed in cancer stem cell (CSC). Overexpression of NUP107 in LUAD suggested a poorer prognosis. Functional enrichment analysis pointed out that NUP107 was mainly linked to the regulation of cell cycle. Both immune cell infiltration and TMB were found to be in connection with NUP107. Cases in the group with high NUP107 expression had poorer immune infiltration, but had higher expression of immune checkpoints, TMB, and proportion of TP53 mutations. NUP107 is a sensitive diagnostic and prognostic factor for LUAD and may be involved in tumor progression through its effects on cell cycle and immune infiltration.

Ferroptosis-related gene MTF-1 as a novel prognostic biomarker in low-grade glioma and its correlation with immune infiltration

BackgroundMetal-responsive transcription factor-1 performs a necessary position in a range of cancers. It is unknown, though, how the prognosis of patients with low-grade gliomas is related to immune infiltration. MethodThe Cancer Genome Atlas database was used in this investigation to evaluate MTF-1 transcription in low-grade glioma and healthy brain tissues, and immunohistochemistry was used to confirm MTF-1 levels. By using functional enrichment analysis and R software, the putative biological roles and signaling pathways connected to MTF-1 in LGG as well as its prognostic significance were investigated. Further research was done on the connection involving MTF-1 and tumor mutational burden in LGG. Finally, the research evaluated how MTF-1 and immune cell infiltration are related. ResultsWe noticed that the WHO grade, 1p/19q codeletion, and older age were all substantially linked with MTF-1 overexpression in low-grade gliomas. OS and disease-specific survival were significantly lowered as a result of MTF-1 transcription. MTF-1 was recognized as an independent OS prognostic predictor with a poor prognosis by multifactorial Cox analysis. Functional enrichment analysis revealed that the primary enrichment pathways were chemical carcinogenesis—receptor activation and the generation of miRNAs implicated in gene suppression by miRNA. Additionally, there was a negative correlation between MTF-1 overexpression and the degree of immune cell infiltration in neutrophils and DC. ConclusionMTF-1 may be a novel prognostic biomarker.

The levels of immunosuppressive checkpoint protein PD-L1 and tumor-infiltrating lymphocytes were integrated to reveal the glioma tumor microenvironment.

In spite of significant strides in the realm of cancer biology and therapeutic interventions, the clinical prognosis for patients afflicted with glioblastoma (GBM) remains distressingly dismal. The tumor immune microenvironment (TIME), a crucial player in the progression, treatment response, and prognostic trajectory of glioma, warrants thorough exploration. Within this intricate microcosm, the immunosuppressive checkpoint protein PD-L1 and tumor-infiltrating lymphocytes (TILs) emerge as pivotal constituents, underscoring their potential role in deciphering glioma biology and informing treatment strategies. However, prognostic models based on the association between PD-L1 expression and TIL infiltration in the tumor immune microenvironment have not been established. The aim of this study was to explore TIME genes associated with PD-L1 expression and TIL invasion and to construct a risk score for predicting the overall survival (OS) of GBM patients based on these genes. The samples were separately classified according to the PD-L1 expression level and TIL score and TIME-related genes were identified using differential expression and weighted gene co-expression network analysis. The DEGs were subjected to least absolute contraction and selection operator (LASSO) -Cox regression to construct TIME associated risk score (TIMErisk). A TIMErisk was developed based on STEAP3 and CXCL13 genes. The STLEAP3 was demonstrated to be involved in glioma progression. The results showed that the patients in the high TIMErisk group had poor OS compared with subjects in the low TIMErisk group. The biological phenotypes associated with TIMErisk were analyzed in terms of functional enrichment, tumor immune profile, and tumor mutation profile. The results on tumor immune dysfunction and exclusion dysfunction (TIDE) score and immune surface score (IPS) showed that GBM patients with different TIME risks had different responses to immunotherapy. Tumor purity analysis indicated that PD-L1 and TIL scores were positively correlated with TIMErisk score and negatively correlated with tumor purity. These results show that the TIMErisk-based prognostic model had high predictive value for the prognosis and immune characteristics of GBM patients. Immunohistochemical staining images of patients in the high and low TIMErisk groups were analyzed, showing that the degree of immune cell infiltration was higher in the high TIMErisk group relative to the low TIMErisk group. The present study provides a basis for understanding glioma tumor microenvironment and a foundation for conducting comprehensive immunogenomic analysis.

Immune-Related Genes in the Pathogenesis of Atherosclerosis: Based on Sex Differences.

Atherosclerosis is still a global public problem with increasing incidence rate and mortality. It has been found that gender factors play an important role in the progression of atherosclerosis. However, few people explore gender related atherosclerosis at the level of genes and immune cells. The purpose of this study was to determine genetic and immune cell differences between male and female samples. This study aims to identify differential genes between male and female samples in the GSE43292 dataset. The focus will be on identifying immune-related genes (IRGs) among these differentially expressed genes. Subsequently, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis will be employed to explore the enrichment of IRGs in biological processes, molecular functions, cellular components, and pathways. Furthermore, a protein-protein interaction (PPI) network for the IRGs will be constructed using Cytoscape software. To estimate the degree of immune cell infiltration, single-sample gene set enrichment analysis (ssGSEA) will be conducted. Moreover, the identified IRGs will be validated using GSE28829 dataset. Finally, we validated in atherosclerotic mice. Seven IRGs (CCL13, IL1RN, FPR2, S100A8, CCL19, CXCL1, CXCL8) were identified as being overexpressed in male atherosclerosis. GO and KEGG analysis revealed that these IRGs are primarily enriched in inflammatory response pathways, cytokine signaling pathways, and cytokine- cytokine receptor interactions. Notably, when compared to females, there was a significant infiltration of immune cells in male specimens. Importantly, all seven IRGs demonstrated high diagnostic value in GSE28829 dataset. The use of animal samples supports our results. This study demonstrates the effectiveness of seven IRGs and reveal sex differences in atherosclerosis. Notably, there is a significant presence of immune cells within the atherosclerotic plaque of men compared to women. These findings have potential implications for the development of personalized treatment approaches targeting gender-related atherosclerosis.

Integration of scRNA-seq and bulk RNA-seq constructs a stemness-related signature for predicting prognosis and immunotherapy responses in hepatocellular carcinoma.

Cancer stem cells are associated with unfavorable prognosis in hepatocellular carcinoma (HCC). However, existing stemness-related biomarkers and prognostic models are limited. The stemness-related signatures were derived from taking the union of the results obtained by performing WGCNA and CytoTRACE analysis at the bulk RNA-seq and scRNA-seq levels, respectively. Univariate Cox regression and the LASSO were applied for filtering prognosis-related signatures and selecting variables. Finally, ten gene signatures were identified to construct the prognostic model. We evaluated the differences in survival, genomic alternation, biological processes, and degree of immune cell infiltration in the high- and low-risk groups. pRRophetic and Tumor Immune Dysfunction and Exclusion (TIDE) algorithms were utilized to predict chemosensitivity and immunotherapy response. Human Protein Atlas (HPA) database was used to evaluate the protein expressions. A stemness-related prognostic model was constructed with ten genes including YBX1, CYB5R3, CDC20, RAMP3, LDHA, MTHFS, PTRH2, SRPRB, GNA14, and CLEC3B. Kaplan-Meier and ROC curve analyses showed that the high-risk group had a worse prognosis and the AUC of the model in four datasets was greater than 0.64. Multivariate Cox regression analyses verified that the model was an independent prognostic indicator in predicting overall survival, and a nomogram was then built for clinical utility in predicting the prognosis of HCC. Additionally, chemotherapy drug sensitivity and immunotherapy response analyses revealed that the high-risk group exhibited a higher likelihood of benefiting from these treatments. The novel stemness-related prognostic model is a promising biomarker for estimating overall survival in HCC.

Infiltration of tumor spheroids by activated immune cells

Recent years have seen a tremendous growth of interest in understanding the role that the adaptive immune system could play in interdicting tumor progression. In this context, it has been shown that the density of adaptive immune cells inside a solid tumor serves as a favorable prognostic marker across different types of cancer. The exact mechanisms underlying the degree of immune cell infiltration is largely unknown. Here, we quantify the temporal dynamics of the density profile of activated immune cells around a solid tumor spheroid. We propose a computational model incorporating immune cells with active, persistent movement and a proliferation rate that depends on the presence of cancer cells, and show that the model able to reproduce semi-quantitatively the experimentally measured infiltration profile. Studying the density distribution of immune cells inside a solid tumor can help us better understand immune trafficking in the tumor micro-environment, hopefully leading towards novel immunotherapeutic strategies.

Machine learning-based identification of cuproptosis-related markers and immune infiltration in severe community-acquired pneumonia.

Severe community-acquired pneumonia (SCAP) is one of the world's most common diseases and a major etiology of acute respiratory distress syndrome (ARDS). Cuproptosis is a novel form of regulated cell death that can occur in various diseases. Our study explored the degree of immune cell infiltration during the onset of severe CAP and identified potential biomarkers related to cuproptosis. Gene expression matrix was obtained from GEO database indexed GSE196399. Three machine learning algorithms were applied: The least absolute shrinkage and selection operator (LASSO), the random forest, and the support vector machine-recursive feature elimination (SVM-RFE). Immune cell infiltration was quantified by single-sample gene set enrichment analysis (ssGSEA) scoring. Nomogram was constructed to verify the applicability of using cuproptosis-related genes to predict the onset of severe CAP and its deterioration toward ARDS. Nine cuproptosis-related genes were differentially expressed between the severe CAP group and the control group: ATP7B, DBT, DLAT, DLD, FDX1, GCSH, LIAS, LIPT1, and SLC31A1. All 13 cuproptosis-related genes were involved in immune cell infiltration. A three-gene diagnostic model was constructed to predict the onset of severe CAP: GCSH, DLD, and LIPT1. Our study confirmed the involvement of the newly discovered cuproptosis-related genes in the progression of SCAP.

BASP1 expression is associated with poor prognosis and is correlated with immune infiltration in gastric cancer.

BASP1 is a membrane-bound protein that plays a promotional or inhibitory role in a variety of tumors; however, its role in gastric cancer (GC) and in the immune microenvironment has not been reported. The objectives of this study were to determine whether BASP1 is a valuable prognostic marker for GC and to explore its role in the immune microenvironment of GC. The expression level of BASP1 in GC was analyzed based on the TCGA dataset and further verified using GSE54129 and GSE161533 datasets, immunohistochemistry, and western blotting. The association between BASP1 and clinicopathological characteristics, as well as its predictive value, were examined using the STAD dataset. Cox regression analysis was performed to determine whether BASP1 can be used as an independent prognostic indicator for GC, and a nomogram was constructed to predict OS. The association between BASP1 and immune cell infiltration, immune checkpoints, and immune cell markers was confirmed by enrichment analysis, as well as analysis based on the TIMER and GEPIA databases. BASP1 was observed to be highly expressed in GC and was associated with a poor prognosis. The expression of BASP1 was positively correlated with the expression of immune checkpoints and immune cell markers, as well as immune cell infiltration. Thus, BASP1 may serve as a standalone prognostic indicator for GC. BASP1 is highly correlated with immune processes, and its expression is positively correlated with the degree of immune cell infiltration, immune checkpoints, and immune cell markers.

Comparison of immune microenvironment between primary and metastatic breast tumors.

1030 Background: Immune evasion is one of the mechanisms by which cancer cells gain the ability to metastasize from the primary tumor to distant sites. In triple-negative breast cancer (TNBC), metastatic tumors are shown to be more immunologically silent than primary tumors. As a result, there are varying degrees of responses to immunotherapy between early-stage and metastatic tumors. Positive clinical responses to immune checkpoint inhibitors (ICIs) are seen in patients with early-stage TNBC regardless of PD-L1 expression. In this study, we investigated the differences in the immune signatures of primary and metastatic breast cancer in a real-world patient population. Methods: We analyzed retrospective comprehensive genomic and immune profiling (CGIP) results from 529 breast tumors tested in the real-world clinical setting. Tumor specimens were classified as primary breast (PB), any lymph nodes (LN; regional and non-regional) or metastatic visceral (MV) sites. LN samples were chosen as positive controls due to expected elevated inflammatory signaling. PD-L1 (CPS positive ≥10) and TMB (high ≥10 Mut/Mb) were determined using IHC and DNA sequencing, respectively. mRNA expression signatures of tumor inflammation (TIGS, strong/moderate/weak) and expression of LAG3, TIGIT and TIM3 were determined by RNA-sequencing from a 395-gene panel. LAG3, TIGIT and TIM3 were selected due to emerging clinical trials in solid tumors. We used over-representation and proportion analysis using chi-squared test to determine the association of specimen sites to various genomic and immune correlates. Results: Among 529 cases, the median patient age was 63.2 years (25.5-93.5). The majority of patients were female (519, 98%), and the most common tumor histology was invasive ductal carcinoma (287, 54%). A total of 224 (42%), 72 (14%), and 232 (44%) of patients had specimens from PB, LN, MV, respectively, while 1 (0.19%) patient had an unknown source. Samples of PB harbored greater degree of immune infiltration, demonstrating higher TIGS score than MV (p=0.014). Primary lesions also demonstrated a greater proportion of PD-L1 positive than metastatic lesions (44% vs 21%, p &lt; 0.001) and higher expressions of immune checkpoints such as TIGIT (p&lt;0.001), LAG3 (p=0.037) and TIM3 (p&lt;0.001). Conclusions: We found that non-lymph node breast cancer metastases harbor a less active immune response than primary breast lesions, showing a lower degree of immune cell infiltration and decreased expression of immune checkpoint markers. These findings support the notion that the immune microenvironment of breast cancer metastases is immunosuppressive and may exhibit a tempered response to ICIs. Therefore, combination treatments of ICIs with chemotherapy, targeted therapies or cancer vaccines may be promising therapeutic approaches to enhance the immune responses and potentially overcome resistance to ICIs in metastatic breast cancer.

B-arrestin deletion abrogates the innate immune response in murine CVB3 myocarditis

β-arrestins (βarrs), initially discovered as desensitizers of GPCR signaling, are now known to function as intracellular scaffolds and signaling transducers mediating a wide array of signaling cascades including immune responses to inflammatory stimuli. An important cause of immune cell infiltration and cardiac inflammation are viral pathogens such as enterovirus coxsackievirus B3 (CVB3) induced myocarditis. While viral myocarditis is a leading cause of dilated cardiomyopathy, the precise molecular mechanisms for the acute immune response to CVB3 infection are not well understood. Given the important role for βarrs in the acute immune response, we tested the hypothesis that βarrs are necessary for the activation of the acute immune response and mediate the progression and severity of cardiotropic CVB3-induced myocarditis in mice. Five to 7-week-old mice devoid of βarr1 (βarr1 KO) or βarr2 (βarr2 KO) were infected intraperitoneally with 1x103-1x104 plaque forming units (PFU) of CVB3 per animal. Wild type (WT) C57BL/6 mice infected with CVB3 were used as controls. The survival rate 7 days post infection (dpi) was significantly improved in male βarr1 KOs (80%) and βarr2 KOs (75%) compared to male WT control mice (35%, p=0.013). Female WT, βarr1 KO, and βarr2 KO mice showed similar survival rates 7 dpi., ranging from 70% to 80%. Early mortality among all groups before 5 dpi was associated with high viral titers (~6.0 ± 0.5 log10PFU/mg) in the liver compared to mortality after 5 dpi (~2.4 ± 1.7 log10PFU/mg) as determined by plaque assay. Viral titers in the heart (WT=3.7 ± 0.9 log10PFU/mg, βarr1KO=3.6 ± 1.3 log10PFU/mg, βarr2KO=3.5 ± 1.2log10PFU/mg) were similar among all groups suggesting that βarrs are not involved in viral replication. Morphometric analysis showed similar weight loss (~18%) across all groups at 7 dpi corroborated by viral cardiac PFU. Immunofluorescent staining of the heart with the pan-inflammatory marker, CD45, revealed high immune cell infiltration in infected WT mice (34.2% ± 4.5%), whereas immune cell infiltration was significantly blunted in infected βarr1 KO (6.0% ± 1.1%; p&lt;0.0001) and βarr2 KO (8.5% ± 0.9%; p&lt;0.0001) mice. The degree of immune cell infiltration in hearts of infected WT mice was directly correlated with an increase in heart viral titer, whereas immune cell infiltration remained blunted across a broad range of heart viral titers in both βarr1 and 2 KO mice. The blunted immune response in both βarr KOs compared to WT infected controls was consistent across multiple immune cell markers including CD4 for helper T cells and CD11b for innate immune cells. In conclusion, we demonstrate that βarrs are necessary for immune cell recruitment to the heart in CVB3 myocarditis and deletion of βarrs in male mice may be cardioprotective as indicated by an increase in survival rate. These data suggest that βarrs may serve as potential therapeutic targets in the treatment of acute viral myocarditis. This work was supported by the National Institutes of Health Grants HL056687 (to H.A.R.). This is the full abstract presented at the American Physiology Summit 2023 meeting and is only available in HTML format. There are no additional versions or additional content available for this abstract. Physiology was not involved in the peer review process.