Comprehensive Analysis of CLCA1 Expression, Immune Infiltration and Immune Checkpoints in Colon Adenocarcinoma / Análisis Completo de la Expresión de CLCA1, Infiltración Inmune y Puntos de Control Inmunológico en Colonadenocarcinoma

SUMMARY: Colon adenocarcinoma (COAD) is a prevalent disease worldwide, known for its high mortality and morbidity rates. Despite this, the extent of investigation concerning the correlation between COAD's CLCA1 expression and immune cell infiltration remains insufficient. This study seeks to examine the expression and prognosis of CLCA1 in COAD, along with its relationship to the tumor immune microenvironment. These findings will offer valuable insights for clinical practitioners and contribute to the existing knowledge in the field. In order to evaluate the prognostic significance of CLCA1 in individuals diagnosed with colorectal cancers, we conducted a comprehensive analysis using univariate and multivariate Cox regression models along with receiver operating characteristic curve (ROC) analysis. This study was performed on the patient data of COAD obtained from The Cancer Genome Atlas (TCGA) database. Nomograms were developed to anticipate CLCA1 prognostic influence. Furthermore, the CLCA1 association with tumor immune infiltration, immune checkpoints, immune checkpoint blockade (ICB) response, interaction network, and functional analysis of CLCA1-related genes was analyzed. We found that Colon adenocarcinoma tissues significantly had decreased CLCA1 expression compared to healthy tissues. Furthermore, the study revealed that the group with high expression of CLCA1 demonstrated a significantly higher overall survival rate (OS) as compared to the group with low expression. Multivariate and Univariate Cox regression analysis revealed the potential of CLCA1 as a standalone risk factor for COAD. These results were confirmed using nomograms and ROC curves. In addition, protein-protein interaction (PPI) network analysis and functional gene enrichment showed that CLCA1 may be associated with functional activities such as pancreatic secretion, estrogen signaling and cAMP signaling, as well as with specific immune cell infiltration. Therefor, as a new independent predictor and potential biomarker of COAD, CLCA1 plays a crucial role in the advancement of colon cancer.

El adenocarcinoma de colon (COAD) es una enfermedad prevalente a nivel mundial, conocida por sus altas tasas de mortalidad y morbilidad. Sin embargo, el alcance de la investigación sobre la correlación entre la expresión de CLCA1 de COAD y la infiltración de células inmunes sigue siendo insuficiente. Este estudio busca examinar la expresión y el pronóstico de CLCA1 en COAD, junto con su relación con el microambiente inmunológico del tumor. Estos hallazgos ofrecerán conocimientos valiosos para los profesionales clínicos y contribuirán al conocimiento existente en el campo. Para evaluar la importancia de pronóstico de CLCA1 en personas diagnosticadas con cáncer colorrectal, realizamos un análisis exhaustivo utilizando modelos de regresión de Cox univariados y multivariados junto con un análisis de la curva característica operativa del receptor (ROC). Este estudio se realizó con los datos de pacientes de COAD obtenidos de la base de datos The Cancer Genome Atlas (TCGA). Se desarrollaron nomogramas para anticipar la influencia pronóstica de CLCA1. Además, se analizó la asociación de CLCA1 con la infiltración inmunitaria tumoral, los puntos de control inmunitarios, la respuesta de bloqueo de los puntos de control inmunitarios (ICB), la red de interacción y el análisis funcional de genes relacionados con CLCA1. Descubrimos que los tejidos de adenocarcinoma de colon tenían una expresión significativamente menor de CLCA1 en comparación con los tejidos sanos. Además, el estudio reveló que el grupo con alta expresión de CLCA1 demostró una tasa de supervivencia general (SG) significativamente mayor en comparación con el grupo con baja expresión. El análisis de regresión de Cox multivariado y univariado reveló el potencial de CLCA1 como factor de riesgo independiente de COAD. Estos resultados se confirmaron mediante nomogramas y curvas ROC. Además, el análisis de la red de interacción proteína- proteína (PPI) y el enriquecimiento de genes funcionales mostraron que CLCA1 puede estar asociado con actividades funcionales como la secreción pancreática, la señalización de estrógenos y la señalización de AMPc, así como con la infiltración de células inmunes específicas. Por lo tanto, como nuevo predictor independiente y biomarcador potencial de COAD, CLCA1 desempeña un papel crucial en el avance del cáncer de colon.

TTYH3 is a prognostic biomarker and associates with immune cell infiltrations of lung adenocarcinoma / TTYH3 es un biomarcador pronóstico y se asocia con infiltraciones de células inmunitarias del adenocarcinoma de pulmón

SUMMARY: We investigated Tweety Family Member 3 (TTYH3) level in lung adenocarcinoma (LUAD) and its relationship with immune infiltration in tumors by bioinformatics. Differential expressions of TTYH3 in lung cancer were analyzed with Oncomine, TIMER, GEO, UALCAN and HPA. Relationship of TTYH3 mRNA/protein levels with clinical parameters was analyzed by UALCAN. Co-expressed genes of TTYH3 in LUAD were analyzed using Cbioportal. Its relationship with LUAD prognosis was analyzed by Kaplan-Meier plotter. GO and KEGG analysis were performed. Correlation between TTYH3 and tumor immune infiltration were tested by TIMER, TISIDB and GEPIA. We found that TTYH3 was significantly increased in LUAD tissues. TTYH3 high expression was closely related to poor overall survival, post progression survival and first progression in LUAD patients. TTYH3 mRNA/protein levels were significantly associated with multiple pathways. Specifically, TTYH3 up-regulation was mostly related to biological regulation, metabolic process, protein blinding, extracellular matrix organization and pathways in cancer. Moreover, TTYH3 was positively associated with immune cell infiltration in LUAD. Finally, TTYH3 was highly expressed in LUAD as revealed by meta-analysis. TTYH3 is closely related to the prognosis of LUAD and immune cell infiltration, and it can be used as a prognostic biomarker for LUAD and immune infiltration.

Investigamos por bioinformática el nivel de Tweety Family Member 3 (TTYH3) con adenocarcinoma de pulmón (LUAD) y su relación con la infiltración inmune en tumores. Las expresiones diferenciales de TTYH3 en cáncer de pulmón se analizaron con Oncomine, TIMER, GEO, UALCAN y HPA. Con UALCAN se analizó la relación de los niveles de ARNm/proteína de TTYH3 con los parámetros clínicos. Los genes coexpresados de TTYH3 en LUAD se analizaron utilizando Cbioportal. Su relación con el pronóstico LUAD se analizó mediante plotter de Kaplan- Meier. Se realizaron análisis GO y KEGG. TIMER, TISIDB y GEPIA probaron la correlación entre TTYH3 y la infiltración inmune tumoral. Encontramos que TTYH3 aumentó significativamente en los tejidos LUAD. La alta expresión de TTYH3 estuvo estrechamente relacionada con una supervivencia general deficiente, supervivencia posterior a la progresión y primera progresión en pacientes con LUAD. Los niveles de ARNm/ proteína de TTYH3 se asociaron significativamente con múltiples vías. Específicamente, la regulación positiva de TTYH3 se relacionó principalmente con la regulación biológica, el proceso metabólico, el cegamiento de proteínas, la organización de la matriz extracelular y las vías en el cáncer. Además, TTYH3 se asoció positivamente con la infiltración de células inmunitarias en LUAD. Finalmente, TTYH3 se expresó altamente en LUAD como lo reveló el metanálisis. TTYH3 está estrechamente relacionado con el pronóstico de LUAD y la infiltración de células inmunitarias, y se puede utilizar como biomarcador pronóstico para LUAD y la infiltración de células inmunitarias.

Identification of key immune related genes in diabetes retinopathy based on weighted gene co-expression network / 国际眼科杂志(Guoji Yanke Zazhi)

AIM: To explore the key genes related to immunity and immune cell infiltration levels in diabetes retinopathy(DR)using bioinformatics.METHODS: Differential expression genes(DEGs)were obtained by “limma” R from Gene Expression Omnibus(GEO)data from September to October 2022, Gene ontology(GO)and Kyoto encyclopedia of genes and genomes(KEGG)were analyzed, and the infiltration of immune cell types in each sample was calculated based on CIBERSORT algorithm. Weighted gene co-expression network analysis(WGCNA)was used to screen for DEGs in immune-related gene modules. The protein-protein interaction(PPI)network was established by STRING online database and Cytoscape, and the hub genes were screened by MCODE and cytoHubba plug-ins.RESULTS: The results showed that 1 426 up-regulated and 206 down-regulated differential genes were screened, where 7 immune cell types, including B cell naive, Plasma cells, CD4+T cells, T cells regulatory(Tregs), Macrophages M0, Macrophages M1 and Neutrophils were significantly overexpressed(P<0.05), while others were low expressed(P<0.05). After WGCNA, a total of 820 DEGs were found in the modules most related to immunity. After constructing the PPI network, 10 key genes were screened using plug-ins, and two key genes were further screened using the expression amount of each differential gene in PPI: DLGAP5 and AURKB.CONCLUSION: This study used bioinformatics to screen the infiltration of immune cells and key genes related to immunity in patients with DR. These findings may provide evidences for future research, diagnosis, and treatment of DR.

A novel defined risk signature of endoplasmic reticulum stress-related genes for predicting the prognosis and immune infiltration status of ovarian cancer / 浙江大学学报（英文版）（B辑：生物医学和生物技术）

Endoplasmic reticulum (ER) stress, as an emerging hallmark feature of cancer, has a considerable impact on cell proliferation, metastasis, invasion, and chemotherapy resistance. Ovarian cancer (OvCa) is one of the leading causes of cancer-related mortality across the world due to the late stage of disease at diagnosis. Studies have explored the influence of ER stress on OvCa in recent years, while the predictive role of ER stress-related genes in OvCa prognosis remains unexplored. Here, we enrolled 552 cases of ER stress-related genes involved in OvCa from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) cohorts for the screening of prognosis-related genes. The least absolute shrinkage and selection operator (LASSO) regression was applied to establish an ER stress-related risk signature based on the TCGA cohort. A seven-gene signature revealed a favorable predictive efficacy for the TCGA, International Cancer Genome Consortium (ICGC), and another GEO cohort (P<0.001, P<0.001, and P=0.04, respectively). Moreover, functional annotation indicated that this signature was enriched in cellular response and senescence, cytokines interaction, as well as multiple immune-associated terms. The immune infiltration profiles further delineated an immunologic unresponsive status in the high-risk group. In conclusion, ER stress-related genes are vital factors predicting the prognosis of OvCa, and possess great application potential in the clinic.

Ferroptosis-related Recurrence Risk Model Predicts Clinical Outcomes and Immune Infiltration in Glioblastoma / 肿瘤防治研究

Objective To construct a ferroptosis-related glioblastoma (GBM) recurrence risk model and evaluate the prognosis of patients. Methods Differentially expressed genes (DEGs) related to ferroptosis in recurrent GBM were screened by CGGA and FerrDb databases. Key genes were obtained by Lasso regression. Then, nomogram was constructed according to the key risk genes, and the prediction efficiency was verified using the TCGA database. GO, KEGG, and GSEA databases were used in exploring the mechanism of prognosis. ESTIMATE and TIMER were used in studying tumor immune infiltration and the expression of immune check points. Results WWTR1, PLIN2, and BID were important prognostic factors for GBM recurrence. The nomogram was constructed according to gender and age, and the observed values were in good agreement with the predicted values. The AUC values were 0.65 (1 year), 0.66 (3 years), and 0.63 (5 years) for CGGA and 0.68 (1 year), 0.76 (3 years), and 0.79 (5 years) for TCGA. Epithelial mesenchymal transition, KRAS pathway, and inflammatory response were significantly upregulated in the high-risk subtypes (P < 0.05). Immune cell infiltration was lower (P < 0.05). Risk score was positively correlated with the expression of immunosuppression check points. Conclusion Ferroptosis-related genes WWTR1, PLIN2, and BID can be used in constructing a nomogram with good predictive performance. These risk genes may affect prognosis through tumor-infiltrating immune cells and immune check points.

Construction of a prognostic model for hepatocellular carcinoma based on pyroptosis-related genes / 中华肝脏病杂志

Objective: To study the construction of a prognostic model for hepatocellular carcinoma (HCC) based on pyroptosis-related genes (PRGs). Methods: HCC patient datasets were obtained from the Cancer Genome Atlas (TCGA) database, and a prognostic model was constructed by applying univariate Cox and least absolute shrinkages and selection operator (LASSO) regression analysis. According to the median risk score, HCC patients in the TCGA dataset were divided into high-risk and low-risk groups. Kaplan-Meier survival analysis, receiver operating characteristic (ROC) curves, univariate and multivariate Cox analysis, and nomograms were used to evaluate the predictive ability of the prognostic models. Functional enrichment analysis and immune infiltration analysis were performed on differentially expressed genes between the two groups. Finally, two HCC datasets (GSE76427 and GSE54236) from the Gene Expression Omnibus database were used to externally validate the prognostic value of the model. Univariate and multivariate Cox regression analysis or Wilcoxon tests were performed on the data. Results: A total of 366 HCC patients were included after screening the HCC patient dataset obtained from the TCGA database. A prognostic model related to HCC was established using univariate Cox regression analysis, LASSO regression analysis, and seven genes (CASP8, GPX4, GSDME, NLRC4, NLRP6, NOD2, and SCAF11). 366 cases were evenly divided into high-risk and low-risk groups based on the median risk score. Kaplan-Meier survival analysis showed that there were statistically significant differences in the survival time between patients in the high-risk and low-risk groups in the TCGA, GSE76427, and GSE54236 datasets (median overall survival time was 1 149 d vs. 2 131 d, 4.8 years vs. 6.3 years, and 20 months vs. 28 months, with P = 0.000 8, 0.034 0, and 0.0018, respectively). ROC curves showed good survival predictive value in both the TCGA dataset and two externally validated datasets. The areas under the ROC curves of 1, 2, and 3 years were 0.719, 0.65, and 0.657, respectively. Multivariate Cox regression analysis showed that the risk score of the prognostic model was an independent predictor of overall survival time in HCC patients. The risk model score accurately predicted the survival probability of HCC patients according to the established nomogram. Functional enrichment analysis and immune infiltration analysis showed that the immune status of the high-risk group was significantly decreased. Conclusion: The prognostic model constructed in this study based on seven PRGs accurately predicts the prognosis of HCC patients.

Correlation of DNA Damage Repair Gene FANCI with Prognosis and Immune Infiltration of Hepatocellular Carcinoma / 中山大学学报(医学科学版)

ObjectiveTo evaluate the expression level of DNA damage repair gene FANCI in hepatocellular carcinoma （HCC） and its relationship with prognosis， clinical stage and immune infiltration. MethodsIn this study， TCGA， GTEx， TIMER2.0， HPA database and qRT-PCR， western blot and immunohistochemistry were used to analyze the expression of FANCI in HCC and its correlation with different clinical stages； Kaplan-Meier Plotter database was used to explore the relationship between FANCI and the prognosis of HCC； the TISIDB database was used to analyze the relationship between FANCI and immune cell infiltration and immune checkpoints in HCC； the STRING database was used to detect the protein binding with FANCI； the TCGA and GTEx databases were used for GO and KEGG enrichment analysis； Cell experiments were used to explore the role of FANCI in HCC. ResultsCompared with normal tissues， the mRNA and protein expression levels of FANCI in tumor tissues were up-regulated （P<0.001）； and HCC patients with high expression of FANCI had poor prognosis （P<0.001）； the expression of FANCI in tumor tissues was positively correlated with the number of activated CD4+ T cells， the number of Th2 cells and the expression of immune checkpoints， and B-cell and macrophage infiltration was significantly lower in the FANCI high expression group （P<0.01）； GO and KEGG enrichment analysis showed that FANCI-related genes were enriched in various biological processes such as amino acid transmembrane transporter activity； Cell experiments showed that knockdown of FANCI could inhibit the proliferation， invasion and migration of HCC （P<0.05）. ConclusionsFANCI is highly expressed in hepatocellular carcinoma tissues， which may play a role in suppressing anti-tumor immunity and acting on pathways such as amino acid transmembrane transport， and is associated with poor prognosis. The proliferation， invasion and migration ability of hepatocellular carcinoma are inhibited after knocking down FANCI.

Effects of immune infiltration-related gene CSAG1 on the progression of renal clear cell carcinoma / 现代泌尿外科杂志

【Objective】 To explore the correlation between CSAG1 expression and the prognosis and tumor-infiltrating lymphocytes in renal clear cell carcinoma (RCCC), and to predict the survival and tumor progression. 【Methods】 The gene expression profiles and clinical information of CSAG1 were downloaded from the Cancer Genome Atlas (TCGA). Based on the differential mRNA expression, GO annotation and KEGG pathway analysis were performed. The relationship between CSAG1 and tumor immune infiltration was assessed with Tumor Immunoassay Resource (Timer 2.0) database. The mRNA expression of CSAG1 in human RCCC specimens was validated with qRT-PCR. 【Results】 CSAG1 expression was significantly higher in RCCC tissues than in normal tissues (P<0.05). The qRT-PCR results revealed that the mRNA level of CSAG1 was consistent with that predicted by bioinformatic analysis. The KEGG analysis and GO annotation indicated high GSAG1 expression in RCCC was related to transmembrane transport, tricarboxylic acid cycle and lysosome. CSAG1 expression was positively related to the infiltration of pDC, aDC, CD8+ T cells, cytotoxic cells, TFH, TH1 cells, Tem, NK CD56dm cells, Treg and T cells, but negatively correlated with macrophage infiltration. 【Conclusion】 CSAG1 may be associated with poor prognosis of RCCC and become a potential immunotherapy target.

Transcriptome analysis of checkpoint kinase 2 in clear cell renal cell carcinoma / 现代泌尿外科杂志

【Objective】 To explore the expression of checkpoint kinase 2 (CHEK2) in clear cell renal cell carcinoma (ccRCC), its association with the clinicopathological features and prognosis, and to predict its relevant molecular signaling pathways and biological functions. 【Methods】 The gene expression data, phenotype data, and corresponding survival information of ccRCC patients were downloaded from TCGA database. The optimal cutoff value of CHEK2 was determined with the "survminer" package. The patients were divided into low and high expression groups, and the association between CHEK2 expression and clinicopathological features was analyzed. The correlation between CHEK2 expression and ccRCC prognosis was evaluated with univariate and multivariate Cox proportional hazard models. The changes of cell signaling pathways involved in different CHEK2 expression levels were explored with gene set variation analysis (GSVA). The correlation between CHEK2 and immune cell infiltration as well as immune checkpoint molecular expression was analyzed. 【Results】 CHEK2 expression was significantly higher in ccRCC tissues than in normal tissues (P<0.01). Higher level of CHEK2 was significantly associated with higher T stage of ccRCC (P<0.01). Kaplan-Meier analysis showed overall survival (OS) of patients with high CHEK2 expression were notably decreased (P<0.001). Univariate and multivariate analyses revealed CHEK2 expression as an independent risk factor of survival (HR=1.950, 95%CI: 1.490-2.570, P<0.001; HR=1.588, 95%CI: 1.185-2.127, P=0.002). GSVA showed that CHEK2 was involved in the following pathways: proximal tubule bicarbonate reclamation, propanoate metabolism, limonene and pinene degradation, fatty acid metabolism, primary immunodeficiency, systemic lupus erythematosus, p53 signaling pathway, homologous recombination, DNA replication and mismatch repair. Correlation analysis suggested that CHEK2 was associated with increased infiltration of multiple immune cells in ccRCC and upregulation of various immune checkpoint molecules. 【Conclusion】 The high level of CHEK2 in ccRCC is an independent predicting factor for poor prognosis. It is probably involved in regulating related events of tumor immune infiltration and may become a new target for ccRCC therapy.

Correlation between biomarker EHD3 and immune cell infiltration in gastric cancer / 西安交通大学学报(医学版)

【Objective】 To investigate the prognostic role of EHD3 and its association with immune cell infiltration in gastric cancer. 【Methods】 In this study, EHD3 expression was analyzed using RNA sequencing data from Cancer Genome Atlas (TCGA). Differential analysis, functional enrichment, immune infiltration, immune checkpoint exploration, and clinical baseline data analysis were performed. Independent prognostic factors were identified using univariate and multivariate Cox regression analysis; a column diagram model was developed and evaluated using C-index and calibration diagrams. 【Results】 EHD3 was significantly upregulated in STAD and functional enrichment analysis showed that EHD3 expression was associated with immune response, with most immune cells and immune checkpoints positively correlated with their expression. Cox regression showed that EHD3 was an independent prognostic factor in STAD patients (HR=2.112, 95% CI: 1.340-3.327, P=0.001). 【Conclusion】 EHD3 is considered to be a novel prognostic biomarker for STAD patients, and this study provides a potential therapeutic target for STAD treatment.

Prognostic index construction and analysis of immune infiltration combined with RNA binding protein and transcription factor in hepatocellular carcinoma / 中华肝胆外科杂志

Objective:To comprehensively analyze the prognostic prediction value of RNA binding protein, transcription factor gene expression and immune infiltration in hepatocellular carcinoma (HCC).Methods:Common gene sets associated with RNA-binding proteins and transcription factors were screened in TCGA ( n=365) , GSE54236 ( n=78) and GSE14520 ( n=221) datasets. Univariate Cox regression was used for primary screening. The survival regression model was constructed by LASSO-Cox. And a complex index [CIRT=(score-min)/max] was calculated. According to the median of CIRT, the HCC patients were divided into CIRT high group ( n=182) and CIRT low group ( n=182). The differences of prognosis, immune infiltration between the two groups were analyzed. Results:Of 37 prognostically relevant RNA binding protein and transcription factor genes were identified. The prognosis prediction model based on seven selected genes was determined by stepwise regression. Patients in the CIRT high group exhibited a lower percentage of macrophages in M1 ( P=0.032), macrophages in M2 ( P=0.009), resting mast cell ( P<0.001), activated NK cells ( P=0.007), and resting memory CD4 + T cells ( P<0.001), while patients in the CIRT low group showed a lower level of resting dendritic cells ( P=0.048), macrophages in M0 ( P<0.001), neutrophils ( P=0.049), follicular helper T cells ( P=0.004) and regulatory T cells ( P=0.001). GSEA analysis has shown that CIRT high groups were highly enriched in cell cycle, DNA repair pathways in TCGA and GSE14520. In the TCGA cohort, the CIRT low group had better overall survival than the CIRT high group. Analysis of 5-year follow-up data in the TCGA cohort showed that CIRT had a good predictive value for long-term survival of patients with liver cancer (area under receiver operating characteristic curve was 0.71). Conclusion:A novel prognostic index and classifier based on RNA-binding protein expression, transcription factors and immune expression profiles were developed and cross-cohort validated. CIRT could be used as an independent predictor.

Effect of ACYP1 on hepatocellular carcinoma immune infiltration and prognosis / 中华肝胆外科杂志

Objective:To investigate the expression, prognostic value of acylphosphatase 1 (ACYP1) and its relationship with hepatocellular carcinoma (HCC) immune cell infiltration.Methods:The expression of ACYP1 in 374 cases of HCC was analyzed by using The Cancer Genome Atlas (TCGA) database. According to the median expression level of ACYP1 in HCC, the patients were divided into high expression (187 cases) and low expression group (187 cases). Fifty normal liver tissue were used as negative control. The differential expression, Kaplan-Meier survival analysis, univariate and multivariate Cox analysis were performed to evaluate the role of ACYP1 in the diagnosis and prognosis of HCC. The relationship between the expression level of ACYP1 and immune cell infiltration and immune checkpoint were analyzed through the TIMER database.Results:The expression level of ACYP1 in HCC (2.18±0.69) was higher than that in normal liver tissue (1.02±0.31), and the difference was statistically significant ( t=11.76, P<0.001). The survival of HCC patients with high ACYP1 was shorter than those HCC patients with low ACYP1 expression, and high expression of ACYP1 was an independent risk factor for poor prognosis of HCC patients ( HR=2.402, 95% CI: 1.483-3.891, P<0.05). The area under the curve of ACYP1 expression level in diagnosis of HCC was 0.965. The expression level of ACYP1 was significantly positively correlated with immune cell infiltration and immune checkpoints programmed cell death protein 1( r=0.288, P<0.001) and cytotoxic T lymphocyte-associated antigen 4 ( r=0.311, P<0.001). Conclusion:ACYP1 is a potential biomarker for HCC diagnosis and prognosis , as well as a potential therapeutic target.

Expression of MAD2L1 in Lung Adenocarcinoma and Its Effect on Immune Microenvironment / 肿瘤防治研究

Objective To investigate the expression of MAD2L1 in lung adenocarcinoma and its effect on the prognosis and immune microenvironment of patients. Methods The difference of MAD2L1 expression in lung adenocarcinoma tissue and normal lung tissue was analyzed by TCGA and GEO database. Survival analysis was carried out to evaluate the prognostic significance of MAD2L1 gene expression in lung adenocarcinoma patients. StarBase database was used to construct miRNA-MAD2L1 regulatory network of lung adenocarcinoma. The relation between the expression of MAD2L1 and immune cell infiltration in lung adenocarcinoma was analyzed by TIMER database. Results The expression of MAD2L1 was up-regulated in lung adenocarcinoma, and the high expression of MAD2L1 was significantly correlated with pathological stage and lymph node metastasis of lung adenocarcinoma. The patients with high expression of MAD2L1 had a poor prognosis. miR-101-3p/MAD2L1 axis was identified as the most potential upstream regulation pathway of MAD2L1 in lung adenocarcinoma. The expression level of MAD2L1 was significantly correlated with tumor immune cell infiltration and immune checkpoint expression. Conclusions MAD2L1 is highly expressed in lung adenocarcinoma, which is related to poor prognosis and tumor immune infiltration. MAD2L1 can be used as a potential target for the treatment of lung adenocarcinoma.

METTL27 is a prognostic biomarker of colon cancer and associated with immune invasion / 南方医科大学学报

OBJECTIVE@#To investigate the expression and gene function of methyltransferase-like protein 27 (METTL27) in colon cancer, its association with immune infiltration and its prognostic significance.@*METHODS@#We analyzed the expression levels of METTL27 in 33 cancers using R language and identified METTL27 as a differential gene in colon cancer. The related signaling pathways of METTL27 were analyzed by gene functional annotation and enrichment. SsGSEA algorithm was used to analyze immune infiltration, and logistic analysis was used to evaluate the correlation between METTL27 expression and clinicopathological features of the patients. Kaplan-meier analysis, univariate and multivariate Cox regression analysis were performed to construct a nomogram for evaluating the correlation between METTL27 expression and clinical prognosis. The expression level of METTL27 was further verified in colorectal cancer cell lines and 16 clinical specimens of colorectal cancer tissues using qPCR and Western blotting.@*RESULTS@#METTL27 was highly expressed in 21 cancers, and its expression was significantly higher in colon cancer than in adjacent tissues (P < 0.001). METTL27-related genes were identified by differential analysis, and functional annotation revealed that METTL27 was significantly enriched in transmembrane transport and lipid metabolism, and 5 related signaling pathways were identified by GSEA. METTL27 expression was negatively correlated with different T helper cells and central memory T cells (P < 0.001). The patients with a high METTL27 mRNA expression had a poor survival outcome. Cox regression analysis showed that METTL27 expression was an independent prognostic factor of the overall survival. The expression level of METTL27 was significantly higher in the colorectal cancer cell line than in normal cells (P < 0.05).@*CONCLUSION@#METTL27 is overexpressed in colon cancer and is associated with a poor prognosis of the patients. A high expression of METTL27 showed is associated less T cell immune infiltration, suggesting the potential of METTL27 as a prognostic marker of colon cancer.

Prognostic implications and functional enrichment analysis of LTB4R in patients with acute myeloid leukemia / 南方医科大学学报

OBJECTIVE@#To explore the expression patterns, prognostic implications, and biological role of leukotriene B4 receptor (LTB4R) in patients with acute myeloid leukemia (AML).@*METHODS@#We collected the data of mRNA expression levels and clinical information of patients with AML from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) database for mRNA expression analyses, survival analyses, Cox regression analyses and correlation analyses using R studio to assess the expression patterns and prognostic value of LTB4R. The correlation of LTB4R expression levels with clinical characteristics of the patients were analyzed using UALCAN. The co-expressed genes LTB4R were screened from Linkedomics and subjected to functional enrichment analysis. A protein-protein interaction network was constructed using STRING. GSEA analyses of the differentially expressed genes (DEGs) were performed based on datasets from TCGA-LAML stratified by LTB4R expression level. We also collected peripheral blood mononuclear cells (PBMCs) from AML patients and healthy donors for examination of the mRNA expression levels of LTB4R and immune checkpoint genes using qRT-PCR. We also examined serum LTB4R protein levels in the patients using ELISA.@*RESULTS@#The mRNA expression level of LTB4R was significantly increased in AML patients (4.898±1.220 vs 2.252±0.215, P < 0.001), and an elevated LTB4R expression level was correlated with a poor overall survival (OS) of the patients (P=0.004, HR=1.74). LTB4R was identified as an independent prognostic factor for OS (P=0.019, HR=1.66) and was associated with FAB subtypes, cytogenetic risk, karyotype abnormalities and NPM1 mutations. The co- expressed genes of LTB4R were enriched in the functional pathways closely associated with AML leukemogenesis, including neutrophil inflammation, lymphocyte activation, signal transduction, and metabolism. The DEGs were enriched in differentiation, activation of immune cells, and cytokine signaling. Examination of the clinical serum samples also demonstrated significantly increased expressions of LTB4R mRNA (P=0.044) and protein (P=0.008) in AML patients, and LTB4R mRNA expression was positively correlated with the expression of the immune checkpoint HAVCR2 (r= 0.466, P=0.040).@*CONCLUSION@#LTB4R can serve as a novel biomarker and independent prognostic indicator of AML and its expression patterns provide insights into the crosstalk of leukemogenesis signaling pathways involving tumor immunity and metabolism.

Bioinformatics Analysis on Key Genes and Immune Infiltration of Osteosarcoma / 中国医学科学院学报

Objective To screen the potential key genes of osteosarcoma by bioinformatics methods and analyze their immune infiltration patterns. Methods The gene expression profiles GSE16088 and GSE12865 associated with osteosarcoma were obtained from the Gene Expression Omnibus(GEO),and the differentially expressed genes(DEGs)related to osteosarcoma were screened by bioinformatics tools.Gene Ontology(GO)annotation,Kyoto Encyclopedia of Genes and Genomes(KEGG)pathway enrichment,and analysis of immune cell infiltration were then carried out for the DEGs.The potential Hub genes of osteosarcoma were identified by protein-protein interaction network,and the expression of Hub genes in osteosarcoma and normal tissue samples was verified via the Cancer Genome Atlas(TCGA). Results A total of 108 DEGs were screened out.GO annotation and KEGG pathway enrichment revealed that the DEGs were mainly involved in integrin binding,extracellular matrix (ECM) structural components,ECM receptor interactions,and phosphatidylinositol 3-kinase/protein kinase B(PI3K/Akt)signaling pathway.Macrophages were the predominant infiltrating immune cells in osteosarcoma.Secreted phosphoprotein 1(SPP1),matrix metallopeptidase 2(MMP2),lysyl oxidase(LOX),collagen type V alpha(II)chain(COL5A2),and melanoma cell adhesion molecule(MCAM)presented differential expression between osteosarcoma and normal tissue samples(all P<0.05). Conclusions SPP1,MMP2,LOX,COL5A2,and MCAM are all up-regulated in osteosarcoma,which may serve as potential biomarkers of osteosarcoma.Macrophages are the key infiltrating immune cells in osteosarcoma,which may provide new perspectives for the treatment of osteosarcoma.

Circular RNA circ_100367 as a diagnostic marker for thyroid cancer and its relationship with immune-related factors / 中华内分泌外科杂志

Objective:To investigate the diagnostic value of circular RNA circ_100367 in thyroid cancer (THCA) and its relationship with immune-related factors.Methods:According to the data chip provided by the National Center for Biotechnology Information (NCBI) website, the differentially expressed circRNAs in THCA were analyzed, then circ_100367 was included in this study. The serum of 175 THCA patients and healthy people were collected, and the expression levels of circ_100367 and its linear transcript DCAF8 mRNA in serum samples were detected by qRT-PCR, and the correlation between circ_100367 and DCAF8 was calculated. The correlation between the expression of circ_100367 and the clinicopathological characteristicsof the patients, immune infiltration level and immunosuppressive factor PD-1 was analyzed.Results:Compared with serum of healthy people (1.00±0.37) , expression level of circ_100367 in serum of THCA patients was significantly increased (1.37±0.41) ( t=8.80, P<0.001) , and there was no significant difference in DCAF8 mRNA expression ( t=1.67, P=0.095) , but circ_100367 was positively correlated with DCAF8 mRNA expression ( r=0.17, P=0.028) . Analysis of expression and clinicopathological characteristics of circ_100367 showed that compared with patients in M0 group (1.26±0.40) , circ_100367 was overexpressed in M1 and Mx patients (1.43±0.40) ( t=2.63, P=0.009) ; compared with N0 patients (1.24±0.36) , circ_100367 was overexpressed in serum of N1 and Nx patients (1.45±0.42) ( t=3.48, P=0.001) ; compared with serum of patients with negative lymph node detection (1.28±0.36) , circ_100367 was overexpressed in serum of positive patients (1.42±0.43) ( t=2.14, P=0.034) ; compared with T1+T2 stage patients (1.30±0.37) , circ_100367 expression was overexpressed in serum ofT3+T4 patients (1.40±0.43) ( t=2.22, P=0.028) . Analysis of the expression and immune infiltration levels of circ_100367 found that highly expressed circ_100367 was associated with CD8+ T cells ( r=0.25, P=0.024) , macrophages ( r=0.22, P=0.038) , CD4+ T cells ( r=0.25, P=0.020) and B cell ( r=0.23, P=0.033) levels. The expression of circ_100367 was also positively correlated with the immunosuppressive factor PD-1 ( r=0.19, P=0.011) . Conclusion:circ_100367 can be used as a marker for the diagnosis of THCA and its expression is strongly correlated with immune-related factors.

Infiltration of immune cells and prognosis in papillary thyroid carcinoma with cervical lymph nodes metastases / 中华内分泌外科杂志

Objective:To investigate the infiltration of immune cells and prognosis in papillary thyroid carcinoma (PTC) with cervical lymph nodes metastases.Methods:The RNA-seq data and clinicopathological data of PTC patients were downloaded from the Cancer Genome Atlas (TCGA) database. There were 85 patients in the PTC with cervical lymph nodes metastases group and 23 patients in the control group, according to the inclusion and exclusion criteria. CIBERSORT deconvolution algorithm was used to calculate the infiltration ratio of 22 kinds of immune cells in PTC with cervical lymph nodes metastases. Different immune infiltrating cells were compared between PTC with cervical lymph nodes metastases and normal thyroid. The correlation between clinical characteristics (age, gender, extra-thyroid invasion and TNM stage) and infiltration of immune cells were evaluated, then different immune cells related to the prognosis of PTC with cervical lymph nodes metastases patients were screened by Kaplan-Meier analysis.Results:The B cells naive, B cells memory, T cells CD8, macrophages M1, mast cells activated and eosinophils were down-regulated in tumor tissue compared with normal. Macrophages M0, macrophages M2, dendritic cells resting, dendritic cells activated and mast cells resting were higher in tumor tissue compared with that of normal. Macrophages M0, macrophages M2 and dendritic cells resting were positively correlated with extra-thyroid invasion and TNM stage, and patients with a high proportion of those immune cells had a shorter progression-free survival (PFS) . The B cells naive and T cells CD8 were negatively correlated with extra-thyroid invasion and TNM stage, and patients with a high proportion of those immune cells had a longer progression-free survival (PFS) .Conclusions:The pattern of immune cell infiltration of PTC with cervical lymph nodes metastases has specificity, and it was related to clinical characteristics and prognosis. This study provides theoretical evidences and new insights for the role of immune cell microenvironment in PTC lymph node metastasis.

Immune Microenvironment Comparation Study between EGFR Mutant and EGFR Wild Type Lung Adenocarcinoma Patients Based on TCGA Database / 中国肺癌杂志

BACKGROUND@#Lung cancer is a malignant with high incidence and mortality and adenocarcinoma is among the most popular subtypes. Epidermal growth factor receptor (EGFR) mutation is one of the most important driver mutations for lung adenocarcinoma and EGFR-tyrosine kinase inhibitor (TKI) will benefit those patients with sensitive EGFR mutations. Recently, immune checkpoint inhibitor (ICI) therapy, provide a new breakthrough treatment for lung cancer patients. Whereas immunotherapy as an emerging treatment does not benefit patients with EGFR mutations, for which mechanistic studies are poorly defined and focused on the link of EGFR mutations and programmed cell death-ligand 1 (PD-L1) expression, we speculate that the different immune microenvironment associated with the two classes of patients.@*METHODS@#Lung adenocarcinoma datasets were collected from the Cancer Genome Atlas (TCGA) database, and clinical information and gene expression profiles were downloaded. The immune related lymphocyte infiltration in TCGA database were generated through timer 2.0 GSEA was used to analyze the difference of pathway expression between EGFR mutant patients and wild type patients.@*RESULTS@#EGFR mutation was more frequently among women and never smokers. Immunoinfiltration analysis showed that patients with EGFR mutation tends to have more tumor associated fibroblasts, common myeloid progenitor cells, hematopoietic stem cells, effector CD4⁺ T cells and natural killer T cells infiltration, and less memory B cells, naïve B cells, plasma B cells, plasmacytoid dendritic cells, memory CD4⁺ T cells, CD4⁺ helper T cells 2, naive CD8⁺ T cells, CD8⁺ T cells and central memory CD8⁺ T cells infiltration. Moreover, patients with more infiltration of CD8⁺ T cells, natural killer T cells, memory B cells and hematopoietic stem cells, tends have better prognosis (Log-rank test, P=0.017, 0.0093, 0.018, 0.016). However, the patients with more CD4⁺ T th2 infiltration in the tumor tends to have worse prognosis (Log-rank test, P=0.016). Furthermore, the results of gene set enrichment analysis showed that compared with the lung adenocarcinoma patients with EGFR wild type, the three pathways positive regulation of natural killer (NK) cell-mediated immune response to tumor cells, NK cell activation involved in immune response, and NK cell-mediated immune response to tumor cells related to natural killer cells in patients with EGFR mutation were down regulated, while the pathway the positive regulation of cytokine secretion involved in immune response was up-regulated in EGFR mutation patients.@*CONCLUSIONS@#The tumour microenvironment of patients with EGFR mutations lacks potent tumour killing effector cells and appears dysfunctional with effector cells. This may be a potential reason for the poor efficacy of immunotherapy in patients with EGFR mutations.

Profiles of immune infiltration in abdominal aortic aneurysm and their associated marker genes: a gene expression-based study

Immune-mediated inflammation plays a key role in the pathology of abdominal aortic aneurysm (AAA). We aimed to use a computational approach to profile the immune infiltration patterns and related core genes in AAA samples based on the overexpression of gene signatures. The microarray datasets of AAA and normal abdominal tissues were acquired from gene expression omnibus (GEO) database. We evaluated the composition of immune infiltrates through microenvironment cell populations (MCP)-counter. Weighted gene correlation network analysis (WGCNA) was employed to construct the co-expression network and extract gene information in the most relevant module. Functional and pathway enrichment analysis was performed and immune infiltration related core genes were screened. AAA tissues had a higher level of infiltration by cytotoxic lymphocytes, NK cells, T cells, fibroblasts, myeloid dendritic cells, and neutrophils than normal aorta. The red module was strongly correlated with the infiltrating levels of T cells and cytotoxic lymphocytes. Gene ontology (GO) and pathway analyses revealed that genes in the most relevant module were mainly enriched in T cell activation, regulation of lymphocyte activation, cytokine-cytokine receptor interaction, and chemokine signaling pathway, etc. The expression of GZMK, CCL5, GZMA, CD2, and EOMES showed significant correlations with cytotoxic lymphocytes, while CD247, CD2, CD6, RASGRP1, and CD48 expression were positively associated with T cell infiltration. In conclusion, we comprehensively analyzed profiles of infiltrated immune cells in AAA tissues and their associated marker genes. Our data may provide a novel clue to indicate the underlying molecular mechanisms of AAA formation in terms of immune infiltration.