Infiltration In Lung Adenocarcinoma Research Articles

MiR-137 mediated high expression of TIGD1 promotes migration, invasion, and suppresses apoptosis of lung adenocarcinoma

ObjectivesTigger transposable element-derived 1 (TIGD1) expression and its underlying functions and regulatory mechanisms in lung adenocarcinoma (LUAD) remain unknown. Therefore, we intended to explore the expression, potential functions, and regulatory mechanisms of TIGD1 in LUAD. Materials and methodsTIGD1 expression in LUAD tissues was determined by immunohistochemistry analysis of a tissue microarray. Functional experiments were conducted to determine how TIGD1 affects LUAD tumorigenesis and metastasis. The molecular mechanisms by which TIGD1 induces LUAD progression were determined. ResultsTIGD1 was upregulated in LUAD tissues and was related to lymph node metastases. TIGD1 knockdown suppressed LUAD cell proliferation, migration, and invasion, while promoted cell apoptosis. Furthermore, decreased metastatic nodules were observed in the TIGD1 knockdown mouse metastasis model. Moreover, microarray analysis was performed to determine the potential downstream genes of TIGD1 in LUAD. Hallmark pathway analysis revealed that the downstream genes of TIGD1 were involved in epithelial-mesenchymal transition (EMT). Western blotting confirmed that vimentin and TWIST was downregulated in TIGD1 knockdown cells, while E-cadherin was upregulated. Ingenuity pathway and hallmark pathway analyses revealed that TIGD1 regulated the interleukin-6 signaling pathway and related gene members. Western blotting, quantitative real-time polymerase chain reaction, enzyme-linked immunosorbent assay indicated that downregulation of TIGD1 decreased interleukin-6 and CXCL1 expression. TIGD1 expression was negatively correlated with immune infiltration in LUAD. The upstream microRNA of TIGD1 was predicted, and subsequent luciferase reporter gene experiments confirmed the interactions between microRNA-137 and TIGD1. The expression of miR-137 was significantly downregulated in LUAD tissues and miR-137 suppressed the proliferation, migration, and invasion of LUAD cells, partially through negatively regulating the expression of TIGD1. ConclusionOur findings suggest that TIGD1, which was regulated by microRNA-137, contributed to LUAD progression by promoting cell proliferation, migration, invasion, and EMT and suppressing cell apoptosis.

The chemokine CCL14 is a potential biomarker associated with immune cell infiltration in lung adenocarcinoma

BackgroundChemokine ligand 14, which has a C–C motif (CCL14), mediates the immunological milieu around tumors. However, its role in the progression of lung adenocarcinoma (LUAD) is still unknown. Our objectives were to study the association between CCL14 and tumor-infiltrating immune cells (TIICs) as well as the predictive significance of CCL14 in LUAD.MethodsThe expression of CCL14 in LUAD was examined by using the Oncomine, The Cancer Genome Atlas (TCGA), The University of Alabama at Birmingham CANcer data analysis Portal (UALCAN), and Human Protein Atlas databases. To determine the prognostic significance of CCL14 in LUAD, researchers used the Kaplan‒Meier plotter and Gene Expression Profiling Interactive Analysis (GEPIA, version 2). We utilized TIMER and GEPIA2 to investigate the connection between CCL14 and TIICs. Gene set enrichment analysis (GSEA) was used to test for functional enrichment of genes. We used RT‒qPCR to measure CCL14 expression and Cell Counting Kit-8, Transwell, and wound healing assays to investigate the biological role of CCL14.ResultsThe prognosis of patients with LUAD was worse when CCL14 expression was low. Statistical analysis revealed that CCL14 mRNA expression was significantly greater in lung epithelial cells than in LUAD cell lines in vitro. Enhancing CCL14 expression reduced cell migration, invasion, and proliferation. The results of the immune infiltration research showed that CCL14 and TIICs were positively correlated. Different immune infiltration patterns associated with CCL14 were also shown by TIIC markers. According to GSEA, histone deacetylases, G2/M checkpoints, and Notch signaling pathways were associated with low CCL14 expression.ConclusionsCCL14 is anticipated to emerge as a prognostic marker and therapeutic target for LUAD due to its role in regulating TIICs, suggesting that it may be an antioncogene.

HES6 Mediates Oxidative Phosphorylation Pathway to Promote Immune Infiltration of CD8+ T Cells in Lung Adenocarcinoma.

Tumor immunotherapy has recently gained popularity as a cancer treatment strategy. The molecular mechanism controlling immune infiltration in lung adenocarcinoma (LUAD) cells, however, is not well characterized. Investigating the immune infiltration modulation mechanism in LUAD is crucial. LUAD patient samples were collected, and HES6 expression and immune infiltration level of CD8+ T cells in patient tissues were analyzed. Bioinformatics was utilized to identify binding relationship between E2F1 and HES6, and enrichment pathway of HES6. The binding of E2F1 to HES6 was verified using dual-luciferase and ChIP experiments. HES6 and E2F1 expression in LUAD cells was detected. LUAD cells were co-cultured with CD8+ T cells, and the CD8+ T cell killing level, IFN-γ secretion, and CD8+ T-cell chemotaxis level were measured. Expression of key genes involved in oxidative phosphorylation was detected, and the oxygen consumption rate of LUAD cells was assessed. A mouse model was constructed to assay Ki67 expression and apoptosis in tumor tissue. High expression of HES6 promoted CD8+ T-cell infiltration and enhanced T-cell killing ability through oxidative phosphorylation. Further bioinformatics analysis, molecular experiments, and cell experiments verified that E2F1 negatively regulated HES6 by oxidative phosphorylation, which suppressed CD8+ T-cell immune infiltration. In addition, in vivo assays illustrated that silencing HES6 repressed tumor cell immune evasion. E2F1 inhibited HES6 transcription, thereby mediating oxidative phosphorylation to suppress immune infiltration of CD8+ T cells in LUAD. The biological functions and signaling pathways of these genes were analyzed, which may help to understand the possible mechanisms regulating immune infiltration in LUAD.

Effect of ZIC2 on immune infiltration and ceRNA axis regulation in lung adenocarcinoma via bioinformatics and experimental studies

ObjectiveThis study aimed to conclude the effect and mechanism of ZIC2 on immune infiltration in lung adenocarcinoma (LUAD). MethodsExpression of ZIC2 in several kinds of normal tissues of TCGA data was analyzed and its correlation with the baseline characteristic of LUAD patients were analyzed. The immune infiltration analysis of LUAD patients was performed by CIBERSORT algorithm. The correlation analysis between ZIC2 and immune cell composition was performed. Additionally, the potential upstream regulatory mechanisms of ZIC2 were predicted to identify the possible miRNAs and lncRNAs that regulated ZIC2 in LUAD. In vitro and in vivo experiments were also conducted to confirm the potential effect of ZIC2 on cell proliferation and invasion ability of LUAD cells. ResultsZIC2 expression was decreased in various normal tissues, but increased in multiple tumors, including LUAD, and correlated with the prognosis of LUAD patients. Enrichment by GO and KEGG suggested the possible association of ZIC2 with cell cycle and p53 signal pathway. ZIC2 expression was significantly correlated with T cells CD4 memory resting, Macrophages M1, and plasma cells, indicating that dysregulated ZIC2 expression in LUAD may directly influence immune infiltration. ZIC2 might be regulated by several different lncRNA-mediated ceRNA mechanisms. In vitro experiments validated the promotive effect of ZIC2 on cell viability and invasion ability of LUAD cells. In vivo experiments validated ZIC2 can accelerate tumor growth in nude mouse. ConclusionZIC2 regulated by different lncRNA-mediated ceRNA mechanisms may play a critical regulatory role in LUAD through mediating the composition of immune cells in tumor microenvironment.

Characteristics of mast cell infiltration in lung adenocarcinoma and its impact on prognosis

BackgroundThe role of mast cells in malignancies remains unclear, and there is no clear correlation between mast cells and tumor microvessels, tumor growth, or lung adenocarcinoma (LUAD) prognosis. This study aims to explore the association between mast cell density (MCD) and intratumoral microvessel density (MVD), clinicopathological parameters, and prognosis in LUAD, by evaluating mast cell infiltration characteristics and their prognostic significance.MethodsThis retrospective investigation involved 238 patients with LUAD undergoing complete resection. Tumor and normal lung tissue sections outside the tumor were immunohistochemically stained for MCD in the intratumoral and outside regions, respectively. CD34 polyclonal antibody was used to measure intratumoral MVD.ResultsIntratumoral regions of LUAD had a higher MCD (P < 0.001) than normal lung tissue. In the intratumoral region, MCD and CD34-MVD were positively correlated (r = 0.411, P < 0.001). Intratumoral MCD correlated with sex, smoking history, tumor differentiation, pathological subtype, and tumor size. Female sex (P = 0.012), no smoking history (P = 0.002), acinar predominant type (P = 0.012), and tumor size ≤ 3 cm (P = 0.009) were associated with a higher MCD, whereas poorly differentiated (P = 0.039) and solid/micropapillary predominant types (P = 0.001) were associated with a lower MCD. Higher intratumoral MCD exhibited a marginally improved overall survival, and individuals with higher MCD infiltration ratios (intratumoral MCD/outside the MCD) had higher disease-free and overall survival rates (log-rank P < 0.001). A high MCD infiltration ratio was associated with decreased risk of tumor progression and death following complete resection.ConclusionThe tumor microenvironment controls mast cell infiltration in LUAD, and patients with increased intratumoral mast cell infiltration have better prognosis.

Chaperonin-containing TCP-1 subunit genes are potential prognostic biomarkers and are correlated with Th2 cell infiltration in lung adenocarcinoma: An observational study

A family of molecular chaperone complexes called chaperonin-containing T-complex protein 1 (TCP-1) subunit genes (CCTs) aids in the folding of numerous proteins. With regard to lung adenocarcinoma (LUAD), this study provided a thorough understanding of the diagnostic and prognostic use of CCTs. The expression of CCTs in LUAD was evaluated by using databases including UALCAN and the Gene Expression Omnibus. Immunohistochemistry (IHC) was conducted to validate the expression of CCTs in LUAD. The mutation in the CCTs was identified through the cBioPortal database, while promoter methylation was measured by the UALCAN database. The prognostic value of CCTs was evaluated using the PrognoScan analysis. The GEPIA2.0 database was used to measure the prognostic value of CCTs and associated Hub genes. Correlation analysis between CCTs expression in LUAD was based on the GEPIA2.0 database. The ROC curves, clinical correlation analysis, gene ontology, Kyoto Encyclopedia of Genes and Genome analysis, and immune cell infiltration analysis were downloaded from The Cancer Genome Atlas database and then analyzed and visualized using the R language. The STRING database was used for protein–protein interaction analysis. Upregulation of CCTs expression in patients with LUAD indicated advanced diseases and a poor prognosis. ROC curve analysis revealed that the CCTs may serve as diagnostic indicators. The functional enrichment analysis showed that CCTs were involved in the mitosis-mediated cell cycle process. Additionally, 10 hub genes associated with CCTs that were linked to LUAD prognosis and tumor progression were identified. Immune cell infiltration analysis showed that CCTs expression in tumor tissues tends to be related to T helper type 2 cell infiltration. This study revealed that CCTs may serve as valuable biomarkers for the diagnosis and targeted therapy of LUAD.

Downregulation of DIP2B as a prognostic marker inhibited cancer proliferation and migration and was associated with immune infiltration in lung adenocarcinoma via CCND1 and MMP2

BackgroundDIP2B is related to cancer progression. This study investigated the roles and pathways of DIP2B in lung adenocarcinoma (LUAD). MethodsDIP2B expression and the relationship between survival time of cancer patients and DIP2B expression were analyzed. The relationship between DIP2B expression and survival time in LUAD patients was evaluated by a meta-analysis. Cox and survival analyses were used to evaluate the prognostic factors and construct a prognostic nomogram. The mechanisms and effects of DIP2B and the relationship between DIP2B expression and the immune microenvironment were investigated using bioinformatics, CCK-8, western blotting, and transwell experiments. ResultsDIP2B was overexpressed in LUAD tissues. DIP2B overexpression was associated with shorter prognosis and was an unfavorable risk factor for prognosis in LUAD patients. DIP2B co-expressed genes were involved in cell division, DNA repair, cell cycle, and others. Inhibition of DIP2B expression could downregulate the proliferation, migration, and invasion of LUAD A549 and H1299 cells, which was related to the decrease in CCND1 and MMP2 protein expression. BRCA1 overexpression was associated with short prognosis, and the nomogram formed by DIP2B and BRCA1 was associated with a poor prognosis in LUAD patients. DIP2B expression correlated with immune cells (such as CD8 T cells, Tcm, and iDCs) and cell markers. ConclusionDIP2B is a potential biomarker of poor prognosis and the immune microenvironment in LUAD. Inhibition of DIP2B expression downregulated cancer cell proliferation, migration, and invasion, which might be related to the decrease in CCND1 and MMP2 protein expression. DIP2B-related nomograms might be useful tools for predicting the prognosis of LUAD patients.

DEP domain containing 1 as a biomarker for poor prognosis in lung adenocarcinoma

ObjectiveThe DEP domain-containing 1 (DEPDC1) gene is essential in the development and advancement of different types of cancer. This study is to examine the levels of DEPDC1 in lung adenocarcinoma (LUAD), and to determine its relationship with clinical results and immune response. The goal is to assess its potential as a biomarker and therapeutic target for LUAD. MethodsBy comprehensively utilizing the Cancer Genome Atlas (TCGA), gene Expression Synthesis (GEO), UALCAN, cBioPortal, TISIDB databases and online platforms, we conducted a bioinformatics analysis to investigate DEPDC1 gene survival analysis, prognostic diagnosis, prognostic survival, immune cell infiltration, DNA methylation, and the correlation of genetic mutations in LUAD. The results were validated through cell assay and immunohistochemical staining. ResultsDEPDC1 shows high levels of expression in the majority of tumors, with its expression being notably elevated in LUAD compablue to normal tissues. The expression of DEPDC1 varies based on the clinical characteristics of patients with LUAD. DEPDC1 expression affects the survival prognosis and prognostic model construction of LUAD patients. In addition, the presence of DEPDC1 is linked to immune infiltration. Various chemokines and chemokine receptors, immunoinhibitors and immune-stimulators in LUAD are significantly correlated with DEPDC1 methylation levels. Cell experiments confirmed through qPCR that the mRNA expression of DEPDC1 in LUAD was markedly elevated in comparison to the normal population, and immunohistochemistry showed positive DEPDC1 expression in LUAD pathological sections. ConclusionSystematic analysis and experiments have verified that DEPDC1 serves as a biomarker for detecting early, prediction of survival, and evaluation of immune cell infiltration in LUAD.

Construction of an immune-related gene prognostic model with experimental validation and analysis of immune cell infiltration in lung adenocarcinoma.

There is a correlation between tumors and immunity with the degree of immune cell infiltration in tumors being closely related to tumor growth and progression. Therefore, the present study identified immune-related prognostic genes and evaluated the immune infiltration level in lung adenocarcinoma (LUAD). This study performed Kyoto Encyclopedia of Genes and Genomes, Gene Ontology, and Gene Set Enrichment Analysis (GSEA) enrichment analyses on differential immune-associated genes. A risk model was created and validated using six immune-related prognostic genes. Reverse transcription-quantitative PCR was used to assess the prognostic gene expression in non-small cell lung cancer cells. Immune cell infiltration in LUAD was analyzed using the CIBERSORT method. Single sample GSEA was used to compare Tumor Immune Dysfunction and Exclusion (TIDE) scores between high and low-risk groups and to assess the activation of thirteen immune-related pathways. Multifactor Cox proportional hazards model analysis identified six prognostic risk genes (S100A16, FURIN, FGF2, LGR4, TNFRSF11A and VIPR1) to construct a risk model. The survival and receiver operating characteristic curves indicated that patients with higher risk scores had lower overall survival rates. The expression levels of prognostic genes S100A16, FURIN, LGR4, TNFRSF11A and VIPR1 were significantly increased in LUAD. B cells naive, plasma cells, T cells CD4 memory activated, T cells follicular helper, T cells regulatory, NK cells activated, macrophages M1, macrophages M2, and Dendritic cells resting cells showed elevated expression in LUAD. The prognostic genes were differentially associated with individual immune cells. Immune-related function scores, such as those for antigen presenting cell (APC) co-stimulation, APC co-inhibition, check-point, Cytolytic-activity, chemokine receptor, parainflammation, major histocompatibility complex-class-I, type-I-IFN-reponse and T-cell-co-inhibition, were higher in the high-risk group compared with the low-risk group. Furthermore, the TIDE score of the high-risk group was significantly lower than the low-risk group. This immune-related gene prognostic model has the potential to predict the prognosis of LUAD patients, supporting the development of a personalized clinical diagnosis and treatment plan.

Low Expression MCEMP1 Promoting Lung Adenocarcinoma Progression by and its Clinical Value.

Lung cancer is a highly prevalent tumor with a lack of biological markers that reflect its progression. Mast cell surface membrane protein 1 (MCEMP1, also known as C19ORF59) has not been reported in lung adenocarcinoma (LUAD). We aimed to investigate the role of MCEMP1 in LUAD. MCEMP1 expression in LUAD was analyzed using The Cancer Genome Atlas (TCGA) data, and conducted univariate and multivariate Cox regression analyses to evaluate the prognostic significance of MCEMP1 expression in TCGA. Tumor Immune Estimation Resource (TIMER) was used for examining the correlation between MCEMP1 expression and immune cell infiltration in LUAD. Furthermore, proliferation, migration, invasion, and colony-forming ability were investigated using LUAD cell lines. MCEMP1 had low expression in LUAD patient tissues and was correlated with lymph node metastasis, differentiation level, and tumor status. The Area under Curve (AUC) value of MCEMP1 for the Receiver Operating Characteristic (ROC) curve analysis was 0.984. The immune infiltration analysis revealed a correlation between MCEMP1 expression and the extent of macrophages and neutrophil infiltration in LUAD. Additionally, MCEMP1 has low expression in clinical samples, MCEMP1 overexpressed in LUAD cells substantially reduced cell growth, migration, and invasion of malignant cells. Low expression MCEMP1 promotes LUAD progression, which provides new insights and a potential biological target for future LUAD therapies.

Prognostic effect of TCF1+ CD8+ T cell and TOX+ CD8+ T cell infiltration in lung adenocarcinoma.

Recent studies have highlighted the pivotal roles of T cell transcription factors TCF-1 and TOX in modulating the immune response in cancer, with TCF-1 maintaining CD8+ T cell stemness and TOX promoting T cell exhaustion. The prognostic significance of these factors in lung adenocarcinoma (LUAD) remains a critical area of investigation. The retrospective study included 191 patients with LUAD who underwent surgery, of whom 83% were in stages II and III. These patients were divided into exploratory (n = 135) and validation (n = 56) groups based on the time of diagnosis. Multiplex fluorescence immunohistochemistry was used to examine the infiltration levels of CD8+ T cells, TCF1+ CD8+ T cells, and TOX+ CD8+ T cells. The percentage of CD8+ T cells in tumor was markedly lower than that in stroma (p < 0.05). In tumor-draining lymph nodes (TDLNs) invaded by tumor, the proportion of stem-like TCF1+ CD8+ T cells was significantly decreased (p < 0.01). Importantly, higher infiltration levels of CD8+ T cells and TCF1+ CD8+ T cells were associated with improved disease-free survival (DFS) (p = 0.009 and p = 0.006, respectively) and overall survival (OS) (p = 0.018 and p = 0.010, respectively). This study underscores the potential of TCF1+ CD8+ T cells as prognostic biomarkers in LUAD, providing insights into the tumor immune microenvironment and guiding future therapeutic strategies.

Identification of immune-associated biomarker for predicting lung adenocarcinoma: bioinformatics analysis and experiment verification of PTK6

BackgroundAbnormal expression of protein tyrosine kinase 6 (PTK6) has been proven to be involved in the development of gynecological tumors. However, its immune-related carcinogenic mechanism in other tumors remains unclear.ObjectiveThe aim of this study was to identify PTK6 as a novel prognostic biomarker in pan-cancer, especially in lung adenocarcinoma (LUAD), which is correlated with immune infiltration, and to clarify its clinicopathological and prognostic significance.MethodsThe prognostic value and immune relevance of PTK6 were investigated by using bio-informatics in this study. PTK6 expression was validated in vitro experiments (lung cancer cell lines PC9, NCI-H1975, and HCC827; human normal lung epithelial cells BEAS-2B). Western blot (WB) revealed the PTK6 protein expression in lung cancer cell lines. PTK6 expression was inhibited by Tilfrinib. Colony formation and the Cell Counting Kit-8 (CCK-8) assay were used to detect cell proliferation. The wound healing and trans-well were performed to analyze the cell migration capacity. Then flow cytometry was conducted to evaluate the cell apoptosis. Eventually, the relationship between PTK6 and immune checkpoints was examined. WB was used to estimate the PD-L1 expression at different Tilfrinib doses.ResultsPTK6 was an independent predictive factor for LUAD and was substantially expressed in LUAD. Pathological stage was significantly correlated with increased PTK6 expression. In accordance with survival analysis, poor survival rate in LUAD was associated with a high expression level of PTK6. Functional enrichment of the cell cycle and TGF-β signaling pathway was demonstrated by KEGG and GSEA analysis. Moreover, PTK6 expression considerably associated with immune infiltration in LUAD, as determined by immune analysis. Thus, the result of vitro experiments indicated that cell proliferation and migration were inhibited by the elimination of PTK6. Additionally, PTK6 suppression induced cell apoptosis. Obviously, PD-L1 protein expression level up-regulated while PTK6 was suppressed.ConclusionPTK6 has predictive value for LUAD prognosis, and could up regulated PD-L1.

Mitochondrial ribosomal protein S24 is associated with immunosuppressive microenvironment and cold tumor in lung adenocarcinoma

ObjectiveMRPS24 (Mitochondrial Ribosomal Protein S24) belongs to the mitochondrial ribosomal protein family, which participates in the protein synthesis of the mitochondrion. However, the relationship of MRPS24 with lung adenocarcinoma (LUAD) remained unknown. We aimed to identify its immunological and functional mechanisms in LUAD. MethodsThe analysis of MRPS24 expression, clinical features, diagnosis, prognosis, function analysis, genetic alteration, copy number variations, methylation, and tumor microenvironment was investigated by the TCGA, UCSC Xena, GEO, HPA, GEPIA, cBioPortal, MethSurv, TIMER, TIMER2.0, and TISIDB databases. ResultsMRPS24 was found to be more abundant in LUAD tumor tissue than in normal tissue. High levels of MRPS24 expression were found to be an independent prognostic factor by multivariate analysis. Functional analysis revealed that MRPS24 expression was associated with the immune, cell cycle and methylation. MRPS24 methylation level was inversely linked with its expression (p < 0.001). Patients with low MRPS24 methylation had a worse prognosis than those with high methylation (p < 0.05). In addition, the result revealed that the MRPS24 expression was inversely linked to the immune cell infiltration in LUAD. Finally, the validations of the expression level, prognosis, and immune cell infiltration of MRPS24 were in accordance with our previous results. ConclusionsThis study systematically explored that MRPS24 expression was significantly correlated with prognosis, tumorigenesis, genetic alteration, copy number variations, methylation, and immune cell infiltration in LUAD. MRPS24 might be a potential immune-related biomarker in the development and treatment of LUAD, thereby acting as a promising predictor of immunotherapy response in LUAD.

Accurate categorization and rapid pathological diagnosis correction with Micro-Raman technique in human lung adenocarcinoma infiltration level.

In the context of surgical interventions for lung adenocarcinoma (LADC), precise determination of the extent of LADC infiltration plays a pivotal role in shaping the surgeon's strategic approach to the procedure. The prevailing diagnostic standard involves the expeditious intraoperative pathological diagnosis of areas infiltrated by LADC. Nevertheless, current methodologies rely on the visual interpretation of tissue images by proficient pathologists, introducing an error margin of up to 15.6%. In this study, we investigated the utilization of Micro-Raman technique on isolated specimens of human LADC with the objective of formulating and validating a workflow for the pathological diagnosis of LADC featuring diverse degrees of infiltration. Our strategy encompasses a thorough pathological characterization of LADC, spanning different tissue types and levels of infiltration. Through the integration of Raman spectroscopy with advanced deep learning models for simultaneous diagnosis, this approach offers a swift, precise, and clinically relevant means of analysis. The diagnostic performance of the convolutional neural network (CNN) model, coupled with the microscopic Raman technique, was found to be exceptional and consistent, surpassing the traditional support vector machine (SVM) model. The CNN model exhibited an area under the curve (AUC) value of 96.1% for effectively distinguishing normal tissue from LADC and an impressive 99.0% for discerning varying degrees of infiltration in LADCs. To comprehensively assess its clinical utility, Raman datasets from patients with intraoperative rapid pathologic diagnostic errors were utilized as test subjects and input into the established CNN model. The results underscored the substantial corrective capacity of the Micro-Raman technique, revealing a misdiagnosis correction rate exceeding 96% in all cases. Ultimately, our discoveries highlight the Micro-Raman technique's potential to augment the intraoperative diagnostic precision of LADC with varying levels of infiltration. And compared to the traditional SVM model, the CNN model has better generalization ability in diagnosing different infiltration levels. This method furnishes surgeons with an objective groundwork for making well-informed decisions concerning subsequent surgical plans.

Identification of CNKSR1 as a biomarker for “cold” tumor microenvironment in lung adenocarcinoma: An integrative analysis based on a novel workflow

BackgroundTherapies targeting PD1/PD-L1 pathway have revolutionized the treatment of lung cancer. However, anti-PD1/PD-L1 therapies have proven beneficial for only a select group of lung adenocarcinoma (LUAD) patients and generally do not work for immuno-cold tumors characterized by a lack of immune cell infiltration. Identifying novel biomarkers is vital to broad therapeutic options for LUAD patients with no response to anti-PD1/PD-L1 immunotherapies. MethodsOur study has developed a novel strategy to identify a promising biomarker that addresses the limitations of anti-PD1/PD-L1 immunotherapy in treating immunological cold tumors. We exacted LUAD RNA-seq data from the Cancer Genome Atlas database (TCGA). Using several machine learning methods, we identified the candidate biomarker. Based on the expression level of PD-L1 and the identified biomarker, samples were categorized into four groups. We further used ESTIMATE, ssGSEA, and CIBERSORT algorithms to calculate the immune infiltration level of each group. The results were validated in three independent bulk datasets and one scRNA-seq dataset. Immunohistochemistry (IHC) assessments were performed in clinical samples to further evaluate the coexpression of CNKSR1 and PD-L1, and to compare CD8 + T cell infiltration among groups. ResultsAfter comprehensive analyses, CNKSR1 was identified as a novel promising biomarker for immuno-cold LUAD. CNKSR1 mRNA expression levels exhibited a negative correlation with both PD-L1 mRNA expression and the extent of immune cell infiltration in LUAD. Besides, in contrast to the significant association between the expression of PD-L1 and the majority of other well-established or widely studied immune checkpoint molecules, a mutually exclusive expression pattern is observed between CNKSR1 and these molecules. The aforementioned results were consistent in validation datasets. The prognostic model built based on the CNKSR1 coexpression module also showed robust predictive performance. Additionally, IHC assessments have confirmed that the coexpression of CNKSR1 and PD-L1 is rare in LUAD samples. Notably, LUADs in the high-CNKSR1 group, characterized by high CNKSR1 but low PD- L1 expression, demonstrated reduced infiltration of CD8+ T cells. ConclusionsIn summary, CNKSR1 emerges as a promising biomarker for immune-cold LUADs, and the study into CNKSR1 modulating T-cell infiltration may lead to the identification of compensatory molecules to enhance the effectiveness of current immunotherapy for LUAD.

Identification of a prognosis-related gene signature and ceRNA regulatory networks in lung adenocarcinoma

The ceRNA network, consisting of both noncoding RNA and protein-coding RNA, governs the occurrence, progression, metastasis, and infiltration of lung adenocarcinoma. Signatures comprising multiple genes can effectively determine survival stratification and prognosis of patients with lung adenocarcinoma. To explore the mechanisms of lung adenocarcinoma progression and identify potential biological targets, we carried out systematic bioinformatics analyses of the genetic profiles of lung adenocarcinoma, such as weighted gene co-expression network analysis (WGCNA), differential expression (DE) assessment, univariate and multivariate Cox proportional hazard regression models, ceRNA modulatory networks generated using the ENCORI and miRcode databases, nomogram models, ROC curve assessment, and Kaplan-Meier survival curve analysis. The ceRNA network encompassed 37 nodes, comprising 12 mRNAs, 22 lncRNAs, and three miRNAs. Simultaneously, we performed integration analysis using the 12 genes from the ceRNA network. Our findings revealed that the signature established by these 12 genes serves as an adverse element in lung adenocarcinoma, contributing to unfavorable patient prognosis. To ensure the credibility of our results, we used in vitro experiments for further verification. In conclusion, our study delved into the potential mechanisms underlying lung adenocarcinoma via the ceRNA regulatory network, specifically focusing on the PIF1 and has-miR-125a-5p axis. Additionally, a signature comprising 12 genes was identified as a biomarker related to the prognosis of lung adenocarcinoma.

Identification and Verification of Metabolism-related Immunotherapy Features and Prognosis in Lung Adenocarcinoma.

Lung cancer is a frequent malignancy with a poor prognosis. Extensive metabolic alterations are involved in carcinogenesis and could, therefore, serve as a reliable prognostic phenotype. Our study aimed to develop a prognosis signature and explore the relationship between metabolic characteristic-related signature and immune infiltration in lung adenocarcinoma (LUAD). TCGA-LUAD and GSE31210 datasets were used as a training set and a validation set, respectively. A total of 513 LUAD samples collected from The Cancer Genome Atlas database (TCGA-LUAD) were used as a training dataset. Molecular subtypes were classified by consensus clustering, and prognostic genes related to metabolism were analyzed based on Differentially Expressed Genes (DEGs), Protein-Protein Interaction (PPI) network, the univariate/multivariate- and Lasso- Cox regression analysis. Two molecular subtypes with significant survival differences were divided by the metabolism gene sets. The DEGs between the two subtypes were identified by integrated analysis and then used to develop an 8-gene signature (TTK, TOP2A, KIF15, DLGAP5, PLK1, PTTG1, ECT2, and ANLN) for predicting LUAD prognosis. Overexpression of the 8 genes was significantly correlated with worse prognostic outcomes. RiskScore was an independent factor that could divide LUAD patients into low- and high-risk groups. Specifically, high-risk patients had poorer prognoses and higher immune escape. The Receiver Operating Characteristic (ROC) curve showed strong performance of the RiskScore model in estimating 1-, 3- and 5-year survival in both training and validation sets. Finally, an optimized nomogram model was developed and contributed the most to the prognostic prediction in LUAD. The current model could help effectively identify high-risk patients and suggest the most effective drug and treatment candidates for patients with LUAD.

Potential association of HSPD1 with dysregulations in ribosome biogenesis and immune cell infiltration in lung adenocarcinoma: An integrated bioinformatic approach.

Lung adenocarcinoma (LUAD) is a major histological subtype of lung cancer with a high mortality rate worldwide. Heat shock protein family D member 1 (HSPD1, also known as HSP60) is reported to be increased in tumor tissues of lung cancer patients compared with healthy control tissues. We aimed to investigate the roles of HSPD1 in prognosis, carcinogenesis, and immune infiltration in LUAD using an integrative bioinformatic analysis. HSPD1 expression in LUAD was investigated in several transcriptome-based and protein databases. Survival analysis was performed using the KM plotter and OSluca databases, while prognostic significance was independently confirmed through univariate and multivariate analyses. Integrative gene interaction network and enrichment analyses of HSPD1-correlated genes were performed to investigate the roles of HSPD1 in LUAD carcinogenesis. TIMER and TISIDB were used to analyze correlation between HSPD1 expression and immune cell infiltration. The mRNA and protein expressions of HSPD1 were higher in LUAD compared with normal tissues. High HSPD1 expression was associated with male gender and LUAD with advanced stages. High HSPD1 expression was an independent prognostic factor associated with poor survival in LUAD patients. HSPD1-correlated genes with prognostic impact were mainly involved in aberrant ribosome biogenesis, while LUAD patients with high HSPD1 expression had low tumor infiltrations of activated and immature B cells and CD4+ T cells. HSPD1 may play a role in the regulation of ribosome biogenesis and B cell-mediated immunity in LUAD. It could serve as a predictive biomarker for prognosis and immunotherapy response in LUAD.

CCND2 is a prognostic biomarker and correlates with immune infiltration in lung adenocarcinoma.

CCND2 expression influences the growth and proliferation of cancer cells and plays a crucial role in immune response of tumor. However, few studies focused on the correlation between CCND2 and lung adenocarcinoma (LUAD) in terms of prognosis and tumor immune infiltration. Original LUAD case data were screened from The Cancer Genome Atlas (TCGA) database. Using R software, we analyzed differently expressed CCND2 between LUAD and adjacent normal tissues. Kaplan-Meier analysis was conducted to determine the relationship between CCND2 expression and the overall survival of LUAD patients, and Cox regression analysis was performed to identify the independently prognostic risk factors for LUAD. Using TIMER (Tumor Immune Estimation Resource) and CIBERSORTx (Cell-type Identification by Estimating Relative Subsets of known RNA Transcripts) databases, the connection between CCND2 expression and LUAD immune infiltration was investigated. The level of CCND2 was significantly lower in LUAD than in adjacent normal tissues [adjusted P<0.05 and log2 fold change (FC) =-1.33]. LUAD patients who expressed lower CCND2 had a shorter overall survival (P=0.046) and CCND2 was an independently prognostic risk factor for LUAD [hazard ratio (HR): 0.77, P=0.049]. In LUAD patients, CCND2 expression was positively associated with the levels of B cells (r=0.159, P=4.00e-04), CD8+ T cells (r=0.287, P=7.88e-11), CD4+ T cells (r=0.301, P=8.14e-12), macrophages (r=0.128, P=4.57e-03), neutrophils (r=0.373, P=1.07e-17), and myeloid dendritic cells (r=0.284, P=1.43e-10). The levels of B cells and macrophages had significantly association with the overall survival of LUAD patients. CIBERSORTx showed that the proportions of naive B cells, resting dendritic cells, and macrophages M1 were higher in the low CCND2 expression group (P<0.05); whereas macrophages M1, activated natural killer (NK) cells, and resting CD4+ memory cells were lower (P<0.05). CCND2 can be exploited as a novel prognostic biomarker involved in immune infiltration of LUAD, hence providing new preventative and therapeutic options for LUAD.

PERP May Affect the Prognosis of Lung Adenocarcinoma by Inhibiting Apoptosis.

PERP, a member of the peripheral myelin protein gene family, is a new therapeutic target in cancer. The relationships between PERP and immune cell infiltration in lung cancer have not been studied. Therefore, the role of PERP in the tumour microenvironment (TME) of lung cancer needs to be further explored. In this study, we explored the association between PERP expression and clinical characteristics by analysing data from the TCGA database. Cox regression and Kaplan‒Meier methods were used to investigate the relationship between the expression of PERP and overall survival in patients with lung adenocarcinoma (LUAD). The relationship between PERP expression and the degree of infiltration of specific immune cell subsets in LUAD was evaluated using the TIMER database and GEPIA. We also performed GO enrichment analysis and KEGG enrichment analysis to reveal genes coexpressed with PERP using the Coexpedia database. Finally, we verified the expression and function of PERP in LUAD tissues and the A549 cell line by RT‒PCR, Western blot, CCK-8, IHC, and wound healing assays. The mouse model was used to study the in vivo effects of PERP. According to our results, PERP expression was significantly higher in LUAD tissues and associated with the clinical characteristics of the disease. Survival was independently associated with PERP in LUAD patients. We further verified that PERP might regulate B-cell infiltration in LUAD to affect the prognosis of LUAD. To identify PERP-related signalling pathways in LUAD, we performed a genome-aggregation analysis (GSEA) between low and high PERP expression datasets. LUAD cells express higher levels of PERP than paracarcinoma cells, and PERP inhibits the proliferation and metastasis of A549 cells through apoptosis. PERP may affect the prognosis of lung adenocarcinoma by inhibiting apoptosis and is associated with immune cell infiltration.