Development of a Phagocytosis-Dependent Gene Signature to Predict Prognosis and Response to Checkpoint Inhibition in Clear-Cell Renal Cell Carcinoma

KDELR3 is transcriptionally activated by FOXM1 and accelerates lung adenocarcinoma growth and metastasis via inhibiting endoplasmic reticulum stress-induced cell apoptosis

Lung cancer is still considered to be the leading cause of cancer-related death worldwide, and lung adenocarcinoma (LUAD) is the most common kind. KDEL Endoplasmic Reticulum Protein Retention Receptor 3 (KDELR3) is a critical regulator of the endoplasmic reticulum (ER) stress and the followed unfolded protein response (UPR) process, which are critical in tumor development. However, the role of KDELR3 in LUAD tumor progression remains poorly understood. In this work, we demonstrated that KDELR3 is significantly upregulated in LUAD tumor tissues and cell lines. Suppression of KDELR3 promoted the phosphorylation level of UPR-related pathways, PERK, and EIF2α in LUAD cell lines. The downregulation of KDELR3 promoted ER stress-induced cell apoptosis, decreased the protein expression of Bcl-2, and increased the protein expression of Bax in LUAD cells. Moreover, the knockdown of KDELR3 inhibits LUAD cell invasion. In vivo animal experiments confirmed that the inhibition of KDELR3 suppresses LUAD tumor growth and metastasis. Mechanistic studies showed that transcription factor FOXM1 may serve as an upstream factor of KDELR3. The upregulation of FOXM1 increased the transcriptional activity of KDELR3. Further results illustrated that FOXM1 directly binds to the promoter of KDELR3, thus upregulating its expression. Finally, rescue experiments demonstrated that FOXM1 inhibition-induced cell apoptosis and invasion could be reversed by KDELR3 overexpression. Overall, our findings indicated that KDELR3 is transcriptionally upregulated by FOXM1 and accelerates tumor growth and lung metastasis in LUAD by inhibiting ER stress-induced cell apoptosis.

An antibody-dependent cellular phagocytosis-related gene signature predicts survival and response to immunotherapy in stomach adenocarcinoma

Antibody-dependent cellular phagocytosis (ADCP) is an immune biological process and plays a biological role in the clearance of tumor cells and the response to immune checkpoint inhibitors. However, the effects of ADCP on stomach adenocarcinoma (STAD) remain unclear. Clinical and genomic data were extracted from multiple datasets. The ADCP-related signature was established using Cox least absolute shrinkage and selection operator regression. Expression of the C5a receptor also known as complement component 5a receptor 1 in the tumor and adjacent-normal tissues was calculated using immunohistochemistry staining. Validation of the signature was conducted in the training and validation cohorts by Cox regression and log-rank tests. Furthermore, the immune infiltrates, the tumor immune dysfunction and exclusion score, and tumor mutation burden score were calculated using the corresponding algorithms, and Mann-Whitney U tests were used to evaluate the differences between groups. Seventy-three hub genes with predictive performance were identified to establish an ADCP-related signature. Accordingly, a 27-gene signature was established, C5a receptor also known as complement component 5a receptor 1, one of the signature genes, had higher expression in tumors than adjacent-normal samples, and its predictive performance was validated in the GSE84437 and The Cancer Genome Atlas cohorts. We found that the ADCP-related signature is an excellent prognostic predictor of STAD. Moreover, the molecular characteristics and some indices of response to immunotherapy differed between the high- and low-risk groups. We constructed a 27-gene signature that is associated with the prognosis and response to STAD-based immunotherapy and provide insights into the biological mechanisms underlying this predictive function.

KDELR3 overexpression as a novel prognostic and diagnostic biomarker in glioma: comprehensive bioinformatic analysis insights

Glioma, the most prevalent primary intracranial malignancy among adults, is distinguished by its high morbidity and recurrence rates, posing a considerable threat to patients' quality of life and survival prospects. Consequently, the pursuit of efficacious molecular prognostic markers holds paramount importance. The exploration of the role of the KDELR3 kinase family in various neoplastic conditions constitutes an emerging area of research. However, the biological functions of KDELR3 and its prognostic implications in brain tumors remain largely undocumented. This study endeavored to ascertain the potential of KDELR3 as a prognostic indicator for glioma. We integrated a comprehensive dataset encompassing 1127 glioma samples, sourced from our cohort, The Cancer Genome Atlas (TCGA), and the Chinese Glioma Genome Atlas (CGGA), to delve into the expression patterns of KDELR3 in glioma and their associated implications. Notably, KDELR3 was markedly overexpressed in glioma and demonstrated a positive correlation with clinical progression. By utilizing Kaplan-Meier survival analysis and the Cox proportional hazards regression model, we evaluated the prognostic significance of KDELR3, revealing it as an independent predictor of adverse outcomes in glioma patients. Furthermore, gene set enrichment analysis unveiled potential signaling pathways associated with KDELR3 expression in glioma, primarily encompassing Cytokine-cytokine receptor interaction, extracellular matrix (ECM)-receptor interaction, and complement and coagulation cascades. In summation, our findings provide profound insights into the potential role of KDELR3 and its application as a novel and promising prognostic biomarker for glioma.

Exploration of the Key Pathways and Genes Involved in Osteoarthritis Genesis: Evidence from Multiple Platforms and Real-World Validation

Background

Osteoarthritis (OA), a degenerative and chronic joint disease, is essential for identifying novel biomarkers for the clinical diagnosis of OA.

Methods

We collected 35 OA patients and 32 healthy controls from four clinical cohorts and 8 real-world samples from our institute. The activation status of 7530 signalling pathways was calculated via the gene set enrichment analysis (GSEA) algorithm. Ten machine learning algorithms and 101 algorithm combinations were further applied to recognize the most diagnostic genes. KDELR3 was chosen for further validation via immunohistochemical staining to determine its diagnostic value in real-world samples.

Results

Sixteen pathways, namely, the cellular respiration chain, protein transport, lysosomal and endocytosis pathways, were activated in OA patients. A total of 101 types of algorithm combinations were considered for the diagnostic model, and 58 were successfully output. The two-step model of glmBoost plus RF had the highest average AUC value of 0.95 and was composed of LY86, SORL1, KDELR3, CSK, PTGS1, and PTGS2. Preferable consistency of the diagnostic mole and real conditions was observed in all four cohorts (GSE55235: Kappa=1.000, P<0.001; GSE55457: Kappa=0.700, P<0.001; GSE82107: Kappa=0.643, P=0.004; GSE1919: Kappa=1.000, P<0.001). KDELR3 was expressed at higher levels in OA patients than were the other genes, and with the help of immunohistochemistry (IHC), we confirmed that OA patients presented high levels of KDELR3 in synovial tissues. The infiltration of immunocytes, macrophages, and natural killer T cells was high in OA patients. KDELR3 might be involved in the activation and infiltration of effector memory CD4 T cells (Rpearson = 0.58, P < 0.001) and natural killer T cells (Rpearson = 0.53, P < 0.001).

Conclusion

We constructed and validated a six-gene diagnostic model for OA patients via machine learning, and KDELR3 emerged as a novel biomarker for OA.

Discovery and Validation of Survival-Specific Genes in Papillary Renal Cell Carcinoma Using a Customized Next-Generation Sequencing Gene Panel

PURPOSE

Papillary renal cell carcinoma (PRCC), the second most common kidney cancer, is morphologically, genetically, and molecularly heterogeneous with diverse clinical manifestations. Genetic variations of PRCC and their association with survival are not yet well-understood. This study aimed to identify and validate survival-specific genes in PRCC and explore their clinical utility.

MATERIALS AND METHODS

Using machine learning, 293 patients from the Cancer Genome Atlas-Kidney Renal Papillary Cell Carcinoma (TCGA-KIRP) database were analyzed to derive genes associated with survival. To validate these genes, DNAs were extracted from the tissues of 60 Korean PRCC patients. Next generation sequencing was conducted using a customized PRCC gene panel of 202 genes, including 171 survival-specific genes. Kaplan-Meier and Log-rank tests were used for survival analysis. Fisher's exact test was performed to assess the clinical utility of variant genes.

RESULTS

A total of 40 survival-specific genes were identified in the TCGA-KIRP database through machine learning and statistical analysis. Of them, 10 (BAP1, BRAF, CFDP1, EGFR, ITM2B, JAK1, NODAL, PCSK2, SPATA13, and SYT5) were validated in the Korean-KIRP database. Among these survival gene signatures, three genes (BAP1, PCSK2, and SPATA13) showed survival specificity in both overall survival (OS) (p = 0.00004, p = 1.38 × 10-7, and p = 0.026, respectively) and disease-free survival (DFS) (p = 0.00002, p = 1.21 × 10-7, and p = 0.036, respectively). Notably, the PCSK2 mutation demonstrated survival specificity uniquely in both the TCGA-KIRP (OS: p = 0.010 and DFS: p = 0.301) and Korean-KIRP (OS: p = 1.38 × 10-7 and DFS: p = 1.21 × 10-7) databases.

CONCLUSIONS

We discovered and verified genes specific for the survival of PRCC patients in the TCGA-KIRP and Korean-KIRP databases. The survival gene signature, including PCSK2 commonly obtained from the 40 gene signature of TCGA and the 10 gene signature of the Korean database, is expected to provide insight into predicting the survival of PRCC patients and developing new treatment.

Epigenomic reprogramming of therapy-resistant circulating tumor cells in colon cancer

Therapy resistance is a major challenge in colorectal cancer management. Epigenetic changes, such as DNA methylation, in tumor cells are involved in the development of acquired resistance during treatment. Here, we characterized the DNA methylation landscape of colon circulating tumor cells (CTCs) during cancer progression and therapy resistance development. To this aim, we used nine permanent CTC lines that were derived from peripheral blood samples of a patient with metastatic colon cancer collected before treatment initiation (CTC-MCC-41) and during treatment and cancer progression (CTC-MCC-41.4 and CTC-MCC-41.5 [A-G]). We analyzed the DNA methylome of these nine CTC lines using EPIC arrays and also assessed the association between DNA methylation and gene expression profiles. We confirmed DNA methylation and gene expression results by pyrosequencing and RT-qPCR, respectively. The global DNA methylation profiles were different in the pre-treatment CTC line and in CTC lines derived during therapy resistance development. These resistant CTC lines were characterized by a more hypomethylated profile compared with the pre-treatment CTC line. Most of the observed DNA methylation differences were localized at CpG-poor regions and some in CpG islands, shore regions and promoters. We identified a distinctive DNA methylation signature that clearly differentiated the pre-treatment CTC line from the others. Of note, the genes involved in this signature were associated with cancer-relevant pathways, including PI3K/AKT, MAPK, Wnt signaling and metabolism. We identified several epigenetically deregulated genes associated with therapy resistance in CTCs, such as AP2M1. Our results bring new knowledge on the epigenomic landscape of therapy-resistant CTCs, providing novel mechanisms of resistance as well as potential biomarkers and therapeutic targets for advanced CRC management.

Establishment of a Seven-Gene Signature Associated with CD8+ T Cells through the Utilization of Both Single-Cell and Bulk RNA-Sequencing Techniques in Clear Cell Renal Cell Carcinoma

Tumor immune microenvironment constituents, such as CD8+ T cells, have emerged as crucial focal points for cancer immunotherapy. Given the absence of reliable biomarkers for clear cell renal cell carcinoma (ccRCC), we aimed to ascertain a molecular signature that could potentially be linked to CD8+ T cells. The differentially expressed genes (DEGs) linked to CD8+ T cells were identified through an analysis of single-cell RNA sequencing (scRNA-seq) data obtained from the Gene Expression Omnibus (GEO) database. Subsequently, immune-associated genes were obtained from the InnateDB and ImmPort datasets and were cross-referenced with CD8+ T-cell-associated DEGs to generate a series of DEGs linked to immune response and CD8+ T cells. Patients with ccRCC from the Cancer Genome Atlas (TCGA) were randomly allocated into testing and training groups. A gene signature was established by conducting LASSO-Cox analysis and subsequently confirmed using both the testing and complete groups. The efficacy of this signature in evaluating immunotherapy response was assessed on the IMvigor210 cohort. Finally, we employed various techniques, including CIBERSORT, ESTIMATE, ssGSEA, and qRT-PCR, to examine the immunological characteristics, drug responses, and expression of the signature genes in ccRCC. Our findings revealed 206 DEGs linked to immune response and CD8+ T cells, among which 65 genes were correlated with overall survival (OS) in ccRCC. A risk assessment was created utilizing a set of seven genes: RARRES2, SOCS3, TNFSF14, XCL1, GRN, CLDN4, and RBP7. The group with a lower risk showed increased expression of CD274 (PD-L1), suggesting a more favorable response to anti-PD-L1 treatment. The seven-gene signature demonstrated accurate prognostic prediction for ccRCC and holds potential as a clinical reference for treatment decisions.

Role of the membrane-spanning 4A gene family in lung adenocarcinoma

Lung adenocarcinoma, which is the second most prevalent cancer in the world, has a poor prognosis and a low 5-year survival rate. The MS4A protein family is crucial to disease development and progression, particularly for cancers, allergies, metabolic disorders, autoimmune diseases, infections, and neurodegenerative disorders. However, its involvement in lung adenocarcinoma remains unclear. In this study, we found that 11 MS4A family genes were upregulated or downregulated in lung adenocarcinoma. Furthermore, we described the genetic variation landscape of the MS4A family in lung adenocarcinoma. Notably, through functional enrichment analysis, we discovered that the MS4A family is involved in the immune response regulatory signaling pathway and the immune response regulatory cell surface receptor signaling pathway. According to the Kaplan-Meier curve, patients with lung adenocarcinoma having poor expression of MS4A2, MS4A7, MS4A14, and MS4A15 had a low overall survival rate. These four prognostic genes are substantially associated with immune-infiltrating cells, and a prognosis model incorporating them may more accurately predict the overall survival rate of patients with lung adenocarcinoma than current models. The findings of this study may offer creative suggestions and recommendations for the identification and management of lung adenocarcinoma.

FKBP11 upregulation promotes proliferation and migration in hepatocellular carcinoma

BACKGROUND

Hepatocellular carcinoma (HCC) is one of the leading causes of cancer related deaths world over. Early diagnosis and effective treatment monitoring significantly improves patients' outcomes. FKBP11 gene is highly expressed in HCC and could play a role in its development, early diagnosis and treatment.

OBJECTIVE

This study aimed to evaluate the expression of FKBP11 in HCC, its correlation with patients' clinical characteristics and potential role in HCC development.

METHODS

Expression was determined by bioinformatics analysis, quantitative real-time PCR, western blot, and immunohistochemistry. CCK-8, Transwell and wound healing assays were used to investigate involvement in HCC development.

RESULTS

FKBP11 was significantly upregulated in HCC cells, tissues and blood (all p< 0.001). Its receiver operator characteristic (ROC) curve had an AUC of 0.864 (95% CI: 0.823-0.904), at a sensitivity of 0.86 and specificity of 0.78 indicating a good diagnostic potential in HCC. Its expression was markedly reduced after surgery (p< 0.0001), indicating a potential application in HCC treatment follow-up. Knockdown of FKBP11 in HCC cells attenuated proliferation and migration, suggesting a possible role in HCC pathogenesis.

CONCLUSION

This study thus found that FKBP11 is upregulated in HCC, and the upregulation promotes HCC development. FKBP11 levels are significantly reduced post-surgery and could be a potential diagnostic and prognostic marker for HCC.

SLC9A1 Binding mTOR Signaling Pathway-Derived Risk Score Predicting Survival and Immune in Clear Cell Renal Cell Carcinoma

Objective. Clear cell renal cell carcinoma (ccRCC) is one of the common renal cell carcinomas (RCC) with a high risk of recurrence. Considering that SLC9A1 is involved in various cellular physiological processes and probably mediates the course of mTOR signaling in tumors, this study constructed a risk model for SLC9A1 combined with mTOR signaling in ccRCC, aiming at better predicting the prognosis of patients. Methods. ccRCC expression matrices were downloaded from TCGA and ICGC databases to compare the expression of SLC9A1 in TCGA, and qRT-PCR was adopted to validate the SLC9A1 expression in different RCC cells and normal kidney cells. The CIBERSORT and ESTIMATE algorithms were used to assess samples for immunity. mTOR signaling-associated genes were downloaded from the KEGG website, and then the genes were adopted to screen genes associated with SLC9A1 expression and mTOR signaling pathway colleagues, based on which univariate COX regression and lasso regression Cox analyses were conducted to construct a ccRCC prognostic risk model. ROC curves and nomograms were used to assess the validity of the models. Results. ccRCC tumor samples showed lower SLC9A1 expression than normal samples, as also evidenced by qRT-PCR. The SLC9A1 expression was highly correlated with tumor immunity. Totally, 564 key genes associated with both SLC9A1 expression and mTOR signaling were screened out, and the risk model consisting of 11 gene signatures was constructed in ccRCC based on the 564 genes. Since patients at a high risk had poorer survival outcomes, the high-risk group presented poorer immunotherapy outcomes. Moreover, a higher clinical grade of patients suggested a higher risk score. The risk score can serve as one independent prognostic factor for the prognosis prediction of ccRCC patients. Conclusion. An extremely promising prognostic indicator for ccRCC based on SLCA9A1 and mTOR signaling has been constructed to provide reference for clinical treatment.

Identification of a claudin-low subtype in clear cell renal cell carcinoma with implications for the evaluation of clinical outcomes and treatment efficacy

Background

In bladder and breast cancer, the claudin-low subtype is widely identified, revealing a distinct tumor microenvironment (TME) and immunological feature. Although we have previously identified individual claudin members as prognostic biomarkers in clear cell renal cell carcinoma (ccRCC), the existence of an intrinsic claudin-low subtype and its interplay with TME and clinical outcomes remains unclear.

Methods

Transcriptomic and clinical data from The Cancer Genome Atlas (TCGA)- kidney clear cell carcinoma (KIRC) cohort and E-MTAB-1980 were derived as the training and validation cohorts, respectively. In addition, GSE40435, GSE53757, International Cancer Genome Consortium (ICGC) datasets, and RNA-sequencing data from local ccRCC patients were utilized as validation cohorts for claudin clustering based on silhouette scores. Using weighted correlation network analysis (WGCNA) and multiple machine learning algorithms, including least absolute shrinkage and selection operator (LASSO), CoxBoost, and random forest, we constructed a claudin-TME related (CTR) risk signature. Furthermore, the CTR associated genomic characteristics, immunity, and treatment sensitivity were evaluated.

Results

A claudin-low phenotype was identified and associated with an inferior survival and distinct TME and cancer immunity characteristics. Based on its interaction with TME, a risk signature was developed with robust prognostic prediction accuracy. Moreover, we found its association with a claudin-low, stem-like phenotype and advanced clinicopathological features. Intriguingly, it was also effective in kidney chromophobe and renal papillary cell carcinoma. The high CTR group exhibited genomic characteristics similar to those of claudin-low phenotype, including increased chromosomal instability (such as deletions at 9p) and risk genomic alterations (especially BAP1 and SETD2). In addition, a higher abundance of CD8 T cells and overexpression of immune checkpoints, such as LAG3, CTLA4 and PDCD1, were identified in the high CTR group. Notably, ccRCC patients with high CTR were potentially more sensitive to immune checkpoint inhibitors; their counterparts could have more clinical benefits when treated with antiangiogenic drugs, mTOR, or HIF inhibitors.

Conclusion

We comprehensively evaluated the expression features of claudin genes and identified a claudin-low phenotype in ccRCC. In addition, its related signature could robustly predict the prognosis and provide guide for personalizing management strategies.