A circadian rhythm-related gene signature associated with tumor immunity, cisplatin efficacy, and prognosis in bladder cancer

Developing and experimental validating a B cell exhaustion-related gene signature to assess prognosis and immunotherapeutic response in bladder cancer

BACKGROUND

B cell exhaustion (BEX) refers to the impairment of normal B cell functions and decreased proliferation capability. However, the prognostic value of BEX-related genes in bladder cancer (BLCA) remains unclear.

METHODS

BLCA cases from TCGA were used for training, while GSE5287, GSE13507, GSE31684, and GSE32894 cohorts from GEO were used for external validation. BEX-related genes were identified through literature retrieval, unsupervised clustering, and genomic difference detection. Gene pairing, LASSO, random forest, and Cox regression were employed to construct a predictive model. B cell samples from scRNAseqDB, GSE111636, and IMvigor210 were utilized to explore immunoprofiles and the predictive ability of the model in immunotherapeutic response. Additionally, 21 pairs of BLCA and paracarcinoma samples from Nanfang Hospital were used to re-confirm our findings through RT-qPCR, immunofluorescence, and flow cytometry.

RESULTS

39 BEX-related genes were identified. A 4-gene-pair signature was constructed and served as a reliable prognostic predictor across multiple datasets (pooled HR = 2.32; 95 % CI = 1.81-2.98). The signature reflected the BEX statuses of B cells (FDR < 0.05) and showed promise in evaluating immunotherapeutic sensitivity (P < 0.001). In the local cohort, CD52, TUBB6, and CAV1 were down-regulated in BLCA tissues, while TGFBI, UBE2L6, TINAGL1, and IL32 were up-regulated (all P < 0.05). Furthermore, the infiltration levels of CD19 + CD52 + and CD19 + TUBB6 + B cells in paracarcinoma samples were higher than those in BLCA samples (all P < 0.05).

CONCLUSION

A BEX-related gene signature was developed to predict prognosis and immunotherapeutic sensitivity in BLCA, providing valuable guidance for personalized treatment.

Relationship between circadian rhythm-related genes and extracellular matrix: implications for sleep deprivation

BACKGROUND

Sleep deprivation (SD) can lead to the development of various pathological disorders. The extracellular matrix (ECM) compositions and circadian rhythm genes are two pivotal variables of SD. However, their relationships remain undefined during SD.

METHODS

A mouse SD model was established using a modified multiplatform water environment method. The expression of nerve growth factor (NGF) in mouse hippocampus was detected by an immunofluorescence (IF) method. Protein expression was assessed by western blot, and mRNA analysis was performed by quantitative real-time PCR (qRT-PCR). The differentially expressed genes after SD, the genes associated with stromal score, and gene expression correlation were analyzed by bioinformatic analysis.

RESULTS

The mouse model of SD was successfully established, as evidenced by the changed morphology, increased Bax and NGF levels, and downregulated Bcl-2 in mouse hippocampus after SD. The differentially expressed genes after SD were closely associated with the ECM compositions. The ECM composition metalloproteinase 9 (MMP9) was under-expressed in mouse hippocampus after SD. The hippocampal MMP9 expression was correlated with the expression levels of circadian genes PER2, PER3, TIMELESS, FBXL3, and NFIL3. PER2 and TIMELESS were upregulated in mouse hippocampus after SD.

CONCLUSION

The current findings suggest a correlation between ECM composition MMP9 and circadian rhythm-related genes PER2 and TIMELESS in mouse hippocampus after SD, providing a novel understanding of the disorders after SD.

Identification of key genes modules linking diabetic retinopathy and circadian rhythm

Background

Diabetic retinopathy (DR) is a leading cause of vision loss worldwide. Recent studies highlighted the crucial impact of circadian rhythms (CR) on normal retinopathy in response to the external light cues. However, the role of circadian rhythms in DR pathogenesis and potential investigational drugs remains unclear.

Methods

To investigate the weather CR affects DR, differential expression analysis was employed to identify differentially expressed genes (DEGs) from the GEO database (GSE160306). Functional enrichment analysis was conducted to identify relevant signaling pathways. LASSO regression was utilized to screen pivotal genes. Weighted gene co-expression network anlaysis (WGCNA) was applied to identify different modules. Additionally, we use the Comparative Toxicogenomics Database (CTD) database to search key genes related to drugs or molecular compounds. The diabetic mouse model received three consecutive intraperitoneal injections of streptozotocin (STZ) during 3 successive days.

Results

We initially identified six key genes associated with circadian rhythm in DR, including COL6A3, IGFBP2, IGHG4, KLHDC7A, RPL26P30, and MYL6P4. Compared to normal tissue, the expression levels of COL6A3 and IGFB2 were significantly increased in DR model. Furthermore, we identified several signaling pathways, including death domain binding, insulin-like growth factor I binding, and proteasome binding. We also observed that COL6A3 was positively correlated with macrophages (cor=0.628296895, p=9.96E-08) and Th17 cells (cor=0.665120835, p=9.14E-09), while IGFBP2 showed a negatively correlated with Tgd (cor=-0.459953045, p=0.000247284) and Th2 cells (cor=-0.442269719, p=0.000452875). Finally, we identified four drugs associated with key genes: Resveratrol, Vitamin E, Streptozocin, and Sulindac.

Conclusion

Our findings revealed several key genes related to circadian rhythms and several relevant drugs in DR, providing a novel insight into the mechanism of DR and potential implications for future DR treatment. This study contributes to a better understanding of CR in DR and its implications for future therapeutic interventions.

Construction and experimental validation of a B cell-related gene signature to predict the prognosis and immunotherapeutic sensitivity in bladder cancer

BACKGROUND

B cells are essential components of tumor microenvironment and exert important functions in anti-tumor immune response. However, the prognosis value of B cell-related genes in bladder cancer (BLCA) remains obscure.

MATERIALS AND METHODS

The infiltrating levels of B cells were measured via the CD20 staining in the local samples and the computational biology analyses in the TCGA-BLCA cohort. The single-cell RNA sequencing analysis, gene-pair strategy, LASSO regression, random forest, and Cox regression were used for B cell-related signature construction. TCGA-BLCA cohort was chosen as the training cohort, and three independent cohorts from GEO and the local cohort were used for external validation. 326 B cells were adopted to explore the association between the model and B cells' biological processes. TIDE algorithm and two BLCA cohorts receiving anti-PD1/PDL1 treatment were utilized to detect its predictive ability to the immunotherapeutic response.

RESULTS

High infiltration levels of B cells heralded favorable prognosis, both in the TCGA-BLCA cohort and the local cohort (all P < 0.05). A 5-gene-pair model was established and served as a significant prognosis predictor across multiple cohorts (pooled hazard ratio = 2.79, 95% confidence interval = 2.22-3.49). The model could evaluate the prognosis effectively in 21 of 33 cancer types (P < 0.05). The signature was negatively associated with B cells' activation, proliferation, and infiltrating levels, and could serve as a potential predictor of immunotherapeutic outcomes.

CONCLUSIONS

A B cell-related gene signature was constructed to predict the prognosis and immunotherapeutic sensitivity in BLCA, helping to guide the personalized treatment.

CRS: a circadian rhythm score model for predicting prognosis and treatment response in cancer patients

BACKGROUND

Circadian rhythm regulates complex physiological activities in organisms. A strong link between circadian dysfunction and cancer has been identified. However, the factors of dysregulation and functional significance of circadian rhythm genes in cancer have received little attention.

METHODS

In 18 cancer types from The Cancer Genome Atlas (TCGA), the differential expression and genetic variation of 48 circadian rhythm genes (CRGs) were examined. The circadian rhythm score (CRS) model was created using the ssGSEA method, and patients were divided into high and low groups based on the CRS. The Kaplan-Meier curve was created to assess the patient survival rate. Cibersort and estimate methods were used to identify the infiltration characteristics of immune cells between different CRS subgroups. Gene Expression Omnibus (GEO) dataset is used as verification queue and model stability evaluation queue. The CRS model's ability to predict chemotherapy and immunotherapy was assessed. Wilcoxon rank-sum test was used to compare the differences of CRS among different patients. We use CRS to identify potential "clock-drugs" by the connective map method.

RESULTS

Transcriptomic and genomic analyses of 48 CRGs revealed that most core clock genes are up-regulated, while clock control genes are down-regulated. Furthermore, we show that copy number variation may affect CRGs aberrations. Based on CRS, patients can be classified into two groups with significant differences in survival and immune cell infiltration. Further studies showed that patients with low CRS were more sensitive to chemotherapy and immunotherapy. Additionally, we identified 10 compounds (e.g. flubendazole, MLN-4924, ingenol) that are positively associated with CRS, and have the potential to modulate circadian rhythms.

CONCLUSIONS

CRS can be utilized as a clinical indicator to predict patient prognosis and responsiveness to therapy, and identify potential "clock-drugs".

Time Matters: Importance of Circadian Rhythms, Disruption, and Chronotherapy in Urologic Malignancies

The human body was evolutionarily programmed to run on cycles, termed circadian rhythms, which integrate human behavior and bodily function with the environment. Disruptions to these rhythms via desynchronization have been deemed a probable carcinogen by the WHO. Subsequent research has identified alterations in multiple core clock genes when comparing tumor and benign tissues. This review will discuss core clock genes associated with urogenital malignancies and highlight impactful research regarding circadian biology use in treatment. Chronotherapy, treatment alignment with an individual's biological rhythm, remains a relatively untouched field within urology that should be explored to possibly enhance therapeutic outcomes.

Clinical Spectrum and Trajectory of Innovative Therapeutic Interventions for Insomnia: A Perspective

Increasing incidences of insomnia in adults, as well as the aging population, have been reported for their negative impact on the quality of life. Insomnia episodes may be associated with neurocognitive, musculoskeletal, cardiovascular, gastrointestinal, renal, hepatic, and metabolic disorders. Epidemiological evidence also revealed the association of insomnia with oncologic and asthmatic complications, which has been indicated as bidirectional. Two therapeutic approaches including cognitive behavioral therapy (CBT) and drugs-based therapies are being practiced for a long time. However, the adverse events associated with drugs limit their wide and long-term application. Further, Traditional Chinese medicine, acupressure, and pulsed magnetic field therapy may also provide therapeutic relief. Notably, the recently introduced cryotherapy has been demonstrated as a potential candidate for insomnia which could reduce pain, by suppressing oxidative stress and inflammation. It seems that the synergistic therapeutic approach of cryotherapy and the above-mentioned approaches might offer promising prospects to further improve efficacy and safety. Considering these facts, this perspective presents a comprehensive summary of recent advances in pathological aetiologies of insomnia including COVID-19, and its therapeutic management with a greater emphasis on cryotherapy.

A circadian rhythm-related biomarker for predicting prognosis and immunotherapy efficacy in lung adenocarcinoma

Lung adenocarcinoma (LUAD) remains a major reason of cancer-associated mortality globally, and there exists a lack of indicators for survival in LUAD patients. Therefore, it is clinically required to obtain a novel prognostically indicator for guiding clinical management. In this study, we established a circadian rhythm (CR) related signature by a combinative investigation of multiple datasets. The newly-established signature showed an acceptable ability to predict survival and could serve as an independent indicator for prognosis. Moreover, the newly-established signature was critically associated with tumor malignancy, including proliferation, invasion, EMT and metastasis. The newly-established signature was predictive of response to immune checkpoint blockade. Collectively, we established a CR-related gene signature that could forecast survival, tumor malignancy and therapeutic response; our findings could help guiding clinical management.

Acircadian rhythm-related gene signature for predicting survival and drug response in HNSC

Head and neck squamous cell carcinoma (HNSC) represents one of the most common malignant carcinomas worldwide. Because the 5-year survival rate of patients with HNSC is poor, it is necessary to develop an effective signature for predicting the risk of HNSC. To identify a circadian rhythm (CR)-related predictive signature, we analyzed the RNA-seq data of patients with HNSC from The Cancer Genome Atlas and Gene Expression Omnibus cohorts. Nine CR-related genes (PER2, PER3, GHRL, CSF2, HDAC3, KLF10, PRKAA2, PTGDS, and RORB) were identified to develop a CR-related signature. The area under the curve values for 5-year overall survival were 0.681, 0.700, and 0.729 in the training set, validation set, and an external independent test set (GSE41613), respectively. The Kaplan‒Meier curve analysis showed that the high-risk group had a reduced relapse-free survival compared with the low-risk group in the training set, validation set, and test set (P < 0.05). Finally, we observed that the CR-related gene signature was associated with the tumor immune microenvironment, somatic nucleotide variation, and drug response in HNSC. In conclusion, we developed a circadian rhythm-related gene signature for predicting overall survival in HNSC.

Development of a Novel Immune-Related Gene Signature to Predict Prognosis and Immunotherapeutic Efficiency in Gastric Cancer

Background: Gastric cancer (GC) is the fifth most common malignancy and the third leading cause of tumor-related deaths globally. Herein, we attempted to build a novel immune-related gene (IRG) signature that could predict the prognosis and immunotherapeutic efficiency for GC patients.

Methods: The mRNA transcription data and corresponding clinical data of GC were downloaded from The Cancer Genome Atlas (TCGA) database as the training group and the GSE84437 data set as the testing cohort, followed by acquisition of IRGs from the InnateDB resource and ImmPort database. Using the univariate Cox regression analysis, an IRG signature was developed. Several immunogenomic analyses were performed to illustrate the associations between the immune risk score and tumor mutational burden, immune cell infiltrations, function of immune infiltration, clinical characteristics, immune subtype, and immunotherapeutic response.

Results: The analysis of 343 GC samples and 30 normal samples from the TCGA database gave rise to 8,713 differentially expressed genes (DEGs) and 513 differentially expressed immune-related genes (DEIRGs) were extracted. The novel IRG signature contained eight DEIRGs (FABP4, PI15, RNASE2, CGB5, INHBE, RLN2, DUSP1, and CD36) and was found to serve as an independent predictive and prognostic factor for GC. Then, the GC patients were separated into the high- and low-risk groups based on the median risk score, wherein the low-risk group presented a better prognosis and was more sensitive to immunotherapy than did the high-risk group. According to the time-dependent ROC curves and AUCs, the immunotherapeutic value of the signature was better than the Tumor Immune Dysfunction and Exclusion (TIDE) and T-cell inflammatory signature (TIS) scores. In addition, the AUCs of the risk score for predicting 1-, 2-, and 3-year OS were 0.675, 0.682, and 0.710, respectively, which indicated that the signature had great predictive power.

Conclusion: This study presents a novel IRG signature based on the tumor immune microenvironment, which could improve the prediction of the prognosis and immunotherapeutic efficiency for GC patients. The powerful signature may serve as novel biomarkers and provide therapeutic targets for precision oncology in clinical practice.