Identification and meta-analysis of copy number variation-driven circadian clock genes for colorectal cancer

LINC01232 promotes ARNTL2 transcriptional activation and inhibits ferroptosis of CRC cells through p300/H3K27ac

Aim: This study investigated the role of lncRNA LINC01232 in ferroptosis of colorectal cancer (CRC).Materials & methods: Real time quantitative polymerase chain reaction or western blot experiments were performed to examine relevant mRNAs and proteins expression. The kit assays evaluated malondialdehyde, iron, Fe2+ and glutathione levels. ROS levels were verified by flow cytometry. Chromatin immunoprecipitation and RNA immunoprecipitation analysis monitored the correlation among LINC01232, H3K27ac, p300 and ARNTL2.Results: LINC01232 or ARNTL2 knockdown facilitated erastin-induced ferroptosis. The interaction between LINC01232 and p300 resulted in the enhancement of H3K27ac levels at ARNTL2 promoter to promote ARNTL2 transcriptional activity. ARNTL2 overexpression reversed the promoting effect of LINC01232 knockdown on ferroptosis.Conclusion: LINC01232 inhibited the ferroptosis in CRC by epigenetically upregulating the transcriptional activity of ARNTL2.

Circadian rhythm-related genes index: A predictor for HNSCC prognosis, immunotherapy efficacy, and chemosensitivity

Background

Head and neck squamous cell carcinoma (HNSCC) is the most common head and neck cancer and is highly aggressive and heterogeneous, leading to variable prognosis and immunotherapy outcomes. Circadian rhythm alterations in tumourigenesis are of equal importance to genetic factors and several biologic clock genes are considered to be prognostic biomarkers for various cancers. The aim of this study was to establish reliable markers based on biologic clock genes, thus providing a new perspective for assessing immunotherapy response and prognosis in patients with HNSCC.

Methods

We used 502 HNSCC samples and 44 normal samples from the TCGA-HNSCC dataset as the training set. 97 samples from GSE41613 were used as an external validation set. Prognostic characteristics of circadian rhythm-related genes (CRRGs) were established by Lasso, random forest and stepwise multifactorial Cox. Multivariate analysis revealed that CRRGs characteristics were independent predictors of HNSCC, with patients in the high-risk group having a worse prognosis than those in the low-risk group. The relevance of CRRGs to the immune microenvironment and immunotherapy was assessed by an integrated algorithm.

Results

6-CRRGs were considered to be strongly associated with HNSCC prognosis and a good predictor of HNSCC. The riskscore established by the 6-CRRG was found to be an independent prognostic factor for HNSCC in multifactorial analysis, with patients in the low-risk group having a higher overall survival (OS) than the high-risk group. Nomogram prediction maps constructed from clinical characteristics and riskscore had good prognostic power. Patients in the low-risk group had higher levels of immune infiltration and immune checkpoint expression and were more likely to benefit from immunotherapy.

Conclusion

6-CRRGs play a key predictive role for the prognosis of HNSCC patients and can guide physicians in selecting potential responders to prioritise immunotherapy, which could facilitate further research in precision immuno-oncology.

Circadian Clock Genes Act as Diagnostic and Prognostic Biomarkers of Glioma: Clinic Implications for Chronotherapy

Gliomas are the most common primary intracranial tumors and closely related to circadian clock. Due to the high mortality and morbidity of gliomas, exploring novel diagnostic and early prognostic markers is necessary. Circadian clock genes (CCGs) play important roles in regulating the daily oscillation of biological processes and the development of tumor. Therefore, we explored the influences that the oscillations of circadian clock genes (CCGs) on diagnosis and prognosis of gliomas using bioinformatics. In this work, we systematically analyzed the rhythmic expression of CCGs in brain and found that some CCGs had strong rhythmic expression; the expression levels were significantly different between day and night. Four CCGs (ARNTL, NPAS2, CRY2, and DBP) with rhythmic expression were not only identified as differentially expressed genes but also had significant independent prognostic ability in the overall survival of glioma patients and were highly correlated with glioma prognosis in COX analysis. Besides, we found that CCG-based predictive model demonstrated higher predictive accuracy than that of the traditional grade-based model; this new prediction model can greatly improve the accuracy of glioma prognosis. Importantly, based on the four CCGs’ circadian oscillations, we revealed that patients sampled at night had higher predictive ability. This may help detect glioma as early as possible, leading to early cancer intervention. In addition, we explored the mechanism of CCGs affecting the prognosis of glioma. CCGs regulated the cell cycle, DNA damage, Wnt, mTOR, and MAPK signaling pathways. In addition, it also affects prognosis through gene coexpression and immune infiltration. Importantly, ARNTL can rhythmically modulated the cellular sensitivity to clinic drugs, temozolomide. The optimal point of temozolomide administration should be when ARNTL expression is highest, that is, the effect is better at night. In summary, our study provided a basis for optimizing clinical dosing regimens and chronotherapy for glioma. The four key CCGs can serve as potential diagnostic and prognostic biomarkers for glioma patients, and ARNTL also has obvious advantages in the direction of glioma chronotherapy.

Exploring the link between chronobiology and drug delivery: effects on cancer therapy

Circadian clock is an impressive timing system responsible for the control of several metabolic, physiological and behavioural processes. Nowadays, the connection between the circadian clock and cancer occurrence and development is consensual. Therefore, the inclusion of circadian timing into cancer therapy may potentially offer a more effective and less toxic approach. This way, chronotherapy has been shown to improve cancer treatment efficacy. Despite this relevant finding, its clinical application is poorly exploited. The conception of novel anticancer drug delivery systems and the combination of chronobiology with nanotechnology may provide a powerful tool to optimize cancer therapy, instigating the incorporation of the circadian timing into clinical practice towards a more personalized drug delivery. This review focuses on the recent advances in the field of cancer chronobiology, on the link between cancer and the disruption of circadian rhythms and on the promising targeted drug nanodelivery approaches aiming the clinical application of cancer chronotherapy.

Low mutation burden and differential tumor-infiltrating immune cells correlate with lymph node metastasis in colorectal cancer

BACKGROUND

Tumor immunotherapy has become an important means of cancer treatment. A response depends on the interaction of tumor cells with immune regulators in the tumor microenvironment, which plays an important role in inhibiting or enhancing the immune response. However, lymph node (LN) metastasis leads to major changes in the tumor microenvironment of patients with colorectal cancer, directly affecting prognosis.

METHODS

Using data downloaded from the Cancer Genome Atlas (TCGA) database, we studied the microenvironmental differences between LN-negative and positive populations by bioinformatic methods.

RESULTS

Patients in the LN-positive group had significantly lower immune scores, cytolytic activity scores, and overall survival than the LN-negative group. In addition, a high mutation burden and a new antigen burden could inhibit lymph node metastasis of CRC. In particular, in the LN positive group, the ratio of monocytes to M1 macrophages was significantly downregulated. After the differentially expressed mRNAs between the LN positive and negative groups were determined, a new CRC model was constructed based on multivariate Cox proportional hazard regression analysis to examine the prognosis of patients. The analyses showed that the model was stable and robust.

CONCLUSIONS

We used multiple scores and details of immune cell infiltration as indicators to assess changes in the tumor microenvironment of CRC patients before and after lymph node metastasis, and quantify and model the immune cells in the microenvironment to predict the overall survival of CRC patients.

Spotlight on Circadian Genes and Colorectal Cancer Crosstalk

Mammalian physiology is regulated by circadian clock through oscillating feedback loops controlling cellular processes and behaviors. Recent findings have led to an interesting connection between circadian disruption and colorectal cancer progression and incidence through controlling the hallmarks of cancer, namely cell cycle, cell metabolism and cell death. Deeper understanding of the circadian mechanisms that define the colorectal cancer pathophysiology is the need of the hour to define a chronotherapy for improving colorectal cancer patient survival. This review identifies the key areas in which circadian genes interact with cellular pathways to modify the outcome with respect to colorectal cancer incidence and progression.