Circadian genes and non-coding RNAs: interactions and implications in cancer

ABSTRACT

Circadian rhythms are 24-hour cycles in various biological processes, such as sleep, wake, and hormone secretion, controlled by an internal clock. Disruption of circadian rhythms has been related to various human diseases. Abnormal expression of circadian rhythm-related genes, such as CLOCK, BMAL1, PER1, PER2, CRY1, CRY2, RORα, NPAS2, REV-ERBα and TIMELESS has also been reported to be associated with cancer. CLOCK, CRY1, NPAS2 and TIMELESS are related to cancer development. In contrast, BMAL1, PER1, PER2, CRY2, RORα and REV-ERBα related to inhibit cancer development and progression. Furthermore, studies suggest that circadian genes related to cancer can be regulated by ncRNAs such as miRNAs, lncRNAs and circRNAs and that dysregulation of these ncRNAs contributes to cancer development. Here, we summarize the mechanisms whereby ncRNA dysregulation leads to the abnormal expression of circadian genes in several cancers and the ncRNA and circadian gene-associated regulatory mechanisms that contribute to resistance to chemo – and radiotherapy. This review provides insights into the mechanistic involvements of the regulatory network of circadian genes and ncRNAs in cancer development.

1. Introduction

Circadian rhythm is an endogenous adaptation mechanism that regulates various physiological processes, including sleep-wake cycles, blood pressure, body temperature, hormone secretion, behavior, immunity, metabolism, and gene expression and is dependent on the involvements of central and peripheral clocks (Dobson 2014; Chaix et al. 2016). The central clock is located in the suprachiasmatic nucleus (SCN) of the hypothalamus. This clock serves as the primary regulator of circadian rhythms (Mohawk et al. 2012) and influences peripheral clocks located in peripheral tissues via neurotransmitters, endocrine factors, and physiological fluids (Dibner et al. 2010; Lowrey and Takahashi 2011). On the other hand, peripheral clocks are found in organs, including liver, brain, lungs, heart, and kidneys, and in mammals, and it is believed that these clocks require physiological stimuli to maintain circadian rhythms (Storch et al. 2002; Mohawk et al. 2012). These physiological stimuli are thought to originate from the SCN or to be triggered by SCN-mediated message (Kramer et al. 2005). Considerable research efforts have been expended on genes associated with circadian rhythm. The clock circadian regulator (CLOCK), basic helix–loop–helix ARNT like 1 (BMAL1; also known as ARNTL1), period circadian regulator (PER), cryptochrome circadian regulator (CRY), RAR related orphan receptor (ROR), neuronal PAS domain protein 2 (NPAS2), nuclear receptor subfamily 1 group D member 1 (NR1D1; also known as REV-ERBα) and timeless circadian regulator (TIMELESS) are well known circadian clock genes (Yu et al. 2019; Zhu et al. 2021; Liu et al. 2023). The entire set of circadian clock genes has been reported to account for 20% of mammalian genes (Steeves et al. 1999; Boiko et al. 2024). Interestingly, circadian genes regulate physiological and behavioral activities that promote the survival and reproduction of organisms (Chaix et al. 2016; Yu et al. 2019). One such advantage is that they restrict DNA synthesis to nighttime, which helps reduce DNA damage caused by UV radiation during the day (Rosato and Kyriacou 2002). This damage and its transmission to daughter cells is associated with cancer, so the advantages conferred by circadian genes appear to be related to cancer suppression (Macheret and Halazonetis 2015). In fact, it has been reported that abnormal circadian gene expression is linked to cancer development and progression, and thus, there is a need to explore the mechanisms responsible for circadian gene dysregulation (Masri and Sassone-Corsi 2018; Selvaraj et al. 2023).

Less than 2% of the human DNA sequence encodes proteins, whereas most DNA sequences are transcribed into RNAs, and many of them regulate gene expression (Ransohoff et al. 2018; Slack and Chinnaiyan 2019). These transcripts are mostly non-coding RNAs (ncRNAs) that are not translated to produce proteins. MicroRNAs (miRNAs) are approximately 22 nucleotide-long ncRNA (Baslund et al. 1993) that mainly bind to the 3'-UTR sequence of mRNAs, where they inhibit or suppress protein translation (Bartel 2009). Long non-coding RNAs (lncRNAs) are ∼200 nucleotide long ncRNAs involved in various stages of gene expression regulation. Circular RNAs (circRNAs) are generated by a specific type of splicing known as back-splicing, in which the 5’ end of an upstream exon is spliced non-collinearly with the 3’ end of a downstream exon on the pre-mRNA (Yu and Kuo 2019). circRNA is generally classified as lncRNA, and like other lncRNA, it has been reported to act as an RNA or protein decoy to regulate gene expression (Abdelmohsen et al. 2017; Li et al. 2020). ncRNAs can also regulate genes involved in circadian rhythms, and accumulating studies indicate that ncRNA dysregulation can cause tumorigenesis and tumor development by affecting circadian rhythm-related genes (Wang et al. 2015; Huang et al. 2023; Kim et al. 2023). Therefore, in this study, we summarize the functions and roles of circadian rhythm-related genes that influence tumorigenesis and cancer development and explore the ncRNA regulatory mechanisms involved in their aberrant regulation. In addition, we provide an overview of the interactions between circadian rhythm-related genes and ncRNAs observed in various cancers.

2. Classification and function of ncRNAs

ncRNAs are RNAs that do not encode proteins and exhibit diverse types and functions. miRNAs, known to play a crucial role in gene expression regulation, are approximately 22 nucleotides in small length and are transcribed by endogenous genes (Gulyaeva and Kushlinskiy 2016). miRNAs are initially processed into by pri-miRNAs by Drosha, and then transported to the cytoplasm with the help to exportin 5, where they are further processed by the Dicer into mature miRNAs consisting of 22 nucleotides single-stranded RNA (Gulyaeva and Kushlinskiy 2016; Matsuyama and Suzuki 2019). miRNAs specifically bind to the 3’-UTRs of mRNAs and are involved in regulating mRNA stability and translation (Gulyaeva and Kushlinskiy 2016) (Figure 1A). In contrast, lncRNAs are long RNAs with a length of over 200 nucleotides that perform diverse functions depending on their location within the cell (Marchese et al. 2017; Bridges et al. 2021). When located in the nucleus, lncRNAs reportedly regulate gene expression at the pre-transcriptional level by modifying chromatin structure (Schmitz et al. 2010; Csorba et al. 2014; Mondal et al. 2015) (Figure 1B). On the other hand, when located in cytoplasm, lncRNAs can regulate gene expression at the post-transcriptional level by interfering with the mRNA splicing of sponging miRNA to regulate mRNA translation (Carrieri et al. 2012; Yap et al. 2018) (Figure 1C). Additionally, these interactions appear to influence cancer development significantly (Chae et al. 2021; Roh et al. 2022; Roh et al. 2023). lncRNAs exhibit tissue-specific expression, making them advantageous as biomarkers for disease diagnosis and prognosis prediction (Qian et al. 2020; Lu et al. 2021; Khawar et al. 2022). Lastly, circRNAs are known to be largely similar to lncRNAs but are distinguished by their unique closed-loop structures, lacking a 5’ cap and poly-A tail (Zhou et al. 2020). Unlike linear RNAs, circRNAs are resistant to exonucleases such as RNase R, which contributes to their high stability (Jeck et al. 2013). Similarly, circRNAs exhibit tissue – and cell-type-specific expression and are found in both the cytoplasm and nucleus, with their functions varying depending on their localization (Yu and Kuo 2019; Huang et al. 2020a) (Figure 1D–E). miRNAs, lncRNAs, and circRNAs are known to be associated not only with cancer but also with various other diseases and have been reported to interact with circadian genes (Bhattacharjee et al. 2023; Guz et al. 2023). This review will focus on the interactions between these ncRNAs and circadian genes.

Figure 1.

The involvement of ncRNAs in regulation of gene expression. (A) miRNA binds to mRNA to negatively regulate its stability and translation. (B) Nuclear lncRNA binds to chromatin and alters its structure to regulate transcription. (C) Cytoplasmic lncRNA regulates gene expression post-transcriptionally by sponging miRNA. (D) Nuclear circRNA binds to chromatin and alters its structure to regulate transcription. (E) Cytoplasmic circRNA regulates gene expression post-transcriptionally by sponging miRNA.

3. Circadian genes and their transcription-translation feedback loops

Circadian rhythms are governed by 24-hour biological cycles and are fundamental to the survival and function of living organisms (Takahashi 2017). These rhythms are orchestrated by a complex network of circadian genes, which regulate diverse physiological and behavioral processes (Partch et al. 2014). Circadian genes maintain 24-hour rhythmicity through precisely timed feedback mechanisms that control their own transcription and translation. The mammalian circadian clock operates through an interlocking system of transcription-translation feedback loops (TTFLs) that regulate gene expression in a 24-hour cycle (Savvidis and Koutsilieris 2012). This rhythmic gene expression occurs as CLOCK/BMAL1 activates target genes including PERs and CRYs, whose protein products then inhibit the activity of CLOCK/BMAL1, creating a self-regulatory loop that defines circadian periodicity (Reppert and Weaver 2002; Partch et al. 2014). The dynamic oscillations of these genes enable cells to synchronize their internal processes with environmental day-night cycles, solidifying their roles as ‘circadian genes’ (Figure 2). The primary TTFL is induced by the CLOCK/BMAL1 complex which binds to E-box elements in the promoter regions of target genes to activate their transcription (Gekakis et al. 1998; Ko and Takahashi 2006). PERs and CRYs, encoded by two of several target gene products, dimerize and accumulate outside of the nucleus. After reaching a threshold concentration in the cytoplasm, they translocate into nucleus and interact with the CLOCK/BMAL1 complex to repress its transcriptional activity (Lee et al. 2001; Cox and Takahashi 2019; Yi et al. 2022). Then, PER proteins are phosphorylated and degraded by CK1. Eventually, the CLOCK/BMAL1 complex would free from transcriptional repression, and the cycle begins again (Gallego and Virshup 2007). The secondary TTFL involves the nuclear receptors REV-ERBs (including REV-ERBα and REV-ERBβ) and RORs (including RORα, RORβ, and RORγ), which regulate the transcription of BMAL1 (Preitner et al. 2002; Guillaumond et al. 2005). REV-ERBα or REV-ERBβ binds to the ROR response element (RORE) and represses BMAL1 transcription, while RORα, RORβ, or RORγ activates BMAL1 transcription, creating a balance that regulates the rhythm of the biological clock (Cho et al. 2012). The last TTFL is associated with D-box elements found in genes including PERs, which are regulated by the D-box binding protein (DBP). DBP, one of target genes transcriptionally activated by CLOCK/BMAL1, promotes transcription of PERs and is repressed by the nuclear factor interleukin 3 (NFIL3), which is downregulated by REV-ERBα and upregulated by RORα (Lin et al. 2015). This loop adds complexity and precision to the circadian clock, harmoniously regulating gene expression across a variety of cellular processes. Together, these three feedback loops synchronize cellular activity to the day-night cycle.

Figure 2.

A Schematic diagram of the core mammalian circadian clockwork. The diagram shows the interplay between various circadian genes and proteins regulating circadian rhythms. In the nucleus, the transcription factors CLOCK and BMAL1 form a heterodimer that binds to E-box elements to activate the transcription of key circadian genes, including PER1, PER2, CRY1, and CRY2. The resulting PER and CRY proteins form complexes that inhibit the activity of the CLOCK/BMAL1 complex, establishing a negative feedback loop. In parallel, REV-ERBs and RORs act on RORE, influencing the transcription of BMAL1 and NFIL3. The transcription factor DBP is also regulated through D-box elements, contributing to the fine-tuning of circadian gene expression. This intricate network maintains the rhythmic expression of clock-controlled genes, sustaining the circadian cycle.

4. Effects of circadian genes on cancer hallmarks

Cancer hallmarks include cell cycle dysregulation, cell proliferation, apoptosis evasion, metabolic reprogramming, angiogenesis, and metastatic conversion. Recent studies have shown that circadian genes are involved in regulating the expression of downstream genes and signaling pathways to influence these features of cancer. Below is a focus on circadian genes associated with cancer development.

4.1. CLOCK and BMAL1

The influence of CLOCK extends beyond circadian control, as it impacts key processes such as cell proliferation, DNA repair, and apoptosis, and thus, its dysregulation can contribute to cancer development (Fu and Lee 2003). Aberrant CLOCK activity disrupts normal circadian rhythm, and fosters tumor progression by promoting cell survival and metabolic dysregulation (Yang et al. 2009). Notably, activated CLOCK regulates metabolic pathways including the oxidative pentose phosphate pathway, which is essential for managing reactive oxygen species detoxification. This regulatory mechanism allows cells to switch between anabolic and homeostatic survival modes, providing metabolic flexibility under stress conditions, such as during cancer progression (Alamoudi 2021). Moreover, silencing CLOCK expression is associated with downregulation of c-Myc and cyclin B1 and upregulation of p53, contributing to induction of apoptosis in glioma cells (Wang et al. 2016). In colorectal cancer, knockdown of BMAL1 results in activation of the PI3K-Akt-MMP2 pathway and induction of cell invasion, which is reversed by treatment of PI3 K, Akt, or MMP2 inhibitors. It indicates that BMAL1 plays a tumor-suppressive role through blocking the PI3K-Akt pathway (Jung et al. 2013). Another study has reported that loss of BMAL1 was associated with downregulation of PER1, PER2, PER3, Wee1, and p53, and upregulation of CDK1, cyclin B1, cyclin D1, and cyclin E (Zeng et al. 2010). It suggests that BMAL1 plays an important role in regulating apoptosis, cell cycle, and DNA damage response and homeostasis in cancer cells. In addition, BMAL1 is involved in inhibition of glycolipid metabolism through transcriptional repression of glycerol-3-phosphate acyltransferase mitochondrial (GPAM) expression in an EZH2-dependent way, resulting in suppression of hepatocellular carcinoma cell growth (Yang et al. 2022). Together, CLOCK as an oncogenic factor and BMAL1 as a tumor-suppressive factor might be inversely involved in cell proliferation, metabolic pathways, and DNA damage response in cancer cells.

4.2. PER1 and PER2

PER1 and PER2 are integral components of DNA damage response, cell cycle regulation, and apoptosis (Fu et al. 2002; Gery et al. 2006; Sun et al. 2010), positioning them as potential tumor suppressors. Reduced expressions of PER1 and PER2 are frequently observed in head and neck, pancreas, and lung cancer, and lead to genomic instability and enhanced malignant cell survival (Xiang et al. 2018; Guo et al. 2020; Yang et al. 2020). In addition, disruption of these genes impairs circadian control and contributes to tumorigenesis (Fu and Lee 2003; Hua et al. 2006). It has been reported that downregulation of PER1 is associated with inhibition of autophagy-mediated cell death and promotion of cell proliferation in an Akt/mTOR pathway-dependent manner, resulting in progression of oral squamous cell carcinoma (Yang et al. 2020). Another study has demonstrated that PER1 is involved in activation of DNA damage response through ATM-CHK2-p53 signaling, leading to inhibition of cell growth and proliferation in pancreatic cancer, which supports anti-tumor effects of PER1 (Guo et al. 2020). Besides, PER2 is responsible for inhibition of cell growth and migration in non-small cell lung cancer through upregulation of apoptosis-related genes, such as Bax, p53, p21, and NM23, and downregulation of metastasis-related genes, such as VEGF, CD44, and c-Myc (Xiang et al. 2018). A study shows that PER2 is capable of binding to p53 and protecting from MDM2-dependent p53 degradation (Gotoh et al. 2014). It indicates that PER2 participates in tumor suppression by increase of p53 stability.

4.3. CRY1 and CRY2

CRY1 acts as a pro-tumorigenic factor by cascading the repair of double-strand breaks (DSBs) in the DNA damage response. A study has reported that, during DSB repair, CRY1 initially activates DSB sensors and mediators, including MRE11A, ATM, RAD50, and RAD51, and subsequently activates DSB effectors, including XRCC3 and POLD2 (Shafi et al. 2021). It indicates that CRY1 is involved in activation of DSB repair genes in chronological order to promote cell survival. On the contrary, CRY2 might play a tumor-suppressive role in cancer cells. It has been shown that CRY2 knockdown results in increase of c-Myc and cyclin D1 expressions, contributing to cell cycle progression in osteosarcoma cells, and increase of ERK phosphorylation and β-catenin expression, promoting cancer cell proliferation and migration (Yu et al. 2018).

4.4. RORα

Interestingly, RORα has been implicated in cancer due to its involvement in metabolic and immune regulation, and its reduced expression has been linked to metabolic imbalances and cancer progression (Lau et al. 2008; Du and Xu 2012; Kadiri et al. 2015; Ma et al. 2021). In gastric cancer, knockout of RORα results in induction of glucose uptake and glycolysis rate, contributing to cell proliferation through metabolic reprogramming. RORα inhibits glycolytic activation by downregulation of G6PD expression, suggesting that RORα functions as a tumor suppressor by reducing aerobic glycolysis (Wang et al. 2024). RORα is involved in regulation of immune microenvironment in melanoma by downregulating the expression of programmed death-ligand 1 (PD-L1). Downregulated PD-L1 results in induction of immune evasion by decreasing the activity of CD8⁺ T cells. It emphasizes that RORα plays a tumor-suppressive role in melanoma by increasing immunosurveillance (Liu et al. 2024). In addition, a previous study has demonstrated a critical role of RORα in the downregulation of the Wnt/β-catenin signaling pathway in colon cancer (Lee et al. 2010). In this study, RORα phosphorylated by PCKα directly binds to β-catenin to inhibit Wnt/β-catenin-downstream gene expressions, including cyclin D1, Axin, c-Myc, and c-Jun, thereby suppressing cancer cell proliferation. In addition, RORα enhances p53 stability by inhibiting its ubiquitination and degradation, which in turn promotes the expression of p53-target genes involved in apoptosis (Kim et al. 2011).

4.5. Other circadian genes

Other circadian genes such as NPAS2, REV-ERBα and TIMELESS are involved in regulation of tumor progression. NPAS2 is a paralog of CLOCK and functions as a transcriptional activator in the circadian clock mechanism. Under certain circumstances such as loss of CLOCK, NPAS2 instead of CLOCK is capable of binding to BMAL1 and regulation of TTFLs, playing a compensatory role in regulating circadian rhythm and metabolic processes (Landgraf et al. 2016). In prostate cancer cells, upregulation of NPAS2 is associated with the increased expression of several genes involving in the glycolytic pathway, such as HIF-1α, HK2, PKM2, GLUT1, and MCT4, indicating that NPAS2 promotes aerobic glycolysis and cell proliferation in cancer cells (Ma et al. 2023). Besides, it has been shown that upregulation of REV-ERBα is correlated with positive prognosis in breast cancer patients (Ka et al. 2023). REV-ERBα is involved in stimulation of anti-tumor immunity through activation of the cGAS-STING pathway, which triggers CD8⁺ T lymphocytes-mediated immune response. Since TIMELESS has been revealed to be a core circadian gene in Drosophila melanogaster, its role in mammals might be limited to the maintenance of the circadian rhythm but primarily linked to genome stability involved in DNA replication and repair pathways (Rageul et al. 2024; Vipat and Moiseeva 2024). TIMELESS is responsible for activation of c-Myc, increasing cell proliferation and invasion of breast cancer cells and self-renewal capability of breast cancer stem cells (Chi et al. 2017). Another study has reported that TIMELESS interacting with c-Myc upregulates PD-L1 expression, contributing to inhibition of CD8⁺ T lymphocyte infiltration in tumor tissues of breast cancer (Dong et al. 2023). It indicates that TIMELESS plays an immunosuppressive role in breast cancer.

5. Associations between circadian genes and ncRNAs in cancer

Interactions between ncRNAs and circadian genes are crucial for maintaining normal cellular processes. However, previous studies have reported that dysregulation of these interactions plays a significant role in the development of various diseases, including cancer. Thus, analyzing the mechanisms by which these molecular interactions, particularly those related to circadian disruption, contribute to tumor formation and development across different cancer types is essential. Many ncRNAs, including lncRNAs, miRNAs, and circRNAs, play critical roles in the regulation of cancer progression by interacting with circadian genes, and these interactions can activate or inhibit cancer-promoting pathways. Below is a summary of key studies that highlight these interactions in different cancers.

5.1. Breast cancer

CLOCK is responsible for downregulation of ALDH, contributing to inhibition of cancer-stemness in breast cancer cells. It has been found that miR-182 downregulates CLOCK in breast cancer cells, enhancing tumorigenicity and invasiveness through induction of ALDH expression (Ogino et al. 2021). TIMELESS participates in upregulation of miR-5188, which direct binds to 3'-UTR of FOXO1 mRNA, contributing to activation of Wnt/β-catenin signaling to promote cell proliferation, stemness, and metastasis in breast cancer cells (Zou et al. 2020b). A study conducting analysis of miRNA downregulated by disruption of the circadian rhythm has presented several miRNAs, including miR-146b and miR-127, playing a role in breast cancer development (Kochan et al. 2015). Downregulation of miR-146b is involved in activation of NF-κB, which promotes cell migration and metastasis in breast cancer cells (Helbig et al. 2003), and downregulation of miR-127 results in upregulation of BCL6, which is known to repress p53 transcription, thereby promoting cell proliferation (Chen et al. 2013).

5.2. Lung cancer

BMAL1 is involved in upregulation of circGUCY1A2, which acts as a sponge for miR-200-3p, thus, increasing the expression of PTEN, a target of miR-200-3p (Zhao et al. 2023). This interaction helps suppress tumorigenic activity by reducing NSCLC cell proliferation and increasing apoptosis. LINC01234, upregulated by c-Myc, is involved in the expression of miR-106b-5p, which targets CRY2 mRNA, and c-Myc is upregulated by LINC01234 and miR-106b-5p (Chen et al. 2020). This positive feedback loop for upregulation of c-Myc and downregulation of CRY2 participates in promotion of NSCLC development. In addition, a study conducting bioinformatics analyses has reported that TIMELESS is suggested as an oncogenic target of tumor-suppressive miR-150-3p in squamous cell carcinoma of the lung (Mizuno et al. 2021). Another study has demonstrated that two lncRNAs, MIR4435-2HG and LINC00152, are involved in upregulation of TIMELESS through sponging miR-1-3p in lung adenocarcinoma based on bioinformatics analyses (Gao et al. 2024). It has been shown that overexpression of TIMELESS is associated with poor prognosis, decreased immune cell infiltration and suppression of antitumor immune response.

5.3. Brain cancer

miR-124 downregulates CLOCK, which reduces NF-κB activity and inhibits glioma cell proliferation and migration (Li et al. 2013). In contrast, lncRNA UCA1 is involved in escalation of CLOCK expression through acting as an endogenous sponge for miR-206, resulting in induction of cell motility and invasion in glioma cells (Huang et al. 2019). A study presents that miR-7239-3p directly targets BMAL1 and suppresses its expression in glioma cells, and downregulation of BMAL1 is associated with decrease of E-cadherin expression and increase of N-cadherin and Vimentin expressions, promoting glioma cell proliferation and migration (Li et al. 2021). RORα acts as a suppressive factor for NF-κB activation through IκBα upregulation in glioma cells. miR-10a promotes the formation of myeloid-derived suppressor cells through targeting RORα mRNA and activating NF-κB signaling, and thus, contributes to tumor immune evasion of glioma (Guo et al. 2018). In addition to miR-10a, miR-18a downregulates RORα expression by binding to 3'-UTR of its mRNA, resulting in activation of NF-κB signaling, thereby promoting glioma cell proliferation and tumorigenesis (Jiang et al. 2020). It has been found that circRELN acts as a ceRNA that sponges miR-1290 and thereby increasing the expression of RORα and exerting a tumor-suppressive function in glioma cells (Kang et al. 2021).

5.4. Liver cancer

In hepatocellular carcinoma, lncRNA HULC increases the expression of CLOCK, resulting in disruption of circadian rhythms, which promotes cell growth and proliferation (Cui et al. 2015). It has been found that the expression of lncRNA HULC is correlated with that of CLOCK in hepatocellular carcinoma tissues from patients. miR-494-3p acts as an oncogenic factor by downregulating the expression of BMAL1, which promotes the expression of GPAM in hepatocellular carcinoma cells (Yang et al. 2022). Increased GPAM facilitates lipid biosynthesis responsible for growth and metastasis of cancer cells. In addition, miR-1246 downregulates RORα, activates the Wnt/β-Catenin pathway and increases the proliferation, invasiveness, and metastasis of cancer cells, thereby promoting EMT in hepatocellular carcinoma cells (Huang et al. 2020b). miR-199b-5p has been reported to retard hepatocellular carcinoma progression by inhibiting NPAS2, which directly regulates HIF-1α (Yuan et al. 2020). Downregulated HIF-1α by silencing of NPAS2 results in decreased expressions of glycolytic genes including GLUT1, HK2, and ALDOA and upregulation of mitochondrial biogenesis in hepatocellular carcinoma cells. It indicates that miR-199b-5p plays a tumor-suppressive role via suppression of glucose metabolism reprogramming.

5.5. Colorectal cancer

It has been reported that CRY2 is direct target of miR-181d in colorectal cancer cells (Guo et al. 2017). C-Myc-induced miR-181d upregulation is responsible for inhibition of CRY2 expression, and thus, enhances glycolysis and promotes proliferation, migration, and invasion. Another study has found that miR-548am-5p promotes cancer cell proliferation and stemness by downregulating RORα (Li et al. 2023). In addition, bioinformatic analysis has revealed that the lncRNA KCNQ1OT1 might play an important role in the development and progression of colon adenocarcinoma through the miR-32-5p/PER2/CRY2 regulatory axis (He et al. 2022).

5.6. Other cancers

Circadian gene interactions with ncRNAs have also been studied in other cancers. In head and neck squamous cell carcinoma, miR-3187-3p represses the expression of PER2, which activates the Wnt/β-catenin signaling pathway to enhance migration and invasion (Xiao et al. 2021). Exosomal miR-24-3p promotes cell proliferation by targeting PER1 directly in oral squamous cell carcinoma (He et al. 2020). In this study, it has been shown that upregulation of miR-24-3p is positively correlated with the expression levels of cyclin B1, cyclin D1, cyclin E1, CDK2, CDK4, and CDK6, and negatively with those of p21 and p27 in oral squamous cell carcinoma cells. In gastric cancer, lncRNA TPTEP1 is involved in the upregulation of PER1 expression by sponging miR-548d-3p (Huang et al. 2022). miR-548d-3p binds to 3'-UTR of KLF9 mRNA to repress its expression, and KLF9 binds to the promoter region for transcriptional activation of PER1, indicating that TPTEP1 regulates the miR-548d-3p/KLF9/PER1 axis to promote the migration and invasion of gastric cancer cells. miR-135b binds directly to 3'-UTR of BMAL1 to inhibit its expression, contributing to cell proliferative capacity and invasiveness in pancreatic cancer cells (Jiang et al. 2018). miR-1290 targets RORα to enhance prostate cancer cell growth and invasion (Li et al. 2022). Knockdown of miR-1290 results in alleviation of tumorigenic properties, indicating that miR-1290 is essential for growth, stemness, and invasion of prostate cancer. It has been reported that RORα acts a common target of miR-1246 and miR-1290 in ovarian cancer (Wang et al. 2022). Both miRNAs existing in extracellular vesicles derived from malignant ascites contribute to induction of invasion and migration in ovarian cancer cells through downregulation of RORα expression. In addition, circ_0061179 induces TIMELESS expression by sponging miR-143-3p, and knockdown of circ_0061179 or overexpression of miR-143-3p increased DNA damage and apoptosis in ovarian cancer cells (Zhang et al. 2024). Modulation of the miR-143-3p/TIMELESS axis thereby promotes proliferation of ovarian cancer cells. A study demonstrates that miR-652 acts as an oncomir that directly targets RORα mRNA to promote proliferation and metastasis in endometrial cancer (Sun et al. 2018; Li and Zou 2019). Since overexpression of miR-652 is involved in activation of the Wnt/β-catenin pathway, endometrial tumor regression would be accomplished by upregulation of RORα or downregulation of β-catenin. Exosomal miR-181a-5p derived from osteosarcoma cells directly inhibits RORα expression in macrophage (Wang et al. 2023). Downregulated RORα results in stimulation of M2 macrophage polarization, which contributes to reprogramming of tumor microenvironment favoring tumorigenesis by facilitating proliferation, angiogenesis, and metastasis of cancer cells.

In this review, we explore the intricate associations between ncRNAs and circadian genes in various cancers (Table 1). In breast, lung, brain, liver, colorectal, and other cancers, ncRNAs modulate key circadian regulators like CLOCK, BMAL1, PERs, and RORα and influence tumor progression, metastasis, and therapy resistance. These ncRNA-circadian gene interactions influence EMT, apoptosis, and metabolic pathways and highlight their roles in oncogenesis (Figure 3). Disruptions in circadian gene regulation by ncRNAs drive changes in cell proliferation, immune evasion, and treatment responses across cancer types and underscore their potential as therapeutic targets.

Table 1.

Correlations between ncRNAs and circadian genes in various cancer types.

Cancer types	Genes	ncRNAs	Roles	Ref.
Breast cancer	CLOCK	miR-182	Invasion	Ogino et al. (2021)
	TIMELESS	miR-5188	Proliferation, stemness, and metastasis	Zou et al. (2020a)
Lung cancer	BMAL1	circGUCY1A2, miR-200-3p	Proliferation and apoptosis	Zhao et al. (2023)
	CRY2	LINC01234, miR-106b-5p	Proliferation	Chen et al. (2020)
Brain tumor	CLOCK	miR-124	Proliferation and migration	Li et al. (2013)
		UCA1, miR-206	Cell motility and invasion	Huang et al. (2019)
	BMAL1	miR-7239-3p	Proliferation and migration	Li et al. (2021)
	RORα	miR-10a	Tumor immune evasion	Guo et al. (2018)
		miR-18a	Proliferation and tumorigenesis	Jiang et al. (2020)
		circRELN, miR-1290	Tumor growth	Kang et al. (2021)
Liver cancer	CLOCK	HULC	Proliferation and cell growth	Cui et al. (2015)
	BMAL1	miR-494-3P	Metastasis	Yang et al. (2022)
	RORα	miR-1246	Proliferation, invasiveness, and metastasis	Huang et al. (2020a)
	NPAS2	miRNA-199b-5p	Metabolism reprogramming	Yuan et al. (2020)
Colorectal cancer	CRY2	miR-181d	Proliferation, migration, and invasion	Guo et al. (2017)
	RORα	miR-548am-5p	Proliferation and stemness	Li et al. (2023)
Head and neck cancer	PER2	miR-3187-3p	Migration and invasion	Xiao et al. (2021)
Oral squamous cell carcinoma	PER1	miR-24-3p	Proliferation	He et al. (2020)
Gastric cancer	PER1	TPTEP1 miR-548-3p	Migration and invasion	Huang et al. (2020b)
Pancreatic cancer	BMAL1	miR-135b	Proliferation and invasion	Jiang et al. (2018)
Prostate cancer	RORα	miR-1290	Cell growth, stemness, and invasion	Li et al. (2022)
Ovarian cancer	RORα	miR-1246 miR-1290	Migration and invasion	Wang et al. (2022)
	TIMELESS	circ_0061179, miR-143-3p	DNA damage and apoptosis	Zhang et al. (2024)
Endometrial cancer	RORα	miR-652	Proliferation and metastasis	Sun et al. (2018)
Osteosarcoma	RORα	miR-181a-5p	Proliferation, angiogenesis, and metastasis	Wang et al. (2023)

Figure 3.

Interaction of circadian clock genes with cancer-related processes. The diagram depicts how core circadian clock components, including CLOCK, BMAL1, NPAS2, RORα, PER1, PER2, CRY2, and TIMELESS, are involved in regulating various hallmarks of cancer. The interaction network indicates both direct and indirect influences, with circadian gene dysregulation potentially impacting cancer progression. Specific non-coding RNAs are highlighted as key regulators that modulate the activity of circadian clock genes, influencing cancer-related outcomes.

6. The clinical value of the link in cancer between clock genes and ncRNAs

Intricate interplay between ncRNAs and circadian rhythm genes significantly impacts cancer progression and therapy. Improved understanding of how ncRNAs modulate the circadian system offers promising therapeutic avenues, particularly for overcoming treatment resistance and improving patient outcomes. Studies show ncRNAs that regulate circadian rhythms are associated with prognosis in cancer and may serve as therapeutic targets (Table 2). For example, the Notch signaling pathway, mediated by miR-20a-5p, which targets the NPAS2 gene, may be involved in the radiation resistance of nasopharyngeal cancer cells (Zhao et al. 2017). In melanoma, LINC01224 enhances REV-ERBβ expression by sponging miR-193a-5p, which increases cell proliferation and reduced radiosensitivity (Cui et al. 2021). miR-708, a direct target of TIMELESS, inhibits cervical cancer cell viability and colony formation, promotes apoptosis, enhances cisplatin efficacy, and impairs DNA repair pathways (Zou et al. 2020a). Furthermore, dysregulation of the miR-135b/BMAL1 axis confers gemcitabine resistance to pancreatic cancer cells (Jiang et al. 2018). miR-5188, whose expression is enhanced by the TIMELESS/Sp1/c-Jun complex, induces chemoresistance to paclitaxel and epirubicin in a dose – and time-dependent manner (Zou et al. 2020b). Moreover, in cancer cells, miR-155 disrupts the DNA repair system and contributes to 5-fluorouracil resistance (Valeri et al. 2010; Geretto et al. 2017), and in nucleus pulposus cells it reduces apoptosis and pyroptosis by inhibiting RORα (Qin et al. 2023). In a recent study, RORα loss in gastric cancer cells leads to reduced glucose uptake and enhances sensitivity to 5-fluorouracil, which suggests that in its absence, cancer cells struggle to manage their energy demands and are more vulnerable to chemotherapy (Wang et al. 2024). Thus, miR-155 appears to play a complex dual role by affecting chemotherapy resistance and cell survival in a tissue-type dependent manner.

Table 2.

Resistance types and mechanisms by circadian genes.

Cancer types	Circadian genes	ncRNAs	Mechanism	Resistance	Ref.
Nasopharyngeal cancer	NPAS2	miR-20a-5p	Inhibiting the Notch signaling pathway by downregulation of NPAS2	Radiation	Zhao et al. (2017)
Melanoma	REV-ERBβ	LINC01224	Upregulating REV-ERBβ by sponging miR-193a-5p	Radiation	Cui et al. (2021)
Cervical cancer	TIMELESS	miR-708	Inhibiting the ATR/CHK1 signaling pathway by downregulation of TIMELESS	Cisplatin	Zou et al. (2020a)
Breast cancer	TIMELESS	miR-5188	Promoting expression by the TIMELESS/Sp1/c-Jun complex	Paclitaxel, epirubicin	Zou et al. (2020b)
Pancreatic cancer	BMAL1	miR-135b	Inhibiting by binding to the 3'UTR of the BMAL1 mRNA	Gemcitabine	Jiang et al. (2018)
Gastric cancer	RORAα	miR-155	Disrupting the DNA repair system and inhibiting RORα	5-fluorouracil	Valeri et al. (2010), Geretto et al. (2017), Qin et al. (2023), Wang et al. (2024)

Circadian genes intricately regulated by TTFLs are involved in promotion or inhibition of tumorigenesis, depending on the balance of these regulatory loops. Restoring the balance of disrupted circadian gene regulatory loops in cancer may provide a promising approach to tumor suppression and enhance the efficacy of therapeutic strategies. The utilization of ncRNAs offers a compelling strategy to restore this balance, modulate circadian gene function, and improve therapeutic outcomes. To achieve this, advanced delivery systems, such as liposomes, nanoparticles, or exosome-based vehicles, have shown potential in targeting ncRNAs or their functional regulators to specific cancer cells or tissues (Zhang et al. 2022; Davodabadi et al. 2024). Numerous clinical trials have been actively conducted to investigate the therapeutic potential of ncRNAs in cancer. However, clinical studies focusing on the interaction between ncRNAs and clock genes in the context of cancer are notably limited. For instance, there are studies evaluating a miR-155 inhibitor, cobomarsen (MRG-106), to show tumor-suppressive potential in hematologic malignancies such as cutaneous T-cell lymphoma (Seto et al. 2018; Witten and Slack 2020). Since miR-155 is associated with inhibition of RORα, further investigations to elucidate the direct involvement of cobomarsen in regulation of circadian rhythm would be required. This highlights the need for clinical studies to target ncRNAs that interact with circadian genes in cancer. However, ncRNA-based modulation of a single clock gene poses a potential challenge, as it may inadvertently alter the entire TTFL network, thereby affecting other clock genes and leading to unforeseen effects on tumor progression or treatment response. Careful characterization of these network interactions and off-target effects will be crucial for designing safe and effective ncRNA-based therapies.

7. Conclusions

The functions and roles of circadian rhythm-regulating genes such as CLOCK, BMAL1, PER1, PER2, CRY1, CRY2, RORα, NPAS2, REV-ERBα and TIMELESS in cancers continue to be topics of study. Many studies have reported that CLOCK, CRY1, NPAS2 and TIMELESS promote cancer formation, whereas BMAL1, PER1, PER2, CRY2, RORα and REV-ERBα inhibit cancer development and progression. In addition, researches have shown that ncRNAs, including miRNA, lncRNA, and circRNA, can regulate the aberrant expressions of circadian rhythm genes and that this phenomenon is associated with chemo – and radiotherapy resistance in diverse cancers. These findings highlight the need to investigate further the molecular mechanisms responsible for the effects of circadian rhythm-regulating genes. This review provides insights into the relationships between circadian genes and regulatory RNAs in cancer, the molecular mechanisms underlying treatment resistance, and development clues for future treatments.

Disclosure statement

No potential conflict of interest was reported by the author(s).