CircFADS2: A potential prognostic biomarker of colorectal cancer

Roles of circRNAs in the progression of colorectal cancer: novel strategies for detection and therapy

Endogenous noncoding RNAs with a covalently closed loop are known as circular RNAs (circRNAs). Recently, published works have revealed that circRNAs, which act as microRNA sponges, are critical for the biological behavior of several kinds of malignancies, including tumor cell proliferation, apoptosis, invasion, and metastasis. Additionally, there is a significant correlation between circRNAs and tumor resistance, stage, prognosis, and size. At present, colorectal cancer (CRC) is one of the most serious malignant tumors for human health. CircRNAs could represent potential targets to use in the prevention, diagnosis, and therapy of CRC, according to many studies. To fully comprehend the role of circRNAs in the incidence and progression of CRC, this review outlines the regulatory role and mechanisms of circRNAs in CRC and assesses their potential relevance as diagnostic and treatment possibilities for CRC. Our goal is to offer meaningful biological information for clinical evaluation and decision-making process for CRC treatment.

FADS2 function at the major cancer hotspot 11q13 locus alters fatty acid metabolism in cancer

Dysregulation of fatty acid metabolism and de novo lipogenesis is a key driver of several cancer types through highly unsaturated fatty acid (HUFA) signaling precursors such as arachidonic acid. The human chromosome 11q13 locus has long been established as the most frequently amplified in a variety of human cancers. The fatty acid desaturase genes (FADS1, FADS2 and FADS3) responsible for HUFA biosynthesis localize to the 11q12-13.1 region. FADS2 activity is promiscuous, catalyzing biosynthesis of several unsaturated fatty acids by Δ6, Δ8, and Δ4 desaturation. Our main aim here is to review known and putative consequences of FADS2 dysregulation due to effects on the 11q13 locus potentially driving various cancer types. FADS2 silencing causes synthesis of sciadonic acid (5Z,11Z,14Z-20:3) in MCF7 cells and breast cancer in vivo. 5Z,11Z,14Z-20:3 is structurally identical to arachidonic acid (5Z,8Z,11Z,14Z-20:4) except it lacks the internal Δ8 double bond required for prostaglandin and leukotriene synthesis, among other eicosanoids. Palmitic acid has substrate specificity for both SCD and FADS2. Melanoma, prostate, liver and lung cancer cells insensitive to SCD inhibition show increased FADS2 activity and sapienic acid biosynthesis. Elevated serum mead acid levels found in hepatocellular carcinoma patients suggest an unsatisfied demand for arachidonic acid. FADS2 circular RNAs are at high levels in colorectal and lung cancer tissues. FADS2 circular RNAs are associated with shorter overall survival in colorectal cancer patients. The evidence thusfar supports an effort for future research on the role of FADS2 as a tumor suppressor in a range of neoplastic disorders.

Glycolysis in human cancers: Emphasis circRNA/glycolysis axis and nanoparticles in glycolysis regulation in cancer therapy

The metabolism of cancer has been an interesting hallmark and metabolic reprogramming, especially the change from oxidative phosphorylation in mitochondria to glucose metabolism known as glycolysis occurs in cancer. The molecular profile of glycolysis, related molecular pathways and enzymes involved in this mechanism such as hexokinase have been fully understood. The glycolysis inhibition can significantly decrease tumorigenesis. On the other hand, circRNAs are new emerging non-coding RNA (ncRNA) molecules with potential biological functions and aberrant expression in cancer cells which have received high attention in recent years. CircRNAs have a unique covalently closed loop structure which makes them highly stable and reliable biomarkers in cancer. CircRNAs are regulators of molecular mechanisms including glycolysis. The enzymes involved in the glycolysis mechanism such as hexokinase are regulated by circRNAs to modulate tumor progression. Induction of glycolysis by circRNAs can significantly increase proliferation rate of cancer cells given access to energy and enhance metastasis. CircRNAs regulating glycolysis can influence drug resistance in cancers because of theirimpact on malignancy of tumor cells upon glycolysis induction. TRIM44, CDCA3, SKA2 and ROCK1 are among the downstream targets of circRNAs in regulating glycolysis in cancer. Additionally, microRNAs are key regulators of glycolysis mechanism in cancer cells and can affect related molecular pathways and enzymes. CircRNAs sponge miRNAs to regulate glycolysis as a main upstream mediator. Moreover, nanoparticles have been emerged as new tools in tumorigenesis suppression and in addition to drug and gene delivery, then mediate cancer immunotherapy and can be used for vaccine development. The nanoparticles can delivery circRNAs in cancer therapy and they are promising candidates in regulation of glycolysis, its suppression and inhibition of related pathways such as HIF-1α. The stimuli-responsive nanoparticles and ligand-functionalized ones have been developed for selective targeting of glycolysis and cancer cells, and mediating carcinogenesis inhibition.

Use of Personalized Biomarkers in Metastatic Colorectal Cancer and the Impact of AI

Colorectal cancer is a major cause of cancer-related death worldwide and is correlated with genetic and epigenetic alterations in the colonic epithelium. Genetic changes play a major role in the pathophysiology of colorectal cancer through the development of gene mutations, but recent research has shown an important role for epigenetic alterations. In this review, we try to describe the current knowledge about epigenetic alterations, including DNA methylation and histone modifications, as well as the role of non-coding RNAs as epigenetic regulators and the prognostic and predictive biomarkers in metastatic colorectal disease that can allow increases in the effectiveness of treatments. Additionally, the intestinal microbiota’s composition can be an important biomarker for the response to strategies based on the immunotherapy of CRC. The identification of biomarkers in mCRC can be enhanced by developing artificial intelligence programs. We present the actual models that implement AI technology as a bridge connecting ncRNAs with tumors and conducted some experiments to improve the quality of the model used as well as the speed of the model that provides answers to users. In order to carry out this task, we implemented six algorithms: the naive Bayes classifier, the random forest classifier, the decision tree classifier, gradient boosted trees, logistic regression and SVM.

CircRNA circFADS2 is under-expressed in sepsis and protects lung cells from LPS-induced apoptosis by downregulating miR-133a

Background

It has been reported that hsa_circRNA_100833 (identified as circFADS2) and miR-133a play opposite roles in LPS-induced cell apoptosis, which contributes to the development of sepsis. This study was carried out to explore the interaction between circFADS2 and miR-133a in sepsis.

Methods

Expression of circFADS2 and miR-133a in plasma from both sepsis patients (n=62) and healthy controls (n=62) was studied by RT-qPCR. Pearson’s correlation coefficient analysis was utilized to analyze the correlation between circFADS2 and miR-133a levels across plasma samples from sepsis patients. Cell viability and apoptosis, levels of proteins associated with apoptosis (cleaved caspase-3 and cleaved caspase-9), and expression of pro-inflammatory cytokines in LPS-treated HBEpCs were detected by MTT assay, cell apoptosis assay, western blot, and ELISA, respectively. In addition, a dual-luciferase reporter assay was performed to verify the interaction between circFADS2 and miR-133a.

Results

CircFADS2 was under-expressed (0.56-fold vs. control) in sepsis, and miR-133a was highly expressed (2.05-fold vs. control) in sepsis. An inverse correlation between circFADS2 and miR-133a was observed across sepsis samples. LPS decreased cell viability, increased cell apoptosis, and elevated productions of tumor necrosis factor (TNF)-α, interleukins (IL)-1β, IL-6, and IL-8 in HBEpCs in a dose-dependent manner. In addition, circFADS2 was identified as a target gene of miR-133a. The further experiment revealed that circFADS2 overexpression and miR-133a inhibition prominently promoted cell viability (1.71-fold vs. pcDNA3.1; 1.65-fold vs. NC miRNA) and decreased apoptosis of LPS-treated HBEpCs (0.44-fold vs. pcDNA3.1; 0.47-fold vs. NC miRNA). Moreover, circFADS2 knockdown and miR-133a overexpression inhibited viability (0.36-fold vs. pcDNA3.1; 0.37-fold vs. NC miRNA) and increased apoptosis (1.54-fold vs. pcDNA3.1; 1.51-fold vs. NC miRNA) of LPS-treated HBEpCs. Notably, circFADS2 overexpression reduced the effects of miR-133a on LPS-treated HBEpCs.

Conclusions

CircFADS2 is under-expressed in sepsis and may protect lung cells from LPS-induced apoptosis by downregulating miR-133a.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12950-022-00300-3.

New understandings of the pathway of long-chain polyunsaturated fatty acid biosynthesis

PURPOSE OF REVIEW

Molecular studies have clarified the roles of the fatty acid desaturase (FADSx) and elongation of very long chain fatty acid (ELOVLx) genes, as well as acyl-coenzyme A synthase long-chain isoforms (ACSLx) required for entry to long-chain polyunsaturated fatty acid (LCPUFA) biosynthetic pathways.

RECENT FINDINGS

FADS1 and FADS2 but not FADS3 are active toward PUFA. FADS1 is a Δ5-desaturase operating on five C20 PUFA, and is strongly regulated by human genetic polymorphisms, modulating circulating arachidonic acid (20:4n-6) levels. In contrast, FADS2 operates on at least 16 substrates, including five saturates, and catalyzes Δ6, Δ4, and Δ8 desaturation. FADS2 silencing in cancer cells leads to FADS1 synthesis of unusual fatty acids. ACSL6 and ACSL4 are required to maintain tissue 22:6n-3 and 20:4n-6, respectively. FADS2AT2, is the first transcript to differentially inhibit desaturation, attenuating 18:3n-3 but not 18:2n-6 desaturation. The PUFA elongases ELOVL5, 2, and 4 are implicated in cancer, age-related methylation, and retinal degeneration, respectively.

SUMMARY

The mixture of fatty acids available to FADS2 in any tissue defines the product mixture available for further synthesis of membrane lipids and signaling molecules and may be relevant in many clinical conditions including cancer. Functional genetic variants define the levels of circulating arachidonic acid via FADS1 regulation; genotypes that drive high arachidonic acid may predispose to disease.

Circular RNA hsa_circ_0006091 as a novel biomarker for hepatocellular carcinoma

Circular RNAs (circRNAs) are stable and extensively distributed non-coding RNA molecules that are differentially expressed in liver cancer tissues in the human body. In this study, we aimed to investigate circRNA as a novel candidate biomarker for hepatocellular carcinoma (HCC). For three groups of HCC and neighboring healthy tissues, the differentially expressed circRNAs were identified through high-throughput sequencing analysis. Reverse transcription PCR (RT-PCR) and quantitative polymerase chain reaction (qPCR) were employed for the evaluation of circRNAs that show an elevated expression level in HCC. The obtained results revealed the significantly differential expression of hsa_circ_0006091 in HCC. Then we obtained their target genes through biological analysis, followed by verifying the underlined target genes, and the regulator of G-protein signaling 12 (RGS12) showed an elevated expression level in HCC tissues. Finally, receiver operating characteristic (ROC) curve analysis was conducted on AFP, RGS12, and hsa_circ_0006091, and combined analysis was performed. Furthermore, hsa_circ_0006091 is a novel candidate biomarker for HCC and could improve the diagnostic strategies, prediction, and follow-up of HCC patients. The joint diagnosis of the hsa_circ_0006091&AFP and hsa_circ_0006091&RGS12 has diagnostic significance and can be used as a molecular marker for HCC diagnosis.

Abbreviations: AUC:area under the ROC curve; ROC:Receptor Operating Characteristics; bp:base pair;mRNA:Messenger Ribonucleic acid;ceRNA:Competing endogenous RNA; RT-qPCR: Real time-quantitativen PCR technology; circRNA: circular RNA; HCC:Hepatocellular carcinoma;miRNA:microRNA;KEGG:Kyoto Encyclopedia of Genes and Genomes; RGS12:regulator of G-protein signaling 12; AFP:alpha fetoprotein; ncRNAs:non-coding RNAs; GEO:Gene Expression Omnibus; FDR:false discovery rate

Circ_0022382 ameliorated intervertebral disc degeneration by regulating TGF-β3 expression through sponge adsorption of miR-4726-5p

Circular RNAs (circRNAs) participate in the progression of many diseases, but knowledge on the role of circRNAs in intervertebral disc degeneration (IDD) is limited. In this study, we discovered the characteristics of a new circRNA (circ_0022382) in human endplate chondrocytes. Currently, real-time quantitative polymerase chain reaction (RT-qPCR) showed that the relative expression level of circ_0022382 was significantly lower under intermittent cyclic tension stimulation than in the control group. circ_0022382, miR-4726-5p and Transforming growth factor 3 (TGF-β3) were evaluated by RT-qPCR, Western Blot and immunofluorescence assay. Additionally, the role and mechanism of circ_0022382 in vivo were also consistent in the rat model. Furthermore, Intermittent cyclic mechanical tension can cause degeneration of endplate chondrocytes. The tension-sensitive circRNA_0022382 was decreased, and we found that circRNA_0022382 promoted morphology of endplate chondrocytes by sponge-binding miR-4726-5p down-regulation of target gene the TGF-β3 expression, thereby alleviating IDD. In a rat model of acupuncture, intervertebral disc injection of circ_0022382 relieved the progression of IDD in vivo. In conclusion, the circ_0022382/miR-4726-5p/TGF-β3 axis plays a key role in the anabolism and catabolism of the endplate chondrocyte extracellular matrix (ECM). It is suggested that circ_0022382 may provide a new approach for the prevention and treatment of IDD.

Robust Glycogene-Based Prognostic Signature for Proficient Mismatch Repair Colorectal Adenocarcinoma

Background

Proficient mismatch repair (pMMR) colorectal adenocarcinoma (CRAC) metastasizes to a greater extent than MMR-deficient CRAC. Prognostic biomarkers are preferred in clinical practice. However, traditional biomarkers screened directly from sequencing are often not robust and thus cannot be confidently utilized.

Methods

To circumvent the drawbacks of blind screening, we established a new strategy to identify prognostic biomarkers in the conserved and specific oncogenic pathway and its regulatory RNA network. We performed RNA sequencing (RNA-seq) for messenger RNA (mRNA) and noncoding RNA in six pMMR CRAC patients and constructed a glycosylation-related RNA regulatory network. Biomarkers were selected based on the network and their correlation with the clinicopathologic information and were validated in multiple centers (n = 775).

Results

We constructed a competing endogenous RNA (ceRNA) regulatory network using RNA-seq. Genes associated with glycosylation pathways were embedded within this scale-free network. Moreover, we further developed and validated a seven-glycogene prognosis signature, GlycoSig (B3GNT6, GALNT3, GALNT8, ALG8, STT3B, SRD5A3, and ALG6) that prognosticate poor-prognostic subtype for pMMR CRAC patients. This biomarker set was validated in multicenter datasets, demonstrating its robustness and wide applicability. We constructed a simple-to-use nomogram that integrated the risk score of GlycoSig and clinicopathological features of pMMR CRAC patients.

Conclusions

The seven-glycogene signature served as a novel and robust prognostic biomarker set for pMMR CRAC, highlighting the role of a dysregulated glycosylation network in poor prognosis.

The effective function of circular RNA in colorectal cancer

Colorectal cancer (CRC) is the 3rd most common type of cancer worldwide. Late detection plays role in one-third of annual mortality due to CRC. Therefore, it is essential to find a precise and optimal diagnostic and prognostic biomarker for the identification and treatment of colorectal tumorigenesis. Covalently closed, circular RNAs (circRNAs) are a class of non-coding RNAs, which can have the same function as microRNA (miRNA) sponges, as regulators of splicing and transcription, and as interactors with RNA-binding proteins (RBPs). Therefore, circRNAs have been investigated as specific targets for diagnostic and prognostic detection of CRC. These non-coding RNAs are also linked to metastasis, proliferation, differentiation, migration, angiogenesis, apoptosis, and drug resistance, illustrating the importance of understanding their involvement in the molecular mechanisms of development and progression of CRC. In this review, we present a detailed summary of recent findings relating to the dysregulation of circRNAs and their potential role in CRC.

CircFADS2 is downregulated in osteoarthritis and suppresses LPS-induced apoptosis of chondrocytes by regulating miR-195-5p methylation

BACKGROUND

CircRNA circFADS2 has been reported to protect cells from LPS (Lipopolysaccharide)-induced cell injury, which contributes to osteoarthritis (OA). This study was carried out to study the role of circFADS2 in OA.

METHODS

The expression of circFADS2 and miR-195-5p in synovial fluid samples from 63 OA patients and 63 healthy controls were detected by RT-qPCRs. The effects of overexpression of circFADS2 on the expression of miR-195-5p and the methylation of miR-195-5p gene in chondrocytes were evaluated by RT-qPCRs and MSPs, respectively. The roles of circFADS2 and miR-195-5p in regulating the LPS-induced apoptosis of chondrocytes were explored by cell apoptosis assay.

RESULTS

CircFADS2 was downregulated in OA and inversely correlated with miR-195-5p. In chondrocytes, overexpression of circFADS2 and downregulation of miR-195-5p were observed after LPS treatment. In chondrocytes, overexpression of circFADS2 decreased the expression levels of miR-195-5p, and increased the methylation of miR-195-5p gene. Cell apoptosis assay showed that overexpression of circFADS2 reduced the apoptosis of chondrocytes under LPS treatment. Overexpression of miR-195-5p increased cell apoptosis and attenuated the effects of overexpression of circFADS2 on cell apoptosis.

CONCLUSION

CircFADS2 may downregulate miR-19-5p through methylation to suppress LPS-induced apoptosis of chondrocytes, thereby suppressing OA.

Circular RNA circFADS2 is overexpressed in sepsis and suppresses LPS-induced lung cell apoptosis by inhibiting the maturation of miR-15a-5p

BACKGROUND

Circular RNA circFADS2 plays protective roles in LPS-induced inflammation, which promotes sepsis, suggesting its involvement in sepsis.

METHODS

Expression of circFADS2, mature miR-15a-5p, and miR-15a-5p precursor in plasma samples from sepsis patients and healthy controls was determined by RT-qPCR. The circFADS2 expression vector was transfected in lung cells, followed by the measurement of the expression levels of mature miR-15a-5p and miR-15a-5p precursor to study the role of circFADS2 in miR-15a-5p maturation. Cell apoptosis was analyzed by cell apoptosis assay.

RESULTS

CircFADS2 was upregulated in sepsis and inversely correlated with mature miR-15a-5p, but not miR-15a-5p precursor. In lung cells, circFADS2 overexpression decreased the level of mature miR-15a-5p, but not miR-15a-5p precursor. LPS treatment decreased miR-15a-5p expression and increased circFADS2 level. Cell apoptosis analysis showed that circFADS2 overexpression reduced miR-15a-5p overexpression-induced apoptosis of LPS-treated lung cells.

CONCLUSIONS

CircFADS2 is upregulated in sepsis to suppress LPS-induced lung cell apoptosis by inhibiting miR-15a-5p maturation.

Up-regulated circBACH2 contributes to cell proliferation, invasion, and migration of triple-negative breast cancer

An increasing amount of evidence has proven the vital role of circular RNAs (circRNAs) in cancer progression. However, there remains a dearth of knowledge on the function of circRNAs in triple-negative breast cancer (TNBC). Utilizing a circRNA microarray dataset, four circRNAs were identified to be abnormally expressed in TNBC. Among them, circBACH2 was most significantly elevated in TNBC cancerous tissues and its high expression was positively correlated to the malignant progression of TNBC patients. In normal human mammary gland cell line, the overexpression of circBACH2 facilitated epithelial to mesenchymal transition and cell proliferation. In TNBC cell lines, circBACH2 knockdown suppressed the malignant progression of TNBC cells. Mechanistically, circBACH2 sponged miR-186-5p and miR-548c-3p, thus releasing the C-X-C chemokine receptor type 4 (CXCR4) expression. The interference of miR-186-5p/miR-548c-3p efficiently promoted the cell proliferation, migration, and invasion suppressed by circBACH2 knockdown in the TNBC cell lines. Finally, circBACH2 knockdown repressed the growth and lung metastasis of TNBC xenografts in nude mice. In summary, circBACH2 functions as an oncogenic circRNA in TNBC through a novel miR-186-5p/miR-548c-3p/CXCR4 axis.

Comprehensive landscape and future perspectives of circular RNAs in colorectal cancer

Colorectal cancer (CRC) is a common hereditary tumor that is often fatal. Its pathogenesis involves multiple genes, including circular RNAs (circRNAs). Notably, circRNAs constitute a new class of noncoding RNAs (ncRNAs) with a covalently closed loop structure and have been characterized as stable, conserved molecules that are abundantly expressed in tissue/development-specific patterns in eukaryotes. Based on accumulating evidence, circRNAs are aberrantly expressed in CRC tissues, cells, exosomes, and blood from patients with CRC. Moreover, numerous circRNAs have been identified as either oncogenes or tumor suppressors that mediate tumorigenesis, metastasis and chemoradiation resistance in CRC. Although the regulatory mechanisms of circRNA biogenesis and functions remain fairly elusive, interesting results have been obtained in studies investigating CRC. In particular, the expression of circRNAs in CRC is comprehensively modulated by multiple factors, such as splicing factors, transcription factors, specific enzymes and cis-acting elements. More importantly, circRNAs exert pivotal effects on CRC through various mechanisms, including acting as miRNA sponges or decoys, interacting with RNA binding proteins, and even translating functional peptides. Finally, circRNAs may serve as promising diagnostic and prognostic biomarkers and potential therapeutic targets in the clinical practice of CRC. In this review, we discuss the dysregulation, functions and clinical significance of circRNAs in CRC and further discuss the molecular mechanisms by which circRNAs exert their functions and how their expression is regulated. Based on this review, we hope to reveal the functions of circRNAs in the initiation and progression of cancer and highlight the future perspectives on strategies targeting circRNAs in cancer research.

Circular RNAs: Emerging Role in Cancer Diagnostics and Therapeutics

Circular RNAs (circRNAs) are rapidly coming to the fore as major regulators of gene expression and cellular functions. They elicit their influence via a plethora of diverse molecular mechanisms. It is not surprising that aberrant circRNA expression is common in cancers and they have been implicated in multiple aspects of cancer pathophysiology such as apoptosis, invasion, migration, and proliferation. We summarize the emerging role of circRNAs as biomarkers and therapeutic targets in cancer.