Hypoxia-induced circular RNA hsa_circ_0008450 accelerates hepatocellular cancer progression via the miR-431/AKAP1 axis

Full-length nanopore sequencing of circular RNA landscape in peripheral blood cells following sequential BNT162b2 mRNA vaccination

Circular RNAs (circRNA) lack 5' or 3' ends; their unique covalently closed structures prevent RNA degradation by exonucleases. These characteristics provide circRNAs with high pharmaceutical stability and biostability relative to current standard-of-care linear mRNAs. CircRNA levels are reportedly associated with certain human diseases, making them novel disease biomarkers and a noncanonical class of therapeutic targets. In this study, the endogenous circRNAs underlying the response to BNT162b2 mRNA vaccination were evaluated. To this end, peripheral blood samples were subjected to full-length sequencing of circRNAs via nanopore sequencing and transcriptome sequencing. Fifteen samples, comprising pre-, first, and second vaccination cohorts, were obtained from five healthcare workers with no history of SARS-CoV-2 infection or previous vaccination. A total of 4706 circRNAs were detected; following full-length sequencing, 4217 novel circRNAs were identified as being specifically expressed during vaccination. These circRNAs were enriched in the binding motifs of stress granule assemblies and SARS-CoV-2 RNA binding proteins, namely poly(A) binding protein cytoplasmic 1 (PABPC1), pumilio RNA binding family member 1 (PUM1), and Y box binding protein 1 (YBX1). Moreover, 489 circRNAs were identified as previously reported miRNA sponges. The differentially expressed circRNAs putatively originated from plasma B cells compared to circRNAs reported in human blood single-cell RNA sequencing datasets. The pre- and post-vaccination differences observed in the circRNA expression landscape in response to the SARS-CoV-2 BNT162b2 mRNA vaccine.

Exploring the impact of circRNAs on cancer glycolysis: Insights into tumor progression and therapeutic strategies

Cancer cells exhibit altered metabolic pathways, prominently featuring enhanced glycolytic activity to sustain their rapid growth and proliferation. Dysregulation of glycolysis is a well-established hallmark of cancer and contributes to tumor progression and resistance to therapy. Increased glycolysis supplies the energy necessary for increased proliferation and creates an acidic milieu, which in turn encourages tumor cells' infiltration, metastasis, and chemoresistance. Circular RNAs (circRNAs) have emerged as pivotal players in diverse biological processes, including cancer development and metabolic reprogramming. The interplay between circRNAs and glycolysis is explored, illuminating how circRNAs regulate key glycolysis-associated genes and enzymes, thereby influencing tumor metabolic profiles. In this overview, we highlight the mechanisms by which circRNAs regulate glycolytic enzymes and modulate glycolysis. In addition, we discuss the clinical implications of dysregulated circRNAs in cancer glycolysis, including their potential use as diagnostic and prognostic biomarkers. All in all, in this overview, we provide the most recent findings on how circRNAs operate at the molecular level to control glycolysis in various types of cancer, including hepatocellular carcinoma (HCC), prostate cancer (PCa), colorectal cancer (CRC), cervical cancer (CC), glioma, non-small cell lung cancer (NSCLC), breast cancer, and gastric cancer (GC). In conclusion, this review provides a comprehensive overview of the significance of circRNAs in cancer glycolysis, shedding light on their intricate roles in tumor development and presenting innovative therapeutic avenues.

Hypoxia-associated autophagy flux dysregulation in human cancers

A general feature of cancer is hypoxia, determined as low oxygen levels. Low oxygen levels may cause cells to alter in ways that contribute to tumor growth and resistance to treatment. Hypoxia leads to variations in cancer cell metabolism, angiogenesis and metastasis. Furthermore, a hypoxic tumor microenvironment might induce immunosuppression. Moreover, hypoxia has the potential to impact cellular processes, such as autophagy. Autophagy refers to the catabolic process by which damaged organelles and toxic macromolecules are broken down. The abnormal activation of autophagy has been extensively recorded in human tumors and it serves as a regulator of cell growth, spread to other parts of the body, and resistance to treatment. There is a correlation between hypoxia and autophagy in human malignancies. Hypoxia can regulate the activity of AMPK, mTOR, Beclin-1, and ATGs to govern autophagy in human malignancies. Furthermore, HIF-1α, serving as an indicator of low oxygen levels, controls the process of autophagy. Hypoxia-induced autophagy has a crucial role in regulating the growth, spread, and resistance to treatment in human malignancies. Hypoxia-induced regulation of autophagy can impact other mechanisms of cell death, such as apoptosis. Chemoresistance and radioresistance have become significant challenges in recent years. Hypoxia-mediated autophagy plays a crucial role in determining the response to these therapeutic treatments.

Hsa_circ_0000129 knockdown attenuates proliferation and migration in keloid fibroblasts by targeting miR-485-3p/SGMS2 pathway

BACKGROUND

Aberrant biofunction of circular RNAs (circRNAs) is potently implicated in keloid formation. However, their roles have been underinvestigated. Recent evidence has demonstrated the pro-tumor role of circ_0000129 in cancers, and yet its role in keloid remains elusive.

METHODS

RT-qPCR analysis and or western blotting of miR-485-3p, circ_0000129, and SGMS2 in keloid tissues and keloid fibroblasts was implemented. CCK8, EdU, scratch wound healing, and Transwell migration assays were perfomed to determine the keloid fibroblast proliferation and migration. Luciferase reporter and RIP assays were adopted to analyze the interaction among circ_0000129, miR-485-3p and SGMS2.

RESULTS

In keloid tissues and keloid fibroblasts, circ_0000129 and SGMS2 were amplified, although miR-485-3p expression was downregulated. Furthermore, siRNAs-targeting endogenous circ_0000129 resulted in proliferation and migration defect of keloid fibroblasts. MiR-485-3p was simultaneously recognized by circ_0000129 and SGMS2 3'UTR. Rescued functional assays also illustrated that miR-485-3p loss was beneficial to the proliferation and migration of keloid fibroblasts, and these promoting changes were nullified by accompanied silence circ_0000129 or SGMS2.

CONCLUSION

Circ_0000129 sponges miR-485-3p and releases expression of SGMS2 from the miR-485-3p suppression, promoting migration and proliferation of keloid fibroblasts, suggesting targeting circ_0000129/miR-485-3p/SGMS2 might be a promising strategy against keloid fibroblasts.

AVAILABILITY OF DATA AND MATERIAL

All data generated or analyzed during this study are included in this article.

Hypoxia-induced circRTN4IP1 promotes progression and glycolysis of hepatocellular carcinoma cells

Hypoxia is one of the hallmarks of solid tumors, especially in hepatocellular carcinoma (HCC). CircRNAs are reported to be tightly connected to hypoxia and also have essential roles in cancer progression. However, many circRNAs implicated in hypoxia-mediated HCC progression are still unclear and require further exploration. In this study, a hypoxia cell model was structured by exposing cells to hypoxia conditions (1% O2) and normoxia conditions (21% O2) as a control. The effects of hypoxia and normoxia on cell viability, migration, invasion, and glycolysis were examined. The expressions of circRNARTN4IP1 under hypoxia were identified. Finally, molecular mechanisms and biological function of circRTN4IP1 were explored. We confirmed that hypoxia treatment facilitated capacities of proliferation, migration, invasion, and glycolysis in tumor cells. Hypoxia induced a significant increase expression of circRTN4IP1 in cells. Functionally, knockdown of circRTN4IP1 inhibited cell malignant progression and glycolysis under hypoxia HCC cells. Mechanistically, HIF1A targeted the promoter region of circRTN4IP1 and positively regulated the expression of circRTN4IP1. In addition, circRTN4IP1 targeted miR-532-5p/G6PC3 axis. In short, hypoxia induced activation of the HIF1A/circRTN4IP1/miR-532-5p/G6PC3 signaling axis, which promoted proliferation, migration, invasion, and glycolysis of HCC cells. This study may reveal a possible mechanism driving the progression of hypoxia HCC, so as to find potential effective candidates for targeting hypoxia microenvironment therapy.

A novel protein encoded by circINSIG1 reprograms cholesterol metabolism by promoting the ubiquitin-dependent degradation of INSIG1 in colorectal cancer

BACKGROUND

Hypoxia is a hallmark of solid tumors and leads to the metabolic reprogramming of cancer cells. The role of epigenetic regulation between hypoxia and aberrant cholesterol metabolism in colorectal cancer (CRC) remains elusive.

METHODS

Hypoxia-responsive circular RNAs (circRNAs) were identified by high throughput RNA sequencing between CRC cells cultured under normoxia or hypoxia. The protein-coding potential of circINSIG1 was identified by polysome profiling and LC-MS. The function of circINSIG1 was validated in vitro and in vivo by gain or loss of function assays. Mechanistic results were concluded by immunoprecipitation analyses.

RESULTS

A novel hypoxia-responsive circRNA named circINSIG1 was identified, which was upregulated in CRC tissues and correlated with advanced clinical stages and poor survival. Mechanistically, circINSIG1 encoded a 121 amino acid protein circINSIG1-121 to promote K48-linked ubiquitination of the critical cholesterol metabolism regulator INSIG1 at lysine 156 and 158 by recruiting CUL5-ASB6 complex, a ubiquitin E3 ligase complex, thereby inducing cholesterol biosynthesis to promote CRC proliferation and metastasis. The orthotopic xenograft tumor models and patient-derived xenograft models further identified the role of circINSIG1 in CRC progression and potential therapeutic target of CRC.

CONCLUSIONS

circINSIG1 presents an epigenetic mechanism which provides insights into the crosstalk between hypoxia and cholesterol metabolism, and provides a promising therapeutic target for the treatment of CRC.

Review of novel functions and implications of circular RNAs in hepatocellular carcinoma

Hepatocellular carcinoma (HCC) is one of the most frequent malignancies, with high incidence and mortality. As the majority of HCC patients are diagnosed at an advanced stage and die of recurrence and metastasis, its pathology and new biomarkers are needed. Circular RNAs (circRNAs) are a large subclass of long non-coding RNAs (lncRNAs) with covalently closed loop structures and abundant, conserved, stable, tissue-specific expression in mammalian cells. CircRNAs exert multiple functions in HCC initiation, growth and progression, serving as promising biomarkers for diagnosis, prognosis and therapeutic targets for this disease. This review briefly describes the biogenesis and biological functions of circRNAs and elucidates the roles of circRNAs in the development and progression of HCC, especially regarding epithelial-mesenchymal transition (EMT), drug resistance and interactions with epigenetic modifications. In addition, this review highlights the implications of circRNAs as potential biomarkers and therapeutic targets for HCC. We hope to provide novel insight into the roles of circRNAs in HCC.

PCLassoLog: A protein complex-based, group Lasso-logistic model for cancer classification and risk protein complex discovery

Risk gene identification has attracted much attention in the past two decades. Since most genes need to be translated into proteins and cooperate with other proteins to form protein complexes to carry out cellular functions, which significantly extends the functional diversity of individual proteins, revealing the molecular mechanism of cancer from a comprehensive perspective needs to shift from identifying individual risk genes toward identifying risk protein complexes. Here, we embed protein complexes into the regularized learning framework and propose a protein complex-based, group Lasso-logistic model (PCLassoLog) to discover risk protein complexes. Experiments on deep proteomic data of two cancer types show that PCLassoLog yields superior predictive performance on independent datasets. More importantly, PCLassoLog identifies risk protein complexes that not only contain individual risk proteins but also incorporate close partners that synergize with them. Furthermore, selection probabilities are calculated and two other protein complex-based models are proposed to complement PCLassoLog in identifying reliable risk protein complexes. Based on PCLassoLog, a pan-cancer analysis is performed to identify risk protein complexes in 12 cancer types. Finally, PCLassoLog is used to discover risk protein complexes associated with gene mutation. We implement all protein complex-based models as an R package PCLassoReg, which may serve as an effective tool to discover risk protein complexes in various contexts.

The Role of ECM Remodeling, EMT, and Adhesion Molecules in Cancerous Neural Invasion: Changing Perspectives

Perineural invasion (PNI) refers to the cancerous invasion of nerves. It provides an alternative route for metastatic invasion and can exist independently in the absence of lymphatic or vascular invasion. It is a prominent characteristic of specific aggressive malignancies where it correlates with poor prognosis. The clinical significance of PNI is widely recognized despite a lack of understanding of the molecular mechanisms underlying its pathogenesis. The interaction between the nerve and the cancer cells is the most pivotal PNI step which is mediated by the activation or inhibition of multiple signaling pathways that include chemokines, interleukins, nerve growth factors, and matrix metalloproteinases, to name a few. The nerve-cancer cell interaction brings about specific changes in the perineural niche, which not only affects the regular nerve functions, but also enhances the migratory, invasive, and adherent properties of the tumor cells. This review aims to elucidate the vital role of adhesion molecules, extracellular matrix, and epithelial-mesenchymal proteins that promote PNI, which may serve as therapeutic targets in the future.

Silencing of circCYP51A1 represses cell progression and glycolysis by regulating miR-490-3p/KLF12 axis in osteosarcoma under hypoxia

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CircCYP51A1 was up-regulated in osteosarcoma cells under hypoxia.

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CircCYP51A1 mediated KLF12 expression through sponging miR-490-3p.

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Under hypoxia condition, circCYP51A1 knockdown inhibited cell progression and glycolysis by regulating miR-490-3p/ KLF12 axis.

Background

Methods

Results

Conclusion

Hypoxia-responsive circRNAs: A novel but important participant in non-coding RNAs ushered toward tumor hypoxia

Given the rapid developments in RNA-seq technologies and bioinformatic analyses, circular RNAs (circRNAs) have gradually become recognized as a novel class of endogenous RNAs, characterized by covalent loop structures lacking free terminals, which perform multiple biological functions in cancer genesis, progression and metastasis. Hypoxia, a common feature of the tumor microenvironments, profoundly affects several fundamental adaptive responses of tumor cells by regulating the coding and non-coding transcriptomes and renders cancer's phenotypes more aggressive. Recently, hypoxia-responsive circRNAs have been recognized as a novel player in hypoxia-induced non-coding RNA transcriptomics to modulate the hypoxic responses and promote the progression and metastasis of hypoxic tumors. Moreover, via extracellular vesicles-exosomes, these hypoxia-responsive circRNAs could transmit hypoxia responses from cancer cells to the cells of surrounding matrices, even more distant cells of other organs. Here, we have summarized what is known about hypoxia-responsive circRNAs, with a focus on their interaction with hypoxia-inducible factors (HIFs), regulation of hypoxic responses and relevance with malignant carcinoma's clinical features, which will offer novel insights on the non-coding RNAs' regulation of cancer cells under hypoxic stress and might aid the identification of new theranostic targets and define new therapeutic strategies for those cancer patients with resistance to radiochemotherapy, because of the ubiquity of tumoral hypoxia.

Hypoxia-regulated microRNAs: the molecular drivers of tumor progression

Hypoxia is a common feature of the tumor microenvironment (TME) of nearly all solid tumors, leading to therapeutic failure. The changes in stiffness of the extracellular matrix (ECM), pH gradients, and chemical balance that contribute to multiple cancer hallmarks are closely regulated by intratumoral oxygen tension via its primary mediators, hypoxia-inducible factors (HIFs). HIFs, especially HIF-1α, influence these changes in the TME by regulating vital cancer-associated signaling pathways and cellular processes including MAPK/ERK, NF-κB, STAT3, PI3K/Akt, Wnt, p53, and glycolysis. Interestingly, research has revealed the involvement of epigenetic regulation by hypoxia-regulated microRNAs (HRMs) of downstream target genes involved in these signaling. Through literature search and analysis, we identified 48 HRMs that have a functional role in the regulation of 5 key cellular processes: proliferation, metabolism, survival, invasion and migration, and immunoregulation in various cancers in hypoxic condition. Among these HRMs, 17 were identified to be directly associated with HIFs which include miR-135b, miR-145, miR-155, miR-181a, miR-182, miR-210, miR-224, miR-301a, and miR-675-5p as oncomiRNAs, and miR-100-5p, miR-138, miR-138-5p, miR-153, miR-22, miR-338-3p, miR-519d-3p, and miR-548an as tumor suppressor miRNAs. These HRMs serve as a potential lead in the development of miRNA-based targeted therapy for advanced solid tumors. Future development of combined HIF-targeted and miRNA-targeted therapy is possible, which requires comprehensive profiling of HIFs-HRMs regulatory network, and improved formula of the delivery vehicles to enhance the therapeutic kinetics of the targeted cancer therapy (TCT) moving forward.

Encouraging specific biomarkers-based therapeutic strategies for hepatocellular carcinoma

The prevention, early discovery and effective treatment of patients with hepatocellular carcinoma (HCC) remain a global medical challenge. At present, HCC is still mainly treated by surgery, supplemented by vascular embolization, radio frequency, radiotherapy, chemotherapy and biotherapy. The application of multikinase inhibitor sorafenib, chimeric antigen receptor T cells, or PD-1/PD-L1 inhibitors can prolong the median survival of HCC patients. However, the treatment efficacy is still unsatisfactory due to HCC metastasis and postoperative recurrence. During the process of hepatocyte malignant transformation, HCC tissues can express and secrete many types of specific biomarkers, or oncogenic antigen molecules into blood, for example, alpha-fetoprotein, glypican-3, Wnt3a (one of the key signaling molecules in the Wnt/β-catenin pathway), insulin-like growth factor (IGF)-II or IGF-I receptor, vascular endothelial growth factor, secretory clusterin and so on. In addition, combining immunotherapy with non-coding RNAs might improve anti-cancer efficacy. These biomarkers not only contribute to HCC diagnosis or prognosis, but may also become molecular targets for HCC therapy under developing or clinical trials. This article reviews the progress in emerging biomarkers in basic research or clinical trials for HCC immunotherapy.

Circular RNA circ_0061140 accelerates hypoxia-induced glycolysis, migration, and invasion in lung adenocarcinoma through the microRNA-653/hexokinase 2 (HK2) axis

Circular RNA (circRNA) is considered to be an essential regulator of multiple human malignancies. However, the role and molecular mechanism of circ_0061140 in lung adenocarcinoma ((LUAD) remain elusive. The levels of circ_0061140, microRNA (miR)-653 and hexokinase 2 (HK2) were examined by RT-qPCR. Downstream targets of circ_0061140 were predicted by circinteractome website and verified by luciferase reporter and RIP assays. HK2 protein level was assessed via Western blotting. The migratory and invasive abilities of LUAD cells were assessed via wound healing and transwell assays. It was uncovered that circ_0061140 level was elevated in LUAD samples, and the high level of circ_0061140 was related to poor survival rate of LUAD patients. Circ_0061140 deletion inhibited glycolysis, migration and invasion of hypoxia-treated LUAD cells. Moreover, circ_0061140 could modulate HK2 level by absorbing miR-653. Furthermore, miR-653 silence or HK2 addition neutralized the effects of circ_0061140 knockdown on LUAD progression under hypoxia. This study elaborated that circ_0061140 accelerated hypoxia-triggered glycolysis, migration and invasion in LUAD cells via downregulating miR-653 and increasing HK2 expression.

miR-199b-5p-AKAP1-DRP1 pathway plays a key role in ox-LDL-induced mitochondrial fission and endothelial apoptosis

BACKGROUND

Atherosclerosis (AS) remains prevalent despite hyperlipidemia-lowering therapies. Although multiple functions of miR-199b-5p have been implicated in cancers, its role in endothelial apoptosis and AS remains unclear. This study aimed to examine the role of miR-199b-5p in mitochondrial dynamics and endothelial apoptosis.

METHODS

Human umbilical vein endothelial cells (HUVECs) treated with oxidized low-density lipoprotein (ox-LDL) were subjected to other treatments, followed by a series analysis. We found that ox-LDL-treated HUVECs were associated with miR-199b-5p downregulation, increased reactive oxygen species level, reduced adenosine triphosphate (ATP) production, mitochondrial fission, and apoptosis, whereas enhanced miR-199b-5p expression or applied mitochondrial division inhibitor 1 (Mdivi-1) markedly reversed these changes.

RESULTS

Mechanistically, A-kinase anchoring protein 1 (AKAP1) was confirmed as a downstream target of miR-199b-5p by dual-luciferase activity reporter assay, AKAP1 overexpression reversed the anti-apoptotic effects of miR-199b-5p through the enhanced interaction of AKAP1 and dynamin protein 1 (DRP1) in ox-LDL-treated HUVECs. Moreover, miR-199b-5p downregulation, AKAP1 upregulation, and excessive mitochondrial fission were verified in human coronary AS endothelial tissues.

CONCLUSION

The miR-199b-5p-dependent regulation of AKAP1/DRP1 is required to inhibit hyperlipidemia-induced mitochondrial fission and endothelial injury and could be a promising therapeutic target for AS.

Development and validation of an immune‐related prognosis signature associated with hypoxia and ferroptosis in hepatocellular carcinoma

Background

Hypoxia and ferroptosis are crucial in the occurrence and development of hepatocellular carcinoma (HCC), and they both affect the immune status of the tumor microenvironment. Previous studies have also shown a link between hypoxia and ferroptosis.

Patients and methods

In all, 814 HCC cases from The Cancer Genome Atlas and Gene Expression Omnibus databases were used as the discovery cohort, and 230 HCC cases from the International Cancer Genome Consortium database were used as the validation cohort. Hypoxia subtypes and ferroptosis subtypes were identified by consensus cluster analysis according to 174 hypoxia‐related genes and 193 ferroptosis‐related genes. The prognostic signature was constructed using the Cox and LASSO regression analyses, and two risk groups were identified. A comprehensive analysis of the clinical and immune characteristics between the two risk groups was further performed.

Results

Two hypoxia subtypes and two ferroptosis subtypes were distinguished and verified; subsequently, a five‐gene prognostic signature was constructed and the risk score could be acquired by the following formula: risk score = 0.0604*Expression (CA9)−0.0714*Expression (ANXA10) + 0.1501*Expression (CDC20)−0.0853*Expression (CYP7A1) + 0.0530*Expression (SPP1). Compared with the low‐risk group, the high‐risk group had a worse prognosis. The high‐risk group also showed a higher level of immune infiltration than the low‐risk group, and immune checkpoints were generally upregulated in the high‐risk group. The antigen presentation ability of the low‐risk group was poor, which may be related to the immune escape mechanism. Drug sensitivity analysis indicated that the high‐ and low‐risk groups were sensitive to tyrosine kinase inhibitors and chemotherapeutic drugs, respectively.

Conclusion

The hypoxia‐, ferroptosis‐, and immune‐associated prognostic signature we constructed could stratify patients with HCC and guide precise treatment.

Biogenesis, Functions, and Role of CircRNAs in Lung Cancer

CircRNAs, a class of endogenous non-coding RNAs with closed-loop structures, have attracted increasing attention because of their good stability, high specificity of tissue expression, long half-life, and highly conserved sequence. CircRNAs have multiple biological functions, including miRNA sponge, transcription regulator, protein translation, interaction with protein, RNA maturation, and so on. These functions indicate the important role of circRNAs in tumorigenesis and malignant progression and their potential as potent diagnostic biomarkers and therapeutic molecules. In recent years, an increasing body of evidence suggests that circRNAs play a crucial role in proliferation, migration, invasion, and apoptosis of lung cancer cells. Therefore, circRNAs have gradually become a research focus in the diagnosis and treatment of lung cancer patients. This review summarizes the classification, biogenesis, and function of circRNAs, and discusses the role of circRNAs in the diagnosis, prognosis, and treatment of lung cancer patients.