Frontiers in Bioengineering and Biotechnology
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2024
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IF 4.3
He Wei,Zhang Xinya,Zou Yangxiaoyu,Li Ji,Chang Le,He Yu-Cai,Jin Qiuheng,Ye Jianren
Introduction: Circular RNAs (circRNAs) are endogenous noncoding RNAs (ncRNAs) with transcriptional lengths ranging from hundreds to thousands. circRNAs have attracted attention owing to their stable structure and ability to treat complicated diseases. Our objective was to create a one-step reaction for circRNA synthesis using wild-type T7 RNA polymerase as the catalyst. However, T7 RNA polymerase is thermally unstable, and we streamlined circRNA synthesis via consensus and folding free energy calculations for hotspot selection. Because of the thermal instability, the permuted intron and exon (PIE) method for circRNA synthesis is conducted via tandem catalysis with a transcription reaction at a low temperature and linear RNA precursor cyclization at a high temperature.Methods: To streamline the process, a multisite mutant T7 RNA polymerase (S430P, N433T, S633P, F849I, F880Y, and G788A) with significantly improved thermostability was constructed, and G788A was used.Results: The resulting mutant exhibited stable activity at 45°C for over an hour, enabling the implementation of a one-pot transcription and cyclization reaction. The simplified circRNA production process demonstrated an efficiency comparable to that of the conventional two-step reaction, with a cyclization rate exceeding 95% and reduced production of immunostimulatory dsRNA byproducts.
研究领域:
分子生物学
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生物化学
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合成生物学
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PubMed
高影响因子
BMC GASTROENTEROLOGY
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2023
·Vol. 23
·期 1
·1-10
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IF 2.4
Xiang Ping,Ge Tingrui,Zhou Jingyi,Zhang Yonggang
Background Increasing research indicates that circular RNAs (circRNAs) play critical roles in the development of ulcerative colitis (UC). This study aimed to determine the role of circRNA CCND1 in UC bio-progression, which has been shown to be downregulated in UC tissues. Methods Reverse transcription quantitative polymerase chain reaction was used to determine the levels of circRNA CCND1 , miR-142-5p, and nuclear receptor coactivator-3 ( NCOA3 ) in UC tissues and in lipopolysaccharide (LPS)-induced Caco-2 cells. Target sites of circRNA CCND1 and miR-142-5p were predicted using StarBase, and TargetScan to forecast potential linkage points of NCOA3 and miR-142-5p, which were confirmed by a double luciferase reporter-gene assay. Cell Counting Kit 8 and flow cytometry assays were performed to assess Caco-2 cell viability and apoptosis. TNF-α, IL-1β, IL-6, and IL-8 were detected using Enzyme-Linked Immunosorbent Assay kits. Results CircRNA CCND1 was downregulated in UC clinical samples and LPS-induced Caco-2 cells. In addition, circRNA CCND1 overexpression suppressed LPS-induced apoptosis and inflammatory responses in Caco-2 cells. Dual-luciferase reporter-gene assays showed that miR-142-5p could be linked to circRNA CCND1 . Moreover, miR-142-5p was found to be highly expressed in UC, and its silencing inhibited LPS-stimulated Caco-2 cell apoptosis and inflammatory responses. Importantly, NCOA3 was found downstream of miR-142-5p. Overexpression of miR-142-5p reversed the inhibitory effect of circRNA CCND1 -plasmid on LPS-stimulated Caco-2 cells, and the effects of miR-142-5p inhibitor were reversed by si- NCOA3 . Conclusion CircRNA CCND1 is involved in UC development by dampening miR-142-5p function, and may represent a novel approach for treating UC patients.
研究领域:
分子生物学
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胃肠病学
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免疫学
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细胞生物学
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DOI
PubMed
高影响因子
CHEMICAL ENGINEERING JOURNAL
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2025
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IF 13.2
Luyun Xu,Yongshi Shen,Zhizhong Lin,Jianqing Ye,Lingna Wang,Xueliang Lin,Shuhang Liu,Duo Lin,Yuanji Xu,Zongyang Yu,Rongcai Zhang,Shangyuan Feng
Lung cancer remains the leading cause of cancer-related deaths worldwide, mainly due to challenges in early detection that often result in poor patient outcomes. In this study, we developed a magnetic biosensing platform based on the coupling of CHA and SERS technologies for one-step detection of lung cancer-related circRNAs. Our approach capitalizes on forming “hot spots” between core–shell SERS nanoprobes and magnetic nanoparticles with precisely defined functionalities, generating a robust Raman signal. This signal is further amplified through magnetic enrichment and calibrated with an internal standard molecule, achieving a remarkably sensitive detection limit of 5.5 aM. Notably, our circRNA detection method significantly surpasses conventional tumor markers’ sensitivity. Validation using human serum samples demonstrated considerably higher circRNA levels in lung cancer patients than healthy controls. Moreover, the core–satellite structured magnetic SERS platform successfully distinguished unique circRNA concentration profiles across early-stage (IA and IB) lung cancers and their subtypes (IA1, IA2, IA3). Collectively, these results underscore the potential of our magnetic SERS platform as a liquid biopsy-based prognostic tool, enhancing early screening sensitivity and thereby facilitating more accurate diagnosis and improved patient stratification.
研究领域:
医学诊断
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纳米技术
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癌症研究
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高影响因子
CELL BIOLOGY AND TOXICOLOGY
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2024
·Vol. 40
·期 1
·1-28
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IF 5.3
Liu Yuhan,Qin Yanling,Zhang Yanning
Uremic encephalopathy (UE) poses a significant challenge in neurology, leading to the need to investigate the involvement of non-coding RNA (ncRNA) in its development. This study employed ncRNA-seq and RNA-seq approaches to identify fundamental ncRNAs, specifically circRNA and miRNA, in the pathogenesis of UE using a mouse model. In vitro and in vivo experiments were conducted to explore the circRNA-PTPN4/miR-301a-3p/FOXO3 axis and its effects on blood–brain barrier (BBB) function and cognitive abilities. The research revealed that circRNA-PTPN4 binds to and inhibits miR-301a-3p, leading to an increase in FOXO3 expression. This upregulation results in alterations in the transcriptional regulation of ZO-1, affecting the permeability of human brain microvascular endothelial cells (HBMECs). The axis also influences the growth, proliferation, and migration of HBMECs. Mice with UE exhibited cognitive deficits, which were reversed by overexpression of circRNA-PTPN4, whereas silencing FOXO3 exacerbated these deficits. Furthermore, the uremic mice showed neuronal loss, inflammation, and dysfunction in the BBB, with the expression of circRNA-PTPN4 demonstrating therapeutic effects. In conclusion, circRNA-PTPN4 plays a role in promoting FOXO3 expression by sequestering miR-301a-3p, ultimately leading to the upregulation of ZO-1 expression and restoration of BBB function in mice with UE. This process contributes to the restoration of cognitive abilities. Graphical Abstract 1. The circRNA-PTPN4/miR-301a-3p/FOXO3 axis is identified as a key regulator of blood–brain barrier integrity and cognitive function in uremic encephalopathy. 2. circRNA-PTPN4 sequestration of miR-301a-3p enhances FOXO3 expression, leading to upregulation of ZO-1 and improved endothelial permeability. 3. Overexpression of circRNA-PTPN4 in uremic mice restores cognitive abilities and reduces neuronal loss and inflammatory infiltration.
研究领域:
神经学
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分子生物学
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非编码RNA
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认知科学
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病理生理学
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DOI
PubMed
高影响因子
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
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2026
·Vol. 27
·期 19
·8593
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IF 5.6
Dongmei Zhong,Faxiang Li,Ziyu Yang,Fang Gou,Yanmei Gao,Tian Bu,Qingfeng Liu,Yinggang Li,Wuhui Li,Qizhi Liu,Kaikun Luo,Rong Yang,Shaojun Liu
Fish gonad development is a central process in reproductive regulation, and elucidating its molecular mechanisms is highly important for developing aquatic genetic resources. However, the involvement of circular RNAs (circRNAs) in the gonad development of freshwater fish is unknown. In this study, a dynamic expression profile of circRNA during the development of red crucian carp testes was systematically constructed via whole-transcriptome sequencing. Notably, the circular characteristics and high testis-specific expression of the key circRNA circdmrt1, formed through the reverse splicing of the fourth exon of thedmrt1gene, have been experimentally validated. The overexpression of circdmrt1 promoted cell proliferation and inhibited the expression of apoptosis-related genes. Furthermore, in the hybrid offspring of red crucian carp and white crucian carp, circdmrt1 expression exhibited a pronounced paternal-line-biased pattern. Our data reveal that circdmrt1 may act as a ceRNA by sequestering miR-122-5p and thereby modulating DHRSX expression, leading to the activation of HEK-293T cell proliferation. This study reveals for the first time the regulatory features of testicular circRNAs in crucian carp, providing support evidence into the mechanisms of gonadal development in teleosts.
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高影响因子
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
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2026
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IF 6.7
Zixuan Liu,Long Sun,Lili Yao,Shengjie Gao,Ling Yan,Yu Mao,Lei Zheng
To address meat adulteration, this study pioneers the use of ultrastable circular RNAs (circRNAs) as species-specific biomarkers for detecting duck meat adulteration in mutton. Three highly abundant duck-specific circRNAs with low cross-species homology were identified via high-throughput sequencing and bioinformatics analysis. Leveraging their unique BSJ, we developed a fluorescence-based dual-recognition platform combining BSJ-targeted reverse transcription rolling circle amplification (RT-RCA) with sequence-specific hairpin probes (HP). This RCA-HP system enables combinatorial hybridization and cascade amplification, achieving a detection limit of 0.1% duck meat in mutton. Notably, the target circRNAs demonstrated remarkable stability under harsh processing (180 °C frying and 121 °C autoclaving) and extended storage. Validation with 60 commercial samples showed 98.89% specificity and 99.26% sensitivity. The modular design allows easy adaptation to other meat species, establishing circRNAs as next-generation biomarkers and providing a robust framework for food authentication resistant to industrial processing.
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PubMed
高影响因子
CHEMICAL ENGINEERING JOURNAL
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2025
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IF 13.2
Xinyu Zhang,Zixin Lin,Huanyu Zhou,Qitao Xie,Yuetao Zhang,Yongmei Chen,Zijie Li,Runlin Lv,Zhiqi Li,Rubing Xiong,Xiaman Chen,Yong Xia,Lei Mou,Honghai Hong
The discovery and sensitive detection of breast cancer biomarkers are significant for cancer diagnosis. Here, to increase the accuracy of breast cancer diagnosis, we show that hsa_circ_044235 and hsa_circ_000250 are effective biomarkers for breast cancer diagnosis. Moreover, we present an integrated electrochemical microfluidic circRNA detection platform (ECMCDP) that combines gold platinum (AuPt) nanoparticle-modified screen-printed electrodes (SPEs), a catalytic hairpin assembly (CHA), an electrochemical microfluidic chip and a customized low-power electronic system for simultaneous detection of the two breast cancer-associated circRNAs. The limits of detection (LODs) are 0.12 fM and 0.01 fM, and the diagnostic accuracies are 92.50 % and 88.75 %, respectively, for clinical blood samples. The platform is validated using paired pre/postoperative blood and tissue samples. By combining five machine learning-based diagnostic models, the ensemble diagnosis model achieves a high accuracy of 93.75 %. This work is aimed at identifying novel breast cancer biomarkers and establishing an innovative circRNA detection platform to improve breast cancer diagnosis and support clinical prognosis assessment.
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高影响因子
Reproductive Biology
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2022
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IF 2.089
Ai-Xue Chen,Rui-Ying Jin,Wei-Mei Zhou,Yong-Ju Ye,Jia-Li Lu,Yue-Fang Ren,Fei-Lan Xuan
abstract Increasing evidence indicates that circular RNAs (CircRNAs) have an important role in human diseases, including polycystic ovary syndrome (PCOS). Recently, circ_0043533, a novel circRNA, was proposed to be involved in the progression of PCOS. However, its role in PCOS has not been explored. In this study, the expression levels of circ_0043533 and miR-1179 in ovarian granulosa cells (OGCs) were examined by qRT-PCR analysis. Moreover, knockdown of circ_0043533 in OGC lines COV434 and KGN, respectively, the cell viability, proliferation, apoptosis, and cycle-related markers of insulin-triggered OGCs were examined by CCK-8, EdU staining, flow cytometry, and western blot assays, respectively. The interaction between circ_0043533 and miR-1179 was examined by bioinformatics, dual-luciferase assay, and RNA immunoprecipitation. Besides, effects of the miR-1179 inhibitor on cell viability and apoptosis in OGC lines with circ_0043533 knockdown were also evaluated. OGCs and insulin-treated OGCs exhibited higher circ_0043533 levels in comparison to the IOSE80 cells. Additionally, knockdown of circ_0043533 remarkably inhibited the cell viability and proliferation and promoted the apoptosis of insulin-treated COV434 and KGN cells, respectively. Meanwhile, circ_0043533 knockdown could down-regulate the Bcl-2, CDK2, and Cyclin D1 expressions, and up-regulate the Bax levels. Furthermore, we demonstrated that circ_0043533 acted as a sponge to absorb miR-1179. Interestingly, miR-1179 inhibition remarkably attenuated the effect of circ_0043533 silence on cell proliferation and apoptosis in insulin-treated COV434 and KGN cells. Taken together, this study revealed that circ_0043533 knockdown restrained the malignant progression of PCOS via targeting miR-1179. Our data suggested that circ_0043533 would serve as a novel therapeutic target for PCOS.
研究领域:
分子生物学
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妇科学
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内分泌学
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DOI
PubMed
高影响因子
JOURNAL OF FOOD BIOCHEMISTRY
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2026
·Vol. 2026
·期 1
·3245873
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IF 2.3
Caijuan Si,Long Shu,Wenjing Cao,Yuliang Feng,Hui Dong,Xingzhen He,Jingjing Yuan,Songtao Li,Feiwei Cao,Qin Zhu,Peifen Zheng
Andrographolide (Andro) is a major bioactive component of Andrographis paniculata, a medicinal and edible plant with anti-inflammatory effects. However, its effects against ulcerative colitis (UC) and circRNA-related mechanism(s) remain unclear. We established the UC mice model by administrating dextran sulfate sodium (DSS) for 14 days. Treatment with Andro for the last 7 days markedly reversed the shortened colon length, decreased the DAI, and abnormal expression of genes related to inflammation and barriers. Besides, sequencing and qRT-PCR revealed circAsxl2 was upregulated in the DSS group while downregulated after Andro treatment. Moreover, knockdown of circAsxl2 corrected gene expression related to inflammation and barriers in lipopolysaccharide-induced HT-29 cells. Then, miRNA and DEmRNAs associated with circAsxl2 were predicted and used to construct a competitive endogenous RNA (ceRNA) network, in which DEmRNAs mRNA was enriched in immune-related pathways by KEGG. Therefore, Andro possesses the potential to serve as a functional food ingredient for the prevention and management of UC.
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高影响因子
BIOSENSORS & BIOELECTRONICS
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2022
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IF 12.545
Min Yang,Hongyu Li,Xiangyang Li,Kunlun Huang,Wentao Xu,Longjiao Zhu
CircRNA, a group of circular, closed, single-stranded non-coding RNA, is an important biomarker for cancer diagnosis and prognosis. Sensitive and selective detection of circRNA can greatly facilitate the early diagnosis of human diseases. Herein, an isothermal amplification system is proposed based on dual-catalyzed hairpin self-assembly (CHA) and chameleon DNA templated silver nanoclusters (DNA-AgNCs) for the label-free ratiometric detection of circRNA. The upstream CHA1 could be specifically triggered by the analyte to form double-stranded DNA (dsDNA) products, leading to the red fluorescence of hairpin DNA-AgNCs decreased due to the destruction of the hairpin structure. The resulting dsDNA, with a trigger sequence, could then further activate downstream CHA2 to generate another dsDNA complex, which induced the other dark AgNCs to approach the G-rich sequence, thereby causing a dramatic increase in green fluorescence. Thus, by measuring the distinct variation in the ratios of green and red fluorescence intensities , the ratiometric system could be used to sensitively detect and visually distinguish the circRNA. In addition, the two-stage signal amplification in the CHA cycle endowed the detection method with ultra-sensitive detection performance, in which the detection limits for the RNA target were honed to 1 pM. Moreover, this novel method can be used as a general strategy to analyze different types of circRNA, thus showing its great potential for the detection of low abundant biomarkers in various clinical research studies.
研究领域:
生物化学
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分子生物学
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纳米技术
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癌症研究
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DOI
PubMed
高影响因子
ACS Applied Nano Materials
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2024
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IF 5.3
Meng-Fan Feng,Li-Miao Qin,Bo Sun,Xianghui Yu,Yuqing Wu
Circular RNA (circRNA) has emerged as a promising class of therapeutics and mRNA vaccines. While possessing greater stability and functionality akin to linear mRNA, circRNA still necessitates an efficient and adaptable delivery system to surmount the primary challenge of cellular uptake and membrane penetration. Inspired by the high invasiveness of the virus, in this study, the virus-like nanoparticles (VLNPs) of human papillomavirus (HPV) have been constructed as robust carriers for circRNA encapsulation and transfer through their coassembly monitoring. Notably, the functionalization of a transmembrane peptide (L17E) on the outer surface of VLNPs has led to the development of a more efficient nanocarrier, which has significantly enhanced both the transmembrane delivery and endosomal escape of circRNA. Validation studies employing VLNPs-L17E-packaged circRNA across various cell types have demonstrated notable improvements in target protein expression, ranging from 1.48- to 2.04-fold. These findings underscore the potential of HPV-VLNPs-L17E as a carrier for circRNA delivery, offering promising prospects for RNA therapy applications in the future.
研究领域:
分子生物学
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纳米医学
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治疗递送系统
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基因工程
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DOI
高影响因子
CANCER BIOTHERAPY AND RADIOPHARMACEUTICALS
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2026
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IF 2.1
Chunyang Lv,Xiaodong Fan,Gaoyuan Wang,Haijian Sun,Dexuan Chen,Tong Shen,Taiyang Zhu,Cunbing Xia,Hong Zhu,Yongkang Zhu
Background:Pancreatic cancer remains one of the most fatal tumors, with a 5-year survival rate of less than 10%, owing mostly to late-stage detection and inadequate treatment efficiency. The pressing need for novel diagnostic and therapeutic approaches has sparked interest in genetic biomarkers and ultrasound-based precision therapies. Circular RNAs (circRNAs) have recently been identified as intriguing regulatory molecules with diagnostic, prognostic, and therapeutic applications.Methods:A comprehensive study of transcriptome and clinical datasets revealed that hsa_circ_0004870 is significantly elevated in pancreatic cancer tissues and is linked with poor patient outcomes. Functional tests, including colony formation, cell counting kit-8, flow cytometry, wound healing, and Transwell invasion studies, were used to evaluate its biological roles. Bioinformatic predictions, along with dual-luciferase reporter assays, revealed the hsa_circ_0004870/miR-3124-3p/TRIM24 regulatory axis. In vivo xenograft research and immunohistochemistry analyses supported these findings. In addition, the authors developed an ultrasound-mediated biophysical modulation model to investigate the potential therapeutic control of this axis.Results:hsa_circ_0004870 was highly overexpressed in pancreatic cancer cells, which increased proliferation, migration, and invasion. It acts as a competitive endogenous RNA, sequestering miR-3124-3p, resulting in increased TRIM24 and tumorigenic behavior. In vivo, silencing hsa_circ_0004870 reduced tumor development significantly. Combining these findings with developments in ultrasound-targeted gene and molecular delivery technology suggests that ultrasound-mediated manipulation of the hsa_circ_0004870 axis might provide a precise and noninvasive therapeutic method to overcome resistance and enhance localized cancer management.Conclusions:hsa_circ_0004870 was overexpressed in pancreatic cancer cells, resulting in enhanced proliferation, migration, and invasion. It works as a competitive endogenous RNA, sequestering miR-3124-3p, leading to enhanced TRIM24 and tumorigenic behavior. In vivo, suppressing hsa_circ_0004870 dramatically decreased tumor growth. Combining these findings with advances in ultrasound-targeted gene and molecular delivery technology, it appears that ultrasound-mediated manipulation of the hsa_circ_0004870 axis could provide a precise and noninvasive therapeutic method for overcoming resistance and improving localized cancer management.
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高影响因子
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