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Xu J, Cui X, Wang L, Chen G, Ji S, Zhao S, Wang H, Luo Z, Zeng A, Fu Q. DNA-functionalized MOF fluorescent probes for the enzyme-free and pretreatment-free detection of MicroRNA in serum. Talanta 2024; 275:126083. [PMID: 38636442 DOI: 10.1016/j.talanta.2024.126083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 03/21/2024] [Accepted: 04/08/2024] [Indexed: 04/20/2024]
Abstract
MicroRNA (miRNA) is a promising biomarker that plays an important role in various biomedical applications, especially in cancer diagnosis. However, the current miRNA detection technology has inherent limitations such as complex operation, expensive testing cost and excessive detection time. In this study, a dual signal amplification biosensor based on DNA-functionalized metal-organic frameworks (MOFs) fluorescent probes, MFPBiosensor, was established for the enzyme-free and pretreatment-free detection of the colon cancer (CC) marker miR-23a. DNA-functionalized MOFs NH2-MIL-53(Al) (DNA@MOFs) were synthesized as fluorescent probes with specific recognition functions. A single DNA@MOF carries a large number of fluorescent ligands 2-aminoterephthalic acid (NH2-H2BDC), which can generate strong fluorescence signals after alkaline hydrolysis. Combined with catalyzed hairpin assembly (CHA), an efficient isothermal amplification technique, the dual signal enhancement strategy reduced matrix interference and sensitized the signal response. The established MFPBiosensor successfully detected extremely low levels of miRNA in complex biological samples with acceptable sensitivity and specificity. With a single detection cost of $0.583 and a test time of 50 min, the excellent inexpensive and rapid advantage of the MFPBiosensor is highlighted. More importantly, the subtle design enables the MFPBiosensor to achieve convenient batch detection, where miRNA in serum can be directly detected without any pretreatment process or enzyme. In conclusion, MFPBiosensor is a promising biosensor with substantial potential for commercial miRNA detection and clinical diagnostic applications of CC.
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Affiliation(s)
- Jiameng Xu
- Department of Pharmaceutical Analysis, School of Pharmacy, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Xia Cui
- Department of Pharmacy, Shaanxi Provincial People's Hospital, Xi'an, 710068, China
| | - Lu Wang
- School of Medicine, Xizang Minzu University, Xianyang, 712082, China
| | - Guoning Chen
- Key Laboratory of Protection, Development and Utilization of Medicinal Resources in Liupanshan Area, Ministry of Education, School of Pharmacy, Ningxia Medical University, Yinchuan, 750004, China
| | - Shuhua Ji
- Department of Pharmaceutical Analysis, School of Pharmacy, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Shiwei Zhao
- Department of Pharmaceutical Analysis, School of Pharmacy, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Hui Wang
- Department of Pharmacy, Shaanxi Provincial People's Hospital, Xi'an, 710068, China
| | - Zhimin Luo
- Department of Pharmaceutical Analysis, School of Pharmacy, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Aiguo Zeng
- Department of Pharmaceutical Analysis, School of Pharmacy, Xi'an Jiaotong University, Xi'an, 710061, China.
| | - Qiang Fu
- Department of Pharmaceutical Analysis, School of Pharmacy, Xi'an Jiaotong University, Xi'an, 710061, China; Department of Pharmaceutical Analysis, College of Pharmacy, Shenzhen Technology University, Shenzhen, 518118, China.
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Peng Y, Xiao S, Zuo W, Xie Y, Xiao Y. Potential diagnostic value of miRNAs in sexually transmitted infections. Gene 2024; 895:147992. [PMID: 37977319 DOI: 10.1016/j.gene.2023.147992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 11/03/2023] [Accepted: 11/13/2023] [Indexed: 11/19/2023]
Abstract
MiRNAs are small endogenous non-coding RNAs that have been demonstrated to be involved in post-transcriptional gene silencing, regulating a number of metabolic functions in the human body, including immune response, cellular physiology, organ development, angiogenesis, signaling, and other aspects. As popular molecules that have been studied in previous years, given their extensive regulatory functions, miRNAs hold considerable promise as non-invasive biomarkers. Sexually transmitted infections(STIs) are still widespread and have an adverse effect on individuals, communities, and society worldwide. miRNAs in the regulatory networks are generally involved in their molecular processes of formation and development. In this review, we discuss the value of miRNAs for the diagnosis of STIs.
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Affiliation(s)
- Yunchi Peng
- Department of Clinical Laboratory, The Second Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang 421001, China
| | - Shuangwen Xiao
- Department of Clinical Laboratory, The Second Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang 421001, China
| | - Wei Zuo
- Department of Clinical Laboratory, The Second Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang 421001, China
| | - Yafeng Xie
- Department of Clinical Laboratory, The Second Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang 421001, China
| | - Yongjian Xiao
- Department of Clinical Laboratory, The Second Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang 421001, China.
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Roh YH, Lee CY, Lee S, Kim H, Ly A, Castro CM, Cheon J, Lee J, Lee H. CRISPR-Enhanced Hydrogel Microparticles for Multiplexed Detection of Nucleic Acids. Adv Sci (Weinh) 2023; 10:e2206872. [PMID: 36725305 PMCID: PMC10074104 DOI: 10.1002/advs.202206872] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 01/11/2023] [Indexed: 06/18/2023]
Abstract
CRISPR/Cas systems offer a powerful sensing mechanism to transduce sequence-specific information into amplified analytical signals. However, performing multiplexed CRISPR/Cas assays remains challenging and often requires complex approaches for multiplexed assays. Here, a hydrogel-based CRISPR/Cas12 system termed CLAMP (Cas-Loaded Annotated Micro-Particles) is described. The approach compartmentalizes the CRISPR/Cas reaction in spatially-encoded hydrogel microparticles (HMPs). Each HMP is identifiable by its face code and becomes fluorescent when target DNA is present. The assay is further streamlined by capturing HMPs inside a microfluidic device; the captured particles are then automatically recognized by a machine-learning algorithm. The CLAMP assay is fast, highly sensitive (attomolar detection limits with preamplification), and capable of multiplexing in a single-pot assay. As a proof-of-concept clinical application, CLAMP is applied to detect nucleic acid targets of human papillomavirus in cervical brushing samples.
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Affiliation(s)
- Yoon Ho Roh
- Institute for Basic Science (IBS)Center for NanomedicineSeoul03722Republic of Korea
- Graduate Program of Nano Biomedical Engineering (NanoBME)Advanced Science Institute Yonsei UniversitySeoul03722Republic of Korea
| | - Chang Yeol Lee
- Institute for Basic Science (IBS)Center for NanomedicineSeoul03722Republic of Korea
- Center for Systems BiologyMassachusetts General Hospital Research InstituteBostonMA02114USA
| | - Sujin Lee
- Institute for Basic Science (IBS)Center for NanomedicineSeoul03722Republic of Korea
- Graduate Program of Nano Biomedical Engineering (NanoBME)Advanced Science Institute Yonsei UniversitySeoul03722Republic of Korea
| | - Hyunho Kim
- Center for Systems BiologyMassachusetts General Hospital Research InstituteBostonMA02114USA
- Department of RadiologyMassachusetts General HospitalHarvard Medical SchoolBostonMA02114USA
| | - Amy Ly
- Department of PathologyMassachusetts General HospitalHarvard Medical SchoolBostonMA02114USA
| | - Cesar M. Castro
- Center for Systems BiologyMassachusetts General Hospital Research InstituteBostonMA02114USA
- Department of MedicineMassachusetts General HospitalHarvard Medical SchoolBostonMA02114USA
| | - Jinwoo Cheon
- Institute for Basic Science (IBS)Center for NanomedicineSeoul03722Republic of Korea
- Graduate Program of Nano Biomedical Engineering (NanoBME)Advanced Science Institute Yonsei UniversitySeoul03722Republic of Korea
- Department of ChemistryYonsei UniversitySeoul03722Republic of Korea
| | - Jae‐Hyun Lee
- Institute for Basic Science (IBS)Center for NanomedicineSeoul03722Republic of Korea
- Graduate Program of Nano Biomedical Engineering (NanoBME)Advanced Science Institute Yonsei UniversitySeoul03722Republic of Korea
| | - Hakho Lee
- Institute for Basic Science (IBS)Center for NanomedicineSeoul03722Republic of Korea
- Graduate Program of Nano Biomedical Engineering (NanoBME)Advanced Science Institute Yonsei UniversitySeoul03722Republic of Korea
- Center for Systems BiologyMassachusetts General Hospital Research InstituteBostonMA02114USA
- Department of RadiologyMassachusetts General HospitalHarvard Medical SchoolBostonMA02114USA
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Masterson AN, Chowdhury NN, Fang Y, Yip-Schneider MT, Hati S, Gupta P, Cao S, Wu H, Schmidt CM, Fishel ML, Sardar R. Amplification-Free, High-Throughput Nanoplasmonic Quantification of Circulating MicroRNAs in Unprocessed Plasma Microsamples for Earlier Pancreatic Cancer Detection. ACS Sens 2023; 8:1085-1100. [PMID: 36853001 DOI: 10.1021/acssensors.2c02105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is a deadly malignancy that is often detected at an advanced stage. Earlier diagnosis of PDAC is key to reducing mortality. Circulating biomarkers such as microRNAs are gaining interest, but existing technologies require large sample volumes, amplification steps, extensive biofluid processing, lack sensitivity, and are low-throughput. Here, we present an advanced nanoplasmonic sensor for the highly sensitive, amplification-free detection and quantification of microRNAs (microRNA-10b, microRNA-let7a) from unprocessed plasma microsamples. The sensor construct utilizes uniquely designed -ssDNA receptors attached to gold triangular nanoprisms, which display unique localized surface plasmon resonance (LSPR) properties, in a multiwell plate format. The formation of -ssDNA/microRNA duplex controls the nanostructure-biomolecule interfacial electronic interactions to promote the charge transfer/exciton delocalization processes and enhance the LSPR responses to achieve attomolar (10-18 M) limit of detection (LOD) in human plasma. This improve LOD allows the fabrication of a high-throughput assay in a 384-well plate format. The performance of nanoplasmonic sensors for microRNA detection was further assessed by comparing with the qRT-PCR assay of 15 PDAC patient plasma samples that shows a positive correlation between these two assays with the Pearson correlation coefficient value >0.86. Evaluation of >170 clinical samples reveals that oncogenic microRNA-10b and tumor suppressor microRNA-let7a levels can individually differentiate PDAC from chronic pancreatitis and normal controls with >94% sensitivity and >94% specificity at a 95% confidence interval (CI). Furthermore, combining both oncogenic and tumor suppressor microRNA levels significantly improves differentiation of PDAC stages I and II versus III and IV with >91% and 87% sensitivity and specificity, respectively, in comparison to the sensitivity and specificity values for individual microRNAs. Moreover, we show that the level of microRNAs varies substantially in pre- and post-surgery PDAC patients (n = 75). Taken together, this ultrasensitive nanoplasmonic sensor with excellent sensitivity and specificity is capable of assaying multiple biomarkers simultaneously and may facilitate early detection of PDAC to improve patient care.
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Affiliation(s)
- Adrianna N Masterson
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University, Indianapolis, Indiana 46202, United States
| | - Nayela N Chowdhury
- Department of Pediatrics, Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, Indiana 46202, United States
- Indiana University Melvin and Bren Simon Comprehensive Cancer Center, Indianapolis, Indiana 46202, United States
| | - Yue Fang
- Department of Biostatistics and Health Data Science, Indiana University School of Medicine, Indianapolis, Indiana 46202, United States
| | - Michele T Yip-Schneider
- Department of Surgery, Indiana University School of Medicine, Indianapolis, Indiana 46202, United States
| | - Sumon Hati
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University, Indianapolis, Indiana 46202, United States
| | - Prashant Gupta
- Department of Mechanical Engineering, Washington University, St. Louis, Missouri 63130, United States
| | - Sha Cao
- Department of Biostatistics and Health Data Science, Indiana University School of Medicine, Indianapolis, Indiana 46202, United States
| | - Huangbing Wu
- Department of Surgery, Indiana University School of Medicine, Indianapolis, Indiana 46202, United States
| | - C Max Schmidt
- Indiana University Melvin and Bren Simon Comprehensive Cancer Center, Indianapolis, Indiana 46202, United States
- Department of Surgery, Indiana University School of Medicine, Indianapolis, Indiana 46202, United States
| | - Melissa L Fishel
- Department of Pediatrics, Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, Indiana 46202, United States
- Indiana University Melvin and Bren Simon Comprehensive Cancer Center, Indianapolis, Indiana 46202, United States
- Department of Pharmacology and Toxicology, Indiana University School of Medicine, Indianapolis, Indiana 46202, United States
| | - Rajesh Sardar
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University, Indianapolis, Indiana 46202, United States
- Indiana University Melvin and Bren Simon Comprehensive Cancer Center, Indianapolis, Indiana 46202, United States
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5
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Al Sulaiman D, Juthani N, Doyle PS. Quantitative and Multiplex Detection of Extracellular Vesicle-Derived MicroRNA via Rolling Circle Amplification within Encoded Hydrogel Microparticles. Adv Healthc Mater 2022; 11:e2102332. [PMID: 35029040 PMCID: PMC9117410 DOI: 10.1002/adhm.202102332] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 01/06/2022] [Indexed: 12/11/2022]
Abstract
Extracellular vesicle-derived microRNA (EV-miRNA) represent a promising cancer biomarker for disease diagnosis and monitoring. However, existing techniques to detect EV-miRNA rely on complex, bias-prone strategies, and preprocessing steps, making absolute quantification highly challenging. This work demonstrates the development and application of a method for quantitative and multiplex detection of EV-miRNA, via rolling circle amplification within encoded hydrogel particles. By a one-pot extracellular vesicle lysis and microRNA capture step, the bias and losses associated with standard RNA extraction techniques is avoided. The system offers a large dynamic range (3 orders of magnitude), ease of multiplexing, and a limit of detection down to 2.3 zmol (46 × 10-18 m), demonstrating its utility in clinical applications based on liquid biopsy tests. Furthermore, orthogonal measurements of EV concentrations coupled with the direct, absolute quantification of miRNA in biological samples results in quantitative measurements of miRNA copy numbers per volume sample, and per extracellular vesicle.
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Affiliation(s)
- Dana Al Sulaiman
- Department of Chemical Engineering Massachusetts Institute of Technology Cambridge MA 02142 USA
- Division of Physical Science and Engineering King Abdullah University of Science and Technology Thuwal 23955‐6900 Kingdom of Saudi Arabia
| | - Nidhi Juthani
- Department of Chemical Engineering Massachusetts Institute of Technology Cambridge MA 02142 USA
| | - Patrick S. Doyle
- Department of Chemical Engineering Massachusetts Institute of Technology Cambridge MA 02142 USA
- Harvard Medical School Initiative for RNA Medicine Boston MA 02115 USA
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Bae SW, Kim J, Kwon S. Recent Advances in Polymer Additive Engineering for Diagnostic and Therapeutic Hydrogels. Int J Mol Sci 2022; 23:ijms23062955. [PMID: 35328375 PMCID: PMC8955662 DOI: 10.3390/ijms23062955] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 03/03/2022] [Accepted: 03/03/2022] [Indexed: 12/13/2022] Open
Abstract
Hydrogels are hydrophilic polymer materials that provide a wide range of physicochemical properties as well as are highly biocompatible. Biomedical researchers are adapting these materials for the ever-increasing range of design options and potential applications in diagnostics and therapeutics. Along with innovative hydrogel polymer backbone developments, designing polymer additives for these backbones has been a major contributor to the field, especially for expanding the functionality spectrum of hydrogels. For the past decade, researchers invented numerous hydrogel functionalities that emerge from the rational incorporation of additives such as nucleic acids, proteins, cells, and inorganic nanomaterials. Cases of successful commercialization of such functional hydrogels are being reported, thus driving more translational research with hydrogels. Among the many hydrogels, here we reviewed recently reported functional hydrogels incorporated with polymer additives. We focused on those that have potential in translational medicine applications which range from diagnostic sensors as well as assay and drug screening to therapeutic actuators as well as drug delivery and implant. We discussed the growing trend of facile point-of-care diagnostics and integrated smart platforms. Additionally, special emphasis was given to emerging bioinformatics functionalities stemming from the information technology field, such as DNA data storage and anti-counterfeiting strategies. We anticipate that these translational purpose-driven polymer additive research studies will continue to advance the field of functional hydrogel engineering.
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Affiliation(s)
- Sang-Wook Bae
- Bio-MAX/N-Bio, Seoul National University, Daehak-dong, Gwanak-gu, Seoul 08826, Korea;
| | - Jiyun Kim
- School of Materials Science and Engineering, Ulsan National Institute of Science and Technology, Ulsan 44919, Korea
- Center for Multidimensional Programmable Matter, Ulsan 44919, Korea
- Correspondence: (J.K.); (S.K.)
| | - Sunghoon Kwon
- Department of Electrical and Computer Engineering, Seoul National University, Daehak-dong, Gwanak-gu, Seoul 08826, Korea
- Correspondence: (J.K.); (S.K.)
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Zhang WC, Skiados N, Aftab F, Moreno C, Silva L, Corbilla PJA, Asara JM, Hata AN, Slack FJ. MicroRNA-21 guide and passenger strand regulation of adenylosuccinate lyase-mediated purine metabolism promotes transition to an EGFR-TKI-tolerant persister state. Cancer Gene Ther 2022; 29:1878-94. [PMID: 35840668 DOI: 10.1038/s41417-022-00504-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 06/15/2022] [Accepted: 06/28/2022] [Indexed: 01/25/2023]
Abstract
In EGFR-mutant lung cancer, drug-tolerant persister cells (DTPCs) show prolonged survival when receiving EGFR tyrosine kinase inhibitor (TKI) treatments. They are a likely source of drug resistance, but little is known about how these cells tolerate drugs. Ribonucleic acids (RNAs) molecules control cell growth and stress responses. Nucleic acid metabolism provides metabolites, such as purines, supporting RNA synthesis and downstream functions. Recently, noncoding RNAs (ncRNAs), such as microRNAs (miRNAs), have received attention due to their capacity to repress gene expression via inhibitory binding to downstream messenger RNAs (mRNAs). Here, our study links miRNA expression to purine metabolism and drug tolerance. MiR-21-5p (guide strand) is a commonly upregulated miRNA in disease states, including cancer and drug resistance. However, the expression and function of miR-21-3p (passenger strand) are not well understood. We found that upregulation of miR-21-5p and miR-21-3p tune purine metabolism leading to increased drug tolerance. Metabolomics data demonstrated that purine metabolism was the top pathway in the DTPCs compared with the parental cells. The changes in purine metabolites in the DTPCs were partially rescued by targeting miR-21. Analysis of protein levels in the DTPCs showed that reduced expression of adenylosuccinate lyase (ADSL) was reversed after the miR-21 knockdown. ADSL is an essential enzyme in the de novo purine biosynthesis pathway by converting succino-5-aminoimidazole-4-carboxamide riboside (succino-AICAR or SAICAR) to AICAR (or acadesine) as well as adenylosuccinate to adenosine monophosphate (AMP). In the DTPCs, miR-21-5p and miR-21-3p repress ADSL expression. The levels of top decreased metabolite in the DTPCs, AICAR was reversed when miR-21 was blocked. AICAR induced oxidative stress, evidenced by increased reactive oxygen species (ROS) and reduced expression of nuclear factor erythroid-2-related factor 2 (NRF2). Concurrently, miR-21 knockdown induced ROS generation. Therapeutically, a combination of AICAR and osimertinib increased ROS levels and decreased osimertinib-induced NRF2 expression. In a MIR21 knockout mouse model, MIR21 loss-of-function led to increased purine metabolites but reduced ROS scavenging capacity in lung tissues in physiological conditions. Our data has established a link between ncRNAs, purine metabolism, and the redox imbalance pathway. This discovery will increase knowledge of the complexity of the regulatory RNA network and potentially enable novel therapeutic options for drug-resistant patients.
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Jang W, Kim J, Mun SJ, Kim SM, Bong KW. Highly Magnetized Encoded Hydrogel Microparticles with Enhanced Rinsing Capabilities for Efficient microRNA Detection. Biomedicines 2021; 9:848. [PMID: 34356912 DOI: 10.3390/biomedicines9070848] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 07/16/2021] [Accepted: 07/16/2021] [Indexed: 11/16/2022] Open
Abstract
Encoded hydrogel microparticles mounting DNA probes are powerful tools for high-performance microRNA (miRNA) detection in terms of sensitivity, specificity, and multiplex detection capability. However, several particle rinsing steps in the assay procedure present challenges for rapid and efficient detection. To overcome this limitation, we encapsulated dense magnetic nanoparticles to reduce the rinsing steps and duration via magnetic separation. A large number of magnetic nanoparticles were encapsulated into hydrogel microparticles based on a discontinuous dewetting technique combined with degassed micromolding lithography. In addition, we attached DNA probes targeting three types of miRNAs related to preeclampsia to magnetically encoded hydrogel microparticles by post-synthesis conjugation and achieved sensitivity comparable to that of conventional nonmagnetic encoded hydrogel microparticles. To demonstrate the multiplex capability of magnetically encoded hydrogel microparticles while maintaining the advantages of the simplified rinsing process when addressing multiple samples, we conducted a triplex detection of preeclampsia-related miRNAs. In conclusion, the introduction of magnetically encoded hydrogel microparticles not only allowed efficient miRNA detection but also provided comparable sensitivity and multiplexed detectability to conventional nonmagnetic encoded hydrogel microparticles.
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Abstract
MicroRNA detection is currently a crucial analytical chemistry challenge: almost 2000 papers were referenced in PubMed in 2018 and 2019 for the keywords "miRNA detection method". MicroRNAs are potential biomarkers for multiple diseases including cancers, neurodegenerative and cardiovascular diseases. Since miRNAs are stably released in bodily fluids, they are of prime interest for the development of non-invasive diagnosis methods, such as liquid biopsies. Their detection is however challenging, as high levels of sensitivity, specificity and robustness are required. The analysis also needs to be quantitative, since the aim is to detect miRNA concentration changes. Moreover, a high multiplexing capability is also of crucial importance, since the clinical potential of miRNAs probably lays in our ability to perform parallel mapping of multiple miRNA concentrations and recognize typical disease signature from this profile. A plethora of biochemical innovative detection methods have been reported recently and some of them provide new solutions to the problem of sensitive multiplex detection. In this review, we propose to analyze in particular the new developments in multiplexed approaches to miRNA detection. The main aspects of these methods (including sensitivity and specificity) will be analyzed, with a particular focus on the demonstrated multiplexing capability and potential of each of these methods.
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Affiliation(s)
- Thomas Jet
- Centre de Recherche des Cordeliers, INSERM, Sorbonne Université, Université de Paris, CNRS SNC5096, Equipe Labellisée Ligue Nationale Contre le Cancer, F-75006 Paris, France.
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Al Sulaiman D, Shapiro SJ, Gomez-Marquez J, Doyle PS. High-Resolution Patterning of Hydrogel Sensing Motifs within Fibrous Substrates for Sensitive and Multiplexed Detection of Biomarkers. ACS Sens 2021; 6:203-211. [PMID: 33351603 DOI: 10.1021/acssensors.0c02121] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
There has been an increasing and urgent demand to develop nucleic acid bioassays which not only offer high analytical performance but which are also amenable with point-of-care testing. Hydrogels present a versatile class of materials with biocompatible antifouling properties and the ability to be engineered for a range of advanced sensing applications. Fibrous substrates like nitrocellulose offer low-cost and durable platforms to run complex bioassays while enabling portability and ease of handling. We demonstrate herein the ability to synergistically combine these two materials into a portable biosensing platform by leveraging projection lithography. We demonstrate the direct polymerization of hydrogel sensing motifs within a range of fibrous substrates with precise control over their shape, size, location, and functionality. Spatial encoding of the hydrogel motifs enables the multiplex detection of multiple biomarkers on the same test. As a proof-of-concept, we apply the platform to the detection of microRNA, an emerging class of circulating biomarkers with promising potential for early diagnosis and monitoring of cancer. The assay offers a large dynamic range (over three orders of magnitude), high sensitivity (limit of detection of 2.5 amol), as well as versatility and ease of handling. Finally, the bioassay is validated using real biological samples, namely, total RNA extracted from the sera of late-stage breast cancer patients, demonstrating its utility and compatibility with clinical biosensing applications.
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Affiliation(s)
- Dana Al Sulaiman
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Sarah J. Shapiro
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Jose Gomez-Marquez
- Little Devices Lab, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Patrick S. Doyle
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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11
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Abstract
We report a platform utilizing a reporter enzyme, which produces a chromogenic indigo precipitate that preferentially localizes within a hydrogel microparticle. The 3D network of the hydrogel maintains the rapid target binding kinetics found in solution, while multiplexed target detection is achieved through shape-encoding of the particles. Moreover, the precipitate-laden hydrogels can be imaged with a simple phone camera setup. We used this system to detect microRNA (miRNA) down to 0.22 fmol. We then showed the compatibility of this system with real samples by performing multiplexed miRNA measurements from total RNA from matched colon cancer and normal adjacent tissue.
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Affiliation(s)
- Nidhi Juthani
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.
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12
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Masterson AN, Liyanage T, Kaimakliotis H, Gholami Derami H, Deiss F, Sardar R. Bottom-Up Fabrication of Plasmonic Nanoantenna-Based High-throughput Multiplexing Biosensors for Ultrasensitive Detection of microRNAs Directly from Cancer Patients' Plasma. Anal Chem 2020; 92:9295-9304. [PMID: 32469524 DOI: 10.1021/acs.analchem.0c01639] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
There is an unmet need in clinical point-of-care (POC) cancer diagnostics for early state disease detection, which would greatly increase patient survival rates. Currently available analytical techniques for early stage cancer diagnosis do not meet the requirements for POC of a clinical setting. They are unable to provide the high demand of multiplexing, high-throughput, and ultrasensitive detection of biomarkers directly from low volume patient samples ("liquid biopsy"). To overcome these current technological bottle-necks, herein we present, for the first time, a bottom-up fabrication strategy to develop plasmonic nanoantenna-based sensors that utilize the unique localized surface plasmon resonance (LSPR) properties of chemically synthesized gold nanostructures, gold triangular nanoprisms (Au TNPs), gold nanorods (Au NRs), and gold spherical nanoparticles (Au SNPs). Our Au TNPs, NRs, and SNPs display refractive index unit (RIU) sensitivities of 318, 225, and 135 nm/RIU respectively. Based on the RIU results, we developed plasmonic nanoantenna-based multiplexing and high-throughput biosensors for the ultrasensitive assay of microRNAs. MicroRNAs are directly linked with cancer development, progression, and metastasis, thus they hold promise as next generation biomarkers for cancer diagnosis and prognosis. The developed biosensors are capable of assaying five different types of microRNAs at an attomolar detection limit. These sets of microRNAs include both oncogenic and tumor suppressor microRNAs. To demonstrate the efficiency as a POC cancer diagnostic tool, we analyzed the plasma of 20-bladder cancer patients without any sample processing steps. Importantly, our liquid biopsy-based biosensing approach is capable of differentiating healthy from early ("non-metastatic") and late ("metastatic") stage cancer with a p value <0.0001. Further, receiver operating characteristic analysis shows that our biosensing approach is highly specific, with an area under the curve of 1.0. Additionally, our plasmonic nanoantenna-based biosensors are regenerative, allowing multiple measurements using the same biosensors, which is essential in low- and middle-income countries. Taken together, our multiplexing and high-throughput biosensors have the unmatched potential to advance POC diagnostics and meet global needs for early stage detection of cancer and other diseases (e.g., infectious, autoimmune, and neurogenerative diseases).
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Affiliation(s)
- Adrianna N Masterson
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis, 402 N Blackford Street, Indianapolis, Indiana 46202, United States
| | - Thakshila Liyanage
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis, 402 N Blackford Street, Indianapolis, Indiana 46202, United States
| | - Hristos Kaimakliotis
- Department of Urology, Indiana University School of Medicine, 535 N. Barnhill Dr. Indianapolis, Indiana 46202, United States
| | - Hamed Gholami Derami
- Department of Mechanical Engineering and Materials Science, Institute of Materials Science and Engineering, Washington University in St. Louis, Saint Louis, Missouri 63130, United States
| | - Frédérique Deiss
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis, 402 N Blackford Street, Indianapolis, Indiana 46202, United States
| | - Rajesh Sardar
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis, 402 N Blackford Street, Indianapolis, Indiana 46202, United States.,Integrated Nanosystems Development Institute, Indiana University-Purdue University Indianapolis, 723 W. Michigan Street, Indianapolis, Indiana 46202, United States
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13
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Abstract
The drive for a simultaneous analysis of multiple targets with excellent accuracy and efficiency, which is often required in both basic biomedical research and clinical applications, demands the development of multiplexed bioassays with desired throughput. With the development of nanotechnologies, innovative multiplex optical bioassays have been achieved. Nanomaterials exhibit unique physical and chemical properties such as easily tunable size, large surface-to-volume ratio, excellent catalysis and the desired signal transduction mechanism, which makes them excellent candidates for the fabrication of novel optical nanoprobes. This mini review summarizes nanomaterial-based optical multiplex sensors from the last 5 years. Specific optical techniques covered in this review are fluorescence, surface-enhanced Raman scattering (SERS), localized surface plasmon resonance (LSPR), chemiluminescence (CL), and the multimodality with fundamentals and examples.
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Affiliation(s)
- Xiaojing Pei
- College of Chemistry and Materials Engineering, Beijing Technology and Business University, Beijing 100048, P. R. China
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14
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Nagarajan MB, Tentori AM, Zhang WC, Slack FJ, Doyle PS. Spatially resolved and multiplexed MicroRNA quantification from tissue using nanoliter well arrays. Microsyst Nanoeng 2020; 6:51. [PMID: 32419951 PMCID: PMC7211184 DOI: 10.1038/s41378-020-0169-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 04/08/2020] [Accepted: 04/09/2020] [Indexed: 05/27/2023]
Abstract
Spatially resolved gene expression patterns are emerging as a key component of medical studies, including companion diagnostics, but technologies for quantification and multiplexing are limited. We present a method to perform spatially resolved and multiplexed microRNA (miRNA) measurements from formalin-fixed, paraffin-embedded (FFPE) tissue. Using nanoliter well arrays to pixelate the tissue section and photopatterned hydrogels to quantify miRNA, we identified differentially expressed miRNAs in tumors from a genetically engineered mouse model for non-small cell lung cancer (K-rasLSL-G12D/+; p53fl/fl). This technology could be used to quantify heterogeneities in tissue samples and lead to informed, biomarker-based diagnostics.
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Affiliation(s)
- Maxwell B. Nagarajan
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139 USA
| | - Augusto M. Tentori
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139 USA
| | - Wen Cai Zhang
- HMS Initiative for RNA Medicine, Department of Pathology, Harvard Medical School, Beth Israel Deaconess Medical Center, Boston, MA 02215 USA
| | - Frank J. Slack
- HMS Initiative for RNA Medicine, Department of Pathology, Harvard Medical School, Beth Israel Deaconess Medical Center, Boston, MA 02215 USA
| | - Patrick S. Doyle
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139 USA
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15
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Gines G, Menezes R, Xiao W, Rondelez Y, Taly V. Emerging isothermal amplification technologies for microRNA biosensing: Applications to liquid biopsies. Mol Aspects Med 2020; 72:100832. [DOI: 10.1016/j.mam.2019.11.002] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2019] [Revised: 11/06/2019] [Accepted: 11/10/2019] [Indexed: 02/07/2023]
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16
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Tang Y, He X, Yuan R, Liu X, Zhao Y, Wang T, Chen H, Feng X. Logic-signal-based multiplex detection of MiRNAs with high tension hybridization and multiple signal amplification. Analyst 2020; 145:4314-4320. [PMID: 32400825 DOI: 10.1039/d0an00550a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A multiplex miRNA detection scheme with simultaneous multiple signal output by single excitation has been reported.
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Affiliation(s)
- Yaqin Tang
- Department of Pharmaceutical Sciences
- Chongqing University
- Chongqing
- China
| | - Xiao He
- Department of Pharmaceutical Sciences
- Chongqing University
- Chongqing
- China
| | - Rui Yuan
- Chongqing University Cancer Hospital
- Chongqing Cancer Hospital
- Chongqing
- China
| | - Xingming Liu
- Chongqing University Cancer Hospital
- Chongqing Cancer Hospital
- Chongqing
- China
| | - Yi Zhao
- Chongqing University Cancer Hospital
- Chongqing Cancer Hospital
- Chongqing
- China
| | - Tingting Wang
- Biochemistry and Molecular Biology Laboratory
- Experimental Teaching and Management Center
- Chongqing Medical University
- Chongqing
- China
| | - Hui Chen
- Department of Pharmaceutical Sciences
- Chongqing University
- Chongqing
- China
| | - Xuli Feng
- Department of Pharmaceutical Sciences
- Chongqing University
- Chongqing
- China
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17
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Zhang WC. microRNAs Tune Oxidative Stress in Cancer Therapeutic Tolerance and Resistance. Int J Mol Sci 2019; 20:E6094. [PMID: 31816897 DOI: 10.3390/ijms20236094] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 11/26/2019] [Accepted: 11/27/2019] [Indexed: 02/07/2023] Open
Abstract
Relapsed disease following first-line therapy remains one of the central problems in cancer management, including chemotherapy, radiotherapy, growth factor receptor-based targeted therapy, and immune checkpoint-based immunotherapy. Cancer cells develop therapeutic resistance through both intrinsic and extrinsic mechanisms including cellular heterogeneity, drug tolerance, bypassing alternative signaling pathways, as well as the acquisition of new genetic mutations. Reactive oxygen species (ROSs) are byproducts originated from cellular oxidative metabolism. Recent discoveries have shown that a disabled antioxidant program leads to therapeutic resistance in several types of cancers. ROSs are finely tuned by dysregulated microRNAs, and vice versa. However, mechanisms of a crosstalk between ROSs and microRNAs in regulating therapeutic resistance are not clear. Here, we summarize how the microRNA-ROS network modulates cancer therapeutic tolerance and resistance and direct new vulnerable targets against drug tolerance and resistance for future applications.
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18
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Manickam P, Vashist A, Madhu S, Sadasivam M, Sakthivel A, Kaushik A, Nair M. Gold nanocubes embedded biocompatible hybrid hydrogels for electrochemical detection of H 2O 2. Bioelectrochemistry 2019; 131:107373. [PMID: 31525638 DOI: 10.1016/j.bioelechem.2019.107373] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Revised: 09/05/2019] [Accepted: 09/05/2019] [Indexed: 10/26/2022]
Abstract
Smart electrochemical biosensors have emerged as a promising alternative analytical diagnostic tool in recent clinical practice. However, improvement in the biocompatibility and electrical conductivity of the biosensor matrix and the immobilization of various bioactive molecules such as enzymes still remain challenging. The present research reports the synthesis of a biocompatible hydrogel network and its integration with gold nanocubes (AuNCs) for developing a novel biosensor with improved functionality. The interpenetrating hydrogel network consist of biopolymers developed using graft co-polymerization of β-cyclodextrin (β-CD) and chitosan (CS). The novelty of this work is in integrating the CS-g-β-CD hydrogel network with conductive AuNCs for improving hydrogel conductivity, biosensor sensitivity and use of the material for a biocompatible sensor. The present protocol advances the state of the art for the utilization of biopolymeric hydrogels system in synergy with an enzymatic biosensing protocol for exclusively detecting hydrogen peroxide (H2O2). Immobilization of the mitochondrial protein, cytochrome c (cyt c) into the hydrogel nanocomposite matrix was performed via thiol cross-linking. This organic-inorganic hybrid nanocomposite hydrogel matrix exhibited high biocompatibility (RAW 264.7 and N2a cell lines), improved electrical conductivity to attain high sensitivity (1.2 mA mM-1 cm-2) and a low detection limit (15 × 10-9 M) for H2O2.
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Affiliation(s)
- Pandiaraj Manickam
- Electrodics and Electrocatalysis Division, CSIR-Central Electrochemical Research Institute, Karaikudi 630 003, Tamil Nadu, India.
| | - Arti Vashist
- Department of Immunology & Nano-Medicine, Institute of NeuroImmune Pharmacology, Center for Personalized Nanomedicine, Herbert Wertheim College of Medicine, Florida International University, Miami, FL 33199, USA
| | - Sekar Madhu
- Department of Nanoscience & Technology, Bharathiar University, Coimbatore 641 046, India
| | - Mohanraj Sadasivam
- Electrodics and Electrocatalysis Division, CSIR-Central Electrochemical Research Institute, Karaikudi 630 003, Tamil Nadu, India
| | - Arunkumar Sakthivel
- Electrodics and Electrocatalysis Division, CSIR-Central Electrochemical Research Institute, Karaikudi 630 003, Tamil Nadu, India; Academy of Scientific and Innovative Research, Ghaziabad 201 002, Uttar Pradesh, India
| | - Ajeet Kaushik
- Department of Natural Sciences, Division of Sciences, Art & Mathematics, Florida Polytechnic University, Lakeland, FL 33805, USA
| | - Madhavan Nair
- Department of Immunology & Nano-Medicine, Institute of NeuroImmune Pharmacology, Center for Personalized Nanomedicine, Herbert Wertheim College of Medicine, Florida International University, Miami, FL 33199, USA
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