Cancer protein biomarker discovery based on nucleic acid aptamers

Xiong, Hongjie; Yan, Jun; Cai, Shundong; He, Qunye; Peng, Dongming; Liu, Zhenbao; Liu, Yanfei

doi:10.1016/j.ijbiomac.2019.03.165

Cited by 66 publications

(30 citation statements)

References 99 publications

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“…Additionally, the detection performance and safety of MOF-based biosensing need to be further verified in vivo due to the complex in vivo environment, and the long-term biological toxicity of metal ion in MOF need to be further evaluated in vivo ( Chen et al, 2019 ), some biocompatible metal ions, such as Fe 2+ /Fe 3+ , Ni 3+ , Zr 4+ , Mn 2+ , Mg 2+ , Ca 2+ , Zn 2+ , or biomaterials, such as liposomal ( Dunne et al, 2019 ), bioconjugates ( Malfanti et al, 2019 ), and green synthetic routes should also be considered. The functional modification of MOFs with target ligands, such as aptamers ( Cai et al, 2018 ; He et al 2020a , 2020b ; Liu et al 2014a , 2015 ; Xiong et al, 2019 ) would endow the MOFs with more functionalities, with detection performances even better than the biosensor platforms based on graphene oxide ( Du et al, 2020 ; Liu et al, 2014b ).…”

Section: Discussion and Prospectivementioning

confidence: 99%

Metal-organic frameworks for virus detection

Wang

et al. 2020

Biosensors and Bioelectronics

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Virus severely endangers human life and health, and the detection of viruses is essential for the prevention and treatment of associated diseases. Metal-organic framework (MOF), a novel hybrid porous material which is bridged by the metal clusters and organic linkers, has become a promising biosensor platform for virus detection due to its outstanding properties including high surface area, adjustable pore size, easy modification, etc. However, the MOF-based sensing platforms for virus detection are rarely summarized. This review systematically divided the detection platforms into nucleic acid and immunological (antigen and antibody) detection, and the underlying sensing mechanisms were interpreted. The nucleic acid sensing was discussed based on the properties of MOF (such as metal ion, functional group, geometry structure, size, porosity, stability, etc.), revealing the relationship between the sensing performance and properties of MOF. Moreover, antibodies sensing based on the fluorescence detection and antigens sensing based on molecular imprinting or electrochemical immunoassay were highlighted. Furthermore, the remaining challenges and future development of MOF for virus detection were further discussed and proposed. This review will provide valuable references for the construction of sophisticated sensing platform for the detection of viruses, especially the 2019 coronavirus.

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Section: Discussion and Prospectivementioning

confidence: 99%

Metal-organic frameworks for virus detection

Wang

et al. 2020

Biosensors and Bioelectronics

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“…We used the SOMAscan ® proteomics platform to carry out a broad assessment of serum proteins. The strengths and weaknesses of the SOMAscan ® platform have been reviewed in detail ( 26 ), and this platform has been used for multiple previous studies of serum from DMD ( 10–12 , 27 ). Briefly, the strength of the aptamer-based platform is that it tests three dilutions of sera over a 10 000-fold concentration range and is highly parallel (1305 serum proteins tested).…”

Section: Discussionmentioning

confidence: 99%

Serum biomarkers associated with baseline clinical severity in young steroid-naïve Duchenne muscular dystrophy boys

Dang

Ziemba

Clemens

et al. 2020

Human Molecular Genetics

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Duchenne muscular dystrophy (DMD) is caused by loss of dystrophin in muscle, and while all patients share the primary gene and biochemical defect, there is considerable patient-patient variability in clinical symptoms. We sought to develop multivariate models of serum protein biomarkers that explained observed variation, using functional outcome measures as proxies for severity. Serum samples from 39 steroid-naïve DMD boys 4 to < 7 years enrolled into a clinical trial of vamorolone were studied (NCT02760264). Four assessments of gross motor function were carried out for each participant over a 6-week interval and their mean was used as response for biomarker models. Weighted correlation network analysis was used for unsupervised clustering of 1305 proteins quantified using SOMAscan® aptamer profiling to define highly representative and connected proteins. Multivariate models of biomarkers were obtained for time to stand performance (strength phenotype; 17 proteins) and 6-minute walk performance (endurance phenotype; 17 proteins) including some shared proteins. Identified proteins were tested with associations of mRNA expression with histological severity of muscle from dystrophinopathy patients (n = 28) and normal controls (n = 6). Strong associations predictive of both clinical and histological severity were found for ERBB4 (reductions in both blood and muscle with increasing severity), SOD1 (reductions in muscle and increases in blood with increasing severity), and CNTF (decreased levels in blood and muscle with increasing severity). We show that performance of DMD boys was effectively modeled with serum proteins, with proximal strength associated with growth and remodeling pathways, and muscle endurance centered on TGFβ and fibrosis pathways in muscle.

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“…Utilizing blind cell SELEX methods, aptamers targeting cancer cell surface structures can be enriched efficiently even without knowledge of the protein expression profile of CTCs. After several rounds of positive and negative selection, aptamers are amplified, sequenced and subjected to protein mass spectrometry to identify the detailed target structure [9]. On one hand this strategy promotes the generation of specific aptamers for detection and therapeutic targeting of cancer cells, on the other hand it facilitates the discovery of novel CTC-based biomarkers.…”

Section: Aptamers For the Detection Of Circulating Cancer Cells (Ctcsmentioning

confidence: 99%

“…Modified aptamers tagged with labeling agents function as sensitive biosensors or targeted imaging tracers. As the selection and generation can be accomplished without structural knowledge of the target molecule, aptamers can also serve as a tool to discover novel biomarkers [ 9 ]. Although they were initially conceived and designed as inhibitors, a rising number of studies reports functionally targeted agent delivery systems employing aptamers [ 10 ].…”

Section: Introductionmentioning

confidence: 99%

Aptamers: a novel targeted theranostic platform for pancreatic ductal adenocarcinoma

Maier

et al. 2020

Radiat Oncol

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Pancreatic ductal adenocarcinoma (PDAC) is an extremely challenging disease with a high mortality rate and a short overall survival time. The poor prognosis can be explained by aggressive tumor growth, late diagnosis, and therapy resistance. Consistent efforts have been made focusing on early tumor detection and novel drug development. Various strategies aim at increasing target specificity or local enrichment of chemotherapeutics as well as imaging agents in tumor tissue. Aptamers have the potential to provide early detection and permit anti-cancer therapy with significantly reduced side effects. These molecules are in-vitro selected single-stranded oligonucleotides that form stable threedimensional structures. They are capable of binding to a variety of molecular targets with high affinity and specificity. Several properties such as high binding affinity, the in vitro chemical process of selection, a variety of chemical modifications of molecular platforms for diverse function, non-immunoreactivity, modification of bioavailability, and manipulation of pharmacokinetics make aptamers attractive targets compared to conventional cell-specific ligands. To explore the potential of aptamers for early diagnosis and targeted therapy of PDAC-as single agents and in combination with radiotherapy-we summarize the generation process of aptamers and their application as biosensors, biomarker detection tools, targeted imaging tracers, and drug-delivery carriers. We are furthermore discussing the current implementation aptamers in clinical trials, their limitations and possible future utilization.

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Cancer protein biomarker discovery based on nucleic acid aptamers

Cited by 66 publications

References 99 publications

Metal-organic frameworks for virus detection

Metal-organic frameworks for virus detection

Serum biomarkers associated with baseline clinical severity in young steroid-naïve Duchenne muscular dystrophy boys

Aptamers: a novel targeted theranostic platform for pancreatic ductal adenocarcinoma

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