Enzyme-free amplified detection of cellular microRNA by light-harvesting fluorescent nanoparticle probes

Xiong

Computational and Mathematical Methods in Medicine

et al. 2022

MicroRNAs (miRNAs) are a kind of noncoding RNA, which plays an essential role in gene regulation by binding to messenger RNAs (mRNAs). Accurate and rapid identification of miRNA target genes is helpful to reveal the mechanism of transcriptome regulation, which is of great significance for the study of cancer and other diseases. Many bioinformatics methods have been proposed to solve this problem, but the previous research did not further study the encoding of the nucleotide sequence. In this paper, we developed a novel method combining word embedding and deep learning for human miRNA targets at the site-level prediction, which is inspired by the similarity between natural language and biological sequences. First, the word2vec model was used to mine the distribution representation of miRNAs and mRNAs. Then, the embedding is extracted automatically via the stacked bidirectional long short-term memory (BiLSTM) network. By testing, our method can effectively improve the accuracy, sensitivity, specificity, and F -measure of other methods. Through our research, it is proved that the distributed representation can improve the accuracy of the deep learning model and better solve the miRNA target site prediction problem.

Section: Resultsmentioning

confidence: 99%

A miRNA Target Prediction Model Based on Distributed Representation Learning and Deep Learning

Xiong

Computational and Mathematical Methods in Medicine

et al. 2022

“…Furthermore, although molecular diagnostic methods have significantly improved CRC screening, similarly to traditional diagnostics, these also carry limitations and challenges. The gold standard technique currently in use, qPCR and RT-qPCR, has been reported to have several restraints [ 19 , 20 , 86 , 87 ]. Thus, CRISPR/Cas-based diagnosis (CRISPR-Dx) technologies may represent a potential opportunity to further improve current molecular diagnosis efforts due to their ultrasensitive and robust bio-sensing properties, especially when there have been significant advances in CRISPR-Dx technologies in clinical research and clinical applications [ 88 ].…”

Section: Current Crc Diagnosis and Their Challenges: Traditional And Molecular Methodsmentioning

confidence: 99%

“…CEx-miRNAs profiles are primarily evaluated through reverse transcription-quantitative polymerase chain reaction (RT-qPCR) [ 11 , 15 , 16 , 17 , 18 ]. However, RT-qPCR has specific challenges, including the limit of detection and limited throughput, consistency, response-time, and portability [ 19 , 20 ], which may affect reported sensitivity, specificity, and turnaround times, ultimately making clinical care decision-making difficult.…”

Section: Introductionmentioning

confidence: 99%

CRISPR/Cas13-Based Platforms for a Potential Next-Generation Diagnosis of Colorectal Cancer through Exosomes Micro-RNA Detection: A Review

Durán-Vinet

Araya‐Castro

Calderón

et al. 2021

Cancers

Colorectal cancer (CRC) is the third most prevalent cancer with the second highest mortality rate worldwide. CRC is a heterogenous disease with multiple risk factors associated, including obesity, smoking, and use of alcohol. Of total CRC cases, 60% are diagnosed in late stages, where survival can drop to about 10%. CRC screening programs are based primarily on colonoscopy, yet this approach is invasive and has low patient adherence. Therefore, there is a strong incentive for developing molecular-based methods that are minimally invasive and have higher patient adherence. Recent reports have highlighted the importance of extracellular vesicles (EVs), specifically exosomes, as intercellular communication vehicles with a broad cargo, including micro-RNAs (miRNAs). These have been syndicated as robust candidates for diagnosis, primarily for their known activities in cancer cells, including immunoevasion, tumor progression, and angiogenesis, whereas miRNAs are dysregulated by cancer cells and delivered by cancer-derived exosomes (CEx). Quantitative polymerase chain reaction (qPCR) has shown good results detecting specific cancer-derived exosome micro-RNAs (CEx-miRNAs) associated with CRC, but qPCR also has several challenges, including portability and sensitivity/specificity issues regarding experiment design and sample quality. CRISPR/Cas-based platforms have been presented as cost-effective, ultrasensitive, specific, and robust clinical detection tools in the presence of potential inhibitors and capable of delivering quantitative and qualitative real-time data for enhanced decision-making to healthcare teams. Thereby, CRISPR/Cas13-based technologies have become a potential strategy for early CRC diagnosis detecting CEx-miRNAs. Moreover, CRISPR/Cas13-based platforms’ ease of use, scalability, and portability also showcase them as a potential point-of-care (POC) technology for CRC early diagnosis. This study presents two potential CRISPR/Cas13-based methodologies with a proposed panel consisting of four CEx-miRNAs, including miR-126, miR-1290, miR-23a, and miR-940, to streamline novel applications which may deliver a potential early diagnosis and prognosis of CRC.

“…[52] Moreover, counterion ensures close proximity of dyes inside polymeric NPs, which induces ultrafast dye-dye energy transfer generating giant light-harvesting nanoantenna that amplifies ∼1000 fluorescence signal through Forster resonance energy transfer (FRET). [53] The latter has already been applied to amplified FRET-based detection of nucleic acids [49,54,55] and oxygen. [47] However, in all these previous works, the counterion function was focused on preventing ACQ and dye leaching; while, theoretically, it could be possible to tailor the structure of the counterion in order to implement new functions into the nanomaterials.…”

Section: Introductionmentioning

confidence: 99%

Lanthanide‐based bulky counterions against aggregation‐caused quenching of dyes in fluorescent polymeric nanoparticles

et al. 2021

Self Cite

Dye‐loaded polymeric nanoparticles (NPs) are promising bioimaging agents because of their available surface chemistry, high brightness, and tunable optical properties. However, high dye loadings can cause the aggregation‐caused quenching (ACQ) of the encapsulated fluorophores. Previously, we proposed to mitigate the ACQ inside polymeric NPs by insulating cationic dyes with bulky hydrophobic counterions. In order to implement new functionalities into dye‐loaded NPs, here, we extend the concept of bulky counterions to anionic lanthanide‐based complexes. We show that by employing Gd‐based counterions with octadecyl rhodamine B loaded NPs at 30 wt% versus polymer, the fluorescence quantum yield can be increased to 10‐fold (to 0.34). Moreover, Gd‐anion provides NPs with enhanced contrast in electron microscopy. A combination of a luminescent Eu‐based counterion with a far‐red to near‐infrared cyanine 5 dye (DiD) yields Forster resonance energy transfer NPs, where the UV‐excited Eu‐based counterion transfers energy to DiD, generating delayed fluorescence and large stokes shift of ∼340 nm. Cellular studies reveal low cytotoxicity of NPs and their capacity to internalize without detectable dye leakage, in contrast to leaky NPs with small counterions. Our findings show that the aggregation behavior of cationic dyes in the polymeric NPs can be controlled by bulky lanthanide anions, which will help in developing bright luminescent multifunctional nanomaterials.