Related Biomedical Research Research Articles

Identify and mitigate bias in electronic phenotyping: A comprehensive study from computational perspective

Electronic phenotyping is a fundamental task that identifies the special group of patients, which plays an important role in precision medicine in the era of digital health. Phenotyping provides real-world evidence for other related biomedical research and clinical tasks, e.g., disease diagnosis, drug development, and clinical trials, etc. With the development of electronic health records, the performance of electronic phenotyping has been significantly boosted by advanced machine learning techniques. In the healthcare domain, precision and fairness are both essential aspects that should be taken into consideration. However, most related efforts are put into designing phenotyping models with higher accuracy. Few attention is put on the fairness perspective of phenotyping. The neglection of bias in phenotyping leads to subgroups of patients being underrepresented which will further affect the following healthcare activities such as patient recruitment in clinical trials. In this work, we are motivated to bridge this gap through a comprehensive experimental study to identify the bias existing in electronic phenotyping models and evaluate the widely-used debiasing methods’ performance on these models. We choose pneumonia and sepsis as our phenotyping target diseases. We benchmark 9 kinds of electronic phenotyping methods spanning from rule-based to data-driven methods. Meanwhile, we evaluate the performance of the 5 bias mitigation strategies covering pre-processing, in-processing, and post-processing. Through the extensive experiments, we summarize several insightful findings from the bias identified in the phenotyping and key points of the bias mitigation strategies in phenotyping.

Nanocounter on cell membrane: In-situ quantification of membrane-bound enzymes with high simplicity and sensitivity via the assembly of branched peptides

The quantitative analysis of membrane-bound enzymes (MBEs) is still challenged by complicated process, expensive equipment, and/or limited sensitivity. Herein, a highly sensitive yet user-friendly colorimetric method is proposed for the in-situ quantification of MBEs via the reasonable assembly of branched peptides. Taking alkaline phosphatase (ALP) as an example, the designed assembly of branched peptides can respond to the membrane-bound enzyme and undergo a spontaneous transformation to load signal reporters, giving rise to a colorimetric signal. Therefore, this method allows for simple in-situ measurements of MBEs without the need for complicated protein isolation or labeling processes or sophisticated equipment. Significantly, the exploitation of branched peptides with multiple functional sites enables both multivalent recognition of targets and large-scale loading of signal reporters, achieving ultra-high sensitivity. As a result, as few as 34 pg of ALP on HepG2 cell membrane can be measured directly in cell suspension in an add-to-respond manner. Furthermore, the successful differentiation of cancer cells with ALP overexpression depicts the potential application of this method. By adjusting the target-responsive peptide sequences, this work can be generally expanded for versatile MBE analysis and other related biomedical research.

Precise quantification of microRNAs based on proximity ligation of AuNPs-immobilized DNA probes.

MiRNAs are critical regulators of target gene expression in many biological processes and are considered promising biomarkers for diseases. In this study, we developed a simple, specific, and sensitive miRNA detection method based on proximity ligation reaction, which is easy to operate. The method uses a pair of target-specific DNA probes immobilized on the same gold nanoparticles (AuNPs), which hybridize to the target miRNA. Hybridization brings the probes close together, allowing the formation of a continuous DNA sequence that can be amplified by Quantitative Real-time PCR (qPCR). This method eliminates the need for complex reverse transcription design and achieves high specificity for discriminating single base mismatches between miRNAs through a simple procedure. This method can sensitively measure three different miRNAs with a detection limit of 20 aM, providing high versatility and sensitivity, even distinguishing single-base variations among members of the miR-200 family with high selectivity. Due to its high selectivity and sensitivity, this method has important implications for the investigation of miRNA biological functions and related biomedical research.

Acid-responsive mediated entropy driven signal amplification nanosystem for sensitive imaging of APE1 activity in living cells

Sensitive imaging of intracellular apurinic/apyrimidinic endonuclease 1 (APE1) activity is helpful to understand its physiological function and pathological role. Herein, an acid-responsive mediated entropy-driven signal amplification all-in-one nanosystem was proposed for sensitive imaging of APE1 activity in living cells. The nanosystem was constructed by modifying recognition probe, entropy-driven reaction (EDR) substrate and acid-responsive components on gold nanoparticles (AuNPs). After the nanosystem was endocytosed into the cell, the triplex in the acid-responsive components folded in the lysosome to free its complementary fuel strand. In the presence of APE1, it specifically cleaved the apurinic/apyrimidinic (AP) site in the recognition probe and released the EDR trigger. With the action of EDR trigger, EDR substrate and fuel strand, the EDR was completed and accompanied by the separation of fluorophore and quenching group in EDR substrate, resulting in obvious fluorescence signal recovery. The nanosystem successfully achieved sensitive imaging of APE1 activity in human cervical cancer cells (Hela cells), human breast cancer cells (MCF-7 cells) and human normal colonic epithelial cells (NCM460 cells) and monitored the changes of APE1 activity in Hela cells. The nanosystem provides a reliable approach for intracellular APE1 analysis and related biomedical research.

In situ formation of copper nanoclusters for efficient analysis of β-glucosidase activity

An efficient and convenient fluorescent method has been developed to detect β-glucosidase via utilizing the in situ synthesis of double-stranded DNA templated copper nanoclusters (dsDNA-Cu NCs). The dsDNA-Cu NCs can be formed by using random dsDNA with (AT-TA) rich sequence as the template. However, with the addition of amygdalin and β-glucosidase, amygdalin was catalyzed by β-glucosidase to generate cyanide ion (CN−). The CN− had the high affinity to bind with Cu2+ to inhibit the production of fluorescent dsDNA-Cu NCs, resulting in low fluorescence intensity. This method exhibits both sensitivity and specificity in detecting β-glucosidase under the optimal conditions. In addition, the technique's detection limit is 0.00084 U mL−1. The serum samples were also used to verify this fluorescent strategy with satisfactory results. In addition, this method does not require complex preparation process of probes and fluorescent dye labelling, greatly simplifying the experimental processes. Thus, it can provide a sensitive method for the β-glucosidase related biomedical research.

Hairpin cascade circuits on programmable DNA-nucleated spherical nucleic acid for intracellular targeted microRNA imaging

DNA molecular probes have been increasingly used for biological imaging and tumor theranostics. In particular, live-cell imaging of low abundance microRNA (miRNA) with high accuracy and efficiency was extremely important for understanding functions and dynamics of miRNA. Herein, an easy-to-obtain DNA-nucleated spherical nucleic acid (DSNA) was constructed by one pair of hairpin probes “sticked” on self-assembled three-dimensional (3D) urchin-like DNA nanostructures (UDNs) to realize sensitive imaging of tumor-related miRNA in living cells. UDNs were prepared through four short single-stranded DNA by a simple “one-pot” annealing process that took only a few minutes. Moreover, sticking the reactants of hairpin probes on the UDNs not only sped up the reaction kinetic rate, but also improved the sensitivity and efficiency of miRNA-triggered hairpin cascade circuits. Compared with traditional AuNP-based spherical nucleic acid, the DSNA possessed superb biocompatibility and stability, excellent cell internalization capability and accessibility, which endowed them tremendous advantages for the monitoring of miRNA in living cells. Therefore, our developed strategy exhibited great potential in sensitive imaging of intracellular miRNA, offering a new avenue for early tumor diagnosis and related biomedical research.

Nanoscale Study of DNA-Cu2+ Interactions by Liquid-Cell Electron Microscopy.

Metal ions are indispensable constituent elements of the human body, among which Cu2+ plays an important role in various biochemical reactions in the human body and is an essential element for maintaining human health. Studying the interaction between Cu2+ and DNA can be helpful to further understand the mechanism of Cu2+ behavior in organisms. In this paper, we investigated the DNA-Cu2+ complex by transmission electron microscopy (TEM) and used in situ liquid-cell TEM to observe the dynamic processes of interactions between DNA and Cu2+. Results show that the binding of Cu2+ to DNA leads to the bending of the DNA strand and provides an anchor site for activating Cu2+ for the nucleation and growth of copper crystals. Bound by the DNA strand, the copper crystals are arranged along the curved strand, showing the same arrangement pattern as guanine on the DNA sequence. It is believed that the study will further elaborate the interaction mechanism by directly observing the DNA-Cu2+ complex at the nanometer scale and benefit the related biomedical research studies.

AIEgen-Peptide Bioprobes for the Imaging of Organelles.

Organelles are important subsystems of cells. The damage and inactivation of organelles are closely related to the occurrence of diseases. Organelles’ functional activity can be observed by fluorescence molecular tools. Nowadays, a series of aggregation-induced emission (AIE) bioprobes with organelles-targeting ability have emerged, showing great potential in visualizing the interactions between probes and different organelles. Among them, AIE luminogen (AIEgen)-based peptide bioprobes have attracted more and more attention from researchers due to their good biocompatibility and photostability and abundant diversity. In this review, we summarize the progress of AIEgen-peptide bioprobes in targeting organelles, including the cell membrane, nucleus, mitochondria, lysosomes and endoplasmic reticulum, in recent years. The structural characteristics and biological applications of these bioprobes are discussed, and the development prospect of this field is forecasted. It is hoped that this review will provide guidance for the development of AIEgen-peptide bioprobes at the organelles level and provide a reference for related biomedical research.

Construction of a fluorescent probe with large stokes shift and deep red emission for sensing of the viscosity in hyperglycemic mice

The detection of viscosity levels in biological systems is of great significance for the research of many diseases. Herein, we constructed a new viscosity probe ND-1 with large Stokes shift (>160 nm) and deep red emission (624 nm). Utilizing its excellent fluorescence performances, the unique probe ND-1 can not only detect the viscosity changes in living cells, zebrafish and tumor mice, but also successfully observe the variation of viscosity in acute hyperglycemia mice for the first time. It is expected that this work may help to promote the progress of related biomedical research and provide a potential tool for the detection and research of viscosity related diseases.

The dumbbell probe mediated triple cascade signal amplification strategy for sensitive and specific detection of uracil DNA glycosylase activity

Uracil DNA glycosylase (UDG) is a key base excision repair (BER) enzyme and its abnormal expression is nearly relevant to several diseases including cancer. The sensitive detection of UDG activity is beneficial for biomedical studies and clinic diagnosis. In this work, we proposed a dumbbell probe mediated triple cascade signal amplification strategy for sensitive and specific detection of UDG activity. The specially designed dumbbell probe contained two uracil bases, two recognition sites for nicking enzyme and a split sequence of DNAzyme. Unsealed dumbbell probes were first connected into sealed dumbbell probes by T4 DNA ligase, and then the unsealed probes were hydrolyzed by exonuclease to ensure the purity of probes. Under the influence of UDG, two uracil bases were removed to produce two apyrimidinic (AP) sites, which were subsequently cleaved by Endo.IV. The probes after cleavage acted as primers and templates for double nicking sites strand displacement amplification (SDA) to produce a mass of two products. The products of SDA continued to act as primers and templates for rolling circle amplification (RCA) to produce repeats containing complete DNAzyme sequences. The DNAzyme repeatedly cleaved multiple molecular beacons (MB), resulting in remarkable fluorescence enhancement. Benefiting from the triple cascade signal amplification, the sensitivity was improved and the detection limit was 7.2 × 10−5 U mL−1. The method could well distinguish UDG from other interfering enzymes and detect UDG activity in real biological samples, showing good specificity. In addition, this method could be used for screening inhibitors. The above results suggested that the method provided a promising analytical means for UDG related biomedical research and clinic diagnosis.

PARP inhibition suppresses topoisomerase 1 poisoning induced Caspase-3 dependent cell death in zebrafish embryos

In the present study the role of poly(ADP)ribosylation on rubitecan induced caspase dependent cell death was evaluated. We show that Top1 poisoning by rubitecan induces caspase mediated apoptosis which was reduced by PARP inhibitor olaparib in zebrafish embryo. Collectively our data introduces zebrafish as a valuable model for PARP related biomedical research.

DNA-Assisted Smart Nanocarriers: Progress, Challenges, and Opportunities.

Due to powerful breakthroughs in nanotechnology, smart delivery mechanisms have rapidly emerged for use in diverse applications across biomedical research and therapeutic development. Recent efforts toward understanding stimuli-responsive strategies have led to substantial improvements in their conceptual application and in vitro efficiency. Because disease targets for therapy are often localized in specific cells, organs, or tissues, an enhanced permeability and retention (EPR)-based strategy remains inadequate for accurate drug delivery and release to target regions, resulting in an insufficient drug concentration reaching the target region and undesired side effects. To address these issues, more precise and remote-controlled stimuli-responsive systems, which recognize and react to changes in the pathophysiological microenvironment, were recently elucidated as feasible on-demand drug-delivery systems. In this Perspective, we focus on progress toward stimuli-responsive drug-delivery systems that utilize dynamic DNA molecules by exploiting DNA nanotechnology. DNA structures can be precisely reconfigured by external and internal stimuli to drive the release of a loaded drug in a target region with appropriate microenvironments. We describe the chemical, physical, and biological engineering principles and strategies for constructing DNA-assisted nanocarriers. We also provide a summary of smart nanocarrier systems, organized with respect to the structural changes in the DNA strand in the microenvironment, resulting from changes in pH and temperature and the presence of intracellular oligonucleotides. To do so, we highlight recent advances in related biomedical research and applications as well as discuss major challenges and opportunities for DNA-assisted nanocarriers to guide the development of future in vivo therapies and clinical translation strategies.

An analysis of the evolution of science-technology linkage in biomedicine

Demonstrating the practical value of public research has been an important subject in science policy. Here we present a detailed study on the evolution of the citation linkage between life science related patents and biomedical research over a 37-year period. Our analysis relies on a newly-created dataset that systematically links millions of non-patent references to biomedical papers. We find a large disparity in the volume of science linkage among technology sectors, with biotechnology and drug patents dominating it. The linkage has been growing exponentially over a long period of time, doubling every 2.9 years. The U.S. has been the largest producer of cited science for years, receiving nearly half of the citations. More than half of citations goes to universities. We use a new paper-level indicator to quantify to what extent a paper is basic research or clinical medicine. We find that the cited papers are likely to be basic research, yet a significant portion of papers cited in patents that are related to FDA-approved drugs are clinical research. The U.S. National Institute of Health continues to be an important funder of cited science. For the majority of companies, more than half of citations in their patents are authored by public research. Taken together, these results indicate a continuous linkage of public science to private sector inventions.

RPI-SE: a stacking ensemble learning framework for ncRNA-protein interactions prediction using sequence information

BackgroundThe interactions between non-coding RNAs (ncRNA) and proteins play an essential role in many biological processes. Several high-throughput experimental methods have been applied to detect ncRNA-protein interactions. However, these methods are time-consuming and expensive. Accurate and efficient computational methods can assist and accelerate the study of ncRNA-protein interactions.ResultsIn this work, we develop a stacking ensemble computational framework, RPI-SE, for effectively predicting ncRNA-protein interactions. More specifically, to fully exploit protein and RNA sequence feature, Position Weight Matrix combined with Legendre Moments is applied to obtain protein evolutionary information. Meanwhile, k-mer sparse matrix is employed to extract efficient feature of ncRNA sequences. Finally, an ensemble learning framework integrated different types of base classifier is developed to predict ncRNA-protein interactions using these discriminative features. The accuracy and robustness of RPI-SE was evaluated on three benchmark data sets under five-fold cross-validation and compared with other state-of-the-art methods.ConclusionsThe results demonstrate that RPI-SE is competent for ncRNA-protein interactions prediction task with high accuracy and robustness. It’s anticipated that this work can provide a computational prediction tool to advance ncRNA-protein interactions related biomedical research.

Proximity-enabled bidirectional enzymatic repairing amplification for ultrasensitive fluorescence sensing of adenosine triphosphate

A novel fluorescence sensing strategy for ultrasensitive and highly specific detection of adenosine triphosphate (ATP) has been developed by the combination of the proximity ligation assay with bidirectional enzymatic repairing amplification (BERA). The strategy relies on proximity binding-triggered the release of palindromic tail that initiates bidirectional cyclic enzymatic repairing amplification reaction with the aid of polymerase and two DNA repairing enzymes, uracil-DNA glycosylase (UDG) and endonuclease IV (Endo IV). A fluorescence-quenched hairpin probe with a palindromic tail at the 3′ end is skillfully designed that functions as not only the recognition element, primer, and polymerization template for BERA but also the indicator for fluorescence signal output. On the basis of the amplification strategy, this biosensor displays excellent sensitivity and selectivity for ATP detection with an outstanding detection limit of 0.81 pM. Through simultaneously enhancing the target response signal value and reducing nonspecific background, this work deducted the background effect, and showed high sensitivity and reproducibility. Moreover, our biosensor also shows promising potential in real sample analysis. Therefore, the proximity-enabled BERA strategy indeed creates a simple and valuable fluorescence sensing platform for ATP identification and related disease diagnosis and biomedical research.

Integrative Construction and Analysis of Molecular Association Network in Human Cells by Fusing Node Attribute and Behavior Information

Detecting whether a pair of biomolecules associate is of great significance in the study of molecular biology. Hence, computational methods are urgently needed as guidance for practice. However, most of the previous prediction models influenced by reductionism focused on isolated research objects, which have their own inherent defects. Inspired by holism, a machine-learning-based framework called MAN-node2vec is proposed to predict multi-type relationships in the molecular associations network (MAN). Specifically, we constructed a large-scale MAN composed of 1,023 miRNAs, 1,649 proteins, 769 long non-coding RNAs (lncRNAs), 1,025 drugs, and 2,062 diseases. Then, each biomolecule in MAN can be represented as a vector by its attribute learned by k-mer, etc. and its behavior learned by node2vec. Finally, the random forest classifier is applied to carry out the relationship prediction task. The proposed model achieved a reliable performance with 0.9677 areas under the curve (AUCs) and 0.9562 areas under the precision curve (AUPRs) under 5-fold cross-validation. Also, additional experiments proved that the proposed global model shows more competitive performance than the traditional local method. All of these provided a systematic insight for understanding the synergistic interactions between various molecules and diseases. It is anticipated that this work can bring beneficial inspiration and advance to related systems biology and biomedical research.

An efficient J-aggregate based fluorescence turn-on and ratiometric sensor for heparin

Heparin is the second most widely used natural drug and an extensively employed blood anticoagulant worldwide. Construction of fluorescent sensors for Heparin has remained heavily dependent on the complex and time-consuming laborious synthetic efforts. However, reports on the direct usage of in-expensive commercially available probe molecule, for sensitive and selective fluorimetric sensing of Heparin, which can greatly simplify the synthetic efforts, has been limited and remains highly desirable. Herein, we report a very sensitive and selective fluorescence turn-on sensor for Heparin, which utilizes a commercially available organic dye molecule, Pseudoisocyanine. The supramolecular interaction between the Pseudoisocyanine and Heparin leads to the J-aggregate formation of Pseudoisocyanine on the surface of Heparin, with an exceptional fluorescence enhancement of ∼400 fold. The J-aggregates of Pseudoisocyanine also display remarkable changes in the absorption features, in the presence of Heparin, which provides a unique advantageous feature of dual sensing of Heparin, by colorimetry and fluorimetry. Pseudoisocyanine also displays high selectivity towards Heparin over its structurally related analogs Chondroitin sulphate and Hyaluronic acid, and other analytes, with a detection limit of 2 nM. More importantly, our sensor system shows good performance in the serum samples, a complex biological media. We further demonstrate that, the interaction of Heparin with its only medically approved antidote, Protamine can also be monitored using Pseudoisocyanine J-aggregates. Thus, our assay is sensitive and selective, rapid, simple, and inexpensive, which can promote the Heparin related biochemical and biomedical research.

A T7 exonuclease assisted dual-cycle signal amplification assay of miRNA using nanospheres-enhanced fluorescence polarization

Based on streptavidin coated nanospheres and T7 exonuclease assisted dual-cycle signal amplification, we developed a novel sensitive fluorescence polarization detection method for miRNA. When target miRNA was present in the system, hairpin probe hybridized with miRNA, forming a double-stranded structure. The 5′ end of hairpin probe was then recognized and digested by T7 exonuclease, releasing the non-degraded single strand DNA fragments and miRNA. The released target miRNA could trigger the next cycle of hybridization and digestion, releasing more non-degraded fragments from hairpin probe. The fragments could hybridize with a signal probe (with carboxyfluorescein modification at 5′-end and biotin modification at 3′-end). The formed blunt 5′-end of signal probe was then recognized and degraded by T7 exonuclease, releasing the fragments and the fluorophore carboxyfluorescein. The next cycle of hybridization and digestion of signal probe was triggered by the released fragment at the same time. The free carboxyfluorescein cannot connect with streptavidin coated nanospheres which were used as the fluorescence polarization signal amplifier. So, there was a big change of fluorescence polarization signal after adding miRNA into the detection system, due to the different fluorescence polarization signal between nanospheres-captured intact signal probe and free carboxyfluorescein. The detection limit of this method is about 0.001 nM, and it has a good selectivity. In addition, it was also applicable to determine target miRNA in total miRNA extracts and compare the expression level of target miRNA in different cells. Consequently, the proposed method is expected to be used for the potential cancer diagnosis and the related biomedical research.

T7 exonuclease-assisted and target-triggered cascade dual recycling signal amplification strategy for the sensitive and specific detection of adenosine

Adenosine is closely related to the development of cancer, and it can be regarded as a biomarker for cancer diagnosis and therapy. Here, a T7 exonuclease (T7 Exo)-assisted and target-triggered cascade dual recycling signal amplification strategy was developed for the sensitive and specific detection of adenosine. In this strategy, a capture strand (Cap)-inhibit strand (Inh) duplex and a DNA hairpin with intact G-quadruplex sequence are designed. In the presence of adenosine, Cap binds with adenosine specifically to form Cap-adenosine complex with recessed 5′-hydroxyl termini, causing the release of Inh. Under the action of T7 Exo, the adenosine is released from Cap-adenosine complex. Then the released adenosine interacts with the next Cap-Inh duplex to promote the release of a new Inh and the recycle I is completed. After that, the released Inh hybridizes with hairpin to form Inh-hairpin duplex with blunt 5′ -hydroxyl termini. Under the same action of T7 Exo, the Inh gets released and a G-quadruplex sequence is obtained. Subsequently, the released Inh continues opening hairpin and the recycle II is accomplished. Finally, plenty of G-quadruplex sequences are generated and then interact with N-methyl-mesoporphyrin IX (NMM) to obtain enhanced fluorescence signal. The limit of detection (LOD) of the proposed strategy is estimated to be 9.8 × 10−7 mol L−1, and the linear range of the strategy is from 5.0 × 10−6 mol L−1 to 7.0 × 10−4 mol L−1. Besides, the proposed strategy is capable of distinguishing adenosine from its analogues. This strategy holds promise in adenosine related biomedical research, clinical diagnosis and disease treatment.

Advances in Microfluidics Applied to Single Cell Operation.

The field of microbiology have traditionally been concerned with and focused on studies at the population level. Microfluidic platforms have emerged as important tools for biology research at a small scale, even down to a single cell level. The spatial and temporal control of cells and stimuli transported by microfluidic channels in well-designed microsystems realized the studies of specific cells in a controlled microenvironment. The true cellular physiology responses, which are obtained mostly by inference from population-level data, could be revealed in this way. Nowadays, significant applications like cell culture, analysis, sorting, genomics, and proteomics at the single cell level have been achieved in microfluidic chips. Highly integrated microfluidic systems with complete bio-analytic functions are also coming forth and of great promise for single cell related physiology, biomedical, and high throughput screening research. Herein, the leads of technologies applied to single cell operation are reviewed. Challenges and potentials of these works are also summarized, to highlight fields for further research.