Combining peptide and DNA for protein assay: CRIP1 detection for breast cancer staging

Demethylation of m1A assisted degradation of the signal probe for rapid electrochemical detection of ALKBH3 activity with practical applications

ALKBH3 is an important marker for early diagnosis and histopathological grading of prostate cancer. However, the lack of a rapid and sensitive method to quantify the enzyme's activity in the current time necessitates the development of a new quantitative assay. Herein, we first tried to quantitative assay for ALKBH3 activity using an electrochemical method based on the degradation of the signal probe due to alkyl group of the m1A removal by ALKBH3. A strong electrochemical signal can be obtained when the ferrocene (Fc) labeled dsDNAs with 1-methyladenine are immobilized on the electrode. In the presence of ALKBH3, the 3' blunt of DNA can be formed because of the removal of alkyl group of the Fc-DNA probe, which can be recognized and degraded by Exonuclease III (Exo III). As a result, the electrochemical signal produced by Fc greatly decreases, and the activity of ALKBH3 can be easily detected via changes in electrochemical signal. Quantitative analysis of ALKBH3 activity showed a wide detection range (0.1 and 20 ng/mL) and low detection limit (0.04 ng/mL). Furthermore, the method can be applied to detect 1-methyladenine through ALKBH3 in cell lysates and tissue samples, providing a new method for clinical detection of prostate cancer.

Weighted Gene Coexpression Network Analysis Identifies Cysteine-Rich Intestinal Protein 1 (CRIP1) as a Prognostic Gene Associated with Relapse in Patients with Acute Myeloid Leukemia

BACKGROUND Acute myeloid leukemia (AML) is associated with a high relapse rate and poor prognosis. This study aimed to use weighted gene coexpression network analysis (WGCNA) of gene coexpression networks to identify candidate prognostic biomarker genes in patients with AML and to investigate the expression of these genes in the human U937 cell line in vitro. MATERIAL AND METHODS RNA-seq data were retrieved from the Cancer Genome Atlas (TCGA) and included bone marrow samples and survival data of patients with AML (N=151), patients who did not relapse after treatment (N=119), and patients with relapse (N=40). Differentially expressed genes were identified, WGCNA was used to detect functional modules, and survival analysis was performed. The Cell Counting Kit-8 (CCK-8) assay investigated the proliferation of U937 cells transfected with short hairpin RNAs (shRNAs), shCRIP1, shHIST1H1C, and shHIST1H1E. RNA-seq analysis identified gene expression following CRIP1 knockdown. RESULTS Eighty-two genes were associated with both relapse and prognosis in patients with AML. There were two prognosis-related gene modules in the coexpression network. In the coexpression network, the histone cluster 1 H1 family member gene, HIST1H1C had the maximum relapse fold change, HIST1H1E had the lowest survival p-value, and the cysteine-rich intestinal protein 1 (CRIP1) gene had the most edge numbers and was significantly associated with poor prognosis (P=0.0165786). RNA-seq data showed that there was a significant difference in gene expression after CRIP1 knockdown in U937 cells. CONCLUSIONS WGCNA of gene coexpression networks identified CRIP1 as a potential prognostic biomarker gene in patients with AML.

Highly sensitive detection of Smoothened based on the drug binding and rolling cycle amplification

Metastases are the leading causes of death in cancer patients. Due to intimate connection with metastasis, Smoothened (Smo) has become a therapeutic target for antimetastatic drugs and can provide early warning of metastasis in breast cancer. Thus, we have developed an electrochemical method in Smo analysis based on small-molecule drugs. Smo on the metastatic cell surface can be internalized after combination with the small-molecule drug. The surplus small-molecule drug and rolling circle amplification (RCA) primer are competitively binding with capture probe on the electrode surface through the click chemical reaction. After RCA reaction, methylene blue is used to label the RCA product. In this process, the more Smo on the metastatic cell surface, the more RCA primer is bound with peptide on the electrode. Therefore, the obtained signal response is positively correlated to Smo on the cancer cells. Moreover, the RCA provides sufficiently high sensitivity, enabling the limit of detection of Smo to be calculated as 0.1 pM (S/N = 3). Owing to its desirable sensitivity, excellent reproducibility, and high selectivity, the proposed method may hold great potential in clinical practice in the future. Graphical abstract.

Dual-aptamer based electrochemical sandwich biosensor for MCF-7 human breast cancer cells using silver nanoparticle labels and a poly(glutamic acid)/MWNT nanocomposite

This paper reports on a sensitive and selective method for the detection of Michigan Cancer Foundation-7 (MCF-7) human breast cancer cells and MUC1 biomarker by using an aptamer-based sandwich assay. A biocompatible nanocomposite consisting of multiwall carbon nanotubes (MWCNT) and poly(glutamic acid) is placed on a glassy carbon electrode (GCE). The sandwich assay relies on the use of a mucin 1 (MUC1)-binding aptamer that is first immobilized on the surface of modified GCE. Another aptamer (labeled with silver nanoparticles) is applied for secondary recognition of MCF-7 cells in order to increase selectivity and produce an amplified signal. Differential pulse anodic stripping voltammetry was used to follow the electrochemical signal of the AgNPs. Under the optimal condition, the sensor responds to MCF-7 cells in the concentration range from 1.0 × 10² to 1.0 × 10⁷ cells·mL^-1 with a detection limit of 25 cells. We also demonstrate that the MUC1 tumor marker can be detected by the present biosensor. The assay is highly selective and sensitive, acceptably stable and reproducible. This warrants the applicability of the method to early diagnosis of breast cancer. Graphical abstract Schematic of the fabrication of an aptamer-based sandwich biosensor for Michigan Cancer Foundation-7 cells (MCF-7). A MWCNT-poly(glutamic acid) nanocomposite was used as a biocompatible matrix for MUC1-aptamer immobilization. Stripping voltammetry analysis of AgNPs was performed using aptamer conjugated AgNPs as signalling probe.

Research progresses on the functional polypeptides in the detection and imaging of breast cancer

Polypeptides as functional groups continue to garner significant interest in the detection and imaging of breast cancer, working as recognition elements, signal sources, building blocks and therapeutic reagents, etc.

A Graphene Oxide-Based Fluorescent Method for the Detection of Human Chorionic Gonadotropin

Human chorionic gonadotropin (hCG) has been regarded as a biomarker for the diagnosis of pregnancy and some cancers. Because the currently used methods (e.g., disposable Point of Care Testing (POCT) device) for hCG detection require the use of many less stable antibodies, simple and cost-effective methods for the sensitive and selective detection of hCG have always been desired. In this work, we have developed a graphene oxide (GO)-based fluorescent platform for the detection of hCG using a fluorescein isothiocyanate (FITC)-labeled hCG-specific binding peptide aptamer (denoted as FITC-PPLRINRHILTR) as the probe, which can be manufactured cheaply and consistently. Specifically, FITC-PPLRINRHILTR adsorbed onto the surface of GO via electrostatic interaction showed a poor fluorescence signal. The specific binding of hCG to FITC-PPLRINRHILTR resulted in the release of the peptide from the GO surface. As a result, an enhanced fluorescence signal was observed. The fluorescence intensity was directly proportional to the hCG concentration in the range of 0.05–20 IU/mL. The detection limit was found to be 20 mIU/mL. The amenability of the strategy to hCG analysis in biological fluids was demonstrated by assaying hCG in the urine samples.

Improvement of Site-Directed Protein-Polymer Conjugates: High Bioactivity and Stability Using a Soft Chain-Transfer Agent

Protein has been widely applied in biotechnology and biomedicine thanks to its unique properties of high catalytic activity, outstanding receptor-ligand specificity, and controllable sequence mutability. Owing to the easily induced structural variation and thus the inactivation of protein, there has been much effort to improve the structural stability and biological activity of proteins by the use of polymers to modify protein to construct protein-polymer conjugates. However, during the conjugation of polymer to protein active center, the great loss in the original biological activity of the protein is still a serious and so far unsolved question. Here, for the purpose of preparing site-directed and highly structurally stable protein-polymer conjugate, which would possess at least a substantially similar level of biological activity as the original unmodified protein, we proposed a new strategy by using a pyridine chain-transfer agent (CTA-Py) with a soft pyridine-terminated chain for visible-light-induced reversible addition-fragmentation chain transfer (RAFT) polymerization specifically on a number of sites close to the protein active center. The results showed that all the intermediate conjugates PPa-CTA-Py at different modification sites could retain full enzymatic activities (about 110-130% of the unmodified PPa). It was demonstrated by dynamic computer simulation that introducing of CTA-Py had little interference to the protein spatial structure as compared to the popular maleimide chain-transfer agent (CTA-Ma) with rigid maleimide-terminated. Moreover, intermediate conjugates PPa-CTA-Py is facile and ready for further light polymerization under mild conditions. Final PPa-PNIPAAm conjugate produced from CTA-Py exhibited excellent temperature responsiveness and maintained its enzymatic activity even at high temperature. These highly stable and responsive protein-polymer conjugates have great potential and could be widely used in various industrial, chemical, biological, and pharmaceutical applications.

An electrochemical peptide cleavage-based biosensor for matrix metalloproteinase-2 detection with exonuclease III-assisted cycling signal amplification

In this work, an electrochemical peptide biosensor was developed for matrix metalloproteinase-2 (MMP-2) detection by conversion of a peptide cleavage event into DNA detection with exonuclease III (Exo III)-assisted cycling signal amplification.

Sandwiched Electrochemiluminescent Peptide Biosensor for the Detection of Prognostic Indicator in Early-Stage Cancer Based on Hollow, Magnetic, and Self-Enhanced Nanosheets

Currently, peptide-based protein-recognition has been recognized as an effective and promising approach for protein assays. However, sandwiched peptide-based biosensor with high sensitivity and low background has not been proposed before. Herein, a sandwiched electrochemiluminescence (ECL) peptide-based biosensor is constructed for Cyclin A(2) (CA2), a prognostic indicator in early stage of multiple cancers, based on nanosheets with hollow, magnetic, and ECL self-enhanced properties. First, hollow and magnetic manganese oxide nanocrystals (H-Mn(3)O(4)) are synthesized using triblock copolymeric micelles with core-shell-corona architecture as templates. Then, polyethyleneimine (PEI) and the composite of platinum nanoparticles and tris (4,4'-dicarboxylicacid-2,2'-bipyridyl) ruthenium (II) (PtNPs-Ru) are immobilized on H-Mn(3)O(4) to form H-Mn(3)O(4) -PEI-PtNPs-Ru nanocomposite, in which PEI as coreactant can effectively enhance the luminous efficiency and PtNPs as nanochannels can greatly accelerate the electron transfer. Finally, due to the coordination between Eu(3+) and carboxyl, the obtained H-Mn(3)O(4) -PEI-PtNPs-Ru aggregates locally to form sheet-like nanostructures ((H-Mn(3)O(4) -PEI-PtNPs-Ru)(n) -Eu(3+)), by which the luminous efficiency is further increased. Based on the nanosheets and two designed peptides, a sandwiched ECL biosensor, using palladium nanocages synthesized through galvanic replacement reaction as substrate, is proposed for CA2 with a linear range from 0.001 to 100 ng mL(-1) and a detection limit of 0.3 pg mL(-1).

Sensitive colorimetric assays for α-glucosidase activity and inhibitor screening based on unmodified gold nanoparticles

A colorimetric sensor has been developed in this work to sensitively detect α-glucosidase activity and screen α-glucosidase inhibitors (AGIs) utilizing unmodified gold nanoparticles (AuNPs). The sensing strategy is based on triple-catalytic reaction triggered by α-glucosidase. In the presence of α-glucosidase, aggregation of AuNPs is prohibited due to the oxidation of cysteine to cystine in the system. However, with addition of AGIs, cysteine induced aggregation of AuNPs occurs. Thus, a new method for α-glucosidase activity detection and AGIs screening is developed by measuring the UV-vis absorption or visually distinguishing. A well linear relation is presented in a range of 0.0025-0.05 U mL(-1). The detection limit is found to be 0.001 U mL(-1) for α-glucosidase assay, which is one order of magnitude lower than other reports. The IC50 values of four kinds of inhibitors observed with this method are in accordance with other reports. The using of unmodified AuNPs in this work avoids the complicated and time-consuming modification procedure. This simple and efficient colorimetric method can also be extended to other enzymes assays.