Biomedical subjects

Yining Zhao

Publications and source records attributed to Yining Zhao.

6 recordsLinked to original sources

PubMed2026

Machine Learning-Based Identification of Survival-Associated CpG Biomarkers in Pancreatic Ductal Adenocarcinoma.

Pancreatic ductal adenocarcinoma (PDAC) is an exceptionally aggressive cancer with a 5-year survival rate of less than 10%, driven by late-stage diagnosis, limited treatment options, and a lack of reliable biomarkers for early detection and prognosis. In this study, we integrated DNA methylation data from TCGA and ICGC cohorts, categorizing samples based on survival time, and identified 688 differentially methylated CpG sites, along with 224 CpG biomarkers significantly associated with patient survival through statistical and machine learning-based analyses. We developed a random forest model to predict patient survival, achieving 85.2% accuracy for short-survival patients and 70.0% for long-survival patients in the validation set. External dataset validation further confirmed the model's robustness and accuracy. De novo motif analysis of genomic regions surrounding the 224 CpG biomarkers identified TWIST1 and FOXA2 as key transcriptional regulators enriched in survival-associated CpG sites, linking their activity to patient survival outcomes. Collectively, our findings highlight valuable epigenetic biomarkers and provide a predictive model to assess PDAC risk levels post-surgery, offering the potential for improved patient stratification and personalized therapeutic strategies.

DNA methylation↗

PubMed2026

CasY7: An optimized Cas12i system for enhanced genome editing in monocot crops.

The CRISPR-Cas12 family nucleases, particularly the Cas12i subtypes, are considered promising alternatives to Cas9 for genome editing in plants. We previously developed a new Cas12i variant, CasY7, which has been successfully applied in clinical trials; its performance in plants remains to be investigated. Initial testing in stable transgenic maize and rice showed that the codon-optimized CasY7 (pCasY7e1) achieved average editing efficiencies of 58.7% and 62.3% across five target sites, respectively, outperforming the typical Cpf1 (pCpf1) control that targets the same sites. To further enhance activity, we fused T5 exonuclease to CasY7 (pCasY7e2), which shifted mutation profiles toward larger deletions, and subsequently integrated an MS2 aptamer into the crRNA scaffold (pCasY7e3). The optimized pCasY7e3 system increased editing efficiencies to 87.7% in maize and 82.9% in rice-approximately 2.7-fold higher than pCpf1. We further demonstrated multiplexed editing in maize, generating biallelic dwarf mutants, and validated functionality in hexaploid wheat with editing efficiencies up to 58.8%. Overall, our comprehensive validation across 942 transgenic plants confirmed robust editing in maize, rice, and wheat, establishing CasY7 as a high-efficiency addition to the CRISPR toolkit.

Zea mays↗

PubMed2025

Machine Learning-Based Identification of Survival-Associated CpG Biomarkers in Pancreatic Ductal Adenocarcinoma.

Pancreatic ductal adenocarcinoma (PDAC) is an exceptionally aggressive cancer with a 5-year survival rate of less than 10%, driven by late-stage diagnosis, limited treatment options, and a lack of reliable biomarkers for early detection and prognosis. In this study, we integrated DNA methylation data from TCGA and ICGC cohorts, categorizing samples based on survival time, and identified 684 differentially methylated CpG sites, along with 224 CpG biomarkers significantly associated with patient survival through statistical and machine learning-based analyses. We developed a random forest model to predict patient survival, achieving 85.2% accuracy for short-survival patients and 70.0% for long-survival patients in the validation set. External dataset validation further confirmed the model's robustness and accuracy. De novo motif analysis of genomic regions surrounding the 224 CpG biomarkers identified TWIST1 and FOXA2 as key transcriptional regulators enriched in survival-associated CpG sites, linking their activity to patient survival outcomes. Collectively, our findings highlight valuable epigenetic biomarkers and provide a predictive model to assess PDAC risk levels post-surgery, offering the potential for improved patient stratification and personalized therapeutic strategies.

Journal Article↗

PubMed2003

Rapid method development for chiral separation in drug discovery using sample pooling and supercritical fluid chromatography-mass spectrometry.

A novel strategy for rapid chiral method development has been implemented using sample pooling and supercritical fluid chromatography-mass spectrometry (SFC-MS) on four chiral stationary phases, namely Chiralpak AD and AS, and Chiralcel OJ and OD, and eight different modifier concentrations (5 to 40% methanol-0.2% isopropylamine). The screening is performed under an outlet pressure of 110 bar at 35 degrees C, and at a flow-rate of 2.5 ml/min for the initial 20 min and then ramped up to 4 ml/min and held for 4.5 min to elute all solutes from the column. The entire process is fully automated from injection to data processing, and operates unattended for 15 h overnight to obtain optimal chiral separation for multiple compounds. A unique feature of using SFC-MS to monitor chiral synthesis is the negligible interferences from achiral impurities. In addition, with SFC-MS, enantiomeric excess can be determined with much lower detection limits than UV and much shorter analysis times compared to normal-phase/reversed-phase liquid chromatography.

Amylose↗

PubMed2003

Photolysis of hop-derived trans-iso-alpha-acids and trans-tetrahydroiso-alpha-acids: product identification in relation to the lightstruck flavour of beer.

The photolysis of hop-derived trans-iso-alpha-acids (2a-c; naturally occurring bitter compounds present in beer) and of trans-tetrahydroiso-alpha-acids (5a-c; semi-synthetic advanced hop products) was investigated at 300 nm in methanol. The complex photoreaction mixtures were separated by high-performance liquid chromatography (HPLC) using diode array detection and the major photoreaction products were identified by HPLC-mass spectroscopy. The main part of the mixture consisted of compounds, which originated from recombination of radicals derived from Norrish Type I photocleavage of the acyloin moiety in both trans-iso-alpha-acids and trans-tetrahydroiso-alpha-acids. The results confirm the intermediacy of radicals that were previously identified by time-resolved electron paramagnetic resonance and they bear relevance to the formation of the lightstruck flavour that is generated when beer is exposed to light. Additionally, new photoproducts were found that are formed by photochemical reactions hitherto undiscovered in hop chemistry, including photoenolization of trans-isohumulone (2a) leading to trans-alloisohumulone (13a) and a retro oxa-di-pi-methane rearrangement in trans-isohumulone (2a) and trans-tetrahydroiso-alpha-acids to humulone (1a) and tetrahydro-alpha-acids (23a-b), respectively.

Journal Article↗

PubMed2002

High-throughput logP measurement using parallel liquid chromatography/ultraviolet/mass spectrometry and sample-pooling.

A novel approach to high-throughput logP measurement based on liquid chromatography/ultraviolet/mass spectrometry (LC/UV/MS) is proposed. The logP value is determined by correlation with the logk value, where k is the capacity factor k = (t(r)-t(0))/t(0), with the logP value using a defined set of standards. Since the analyte retention time (t(r)) is determined from the appropriate extracted ion chromatogram (EIC), there are no interferences from impurities and this allows the pooling of multiple compounds into one injection. To ensure the accuracy and instrument robustness in a routine high-throughput environment, a simple and MS-friendly mobile phase consisting of 20 mM ammonium carbonate (pH 8.0) for basic compounds or 20 mM ammonium formate (pH 1.0) for acidic compounds, both in combination with methanol at a ratio of 45:55, is used. This approach has been successfully used on single as well as parallel multi-channel LC/UV/MS systems to screen small to large sets of lead compounds and their analogs. A high-throughput capability to analyze over 1000 compounds per day has been achieved.

Animals↗