Changkai Sun

Xinyu Liu, Siyu Xu, Chunying Liu, Zhenghao Wang, Bo Wu, Meijuan Guo, Changkai Sun, and Hongshan Yu. J. Microbiol. Biotechnol. 2024;34:1-10. https://doi.org/10.4014/jmb.2408.08046

Scholars have recently used various methods to study the human body’s characteristics, propose improvements, and rely on medical data. This research introduces a new real−time data collection and analysis system comprising two components: a smart mask for data collection and a processing unit for analysis and storage. The medical mask incorporates four sensors: three heat sensors to measure the nose tip and exhaled air temperature from the nostrils and mouth, along with a microphone for audio data. Collected data is instantly transmitted to the processing unit. Temperature readings are labeled and stored for analysis, while audio data is classified into breathing, coughing, and speaking categories using the Support Vector Machine (SVM) algorithm. The SVM’s performance is further optimized using the Lion Algorithm. Evaluation results indicate satisfactory accuracy for temperature data collected from the mask. The SVM achieved 84.3% accuracy for sound data classification, while the Lion algorithm−optimized SVM achieved an even higher accuracy of 93.6%. Future work aims to establish a reliable data collection tool that will serve as the foundation for developing an intelligent human body analysis model called the real human body neural network (rhBNN+).

Zhenghao Wang, Chunying Liu, Hongshan Yu, Bo Wu, Baoyu Huai, Ziyu Zhuang, Changkai Sun, Longquan Xu, and Fengxie Jin. J. Microbiol. Biotechnol. 2022;32:437-46. https://doi.org/10.4014/jmb.2112.12036

Highly efficient gene knockout (KO) editing of CRISPR–Cas9 has been achieved in iPSCs, whereas homology-directed repair (HDR)-mediated precise gene knock-in (KI) and high-level expression are still bottlenecks for the clinical applications of iPSCs. Here, we developed a novel editing strategy that targets introns. By targeting the intron before the stop codon, this approach tolerates reading frameshift mutations caused by nonhomologous end-joining (NHEJ)-mediated indels, thereby maintaining gene integrity without damaging the non-HDR-edited allele. Furthermore, to increase the flexibility and screen for the best intron-targeting sgRNA, we designed an HDR donor with an artificial intron in place of the endogenous intron. The presence of artificial introns, particularly an intron that carries an enhancer element, significantly increased the reporter expression levels in iPSCs compared to the intron-deleted control. In addition, a combination of the small molecules M3814 and trichostatin A (TSA) significantly improves HDR efficiency by inhibiting NHEJ. These results should find applications in gene therapy and basic research, such as creating reporter cell lines.

During the course of a review of our publication, an error in the title paper

Genome editing of human induced pluripotent stem cells (iPSCs) is instrumental for functional genomics, disease modeling, and regenerative medicine. However, low editing efficiency has hampered the applications of CRISPR–Cas9 technology in creating knockin (KI) or knockout (KO) iPSC lines, which is largely due to massive cell death after electroporation with editing plasmids. Here, we report that the transient delivery of BCL-XL increases iPSC survival by ∼10-fold after plasmid transfection, leading to a 20- to 100-fold increase in homology-directed repair (HDR) KI efficiency and a 5-fold increase in non-homologous end joining (NHEJ) KO efficiency. Treatment with a BCL inhibitor ABT-263 further improves HDR efficiency by 70% and KO efficiency by 40%. The increased genome editing efficiency is attributed to higher expressions of Cas9 and sgRNA in surviving cells after electroporation. HDR or NHEJ efficiency reaches 95% with dual editing followed by selection of cells with HDR insertion of a selective gene. Moreover, KO efficiency of 100% can be achieved in a bulk population of cells with biallelic HDR KO followed by double selection, abrogating the necessity for single cell cloning. Taken together, these simple yet highly efficient editing strategies provide useful tools for applications ranging from manipulating human iPSC genomes to creating gene-modified animal models.

Epilepsy is a complex neurological disorder and a significant health problem. The pathogenesis of epilepsy remains obscure in a significant number of patients and the current treatment options are not adequate in about a third of individuals which were known as refractory epilepsies (RE). Network medicine provides an effective approach for studying the molecular mechanisms underlying complex diseases. Here we integrated 1876 disease-gene associations of RE and located those genes to human protein-protein interaction (PPI) network to obtain 42 significant RE-associated disease modules. The functional analysis of these disease modules showed novel molecular pathological mechanisms of RE, such as the novel enriched pathways (e.g., “presynaptic nicotinic acetylcholine receptors”, “signaling by insulin receptor”). Further analysis on the relationships between current drug targets and the RE-related disease genes showed the rational mechanisms of most antiepileptic drugs. In addition, we detected ten potential novel drug targets (e.g., KCNA1, KCNA4-6, KCNC3, KCND2, KCNMA1, CAMK2G, CACNB4 and GRM1) located in three RE related disease modules, which might provide novel insights into the new drug discovery for RE therapy.