Bioinformatics analysis for structure and function of CPR of Plasmodium falciparum

Objective:To analyse the structure and function of NADPH-cytochrome p450 reductase(CYPOR or CPR) from Plasmodium falciparum(Pf),and to predict its’ drug target and vaccine target. Methods:The structure,function,drug target and vaccine target of CPR from Plasmodium falciparum were analyzed and predicted by bioinformatics methods.Results:PfCPR,which was older CPR,had close relationship with the CPR from other Plasmodium species,but it was distant from its hosts,such as Homo sapiens and Anopheles.PfCPR was located in the cellular nucleus of Plasmodium falciparum.335aa-352aa and 591aa - 608aa were inserted the interior side of the nuclear membrane,while 151aa-265aa was located in the nucleolus organizer regions.PfCPR had 40 function sites and 44 protein-protein binding sites in amino acid sequence.The teriary structure of laa-700aa was forcep-shaped with wings.15 segments of PfCPR had no homology with Homo sapien CPR and most were exposed on the surface of the protein.These segments had 25 protein-protein binding sites.While 13 other segments all possessed function sites. Conclusions:The evolution or genesis of Plasmodium falciparum is earlier than those of Homo sapiens.PfCPR is a possible resistance site of antimalarial drug and may involve immune evasion, which is associated with parasite of sporozoite in hepatocytes.PfCPR is unsuitable as vaccine target,but it has at least 13 ideal drug targets.

机器学习方法在CRISPR/Cas9系统中的应用

基于CRISPR/Cas9系统介导的第三代基因组定点编辑技术,已被广泛应用于基因编辑和基因表达调控等研究领域。如何提高该技术对基因组编辑的效率与特异性、最大限度降低脱靶风险一直是该领域的难点。近年来,机器学习为解决CRISPR/Cas9系统所面临的问题提供了新思路,基于机器学习的CRISPR/Cas9系统已逐渐成为研究热点。本文阐述了CRISPR/Cas9的作用机理,总结了现阶段该技术面临的基因组编辑效率低、存在潜在的脱靶效应、前间区序列邻近基序(PAM)限制识别序列等问题,最后对机器学习应用于优化设计高效向导RNA(sg RNA)序列、预测sg RNA的活性、脱靶效应评估、基因敲除、高通量功能基因筛选等领域的研究现状与发展前景进行了展望,以期为基因组编辑领域的研究提供参考。

Bioinformatics analysis and prediction for structure and function of nitric oxide synthase and similar proteins from Plasmodium berghei

ObjectiveTo search and analyze nitric oxide synthase (NOS) and similar proteins from Plasmodium berghei(Pb).MethodsThe structure and function of nitric oxide synthase and similar proteins from Plasmodium berghei were analyzed and predicted by bioinformatics.ResultsPbNOS were not available, but nicotinamide adenine dinucleotide 2′–phosphate reduced tetrasodium (NADPH)–cytochrome p450 reductase(CPR) were gained. PbCPR was in the nucleus of Plasmodium berghei, while 134aa–229aa domain was localize in nucleolar organizer. The amino acids sequence of PbCPR had the closest genetic relationship with Plasmodium vivax showing a 73% homology. The tertiary structure of PbCPR displayed the forcep–shape with wings, but no wings existed in the tertiary structure of its' host, Mus musculus(Mm). 137aa–200aa, 201aa–218aa, 220aa–230aa, 232aa–248, 269aa–323aa, 478aa–501aa and 592aa–606aa domains of PbCPR showed no homology with MmCPRs', and all domains were exposed on the surface of the protein.ConclusionsNOS can't be found in Plasmodium berghei and other Plasmodium species. PbCPR may be a possible resistance site of antimalarial drug, and the targets of antimalarial drug and vaccine. It may be also one of the mechanisms of immune evasion. This study on Plasmodium berghei may be more suitable to Plasmodium vivax. And 137aa–200aa, 201aa–218aa, 220aa–230aa, 232aa–248, 269aa–323aa, 478aa–501aa and 592aa–606aa domains of PbCPR are more ideal targets of antimalarial drug and vaccine.

A zwitterionic polymer-inspired material mediated efficient CRISPR-Cas9 gene editing

The typeⅡ prokaryotic CRISPR (clustered regularly interspaced short palindromic repeats)/Cas9 (CRISPR/Cas9) adaptive immune system is a cutting-edge genome-editing toolbox.However,its applications are still limited by its inefficient transduction.Herein,we present a novel gene vector,the zwitterionic polymer-inspired material with branched structure (ZEBRA) for efficient CRISPR/Cas9 delivery.Polo-like kinase 1 (PLK1) acts as a master regulator of mitosis and overexpresses in multiple tumor cells.The Cas9 and single guide sgRNA (sgRNA)-encoded plasmid was transduced to knockout Plk1 gene,which was expected to inhibit the expression of PLK1.Our studies demonstrated that ZEBRA enabled to transduce the CRISPR/Cas9 system with large size into the cells efficiently.The transduction with ZEBRA was cell line dependent,which showed~10-fold higher in CD44-positive cancer cell lines compared with CD44-negative ones.Furthermore,ZEBRA induced highlevel expression of Cas9 proteins by the delivery of CRISPR/Cas9 and efficient gene editing of Plk1 gene,and inhibited the tumor cell growth significantly.This zwitterionic polymerinspired material is an effective and targeted gene delivery vector and further studies are required to explore its potential in gene delivery applications.

MiR-142-3p enhances chemosensitivity of breast cancer cells and inhibits autophagy by targeting HMGB1

MiR-142-3p has been reported to act as a tumor suppressor in breast cancer.However,the regulatory effect of miR-142-3p on drug resistance of breast cancer cells and its underlying mechanism remain unknown.Here,we found that miR-142-3p was significantly downregulated in the doxorubicin(DOX)-resistant MCF-7 cell line(MCF-7/DOX).MiR-142-3p overexpression increased DOX sensitivity and enhanced DOXinduced apoptosis in breast cancer cells.High-mobility group box 1(HMGB1)is a direct functional target of miR-142-3p in breast cancer cells and miR-142-3p negatively regulated HMGB1 expression.Moreover,overexpres sion of HMGB1 dramatically reversed the promotion of apoptosis and inhibition of autophagy mediated by miR-142-3p up-regulation.In conclusion,miR-142-3p overexpression may inhibit autophagy and promote the drug sensitivity of breast cancer cells to DOX by targeting HMGB 1.The miR-142-3 p/HMGB1 axis might be a novel target to regulate the drug resistance of breast cancer patients.

Lineage reprogramming of fibroblasts into induced cardiac progenitor cells by CRISPR/Cas9-based transcriptional activators

Overexpression of exogenous lineage-determining factors succeeds in directly reprogramming fibroblasts to various cell types.Several studies have reported reprogramming of fibroblasts into induced cardiac progenitor cells(iCPCs).CRISPR/Cas9-mediated gene activation is a potential approach for cellular reprogramming due to its high precision and multiplexing capacity.Here we show lineage reprogramming to iCPCs through a dead Cas9(dCas9)-based transcription activation system.Targeted and robust activation of endogenous cardiac factors,including GATA4,HAND2,MEF2 C and TBX5(G,H,M and T;GHMT),can reprogram human fibroblasts toward iCPCs.The iCPCs show potentials to differentiate into cardiomyocytes,smooth muscle cells and endothelial cells in vitro.Addition of MEIS1 to GHMT induces cell cycle arrest in G2/M and facilitates cardiac reprogramming.Lineage reprogramming of human fibroblasts into iCPCs provides a promising cellular resource for disease modeling,drug discovery and individualized cardiac cell therapy.

The construction of drug-resistant cancer cell lines by CRISPR/Cas9 system for drug screening

Cancer therapy is often hampered by the rapid emergence of drug resistance. Drug-resistant cellular models are essential for understanding the drug resistance and developing new therapeutics. The low efficiency and long time required in creating these models are major obstacles hindering drug resistance research and drug screening. Herein, we report an approach that can accelerate(shortening the time from years to 3 weeks) the establishment of cancer cell line-based, inheritable drug resistance models by specific knockout of MED12 gene using CRISPR/Cas9 system. The resultant MED12^(KO) A375(melanoma)cell line was resistant to inhibitors of B-Raf proto-oncogene, serine/threonine kinase(BRAF), whereas the resultant MED12^(KO) PC9(non-small cell lung cancer) cell line was resistant to inhibitors of epidermal growth factor receptor(EGFR). Evaluation of anti-cancer drugs and their combinations shows that certain combinations of BRAF inhibitors and TGF-β receptor(TGF-βR) inhibitors are active in suppressing the growth of MED12^(KO) A375 cells, and a few combinations of EGFR inhibitors and TGF-βR inhibitors were active in suppressing the growth of MED12^(KO) PC9 cells. The drug-resistant models will be useful in screening novel drugs and drug combinations for multi-drug-resistant cancer therapy.

A splice variant of PGRP-LC required for expression of antimicrobial peptides in Anopheles gambiae

Members of the peptidoglycan recognition protein （PGRP） family play essential roles in different manifestations of immune responses in insects. PGRP-LC, one of seven members of this family in the malaria vector Anopheles gambiae produced several spliced variants. Here we show that PGRP-LC, and not other members of the PGRP family nor the six members of the Gram-negative binding protein families, is required for the expression of antimicrobial peptide genes （such as CEC1 and GAM1） under the control of the Imd-Rel2 pathway in an A. gambiae cell line, 4a3A. PGRP-LC produces many splice variants that can be classified into three sub-groups （LC1, LC2 and LC3）, based on the carboxyl terminal sequences. RNA interference against one LC1 sub-group resulted in dramatic reduction of CEC1 and GAM1. Over-expression of LCla and to a lesser extent LC3a （a member of the LC1 and LC3 sub-group, respectively） in the 4a3A cell line enhances the expression of CEC1 and GAM1. These results demonstrate that the LC1-subgroup splice variants are essential for the expression of CEC1 and GAM1 in A. gambiae cell line.