A New Optimized Wrapper Gene Selection Method for Breast Cancer Prediction

Machine-learning algorithms have been widely used in breast cancer diagnosis to help pathologists and physicians in the decision-making process. However, the high dimensionality of genetic data makes the classification process a challenging task. In this paper, we propose a new optimized wrapper gene selection method that is based on a nature-inspired algorithm (simulated annealing (SA)), which will help select the most informative genes for breast cancer prediction. These optimal genes will then be used to train the classifier to improve its accuracy and efficiency. Three supervised machine-learning algorithms, namely, the support vector machine, the decision tree, and the random forest were used to create the classifier models that will help to predict breast cancer. Two different experiments were conducted using three datasets: Gene expression (GE), deoxyribonucleic acid (DNA) methylation, and a combination of the two. Six measures were used to evaluate the performance of the proposed algorithm, which include the following: Accuracy, precision, recall, specificity, area under the curve (AUC), and execution time. The effectiveness of the proposed classifiers was evaluated through comprehensive experiments. The results demonstrated that our approach outperformed the conventional classifiers as expected in terms of accuracy and execution time. High accuracy values of 99.77%, 99.45%, and 99.45% have been achieved by SA-SVM for GE, DNA methylation, and the combined datasets, respectively. The execution time of the proposed approach was significantly reduced, in comparison to that of the traditional classifiers and the best execution time has been reached by SA-SVM, which was 0.02, 0.03, and 0.02 on GE, DNA methylation, and the combined datasets respectively. In regard to precision and specificity, SA-RF obtained the best result of 100 on GE dataset. While SA-SVM attained the best recall result of 100 on GE dataset.     

Aptamer/Peptide-Functionalized Genome-Editing System for Effective Immune Restoration through Reversal of PD-L1-Mediated Cancer Immunosuppression

Effective reversal of tumor immunosuppression is of critical importance in cancer therapy. A multifunctional delivery vector that can effectively deliver CRISPR-Cas9 plasmid for β-catenin knockout to reverse tumor immunosuppression is constructed. The multi-functionalized delivery vector is decorated with aptamer-conjugated hyaluronic acid and peptide-conjugated hyaluronic acid to combine the tumor cell/nuclear targeting function of AS1411 with the cell penetrating/nuclear translocation function of TAT-NLS. Due to the significantly enhanced plasmid enrichment in malignant cell nuclei, the genome editing system can induce effective β-catenin knockout and suppress Wnt/β-catenin pathway, resulting in notably downregulated proteins involved in tumor progression and immunosuppression. Programmed death-ligand 1 (PD-L1) downregulation in edited tumor cells not only releases the PD-1/PD-L1 brake to improve the cancer killing capability of CD8⁺ T cells, but also enhances antitumor immune responses of immune cells. This provides a facile strategy to reverse tumor immunosuppression and to restore immunosurveillance and activate anti-tumor immunity.     

重组人淋巴细胞活化基因-3蛋白胞外段的真核表达及鉴定

目的真核表达重组人淋巴细胞活化基因-3(lymphocyte activation gene-3,LAG-3)蛋白胞外段,并进行鉴定。方法用植物血球凝集素(phytohaemagg lutinin,PHA)刺激Jurkat细胞,流式细胞术检测Jurkat细胞中LAG-3蛋白的表达;提取Jurkat细胞总mRNA,RT-PCR法扩增人LAG-3蛋白胞外段基因片段,同时在蛋白C-末端引入His标签,将其克隆入载体pcDNA3. 1+,构建重组质粒,转染Expi293F真核细胞,当细胞活率低于50%时收获细胞上清,经镍柱亲合层析纯化。纯化产物进行4%~20%SDS-PAGE、HPLC及Western blot分析,BCA法测定浓度。结果经菌液PCR、双酶切及测序鉴定,表明质粒构建正确。重组表达蛋白的相对分子质量约60 000,纯化后纯度达95%以上,与鼠抗LAG-3单克隆抗体可发生特异性结合,浓度为2. 4 mg/mL。结论成功构建了重组真核表达质粒LAG-3/pcDNA3. 1+,并于Expi293F细胞中表达,纯化获得了纯度较高的LAG-3蛋白,为后期LAG-3蛋白的相关研究及其单抗的制备奠定了基础。     

Polymorphisms of Encoding Genes IL1RN and P2RX7 in Apical Root Resorption in Patients after Orthodontic Treatment

External apical root resorption (EARR) is one of the most serious complications associated with orthodontic treatment. The aim of the study was to analyze the relationships between selected single nucleotide polymorphisms (SNPs) in Interleukin 1 receptor antagonist (IL1RN), purinoreceptor P2X7 (P2RX7) and EARR in patients after orthodontic treatment. The study comprised 101 patients who underwent a complex orthodontic treatment with a combination of fixed appliances. Roots were measured based on orthopantomograms and lateral cephalometric radiographs taken before and at the end of the treatment using diagnostic software. Proportional measurements of selected teeth were made using the modified Linge and Linge methods. Based on the presence or absence of EARR, patients were divided into two groups: control group, 61 patients without EARR (with 0.90 ≤ rRCR ≤ 1.00), and EARR group, 40 patients with EARR (rRCR < 0.90). Root resorption in selected groups was also evaluated with the scores of Malmgren and Levander. SNP analysis was performed using the real-time polymerase chain reaction (PCR) method. The analysis indicated that a specific haplotype of P2RX7 (rs208294) and IL1RN (rs419598) modified the risk of EARR development (p < 0.05), with a Bonferroni correction. The analysis of the P2RX7 and IL1RN gene polymorphisms showed that the presence of SNPs of these genes may predispose individuals to EARR. These findings indicate that EARR is a complex condition influenced not only by environmental factors and needs further study on the genetic risk factors.     

安徽地区汉族心血管疾病患者SLCO1B1与ApoE基因多态性分布及其在他汀类药物临床个体化应用中的意义

目的：探讨脂质及药物代谢相关基因SLCO1B1和ApoE的基因多态性在安徽地区汉族心血管疾病患者中的分布，以评估他汀类药物个体化用药的效益/风险比。方法：利用PCR-荧光探针法技术检测2019年1月至2020年8月合肥市第二人民医院736例心血管疾病患者外周血基因组中SLCO1B1基因的rs2306283（388A>G）和rs4149056（521T>C）位点和ApoE基因的rs429358（388T>C）和rs7412（526C>T）位点的基因多态性分布特点，并与已报道的中国其他地区汉族心血管疾病患者的数据进行比较，分析不同地区间的基因型分布差异。结果：检测到安徽地区汉族心血管疾病患者中SLCO1B1基因型有6种，分别为*1a/*1a型（6.11%）、*1a/*1b型（29.08%）、*1b/*1b型（44.57%）、*1a/*15型（4.08%）、*1b/*15型（15.49%）、*15/*15型（0.68%），未检测到*1a/*5型、*5/*5型和*5/*15型；ApoE基因有6种表型，分别为E2/E2型（0.41%）、E2/E3型（11.96%）、E2/E4型（1.09%）、E3/E3型（67.66%）、E3/E4型（17.93%）、E4/E4型（0.95%）。两种基因的基因多态性频率分布满足Hardy-Weinberg遗传平衡，具有群体代表性。本研究人群中携带SLCO1B1正常肌病风险型的比例最高，约占79.76%；SLCO1B1中度肌病风险型和高度肌病风险型的人群比例较低，分别为19.57%和0.68%。ApoE大众类基因型比例最高，约占68.75%；ApoE保护类基因型及风险类基因型的人群比例分别为12.37%和18.88%。不同性别间SLCO1B1和ApoE基因表型患者差异无统计学意义。与华南地区心血管疾病患者相比，安徽地区ApoE基因多态性分布差异有统计学意义（P<0.05）。结论：安徽地区736例心血管疾病患者SLCO1B1和ApoE基因型分别以他汀药物剂量耐受性较高的正常肌病风险型和对他汀药物敏感的大众类基因型为主，服用他汀类药物诱发肌病的风险较低，降脂疗效较好；且两种基因的多态性分布均不受性别的影响，但ApoE基因多态性分布特征可能在地域上存在差异。因此，检测SLCO1B1和APOE基因多态性对于临床评估效益/风险比有重要的指导意义。     

A Nanochannel Platform for Single DNA Studies: From Crowding,Protein DNA Interaction,to Sequencing of Genomic Information

The study of nanochannel-confined DNA is important from biotechnological and biophysical points of view. We produce nanochannels in elastomer with soft lithography and proton beam writing. Issues concerning DNA confined in such quasi one-dimensional channels are discussed. We describe DNA stretching via the control of channel diameter and buffer conditions and how the extension can be interpreted with theory and computer simulation. We then discuss the conformation of nano-confined DNA crowded by neutral polymers and like-charged proteins. As an example of a protein that has an affinity to DNA, the effect of heat-stable nucleoid-structuring protein, H-NS, on the folding and compaction of DNA is reviewed. Compaction of DNA by eukaryotic protamine and unpacking of pre-compacted DNA through an increase in salt concentration are discussed. We review results obtained with a novel, cross-channel device that allows the monitoring of the dynamic, conformational response of DNA after exposure to a ligand or protein and/or a change in buffer conditions in situ. As a biotechnological application, linearization of DNA by bottlebrush coating with a polypeptide copolymer is discussed. It is demonstrated that large-scale genomic organization can be sequenced using single DNA molecules on an array of elastomeric nanochannels. Overall, our results show that the effects of ligands and proteins on the conformation, folding, and condensation of DNA are not only related to classical controlling factors, such as osmotic pressure, charge, and binding, but that the interplay with confinement in a nanospace is of paramount importance.