Genomics, Proteomics & Bioinformatics最新文献

{"title":"TransCell: In silico Characterization of Genomic Landscape and Cellular Responses by Deep Transfer Learning","authors":"Shan-Ju Yeh, Shreya Paithankar, Ruoqiao Chen, Jing Xing, Mengying Sun, Ke Liu, Jiayu Zhou, Bin Chen","doi":"10.1093/gpbjnl/qzad008","DOIUrl":"https://doi.org/10.1093/gpbjnl/qzad008","url":null,"abstract":"<jats:title>Abstract</jats:title> Gene expression profiling of new or modified cell lines becomes routine today; however, obtaining comprehensive molecular characterization and cellular responses for a variety of cell lines, including those derived from underrepresented groups, is not trivial when resources are minimal. Using gene expression to predict other measurements has been actively explored; however, systematic investigation of its predictive power in various measurements has not been well studied. We evaluated commonly used machine learning methods and presented TransCell, a two-step deep transfer learning framework that utilized the knowledge derived from pan-cancer tumor samples to predict molecular features and responses. Among these models, TransCell has the best performance in predicting metabolite, gene effect score (or genetic dependency), and drug sensitivity, and has comparable performance in predicting mutation, copy number variation, and protein expression. Notably, TransCell improved the performance by over 50% in drug sensitivity prediction and achieved a correlation of 0.7 in gene effect score prediction. Furthermore, predicted drug sensitivities revealed potential repurposing candidates for new 100 pediatric cancer cell lines, and predicted gene effect scores reflected BRAF resistance in melanoma cell lines. Together, we investigated the predictive power of gene expression in six molecular measurement types and developed a web portal (http://apps.octad.org/transcell/) that enables the prediction of 352,000 genomic and cellular response features solely from gene expression profiles.","PeriodicalId":12528,"journal":{"name":"Genomics, Proteomics & Bioinformatics","volume":"12 1","pages":""},"PeriodicalIF":9.5,"publicationDate":"2024-01-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139921997","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Microbiome in Female Reproductive Health: Implications for Fertility and Assisted Reproductive Technologies","authors":"Liwen Xiao, Zhenqiang Zuo, Fangqing Zhao","doi":"10.1093/gpbjnl/qzad005","DOIUrl":"https://doi.org/10.1093/gpbjnl/qzad005","url":null,"abstract":"<jats:title>Abstract</jats:title> The microbiome plays a critical role in the process of conception and the outcomes of pregnancy. Disruptions in microbiome homeostasis in women of reproductive age can lead to various pregnancy complications, which significantly impact maternal and fetal health. Recent studies have associated the microbiome in the female reproductive tract (FRT) with assisted reproductive technology (ART) outcomes, and restoring microbiome balance has been shown to improve fertility in infertile couples. This review provides an overview of the role of the microbiome in female reproductive health, including its implications for pregnancy outcomes and ARTs. Additionally, recent advances in the use of microbial biomarkers as indicators of pregnancy disorders are summarized. A comprehensive understanding of the characteristics of the microbiome before and during pregnancy and its impact on reproductive health will greatly promote maternal and fetal health. Such knowledge can also contribute to the development of ARTs and microbiome-based interventions.","PeriodicalId":12528,"journal":{"name":"Genomics, Proteomics & Bioinformatics","volume":"7 1","pages":""},"PeriodicalIF":9.5,"publicationDate":"2024-01-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139922077","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Q-BioLiP: A Comprehensive Resource for Quaternary Structure-based Protein–ligand Interactions","authors":"Hong Wei, Wenkai Wang, Zhenling Peng, Jianyi Yang","doi":"10.1093/gpbjnl/qzae001","DOIUrl":"https://doi.org/10.1093/gpbjnl/qzae001","url":null,"abstract":"<jats:title>Abstract</jats:title> Since its establishment in 2013, BioLiP has become one of the widely used resources for protein–ligand interactions. Nevertheless, several known issues occurred with it over the past decade. For example, the protein–ligand interactions are represented in the form of single-chain-based tertiary structures, which may be inappropriate as many interactions involve multiple protein chains (known as quaternary structures). We sought to address these issues, resulting in Q-BioLiP, a comprehensive resource for quaternary structure-based protein–ligand interactions. The major features of Q-BioLiP include: (1) representing protein structures in the form of quaternary structures rather than single-chain-based tertiary structures; (2) pairing DNA/RNA chains properly rather than separation; (3) providing both experimental and predicted binding affinities; (4) retaining both biologically relevant and irrelevant interactions to alleviate the problem of the wrong justification of ligands’ biological relevance; and (5) developing a new quaternary structure-based algorithm for the modelling of protein–ligand complex structure. With these new features, Q-BioLiP is expected to be a valuable resource for studying biomolecule interactions, including protein–small molecule interaction, protein–metal ion interaction, protein–peptide interaction, protein–protein interaction, protein–DNA/RNA interaction, and RNA–small molecule interaction. Q-BioLiP is freely available at https://yanglab.qd.sdu.edu.cn/Q-BioLiP/.","PeriodicalId":12528,"journal":{"name":"Genomics, Proteomics & Bioinformatics","volume":"118 1","pages":""},"PeriodicalIF":9.5,"publicationDate":"2024-01-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139921994","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Systematic Exploration of Optimized Base Editing gRNA Design and Pleiotropic Effects with BExplorer","authors":"Gongchen Zhang ,&nbsp;Chenyu Zhu ,&nbsp;Xiaohan Chen ,&nbsp;Jifang Yan,&nbsp;Dongyu Xue,&nbsp;Zixuan Wei,&nbsp;Guohui Chuai,&nbsp;Qi Liu","doi":"10.1016/j.gpb.2022.06.005","DOIUrl":"10.1016/j.gpb.2022.06.005","url":null,"abstract":"<div><div><strong>Base editing</strong> technology is being increasingly applied in genome engineering, but the current strategy for designing guide RNAs (gRNAs) relies substantially on empirical experience rather than a dependable and efficient <em>in silico</em> design. Furthermore, the pleiotropic effect of base editing on disease treatment remains unexplored, which prevents its further clinical usage. Here, we presented BExplorer, an integrated and comprehensive computational pipeline to optimize the design of gRNAs for 26 existing types of base editors <em>in silico</em>. Using BExplorer, we described its results for two types of mainstream base editors, BE3 and ABE7.10, and evaluated the pleiotropic effects of the corresponding base editing loci. BExplorer revealed 524 and 900 editable pathogenic single nucleotide polymorphism (SNP) loci in the human genome together with the selected optimized gRNAs for BE3 and ABE7.10, respectively. In addition, the impact of 707 edited pathogenic SNP loci following base editing on 131 diseases was systematically explored by revealing their pleiotropic effects, indicating that base editing should be carefully utilized given the potential pleiotropic effects. Collectively, the systematic exploration of optimized base editing <strong>gRNA design</strong> and the corresponding pleiotropic effects with BExplorer provides a computational basis for applying base editing in disease treatment.</div></div>","PeriodicalId":12528,"journal":{"name":"Genomics, Proteomics & Bioinformatics","volume":"21 6","pages":"Pages 1237-1245"},"PeriodicalIF":11.5,"publicationDate":"2023-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11082405/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40475056","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Sequence-based Functional Metagenomics Reveals Novel Natural Diversity of Functional CopA in Environmental Microbiomes","authors":"Wenjun Li ,&nbsp;Likun Wang ,&nbsp;Xiaofang Li ,&nbsp;Xin Zheng ,&nbsp;Michael F. Cohen ,&nbsp;Yong-Xin Liu","doi":"10.1016/j.gpb.2022.08.006","DOIUrl":"10.1016/j.gpb.2022.08.006","url":null,"abstract":"<div><div>Exploring the <strong>natural diversity</strong> of functional genes/proteins from environmental DNA in high throughput remains challenging. In this study, we developed a sequence-based <strong>functional metagenomics</strong> procedure for mining the diversity of copper (Cu) resistance gene <strong><em>copA</em></strong> in global microbiomes, by combining the metagenomic assembly technology, local BLAST, <strong>evolutionary trace analysis</strong> (ETA), chemical synthesis, and conventional functional genomics. In total, 87 metagenomes were collected from a public database and subjected to <em>copA</em> detection, resulting in 93,899 hits. Manual curation of 1214 hits of high confidence led to the retrieval of 517 unique CopA candidates, which were further subjected to ETA. Eventually, 175 novel <em>copA</em> sequences of high quality were discovered. Phylogenetic analysis showed that almost all these putative CopA proteins were distantly related to known CopA proteins, with 55 sequences from totally unknown species. Ten novel and three known <em>copA</em> genes were chemically synthesized for further functional genomic tests using the Cu-sensitive <em>Escherichia coli</em> (Δ<em>copA</em>). The growth test and Cu uptake determination showed that five novel clones had positive effects on host <strong>Cu resistance</strong> and uptake. One recombinant harboring <em>copA</em>-like 15 (<em>copAL15</em>) successfully restored Cu resistance of the host with a substantially enhanced Cu uptake. Two novel <em>copA</em> genes were fused with the <em>gfp</em> gene and expressed in <em>E. coli</em> for microscopic observation. Imaging results showed that they were successfully expressed and their proteins were localized to the membrane. The results here greatly expand the diversity of known CopA proteins, and the sequence-based procedure developed overcomes biases in length, screening methods, and abundance of conventional functional metagenomics.</div></div>","PeriodicalId":12528,"journal":{"name":"Genomics, Proteomics & Bioinformatics","volume":"21 6","pages":"Pages 1182-1194"},"PeriodicalIF":11.5,"publicationDate":"2023-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11082258/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33458568","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"High Sensitivity of Shotgun Metagenomic Sequencing in Colon Tissue Biopsy by Host DNA Depletion","authors":"Wing Yin Cheng ,&nbsp;Wei-Xin Liu ,&nbsp;Yanqiang Ding ,&nbsp;Guoping Wang ,&nbsp;Yu Shi ,&nbsp;Eagle S.H. Chu ,&nbsp;Sunny Wong ,&nbsp;Joseph J.Y. Sung ,&nbsp;Jun Yu","doi":"10.1016/j.gpb.2022.09.003","DOIUrl":"10.1016/j.gpb.2022.09.003","url":null,"abstract":"<div><div>The high host genetic background of tissue biopsies hinders the application of <strong>shotgun metagenomic sequencing</strong> in characterizing the tissue microbiota. We proposed an optimized method that removed host DNA from colon biopsies and examined the effect on metagenomic analysis. Human or mouse colon biopsies were divided into two groups, with one group undergoing <strong>host DNA depletion</strong> and the other serving as the control. Host DNA was removed through differential lysis of mammalian and bacterial cells before sequencing. The impact of host DNA depletion on microbiota was compared based on phylogenetic diversity analyses and regression analyses. Removing host DNA enhanced bacterial sequencing depth and improved species discovery, increasing bacterial reads by 2.46 ± 0.20 folds while reducing host reads by 6.80% ± 1.06%. Moreover, 2.40 times more of bacterial species were detected after host DNA depletion. This was confirmed from mouse <strong>colon tissues</strong>, increasing bacterial reads by 5.46 ± 0.42 folds while decreasing host reads by 10.2% ± 0.83%. Similarly, significantly more bacterial species were detected in the mouse colon tissue upon host DNA depletion (<em>P</em> &lt; 0.001). Furthermore, an increased microbial richness was evident in the host DNA-depleted samples compared with non-depleted controls in human colon biopsies and mouse colon tissues (<em>P</em> &lt; 0.001). Our optimized method of host DNA depletion improves the sensitivity of shotgun metagenomic sequencing in bacteria detection in the biopsy, which may yield a more accurate taxonomic profile of the tissue microbiota and identify bacteria that are important for disease initiation or progression.</div></div>","PeriodicalId":12528,"journal":{"name":"Genomics, Proteomics & Bioinformatics","volume":"21 6","pages":"Pages 1195-1205"},"PeriodicalIF":11.5,"publicationDate":"2023-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11082407/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40382461","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"T2T-YAO: A Telomere-to-telomere Assembled Diploid Reference Genome for Han Chinese","authors":"Yukun He ,&nbsp;Yanan Chu ,&nbsp;Shuming Guo ,&nbsp;Jiang Hu ,&nbsp;Ran Li ,&nbsp;Yali Zheng ,&nbsp;Xinqian Ma ,&nbsp;Zhenglin Du ,&nbsp;Lili Zhao ,&nbsp;Wenyi Yu ,&nbsp;Jianbo Xue ,&nbsp;Wenjie Bian ,&nbsp;Feifei Yang ,&nbsp;Xi Chen ,&nbsp;Pingan Zhang ,&nbsp;Rihan Wu ,&nbsp;Yifan Ma ,&nbsp;Changjun Shao ,&nbsp;Jing Chen ,&nbsp;Jian Wang ,&nbsp;Zhancheng Gao","doi":"10.1016/j.gpb.2023.08.001","DOIUrl":"10.1016/j.gpb.2023.08.001","url":null,"abstract":"<div><div>Since its initial release in 2001, the human reference genome has undergone continuous improvement in quality, and the recently released telomere-to-telomere (T2T) version — T2T-CHM13 — reaches its highest level of continuity and accuracy after 20 years of effort by working on a simplified, nearly homozygous genome of a hydatidiform mole cell line. Here, to provide an authentic complete <strong>diploid</strong> human genome reference for the <strong>Han Chinese</strong>, the largest population in the world, we assembled the genome of a male Han Chinese individual, T2T-YAO, which includes T2T assemblies of all the 22 + X + M and 22 + Y chromosomes in both haploids. The quality of T2T-YAO is much better than those of all currently available diploid assemblies, and its haploid version, T2T-YAO-hp, generated by selecting the better assembly for each autosome, reaches the top quality of fewer than one error per 29.5 Mb, even higher than that of T2T-CHM13. Derived from an individual living in the aboriginal region of the Han population, T2T-YAO shows clear ancestry and potential genetic continuity from the ancient ancestors. Each haplotype of T2T-YAO possesses ∼ 330-Mb exclusive sequences, ∼ 3100 unique genes, and tens of thousands of nucleotide and structural variations as compared with CHM13, highlighting the necessity of a population-stratified reference genome. The construction of T2T-YAO, an accurate and authentic representative of the Chinese population, would enable precise delineation of genomic variations and advance our understandings in the hereditability of diseases and phenotypes, especially within the context of the unique variations of the Chinese population.</div></div>","PeriodicalId":12528,"journal":{"name":"Genomics, Proteomics & Bioinformatics","volume":"21 6","pages":"Pages 1085-1100"},"PeriodicalIF":11.5,"publicationDate":"2023-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11082261/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10023539","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The Proteome Landscape of Human Placentas for Monochorionic Twins with Selective Intrauterine Growth Restriction","authors":"Xin-Lu Meng ,&nbsp;Peng-Bo Yuan ,&nbsp;Xue-Ju Wang ,&nbsp;Jing Hang ,&nbsp;Xiao-Ming Shi ,&nbsp;Yang-Yu Zhao ,&nbsp;Yuan Wei","doi":"10.1016/j.gpb.2023.03.002","DOIUrl":"10.1016/j.gpb.2023.03.002","url":null,"abstract":"<div><div>In perinatal medicine, intrauterine growth restriction (IUGR) is one of the greatest challenges. The etiology of IUGR is multifactorial, but most cases are thought to arise from placental insufficiency. However, identifying the placental cause of IUGR can be difficult due to numerous confounding factors. Selective IUGR (sIUGR) would be a good model to investigate how impaired placentation affects fetal development, as the growth discordance between monochorionic twins cannot be explained by confounding genetic or maternal factors. Herein, we constructed and analyzed the placental proteomic profiles of IUGR twins and normal cotwins. Specifically, we identified a total of 5481 proteins, of which 233 were differentially expressed (57 up-regulated and 176 down-regulated) in IUGR twins. Bioinformatics analysis indicates that these differentially expressed proteins (DEPs) are mainly associated with cardiovascular system development and function, organismal survival, and organismal development. Notably, 34 DEPs are significantly enriched in <strong>angiogenesis</strong>, and diminished placental angiogenesis in IUGR twins has been further elaborately confirmed. Moreover, we found decreased expression of <strong>metadherin</strong> (MTDH) in the <strong>placentas</strong> of IUGR twins and demonstrated that MTDH contributes to placental angiogenesis and fetal growth <em>in vitro</em>. Collectively, our findings reveal the comprehensive proteomic signatures of placentas for sIUGR twins, and the DEPs identified may provide in-depth insights into the pathogenesis of placental dysfunction and subsequent impaired fetal growth.</div></div>","PeriodicalId":12528,"journal":{"name":"Genomics, Proteomics & Bioinformatics","volume":"21 6","pages":"Pages 1246-1259"},"PeriodicalIF":11.5,"publicationDate":"2023-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11082409/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9375205","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Comprehensive Characterization and Global Transcriptome Analysis of Human Fetal Liver Terminal Erythropoiesis","authors":"Yongshuai Han ,&nbsp;Shihui Wang ,&nbsp;Yaomei Wang ,&nbsp;Yumin Huang ,&nbsp;Chengjie Gao ,&nbsp;Xinhua Guo ,&nbsp;Lixiang Chen ,&nbsp;Huizhi Zhao ,&nbsp;Xiuli An","doi":"10.1016/j.gpb.2023.07.001","DOIUrl":"10.1016/j.gpb.2023.07.001","url":null,"abstract":"<div><div>The fetal liver (FL) is the key erythropoietic organ during fetal development, but knowledge on human FL erythropoiesis is very limited. In this study, we sorted primary erythroblasts from FL cells and performed RNA sequencing (RNA-seq) analyses. We found that temporal gene expression patterns reflected changes in function during primary human FL <strong>terminal erythropoiesis</strong>. Notably, the expression of genes enriched in proteolysis and autophagy was up-regulated in orthochromatic erythroblasts (OrthoEs), suggesting the involvement of these pathways in <strong>enucleation</strong>. We also performed RNA-seq of <em>in vitro</em> cultured erythroblasts derived from FL CD34⁺ cells. Comparison of <strong>transcriptomes</strong> between the primary and cultured erythroblasts revealed significant differences, indicating impacts of the culture system on gene expression. Notably, the expression of lipid metabolism-related genes was increased in cultured erythroblasts. We further <strong>immortalized erythroid cell lines</strong> from FL and cord blood (CB) CD34⁺ cells (FL-iEry and CB-iEry, respectively). FL-iEry and CB-iEry were immortalized at the proerythroblast stage and can be induced to differentiate into OrthoEs, but their enucleation ability was very low. Comparison of the transcriptomes between OrthoEs with and without enucleation capability revealed the down-regulation of pathways involved in chromatin organization and mitophagy in OrthoEs without enucleation capacity, indicating that defects in chromatin organization and mitophagy contribute to the inability of OrthoEs to enucleate. Additionally, the expression of <em>HBE1</em>, <em>HBZ</em>, and <em>HBG2</em> was up-regulated in FL-iEry compared with CB-iEry, and such up-regulation was accompanied by down-regulated expression of <em>BCL11A</em> and up-regulated expression of <em>LIN28B</em> and <em>IGF2BP1</em>. Our study provides new insights into human FL erythropoiesis and rich resources for future studies.</div></div>","PeriodicalId":12528,"journal":{"name":"Genomics, Proteomics & Bioinformatics","volume":"21 6","pages":"Pages 1117-1132"},"PeriodicalIF":11.5,"publicationDate":"2023-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11082260/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10135733","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Superior Fidelity and Distinct Editing Outcomes of SaCas9 Compared with SpCas9 in Genome Editing","authors":"Zhi-Xue Yang ,&nbsp;Ya-Wen Fu ,&nbsp;Juan-Juan Zhao ,&nbsp;Feng Zhang ,&nbsp;Si-Ang Li ,&nbsp;Mei Zhao ,&nbsp;Wei Wen ,&nbsp;Lei Zhang ,&nbsp;Tao Cheng ,&nbsp;Jian-Ping Zhang ,&nbsp;Xiao-Bing Zhang","doi":"10.1016/j.gpb.2022.12.003","DOIUrl":"10.1016/j.gpb.2022.12.003","url":null,"abstract":"<div><div>A series of clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR associated protein 9 (Cas9) systems have been engineered for genome editing. The most widely used Cas9 is <strong>SpCas9</strong> from <em>Streptococcus pyogenes</em> and <strong>SaCas9</strong> from <em>Staphylococcus aureus</em>. However, a comparison of their detailed gene editing outcomes is still lacking. By characterizing the editing outcomes of 11 sites in human induced pluripotent stem cells (iPSCs) and K562 cells, we found that SaCas9 could edit the genome with greater efficiencies than SpCas9. We also compared the effects of <strong>spacer lengths</strong> of single-guide RNAs (sgRNAs; 18–21 nt for SpCas9 and 19–23 nt for SaCas9) and found that the optimal spacer lengths were 20 nt and 21 nt for SpCas9 and SaCas9, respectively. However, the optimal spacer length for a particular sgRNA was 18–21 nt for SpCas9 and 21–22 nt for SaCas9. Furthermore, SpCas9 exhibited a more substantial bias than SaCas9 for nonhomologous end-joining (NHEJ) +1 insertion at the fourth nucleotide upstream of the protospacer adjacent motif (PAM), indicating a characteristic of a staggered cut. Accordingly, editing with SaCas9 led to higher efficiencies of NHEJ-mediated double-stranded oligodeoxynucleotide (dsODN) insertion or homology-directed repair (HDR)-mediated adeno-associated virus serotype 6 (AAV6) donor knock-in. Finally, GUIDE-seq analysis revealed that SaCas9 exhibited significantly reduced <strong>off-target</strong> effects compared with SpCas9. Our work indicates the superior performance of SaCas9 to SpCas9 in transgene integration-based therapeutic gene editing and the necessity to identify the optimal spacer length to achieve desired editing results.</div></div>","PeriodicalId":12528,"journal":{"name":"Genomics, Proteomics & Bioinformatics","volume":"21 6","pages":"Pages 1206-1220"},"PeriodicalIF":11.5,"publicationDate":"2023-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11082263/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10419418","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}