| Title |
Comprehensive off-target analysis of dCas9-SAM-mediated HIV reactivation via long noncoding RNA and mRNA profiling
|
|---|---|
| Published in |
BMC Medical Genomics, September 2018
|
| DOI | 10.1186/s12920-018-0394-2 |
| Pubmed ID | |
| Authors |
Yonggang Zhang, Gustavo Arango, Fang Li, Xiao Xiao, Raj Putatunda, Jun Yu, Xiao-Feng Yang, Hong Wang, Layne T. Watson, Liqing Zhang, Wenhui Hu |
| Abstract |
CRISPR/CAS9 (epi)genome editing revolutionized the field of gene and cell therapy. Our previous study demonstrated that a rapid and robust reactivation of the HIV latent reservoir by a catalytically-deficient Cas9 (dCas9)-synergistic activation mediator (SAM) via HIV long terminal repeat (LTR)-specific MS2-mediated single guide RNAs (msgRNAs) directly induces cellular suicide without additional immunotherapy. However, potential off-target effect remains a concern for any clinical application of Cas9 genome editing and dCas9 epigenome editing. After dCas9 treatment, potential off-target responses have been analyzed through different strategies such as mRNA sequence analysis, and functional screening. In this study, a comprehensive analysis of the host transcriptome including mRNA, lncRNA, and alternative splicing was performed using human cell lines expressing dCas9-SAM and HIV-targeting msgRNAs. The control scrambled msgRNA (LTR_Zero), and two LTR-specific msgRNAs (LTR_L and LTR_O) groups show very similar expression profiles of the whole transcriptome. Among 839 identified lncRNAs, none exhibited significantly different expression in LTR_L vs. LTR_Zero group. In LTR_O group, only TERC and scaRNA2 lncRNAs were significantly decreased. Among 142,791 mRNAs, four genes were differentially expressed in LTR_L vs. LTR_Zero group. There were 21 genes significantly downregulated in LTR_O vs. either LTR_Zero or LTR_L group and one third of them are histone related. The distributions of different types of alternative splicing were very similar either within or between groups. There were no apparent changes in all the lncRNA and mRNA transcripts between the LTR_L and LTR_Zero groups. This is an extremely comprehensive study demonstrating the rare off-target effects of the HIV-specific dCas9-SAM system in human cells. This finding is encouraging for the safe application of dCas9-SAM technology to induce target-specific reactivation of latent HIV for an effective "shock-and-kill" strategy. |
X Demographics
The data shown below were collected from the profiles of 6 X users who shared this research output. Click here to find out more about how the information was compiled.
Geographical breakdown
| Country | Count | As % |
|---|---|---|
| Argentina | 1 | 17% |
| Unknown | 5 | 83% |
Demographic breakdown
| Type | Count | As % |
|---|---|---|
| Members of the public | 6 | 100% |
Mendeley readers
The data shown below were compiled from readership statistics for 43 Mendeley readers of this research output. Click here to see the associated Mendeley record.
Geographical breakdown
| Country | Count | As % |
|---|---|---|
| Unknown | 43 | 100% |
Demographic breakdown
| Readers by professional status | Count | As % |
|---|---|---|
| Student > Ph. D. Student | 8 | 19% |
| Student > Bachelor | 7 | 16% |
| Researcher | 4 | 9% |
| Student > Master | 3 | 7% |
| Other | 2 | 5% |
| Other | 2 | 5% |
| Unknown | 17 | 40% |
| Readers by discipline | Count | As % |
|---|---|---|
| Biochemistry, Genetics and Molecular Biology | 7 | 16% |
| Agricultural and Biological Sciences | 6 | 14% |
| Medicine and Dentistry | 3 | 7% |
| Nursing and Health Professions | 2 | 5% |
| Immunology and Microbiology | 2 | 5% |
| Other | 5 | 12% |
| Unknown | 18 | 42% |
Attention Score in Context
This research output has an Altmetric Attention Score of 5. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 01 August 2019.
All research outputs
#6,314,489
of 23,325,355 outputs
Outputs from BMC Medical Genomics
#281
of 1,252 outputs
Outputs of similar age
#110,709
of 337,886 outputs
Outputs of similar age from BMC Medical Genomics
#5
of 22 outputs
Altmetric has tracked 23,325,355 research outputs across all sources so far. This one has received more attention than most of these and is in the 72nd percentile.
So far Altmetric has tracked 1,252 research outputs from this source. They receive a mean Attention Score of 4.7. This one has done well, scoring higher than 77% of its peers.
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We're also able to compare this research output to 22 others from the same source and published within six weeks on either side of this one. This one has done well, scoring higher than 81% of its contemporaries.