Cas9 Protein Triggers Differential Expression of Inherent Genes Especially NGFR Expression in 293T Cells

  • Liqun Chen
  • Huilian Zhang
  • Linteng Zhang
  • Wenbo Li
  • Fengtian Fan
  • Xiaoyun Wu
  • Xueling Wu
  • Jun LinEmail author
Original Article



CRISPR/CAS9 systems, which can be utilized in vitro biological experiments, have recently captured much attention for their important roles and benefits. However, full realization of the potential of CRISPR/CAS9 approaches requires addressing many challenges and side effects. The expression of genes and potential side effects of CRISPR/CAS9 in human cells remains to be elucidated. The aim of our study was to explore the effect of CRISPR/CAS9 on gene expression in 293T cells.


A Cas9-expressing PX458 plasmid and Cas9-deactivated PX458-T2A plasmid were used to study the role of CRISPR/CAS9 on regulating gene expression in 293T cells. Gene expression in 293T cells after transfection of the PX458 plasmid or PX458-T2A plasmid was detected by RNA sequencing and correlative statistical analysis. Differential gene expression in both PX458 transfected 293T cells and PX458-T2A transfected 293T cells compared with normal 293T cells was detected using quantitative reverse transcription polymerase chain reaction (RT qPCR). The mRNA and protein levels were measured using reverse transcription PCR and Western blot. Co-IP assay combined with shotgun LC-MS/MS were used to investigate the differences of NGFR-interaction proteins between PX458 transfected 293T cells and PX458-T2A transfected 293T cells.


In this study, we observed that PX458 plasmid transfection and Cas9 expression can affect the expression of different genes, including FOSB (FBJ murine osteosarcoma viral oncogene homolog B), IL-11 (Interleukin-11), MMP1 (matrix metalloproteinase), CYP2D6 (CytochromeP4502D6), and NGFR (matrix metalloproteinase 1). Downregulation of NGFR after PX458 transfection was confirmed by RT qPCR and western blot analysis. NGFR expression was significantly lower in PX458 transfected 293T cells than in normal 293T cells and PX458-T2A transfected 293T cells. The co-IP dilutions analyzed by shotgun LC-MS/MS showed a total of 183 proteins interact with NGFR in PX458 transfected 293T cells while 221 proteins interact with NGFR were identified in PX458-T2A transfected 293T cells using the MASCOT engine.


Cas9 expression by transfection of the PX458 plasmid was negatively correlated with the NGFR mRNA level and NGFR protein expression in 293T cells, while PX458-T2A, in which Cas9 is deactivated, did not affect NGFR expression. The decrease in NGFR expression also affects the amount of proteins that interact with NGFR. These results suggest that the effect of Cas9 on NGFR expression and the expression of other genes should be noticed when developing cell-based studies and therapies utilizing CRISPR/CAS9 systems.


CRISPR/CAS9 PX458 PX458-T2A RNA sequencing Gene expression NGFR 



2A peptide derived from insect Thosea asigna virus


Glyceraldehyde-3-phosphate dehydrogenase


Human embryonic kidney cell line


Dulbecco’s modified Eagle’s medium


Nerve growth factor receptor



We are grateful to the WuXi NextCODE company for RNA sequencing. We thank LetPub ( for its linguistic assistance during the preparation of this manuscript. We acknowledge supports from the National Natural Science Foundation of China (Grant No. 31500616) and the Natural Science Foundation of Fujian Province (Grant No. 2017 J01445).

Research Involved in Human and Animal Rights

No human studies were carried out by the authors for this article. No animal studies were carried out by the authors for this article.

Competing interests

All authors, including Liqun Chen, Huilian Zhang Linteng Zhang, Wenbo Li, Fengtian Fan, Xiaoyun Wu, Xueling Wu, Jun Lin, declare that they have no competing interests.


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Copyright information

© Biomedical Engineering Society 2019

Authors and Affiliations

  1. 1.College of Biological Science and EngineeringFuzhou UniversityFuzhouChina
  2. 2.Institute of Apply GenomicsFuzhou UniversityFuzhouChina
  3. 3.Fujian Key Laboratory of Marine Enzyme EngineeringFuzhou UniversityFuzhouChina

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