Heterozygous IDH1R132H/WT created by “single base editing” inhibits human astroglial cell growth by downregulating YAP

Shuang Wei, Jie Wang, Olutobi Oyinlade, Ding Ma, Shuyan Wang, Lisa Kratz, Bachchu Lal, Qingfu Xu, Senquan Liu, Sagar R. Shah, Hao Zhang, Yunqing Li, Alfredo Quinones-Hinojosa, Heng Zhu, Zhi yong Huang, Linzhao Cheng, Jiang Qian, Shuli Xia

Research output: Contribution to journalArticle

3 Citations (Scopus)

Abstract

Mutations in the isocitrate dehydrogenase 1 (IDH1) gene have been identified in a number of cancer types, including brain cancer. The Cancer Genome Atlas project has revealed that IDH1 mutations occur in 70–80% of grade II and grade III gliomas. Until recently, most of the functional studies of IDH1 mutations in cellular models have been conducted in overexpression systems with the IDH1 wild type background. In this study, we employed a modified CRISPR/Cas9 genome editing technique called “single base editing”, and efficiently introduced heterozygous IDH1 R132H mutation (IDH1R132H/WT) in human astroglial cells. Global DNA methylation profiling revealed hypermethylation as well as hypomethylation induced by IDH1R132H/WT. Global gene expression analysis identified molecular targets and pathways altered by IDH1R132H/WT, including cell proliferation, extracellular matrix (ECM), and cell migration. Our phenotype analysis indicated that compared with IDH1 wild type cells, IDH1R132H/WT promoted cell migration by upregulating integrin β4 (ITGB4); and significantly inhibited cell proliferation. Using our mutated IDH1 models generated by “single base editing”, we identified novel molecular targets of IDH1R132H/WT, namely Yes-associated protein (YAP) and its downstream signaling pathway Notch, to mediate the cell growth-inhibiting effect of IDH1R132H/WT. In summary, the “single base editing” strategy has successfully created heterozygous IDH1 R132H mutation that recapitulates the naturally occurring IDH1 mutation. Our isogenic cellular systems that differ in a single nucleotide in one allele of the IDH1 gene provide a valuable model for novel discoveries of IDH1R132H/WT-driven biological events.

Original languageEnglish (US)
Pages (from-to)1-15
Number of pages15
JournalOncogene
DOIs
StateAccepted/In press - May 30 2018

Fingerprint

Isocitrate Dehydrogenase
Down-Regulation
Growth
Proteins
Mutation
Brain Neoplasms
Cell Movement
Clustered Regularly Interspaced Short Palindromic Repeats
Cell Proliferation
DNA Fingerprinting
Atlases
DNA Methylation
Integrins
Glioma
Genes
Extracellular Matrix
Nucleotides
Alleles
Genome
Phenotype

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics
  • Cancer Research

Cite this

Heterozygous IDH1R132H/WT created by “single base editing” inhibits human astroglial cell growth by downregulating YAP. / Wei, Shuang; Wang, Jie; Oyinlade, Olutobi; Ma, Ding; Wang, Shuyan; Kratz, Lisa; Lal, Bachchu; Xu, Qingfu; Liu, Senquan; Shah, Sagar R.; Zhang, Hao; Li, Yunqing; Quinones-Hinojosa, Alfredo; Zhu, Heng; Huang, Zhi yong; Cheng, Linzhao; Qian, Jiang; Xia, Shuli.

In: Oncogene, 30.05.2018, p. 1-15.

Research output: Contribution to journalArticle

Wei, S, Wang, J, Oyinlade, O, Ma, D, Wang, S, Kratz, L, Lal, B, Xu, Q, Liu, S, Shah, SR, Zhang, H, Li, Y, Quinones-Hinojosa, A, Zhu, H, Huang, ZY, Cheng, L, Qian, J & Xia, S 2018, 'Heterozygous IDH1R132H/WT created by “single base editing” inhibits human astroglial cell growth by downregulating YAP', Oncogene, pp. 1-15. https://doi.org/10.1038/s41388-018-0334-9
Wei, Shuang ; Wang, Jie ; Oyinlade, Olutobi ; Ma, Ding ; Wang, Shuyan ; Kratz, Lisa ; Lal, Bachchu ; Xu, Qingfu ; Liu, Senquan ; Shah, Sagar R. ; Zhang, Hao ; Li, Yunqing ; Quinones-Hinojosa, Alfredo ; Zhu, Heng ; Huang, Zhi yong ; Cheng, Linzhao ; Qian, Jiang ; Xia, Shuli. / Heterozygous IDH1R132H/WT created by “single base editing” inhibits human astroglial cell growth by downregulating YAP. In: Oncogene. 2018 ; pp. 1-15.
@article{05200fdd2064427bb74d8b298a64aa3e,
title = "Heterozygous IDH1R132H/WT created by “single base editing” inhibits human astroglial cell growth by downregulating YAP",
abstract = "Mutations in the isocitrate dehydrogenase 1 (IDH1) gene have been identified in a number of cancer types, including brain cancer. The Cancer Genome Atlas project has revealed that IDH1 mutations occur in 70–80{\%} of grade II and grade III gliomas. Until recently, most of the functional studies of IDH1 mutations in cellular models have been conducted in overexpression systems with the IDH1 wild type background. In this study, we employed a modified CRISPR/Cas9 genome editing technique called “single base editing”, and efficiently introduced heterozygous IDH1 R132H mutation (IDH1R132H/WT) in human astroglial cells. Global DNA methylation profiling revealed hypermethylation as well as hypomethylation induced by IDH1R132H/WT. Global gene expression analysis identified molecular targets and pathways altered by IDH1R132H/WT, including cell proliferation, extracellular matrix (ECM), and cell migration. Our phenotype analysis indicated that compared with IDH1 wild type cells, IDH1R132H/WT promoted cell migration by upregulating integrin β4 (ITGB4); and significantly inhibited cell proliferation. Using our mutated IDH1 models generated by “single base editing”, we identified novel molecular targets of IDH1R132H/WT, namely Yes-associated protein (YAP) and its downstream signaling pathway Notch, to mediate the cell growth-inhibiting effect of IDH1R132H/WT. In summary, the “single base editing” strategy has successfully created heterozygous IDH1 R132H mutation that recapitulates the naturally occurring IDH1 mutation. Our isogenic cellular systems that differ in a single nucleotide in one allele of the IDH1 gene provide a valuable model for novel discoveries of IDH1R132H/WT-driven biological events.",
author = "Shuang Wei and Jie Wang and Olutobi Oyinlade and Ding Ma and Shuyan Wang and Lisa Kratz and Bachchu Lal and Qingfu Xu and Senquan Liu and Shah, {Sagar R.} and Hao Zhang and Yunqing Li and Alfredo Quinones-Hinojosa and Heng Zhu and Huang, {Zhi yong} and Linzhao Cheng and Jiang Qian and Shuli Xia",
year = "2018",
month = "5",
day = "30",
doi = "10.1038/s41388-018-0334-9",
language = "English (US)",
pages = "1--15",
journal = "Oncogene",
issn = "0950-9232",
publisher = "Nature Publishing Group",

}

TY - JOUR

T1 - Heterozygous IDH1R132H/WT created by “single base editing” inhibits human astroglial cell growth by downregulating YAP

AU - Wei, Shuang

AU - Wang, Jie

AU - Oyinlade, Olutobi

AU - Ma, Ding

AU - Wang, Shuyan

AU - Kratz, Lisa

AU - Lal, Bachchu

AU - Xu, Qingfu

AU - Liu, Senquan

AU - Shah, Sagar R.

AU - Zhang, Hao

AU - Li, Yunqing

AU - Quinones-Hinojosa, Alfredo

AU - Zhu, Heng

AU - Huang, Zhi yong

AU - Cheng, Linzhao

AU - Qian, Jiang

AU - Xia, Shuli

PY - 2018/5/30

Y1 - 2018/5/30

N2 - Mutations in the isocitrate dehydrogenase 1 (IDH1) gene have been identified in a number of cancer types, including brain cancer. The Cancer Genome Atlas project has revealed that IDH1 mutations occur in 70–80% of grade II and grade III gliomas. Until recently, most of the functional studies of IDH1 mutations in cellular models have been conducted in overexpression systems with the IDH1 wild type background. In this study, we employed a modified CRISPR/Cas9 genome editing technique called “single base editing”, and efficiently introduced heterozygous IDH1 R132H mutation (IDH1R132H/WT) in human astroglial cells. Global DNA methylation profiling revealed hypermethylation as well as hypomethylation induced by IDH1R132H/WT. Global gene expression analysis identified molecular targets and pathways altered by IDH1R132H/WT, including cell proliferation, extracellular matrix (ECM), and cell migration. Our phenotype analysis indicated that compared with IDH1 wild type cells, IDH1R132H/WT promoted cell migration by upregulating integrin β4 (ITGB4); and significantly inhibited cell proliferation. Using our mutated IDH1 models generated by “single base editing”, we identified novel molecular targets of IDH1R132H/WT, namely Yes-associated protein (YAP) and its downstream signaling pathway Notch, to mediate the cell growth-inhibiting effect of IDH1R132H/WT. In summary, the “single base editing” strategy has successfully created heterozygous IDH1 R132H mutation that recapitulates the naturally occurring IDH1 mutation. Our isogenic cellular systems that differ in a single nucleotide in one allele of the IDH1 gene provide a valuable model for novel discoveries of IDH1R132H/WT-driven biological events.

AB - Mutations in the isocitrate dehydrogenase 1 (IDH1) gene have been identified in a number of cancer types, including brain cancer. The Cancer Genome Atlas project has revealed that IDH1 mutations occur in 70–80% of grade II and grade III gliomas. Until recently, most of the functional studies of IDH1 mutations in cellular models have been conducted in overexpression systems with the IDH1 wild type background. In this study, we employed a modified CRISPR/Cas9 genome editing technique called “single base editing”, and efficiently introduced heterozygous IDH1 R132H mutation (IDH1R132H/WT) in human astroglial cells. Global DNA methylation profiling revealed hypermethylation as well as hypomethylation induced by IDH1R132H/WT. Global gene expression analysis identified molecular targets and pathways altered by IDH1R132H/WT, including cell proliferation, extracellular matrix (ECM), and cell migration. Our phenotype analysis indicated that compared with IDH1 wild type cells, IDH1R132H/WT promoted cell migration by upregulating integrin β4 (ITGB4); and significantly inhibited cell proliferation. Using our mutated IDH1 models generated by “single base editing”, we identified novel molecular targets of IDH1R132H/WT, namely Yes-associated protein (YAP) and its downstream signaling pathway Notch, to mediate the cell growth-inhibiting effect of IDH1R132H/WT. In summary, the “single base editing” strategy has successfully created heterozygous IDH1 R132H mutation that recapitulates the naturally occurring IDH1 mutation. Our isogenic cellular systems that differ in a single nucleotide in one allele of the IDH1 gene provide a valuable model for novel discoveries of IDH1R132H/WT-driven biological events.

UR - http://www.scopus.com/inward/record.url?scp=85047816917&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=85047816917&partnerID=8YFLogxK

U2 - 10.1038/s41388-018-0334-9

DO - 10.1038/s41388-018-0334-9

M3 - Article

C2 - 29849122

AN - SCOPUS:85047816917

SP - 1

EP - 15

JO - Oncogene

JF - Oncogene

SN - 0950-9232

ER -