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Identifying novel therapeutic targets in gastric cancer using genome-wide CRISPR-Cas9 screening

Oncogene volume 41, pages 2069–2078 (2022)Cite this article

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Abstract

Genome-scale CRISPR-Cas9 screening technology is a powerful tool to systematically identify genes essential for cancer cell survival. Herein, TKOv3, a genome-scale CRISPR-Cas9 knock-out library, was screened in the gastric cancer (GC) cells, and relevant validation experiments were performed. We obtained 854 essential genes for the AGS cell line, and 184 were novel essential genes. After knocking down essential genes: SPC25, DHX37, ABCE1, SNRPB, TOP3A, RUVBL1, CIT, TACC3 and MTBP, cell viability and proliferation were significantly decreased. Then, we analysed the detected essential genes at different time points and proved more characteristic genes might appear with the extension of selection. After progressive selection using a series of open datasets, 41 essential genes were identified as potential drug targets. Among them, methyltransferase 1 (METTL1) was over expressed in GC tissues. High METTL1 expression was associated with poor prognosis among 3 of 6 GC cohorts. Furthermore, GC cells growth was significantly inhibited after the down-regulation of METTL1 in vitro and in vivo. Function analysis revealed that METTL1 might play a role in the cell cycle through AKT/STAT3 pathways. In conclusion, compared with existing genome-scale screenings, we obtained 184 novel essential genes. Among them, METTL1 was validated as a potential therapeutic target of GC.

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Fig. 1: Genome-wide CRISPR-Cas9 screens of negative selection in AGS cell line.
Fig. 2: Essential genes detected by TKOv3 library at different time points.
Fig. 3: The evaluation of nine essential genes.
Fig. 4: The selection of potential drug targets.
Fig. 5: METTL1 knock-down inhibited GC tumor growth in vivo.
Fig. 6: The function of METTL1 in AGS cell line.
Fig. 7: METTL1 in GC tissues.

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References

  1. Ho SWT, Tan P. Dissection of gastric cancer heterogeneity for precision oncology. Cancer Sci. 2019;110:3405–14.

    Article  CAS  Google Scholar 

  2. Bray F, Ferlay J, Soerjomataram I, Siegel RL, Torre LA, Jemal A. Global cancer statistics 2018: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries. CA: Cancer J Clin. 2018;68:394–424.

    Google Scholar 

  3. Venerito M, Link A, Rokkas T, Malfertheiner P. Review: gastric cancer-clinical aspects. Helicobacter 2019;24:e12643. Suppl 1.

    Article  Google Scholar 

  4. Tzelepis K, Koike-Yusa H, De Braekeleer E, Li Y, Metzakopian E, Dovey OM, et al. A CRISPR dropout screen identifies genetic vulnerabilities and therapeutic targets in acute myeloid leukemia. Cell Rep. 2016;17:1193–205.

    Article  CAS  Google Scholar 

  5. Evers B, Jastrzebski K, Heijmans JP, Grernrum W, Beijersbergen RL, Bernards R. CRISPR knockout screening outperforms shRNA and CRISPRi in identifying essential genes. Nat Biotechnol. 2016;34:631–3.

    Article  CAS  Google Scholar 

  6. Zhou Y, Zhu S, Cai C, Yuan P, Li C, Huang Y, et al. High-throughput screening of a CRISPR/Cas9 library for functional genomics in human cells. Nature 2014;509:487–91.

    Article  CAS  Google Scholar 

  7. Mali P, Yang L, Esvelt KM, Aach J, Guell M, DiCarlo JE, et al. RNA-guided human genome engineering via Cas9. Science. 2013;339:823–6.

    Article  CAS  Google Scholar 

  8. Cong L, Ran FA, Cox D, Lin S, Barretto R, Habib N, et al. Multiplex genome engineering using CRISPR/Cas systems. Science 2013;339:819–23.

    Article  CAS  Google Scholar 

  9. Kurata M, Yamamoto K, Moriarity BS, Kitagawa M, Largaespada DA. CRISPR/Cas9 library screening for drug target discovery. J Hum Gen. 2018;63:179–86.

    Article  CAS  Google Scholar 

  10. Balusamy SR, Perumalsamy H, Huq MA, Balasubramanian B. Anti-proliferative activity of Origanum vulgare inhibited lipogenesis and induced mitochondrial mediated apoptosis in human stomach cancer cell lines. Biomed Pharmacother. 2018;108:1835–44.

    Article  CAS  Google Scholar 

  11. Shang W, Wang Y, Liang X, Li T, Shao W, Liu F, et al. SETDB1 promotes gastric carcinogenesis and metastasis via upregulation of CCND1 and MMP9 expression. J Pathol. 2021;253:148–59.

    Article  CAS  Google Scholar 

  12. Lu X, Wu N, Yang W, Sun J, Yan K, Wu J. OGDH promotes the progression of gastric cancer by regulating mitochondrial bioenergetics and Wnt/beta-catenin signal pathway. OncoTargets Ther. 2019;12:7489–500.

    Article  CAS  Google Scholar 

  13. Chen Z, Raghoonundun C, Chen W, Zhang Y, Tang W, Fan X, et al. SETD2 indicates favourable prognosis in gastric cancer and suppresses cancer cell proliferation, migration, and invasion. Biochem Biophys Res Commun. 2018;498:579–85.

    Article  CAS  Google Scholar 

  14. Tsai MM, Lin PY, Cheng WL, Tsai CY, Chi HC, Chen CY, et al. Overexpression of ADP-ribosylation factor 1 in human gastric carcinoma and its clinicopathological significance. Cancer Sci. 2012;103:1136–44.

    Article  CAS  Google Scholar 

  15. Chushi L, Wei W, Kangkang X, Yongzeng F, Ning X, Xiaolei C. HMGCR is up-regulated in gastric cancer and promotes the growth and migration of the cancer cells. Gene. 2016;587:42–47.

    Article  Google Scholar 

  16. Sheng Y, Wang W, Hong B, Jiang X, Sun R, Yan Q, et al. Upregulation of KIF20A correlates with poor prognosis in gastric cancer. Cancer Manag Res. 2018;10:6205–16.

    Article  CAS  Google Scholar 

  17. Yuan L, Li JX, Yang Y, Chen Y, Ma TT, Liang S, et al. Depletion of MRPL35 inhibits gastric carcinoma cell proliferation by regulating downstream signaling proteins. World J Gastroenterol. 2021;27:1785–804.

    Article  CAS  Google Scholar 

  18. Tao J, Zhi X, Tian Y, Li Z, Zhu Y, Wang W, et al. CEP55 contributes to human gastric carcinoma by regulating cell proliferation. Tumour Biol. 2014;35:4389–99.

    Article  CAS  Google Scholar 

  19. Hart T, Tong AHY, Chan K, Van Leeuwen J, Seetharaman A, Aregger M, et al. Evaluation and design of genome-wide CRISPR/SpCas9 knockout screens. G3. 2017;7:2719–27.

    Article  CAS  Google Scholar 

  20. Marcotte R, Brown KR, Suarez F, Sayad A, Karamboulas K, Krzyzanowski PM, et al. Essential gene profiles in breast, pancreatic, and ovarian cancer cells. Cancer Discov. 2012;2:172–89.

    Article  CAS  Google Scholar 

  21. Shalem O, Sanjana NE, Hartenian E, Shi X, Scott DA, Mikkelson T, et al. Genome-scale CRISPR-Cas9 knockout screening in human cells. Science. 2014;343:84–7.

    Article  CAS  Google Scholar 

  22. Wang T, Wei JJ, Sabatini DM, Lander ES. Genetic screens in human cells using the CRISPR-Cas9 system. Science. 2014;343:80–4.

    Article  CAS  Google Scholar 

  23. Morgens DW, Deans RM, Li A, Bassik MC. Systematic comparison of CRISPR/Cas9 and RNAi screens for essential genes. Nat Biotechnol. 2016;34:634–6.

    Article  CAS  Google Scholar 

  24. Hart T, Chandrashekhar M, Aregger M, Steinhart Z, Brown KR, MacLeod G, et al. High-resolution CRISPR screens reveal fitness genes and genotype-specific cancer liabilities. Cell. 2015;163:1515–26.

    Article  CAS  Google Scholar 

  25. Ghandi M, Huang FW, Jane-Valbuena J, Kryukov GV, Lo CC, McDonald ER, 3rd. et al. Next-generation characterization of the Cancer Cell Line Encyclopedia. Nature. 2019;569:503–8.

  26. Meyers RM, Bryan JG, McFarland JM, Weir BA, Sizemore AE, Xu H, et al. Computational correction of copy number effect improves specificity of CRISPR-Cas9 essentiality screens in cancer cells. Nat Gen. 2017;49:1779–84.

    Article  CAS  Google Scholar 

  27. Behan FM, Iorio F, Picco G, Gonçalves E, Beaver CM, Migliardi G, et al. Prioritization of cancer therapeutic targets using CRISPR-Cas9 screens. Nature. 2019;568:511–6.

    Article  CAS  Google Scholar 

  28. Davies R, Liu L, Taotao S, Tuano N, Chaturvedi R, Huang KK, et al. CRISPRi enables isoform-specific loss-of-function screens and identification of gastric cancer-specific isoform dependencies. Genome Biol. 2021;22:47.

    Article  CAS  Google Scholar 

  29. Costa R, Carneiro BA, Taxter T, Tavora FA, Kalyan A, Pai SA, et al. FGFR3-TACC3 fusion in solid tumors: mini review. Oncotarget. 2016;7:55924–38.

    Article  Google Scholar 

  30. Katoh M, Nakagama H. FGF receptors: cancer biology and therapeutics. Med Res Rev. 2014;34:280–300.

    Article  CAS  Google Scholar 

  31. Pandolfini L, Barbieri I, Bannister AJ, Hendrick A, Andrews B, Webster N, et al. METTL1 Promotes let-7 MicroRNA Processing via m7G Methylation. Mol Cell. 2019;74:1278–90. e9.

    Article  CAS  Google Scholar 

  32. Liu Y, Zhang Y, Chi Q, Wang Z, Sun B. Methyltransferase-like 1 (METTL1) served as a tumor suppressor in colon cancer by activating 7-methylguanosine (m7G) regulated let-7e miRNA/HMGA2 axis. Life Sci. 2020;249:117480.

    Article  CAS  Google Scholar 

  33. Okamoto M, Fujiwara M, Hori M, Okada K, Yazama F, Konishi H, et al. tRNA modifying enzymes, NSUN2 and METTL1, determine sensitivity to 5-fluorouracil in HeLa cells. PLoS Gen. 2014;10:e1004639.

    Article  Google Scholar 

  34. Wang C, Wang W, Han X, Du L, Li A, Huang G. Methyltransferase-like 1 regulates lung adenocarcinoma A549 cell proliferation and autophagy via the AKT/mTORC1 signaling pathway. Oncol Lett. 2021;21:330.

    Article  CAS  Google Scholar 

  35. Tian QH, Zhang MF, Zeng JS, Luo RG, Wen Y, Chen J, et al. METTL1 overexpression is correlated with poor prognosis and promotes hepatocellular carcinoma via PTEN. J Mol Med. 2019;97:1535–45.

    Article  CAS  Google Scholar 

  36. Lin S, Liu Q, Lelyveld VS, Choe J, Szostak JW, Gregory RI. Mettl1/Wdr4-mediated m(7)G tRNA methylome is required for normal mRNA translation and embryonic stem cell self-renewal and differentiation. Mol Cell. 2018;71:244–55. e5.

    Article  CAS  Google Scholar 

  37. Orellana EA, Liu Q, Yankova E, Pirouz M, De, Braekeleer E, et al. METTL1-mediated m7G modification of Arg-TCT tRNA drives oncogenic transformation. Mol Cell. 2021;81:3323–38. e14.

    Article  CAS  Google Scholar 

  38. Wang B, Wang M, Zhang W, Xiao T, Chen CH, Wu A, et al. Integrative analysis of pooled CRISPR genetic screens using MAGeCKFlute. Nat Prot. 2019;14:756–80.

    Article  CAS  Google Scholar 

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Acknowledgements

We thank Yue Zhao for her assistance with algorithm improvement. Also, we appreciate Jeffery Parvin for his guidance of experiments design.

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Author notes

  1. These authors contributed equally: Zhi Zeng, Xu Zhang, Cong-Qing Jiang.

Authors and Affiliations

  1. Department of Pathology, Renmin Hospital of Wuhan University, Wuhan, Hubei, China

    Zhi Zeng

  2. Central Laboratory, Renmin Hospital of Wuhan University, Wuhan, Hubei, China

    Xu Zhang, Yong-Gang Zhang & Li-Juan Gu

  3. Department of Colorectal and Anal Surgery, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China

    Cong-Qing Jiang & Xiao-Yu Xie

  4. Department of Biomedical informatics, The Ohio State University, Columbus, OH, USA

    Xue Wu, Jin Li, Shan Tang & Lang Li

  5. Department of Infectious Diseases, Renmin Hospital of Wuhan University, Wuhan, Hubei, China

    Ying-An Jiang

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Contributions

ZZ and X-YX conceptualized and designed the study. ZZ, XZ, and Y-GZ conducted the experiments. XW, JL, and ST analysed and interpreted the data. ZZ, XZ, and L-JG contributed to the sample collection. LL and Y-AJ provided technical support. ZZ, C-QJ, X-YX, and Y-AJ wrote and revised the manuscript. All authors read and approved the final manuscript.

Corresponding authors

Correspondence to Xiao-Yu Xie or Ying-An Jiang.

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This study was approved by the Ethics Committee of Renmin Hospital of Wuhan University and Registration number is 2018K-C059.

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Zeng, Z., Zhang, X., Jiang, CQ. et al. Identifying novel therapeutic targets in gastric cancer using genome-wide CRISPR-Cas9 screening. Oncogene 41, 2069–2078 (2022). https://doi.org/10.1038/s41388-022-02177-1

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