Citation: Wan-Bing Tao, Neng-Bin Xie, Qing-Yun Cheng, Yu-Qi Feng, Bi-Feng Yuan. Sensitive determination of inosine RNA modification in single cell by chemical derivatization coupled with mass spectrometry analysis[J]. Chinese Chemical Letters, ;2023, 34(10): 108243. doi: 10.1016/j.cclet.2023.108243 shu

Sensitive determination of inosine RNA modification in single cell by chemical derivatization coupled with mass spectrometry analysis

Wan-Bing Tao ^a ,
Neng-Bin Xie ^{a, b} ,
Qing-Yun Cheng ^a ,
Yu-Qi Feng ^{a, b} ,
Bi-Feng Yuan ^{a, b, c, d, *,}

a.
College of Chemistry and Molecular Sciences, Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China
b.
School of Public Health, Wuhan University, Wuhan 430071, China
c.
Research Center of Public Health, Renmin Hospital of Wuhan University, Wuhan 430060, China
d.
Cancer Precision Diagnosis and Treatment and Translational Medicine Hubei Engineering Research Center, Zhongnan Hospital of Wuhan University, Wuhan Research Center for Infectious Diseases and Cancer, Chinese Academy of Medical Sciences, Wuhan 430071, China

bfyuan@whu.edu.cn

Received Date: 25 October 2022
Revised Date: 30 January 2023
Accepted Date: 16 February 2023
Available Online: 19 February 2023

Figures(4)

Inosine is a vital RNA modification across three kingdoms of life. It has been demonstrated that inosine plays important roles in modulation of the fate of RNAs. In the current study, we developed a highly sensitive method to determine inosine in a single cell by N-cyclohexyl-N'-β-(4-methylmorpholinium)ethylcarbodiimide p-toluenesulfonate (CMCT) derivatization in combination with mass spectrometry analysis. The results showed that the detection sensitivity of inosine was increased by 556-fold after CMCT derivatization, with the limit of detection (LOD) being 4.5 amol. With the established method, we could detect inosine from 13.0 pg of total RNA of HEK293T cells. Meanwhile, inosine in RNA from a single cell could also be clearly detected due to the improved detection sensitivity. Moreover, we found the level of inosine in RNA of sleep-deprived mice was significantly increased compared to the control mice, indicating that inosine is associated with sleep behavior and might be a potential indicator of sleep disorder. Taken together, the chemical derivatization coupled with mass spectrometry analysis offers a valuable tool in determination of endogenous RNA modifications in a single cell, which should benefit the functional study of RNA modification in rare clinical samples.
- Inosine,
- RNA modification,
- CMCT,
- Derivatization,
- Mass spectrometry,
- Single cell
1. [1]
  I.A. Roundtree, M.E. Evans, T. Pan, C. He, Cell 169 (2017) 1187-1200. doi: 10.1016/j.cell.2017.05.045
2. [2]
  T. Liu, C.J. Ma, B.F. Yuan, Y.Q. Feng, Sci. China Chem. 61 (2018) 381-392. doi: 10.1007/s11426-017-9186-y
3. [3]
  J. Song, C. Yi, ACS Chem. Biol. 12 (2017) 316-325. doi: 10.1021/acschembio.6b00960
4. [4]
  M. Frye, B.T. Harada, M. Behm, C. He, Science 361 (2018) 1346-1349. doi: 10.1126/science.aau1646
5. [5]
  Q. Wang, J.H. Ding, J. Xiong, et al., Chin. Chem. Lett. 32 (2021) 3426-3430. doi: 10.1016/j.cclet.2021.05.020
6. [6]
  P. Boccaletto, F. Stefaniak, A. Ray, et al., Nucleic Acids Res 50 (2022) D231-D235. doi: 10.1093/nar/gkab1083
7. [7]
  X.J. You, S. Zhang, J.J. Chen, et al., Nucleic Acids Res. 50 (2022) 9858-9872. doi: 10.1093/nar/gkac770
8. [8]
  M.Y. Cheng, X.J. You, J.H. Ding, et al., Chem. Sci. 12 (2021) 8149–8156. doi: 10.1039/d1sc01972d
9. [9]
  M.Y. Chen, Z. Gui, K.K. Chen, et al., Chin. Chem. Lett. 33 (2022) 2086-2090. doi: 10.1016/j.cclet.2021.08.094
10. [10]
  A.A. Schaffer, E. Kopel, A. Hendel, et al., Nucleic Acids Res. 48 (2020) 5849-5858. doi: 10.1093/nar/gkaa305
11. [11]
  X.J. You, L. Li, T.T. Ji, et al., Chin. Chem. Lett. 34 (2023) 107181. doi: 10.1016/j.cclet.2022.01.074
12. [12]
  M.W. Gray, Biochemistry 51 (2012) 5235-5242. doi: 10.1021/bi300419r
13. [13]
  B.L. Bass, Annu. Rev. Biochem. 71 (2002) 817-846. doi: 10.1146/annurev.biochem.71.110601.135501
14. [14]
  R.W. Holley, G.A. Everett, J.T. Madison, A. Zamir, J. Biol. Chem. 240 (1965) 2122-2128. doi: 10.1016/S0021-9258(18)97435-1
15. [15]
  K. Nishikura, Annu. Rev. Biochem. 79 (2010) 321-349. doi: 10.1146/annurev-biochem-060208-105251
16. [16]
  I. Alseth, B. Dalhus, M. Bjoras, Curr. Opin. Genet. Dev. 26 (2014) 116-123. doi: 10.1016/j.gde.2014.07.008
17. [17]
  Y. Yang, S. Okada, M. Sakurai, RNA Biol. 18 (2021) 999-1013. doi: 10.1080/15476286.2020.1867797
18. [18]
  X. Xu, Y. Wang, H. Liang, Curr. Opin. Genet. Dev. 48 (2018) 51-56. doi: 10.1016/j.gde.2017.10.009
19. [19]
  T. Nakahama, Y. Kawahara, Cell. Mol. Life Sci. 77 (2020) 2931-2948. doi: 10.1007/s00018-020-03466-2
20. [20]
  Y. Dai, B.F. Yuan, Y.Q. Feng, RSC Chem. Biol. 2 (2021) 1096–1114. doi: 10.1039/d1cb00022e
21. [21]
  B. Chen, B.F. Yuan, Y.Q. Feng, Anal. Chem. 91 (2019) 743-756. doi: 10.1021/acs.analchem.8b04078
22. [22]
  M.C. Owens, C. Zhang, K.F. Liu, Mol. Cell. 81 (2021) 4116-4136. doi: 10.1016/j.molcel.2021.07.036
23. [23]
  M.Y. Chen, C.B. Qi, X.M. Tang, et al., Chin. Chem. Lett. 33 (2022) 3772-3776. doi: 10.1016/j.cclet.2021.12.008
24. [24]
  Y.J. Feng, X.J. You, J.H. Ding, et al., Anal. Chem. 94 (2022) 4747-4755. doi: 10.1021/acs.analchem.1c05292
25. [25]
  R. Zhang, W. Lai, H. Wang, Anal. Chem. 93 (2021) 15567-15572. doi: 10.1021/acs.analchem.1c04151
26. [26]
  H.Y. Pan, Y. Yu, T. Cao, et al., Anal. Chem. 93 (2021) 14907-14911. doi: 10.1021/acs.analchem.1c03869
27. [27]
  X.M. Tang, T.T. Ye, X.J. You, et al., Chin. Chem. Lett. 34 (2023) 107531. doi: 10.1016/j.cclet.2022.05.045
28. [28]
  B.L. Qi, P. Liu, Q.Y. Wang, et al., TrAC Trend. Anal. Chem. 59 (2014) 121-132. doi: 10.1016/j.trac.2014.03.013
29. [29]
  Q.F. Zhang, H.M. Xiao, J.T. Zhan, B.F. Yuan, Y.Q. Feng, Chin. Chem. Lett. 33 (2022) 4746-4749. doi: 10.1016/j.cclet.2022.01.004
30. [30]
  J.M. Chu, C.B. Qi, Y.Q. Huang, et al., Anal. Chem. 87 (2015) 7364-7372. doi: 10.1021/acs.analchem.5b01614
31. [31]
  H. Shintaku, H. Nishikii, L.A. Marshall, H. Kotera, J.G. Santiago, Anal. Chem. 86 (2014) 1953-1957. doi: 10.1021/ac4040218
32. [32]
  J. Wen, L.A. Legendre, J.M. Bienvenue, J.P. Landers, Anal. Chem. 80 (2008) 6472-6479. doi: 10.1021/ac8014998
33. [33]
  F.L. Liu, T.T. Ye, J.H. Ding, et al., Anal. Chem. 93 (2021) 6848-6856. doi: 10.1021/acs.analchem.1c00915
34. [34]
  W. Huang, C.B. Qi, S.W. Lv, et al., Anal. Chem. 88 (2016) 1378-1384. doi: 10.1021/acs.analchem.5b03962
35. [35]
  T.M. Prince, M. Wimmer, J. Choi, et al., Neurobiol. Learn. Mem. 109 (2014) 122-130. doi: 10.1016/j.nlm.2013.11.021
36. [36]
  J.E. Kang, M.M. Lim, R.J. Bateman, et al., Science 326 (2009) 1005-1007. doi: 10.1126/science.1180962
37. [37]
  M. Guidolin, M. Gradisar, Sleep Med. 13 (2012) 779-786. doi: 10.1016/j.sleep.2012.03.016
38. [38]
  J.H. Ding, M.Y. Chen, N.B. Xie, et al., Biosens. Bioelectron. 219 (2023) 114821. doi: 10.1016/j.bios.2022.114821
1. [1]
  Tian Feng , Yun-Ling Gao , Di Hu , Ke-Yu Yuan , Shu-Yi Gu , Yao-Hua Gu , Si-Yu Yu , Jun Xiong , Yu-Qi Feng , Jie Wang , Bi-Feng Yuan . Chronic sleep deprivation induces alterations in DNA and RNA modifications by liquid chromatography-mass spectrometry analysis. Chinese Chemical Letters, 2024, 35(8): 109259-. doi: 10.1016/j.cclet.2023.109259
2. [2]
  Cheng Guo , Xiaoxiao Zhang , Xiujuan Hong , Yiqiu Hu , Lingna Mao , Kezhi Jiang . Graphene as adsorbent for highly efficient extraction of modified nucleosides in urine prior to liquid chromatography-tandem mass spectrometry analysis. Chinese Chemical Letters, 2024, 35(4): 108867-. doi: 10.1016/j.cclet.2023.108867
3. [3]
  Jun Xiong , Ke-Ke Chen , Neng-Bin Xie , Wei Chen , Wen-Xuan Shao , Tong-Tong Ji , Si-Yu Yu , Yu-Qi Feng , Bi-Feng Yuan . Demethylase-assisted site-specific detection of N¹-methyladenosine in RNA. Chinese Chemical Letters, 2024, 35(5): 108953-. doi: 10.1016/j.cclet.2023.108953
4. [4]
  Qiongqiong Wan , Yanan Xiao , Guifang Feng , Xin Dong , Wenjing Nie , Ming Gao , Qingtao Meng , Suming Chen . Visible-light-activated aziridination reaction enables simultaneous resolving of C=C bond location and the sn-position isomers in lipids. Chinese Chemical Letters, 2024, 35(4): 108775-. doi: 10.1016/j.cclet.2023.108775
5. [5]
  Jing Chen , Peisi Xie , Pengfei Wu , Yu He , Zian Lin , Zongwei Cai . MALDI coupled with laser-postionization and trapped ion mobility spectrometry contribute to the enhanced detection of lipids in cancer cell spheroids. Chinese Chemical Letters, 2024, 35(4): 108895-. doi: 10.1016/j.cclet.2023.108895
6. [6]
  Dan Ouyang , Huan Huang , Yanting He , Jiajing Chen , Jiali Lin , Zhuling Chen , Zongwei Cai , Zian Lin . Utilization of hydralazine as a reactive matrix for enhanced detection and on-MALDI-target derivatization of saccharides. Chinese Chemical Letters, 2024, 35(5): 108885-. doi: 10.1016/j.cclet.2023.108885
7. [7]
  Fengyu Zhang , Yali Liang , Zhangran Ye , Lei Deng , Yunna Guo , Ping Qiu , Peng Jia , Qiaobao Zhang , Liqiang Zhang . Enhanced electrochemical performance of nanoscale single crystal NMC811 modification by coating LiNbO₃. Chinese Chemical Letters, 2024, 35(5): 108655-. doi: 10.1016/j.cclet.2023.108655
8. [8]
  Yan Liu , Yang Wang , Jiayi Zhu , Xuxian Su , Xudong Lin , Liang Xu , Xiwen Xing . Employing pH-responsive RNA triplex to control CRISPR/Cas9-mediated gene manipulation in mammalian cells. Chinese Chemical Letters, 2024, 35(9): 109427-. doi: 10.1016/j.cclet.2023.109427
9. [9]
  Yunan Yuan , Zhimin Luo , Jie Chen , Chaoliang He , Kai Hao , Huayu Tian . Constructing thermoresponsive PNIPAM-based microcarriers for cell culture and enzyme-free cell harvesting. Chinese Chemical Letters, 2024, 35(7): 109549-. doi: 10.1016/j.cclet.2024.109549
10. [10]
  Kexin Yuan , Yulei Liu , Haoran Feng , Yi Liu , Jun Cheng , Beiyang Luo , Qinglian Wu , Xinyu Zhang , Ying Wang , Xian Bao , Wanqian Guo , Jun Ma . Unlocking the potential of thin-film composite reverse osmosis membrane performance: Insights from mass transfer modeling. Chinese Chemical Letters, 2024, 35(5): 109022-. doi: 10.1016/j.cclet.2023.109022
11. [11]
  Haoyang Wang , Ronghao Zhang , Yanlun Ren , Li Zhang . A convenient method for measuring gas-liquid volumetric mass transfer coefficient in micro reactors. Chinese Chemical Letters, 2024, 35(4): 108833-. doi: 10.1016/j.cclet.2023.108833
12. [12]
  Wenbi Wu , Yinchu Dong , Haofan Liu , Xuebing Jiang , Li Li , Yi Zhang , Maling Gou . Modification of plasma protein for bioprinting via photopolymerization. Chinese Chemical Letters, 2024, 35(8): 109260-. doi: 10.1016/j.cclet.2023.109260
13. [13]
  Lijun Mao , Shuo Li , Xin Zhang , Zhan-Ting Li , Da Ma . Cucurbit[n]uril-based nanostructure construction and modification. Chinese Chemical Letters, 2024, 35(8): 109363-. doi: 10.1016/j.cclet.2023.109363
14. [14]
  Fangling Cui , Zongjie Hu , Jiayu Huang , Xiaoju Li , Ruihu Wang . MXene-based materials for separator modification of lithium-sulfur batteries. Chinese Journal of Structural Chemistry, 2024, 43(7): 100337-100337. doi: 10.1016/j.cjsc.2024.100337
15. [15]
  Chenghao Ge , Peng Wang , Pei Yuan , Tai Wu , Rongjun Zhao , Rong Huang , Lin Xie , Yong Hua . Tuning hot carrier transfer dynamics by perovskite surface modification. Chinese Chemical Letters, 2024, 35(10): 109352-. doi: 10.1016/j.cclet.2023.109352
16. [16]
  Yukai Tong , Zhijun Wu , Bo Zhou , Min Hu , Anpei Ye . Surface tension of single suspended aerosol microdroplets. Chinese Chemical Letters, 2024, 35(4): 109062-. doi: 10.1016/j.cclet.2023.109062
17. [17]
  Kun Tang , Yu-Wu Zhong . Water reduction by an organic single-chromophore photocatalyst. Chinese Journal of Structural Chemistry, 2024, 43(8): 100376-100376. doi: 10.1016/j.cjsc.2024.100376
18. [18]
  Kun-Heng Li , Hong-Yang Zhao , Dan-Dan Wang , Ming-Hui Qi , Zi-Jian Xu , Jia-Mi Li , Zhi-Li Zhang , Shi-Wen Huang . Mitochondria-targeted nano-AIEgens as a powerful inducer for evoking immunogenic cell death. Chinese Chemical Letters, 2024, 35(5): 108882-. doi: 10.1016/j.cclet.2023.108882
19. [19]
  Yang Liu , Yan Liu , Kaiyin Yang , Zhiruo Zhang , Wenbo Zhang , Bingyou Yang , Hua Li , Lixia Chen . A selective HK2 degrader suppresses SW480 cancer cell growth by degrading HK2. Chinese Chemical Letters, 2024, 35(8): 109264-. doi: 10.1016/j.cclet.2023.109264
20. [20]
  Boran Cheng , Lei Cao , Chen Li , Fang-Yi Huo , Qian-Fang Meng , Ganglin Tong , Xuan Wu , Lin-Lin Bu , Lang Rao , Shubin Wang . Fluorine-doped carbon quantum dots with deep-red emission for hypochlorite determination and cancer cell imaging. Chinese Chemical Letters, 2024, 35(6): 108969-. doi: 10.1016/j.cclet.2023.108969

Get Citation

PDF

XML

Metrics

PDF Downloads(3)
Abstract views(200)
HTML views(18)

通讯作者: 陈斌, bchen63@163.com

1.
沈阳化工大学材料科学与工程学院沈阳 110142