Binding target and sequencing analysis of aldehyde dehydrogenase 18 family member A1 in esophageal cancer cells_West China Medical Journal

Authors：

WANG Yongkang ¹ , YU Wei ¹ , Kelimu Abudureyimu ² ,  Maimaiti Yisireyili ^1,2,3

1. Graduate School of Xinjiang Medical University, Urumqi, Xinjiang 830017, P. R. China;
2. Research Institute for General and Minimally Invasive Surgery, People’s Hospital of Xinjiang Uygur Autonomous Region , Urumqi, Xinjiang 830001, P. R. China;
3. Research and Education Center, People’s Hospital of Xinjiang Uygur Autonomous Region, Urumqi, Xinjiang 830001, P. R. China;

Corresponding author：

Maimaiti Yisireyili, Email: maimaiti727@sina.com

Keywords：

Esophageal cancer cells; aldehyde dehydrogenase 18 family member A1; RNA binding protein; RNA immunocoprecipitation

DOI：

10.7507/1002-0179.202401287

Video：

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Abstract Full text Figures/Tables Video References Cited by

Objective To study the molecular characteristics of RNA binding protein aldehyde dehydrogenase 18 family member A1 (ALDH18A1) in esophageal carcinoma cells (KYSE150 cells) and its effect on tumor growth. Methods Human esophageal squamous cell (KYSE150 cells) was cultured in vitro. At the same time, RNA co-immuno precipitation technology was used to study the binding of RNA and protein in the cell, and the corresponding RNA-protein complex was precipitated by the antibody of the target protein to separate and purify the captured RNA. The molecular characteristics of ALDH18A1 binding RNA were analyzed, and KyotoEncyclopedia of Genes and Genomes cluster analysis was performed for ALDH18A1 binding target genes. Results Protein immunoblotting experiments showed that the target protein was well enriched by antibodies. ALDH18A1 had extensive RNA binding activity, with significant enrichment in regions such as coding sequences, intron, and 5’untranslated region. ALDH18A1 mainly bound to the UGUAAUC motif of RNA. The cluster analysis showed that the RNA molecules bound to ALDH18A1 mainly participated in focal adhesion, central carbon metabolism in cancer, cell cycle, spliceosome, RNA transport, and ubiquitin mediated protein hydrolysis. Conclusion ALDH18A1 has the function of binding to RNA molecules and may play a role in the expression of esophageal cancer-related genes and related biological processes.

Citation： WANG Yongkang, YU Wei, Kelimu Abudureyimu, Maimaiti Yisireyili. Binding target and sequencing analysis of aldehyde dehydrogenase 18 family member A1 in esophageal cancer cells. West China Medical Journal, 2024, 39(8): 1188-1194. doi: 10.7507/1002-0179.202401287 Copy

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11.	马艳荣, 罗蕴之, 马福慧, 等. SRSF6 在大鼠胰岛细胞中结合的靶标及测序分析. 中华保健医学杂志, 2022, 24(4): 336-338.
12.	David G, Reboutier D, Deschamps S, et al. The RNA-binding proteins CELF1 and ELAVL1 cooperatively control the alternative splicing of CD44. Biochem Biophys Res Commun, 2022, 626: 79-84.
13.	Van Nostrand EL, Freese P, Pratt GA, et al. A large-scale binding and functional map of human RNA-binding proteins. Nature, 2020, 583(7818): 711-719.
14.	Jonas K, Calin GA, Pichler M. RNA-binding proteins as important regulators of long non-coding RNAs in cancer. Int J Mol Sci, 2020, 21(8): 2969.
15.	Li W, Deng X, Chen J. RNA-binding proteins in regulating mRNA stability and translation: roles and mechanisms in cancer. Semin Cancer Biol, 2022, 86(Pt 2): 664-677.
16.	Li X, Liang QX, Lin JR, et al. Epitranscriptomic technologies and analyses. Sci China Life Sci, 2020, 63(4): 501-515.
17.	Geng P, Qin W, Xu G. Proline metabolism in cancer. Amino Acids, 2021, 53(12): 1769-1777.
18.	Shenoy A, Belugali Nataraj N, Perry G, et al. Proteomic patterns associated with response to breast cancer neoadjuvant treatment. Mol Syst Biol, 2020, 16(9): e9443.
19.	Qin H, Ni H, Liu Y, et al. RNA-binding proteins in tumor progression. J Hematol Oncol, 2020, 13(1): 90.
20.	Jiang F, Hedaya OM, Khor E, et al. RNA binding protein PRRC2B mediates translation of specific mRNAs and regulates cell cycle progression. Nucleic Acids Res, 2023, 51(11): 5831-5846.
21.	Zhu Z, Chen D, Zhang W, et al. Modulation of alternative splicing induced by paclitaxel in human lung cancer. Cell Death Dis, 2018, 9(5): 491.
22.	Castello A, Hentze MW, Preiss T. Metabolic enzymes enjoying new partnerships as RNA-binding proteins. Trends Endocrinol Metab, 2015, 26(12): 746-757.

1. Morgan E, Soerjomataram I, Rumgay H, et al. The global landscape of esophageal squamous cell carcinoma and esophageal adenocarcinoma incidence and mortality in 2020 and projections to 2040: new estimates from GLOBOCAN 2020. Gastroenterology, 2022, 163(3): 649-658. e2.
2. Chang J, Zhao X, Wang Y, et al. Genomic alterations driving precancerous to cancerous lesions in esophageal cancer development. Cancer Cell, 2023, 41(12): 2038-2050. e5.
3. Hashimoto S, Kishimoto T. Roles of RNA-binding proteins in immune diseases and cancer. Semin Cancer Biol, 2022, 86(Pt 3): 310-324.
4. Wang S, Sun Z, Lei Z, et al. RNA-binding proteins and cancer metastasis. Semin Cancer Biol, 2022, 86(Pt 2): 748-768.
5. Nag S, Goswami B, Das Mandal S, et al. Cooperation and competition by RNA-binding proteins in cancer. Semin Cancer Biol, 2022, 86(Pt 3): 286-297.
6. Cava C, Armaos A, Lang B, et al. Identification of long non-coding RNAs and RNA binding proteins in breast cancer subtypes. Sci Rep, 2022, 12(1): 693.
7. Craze ML, Cheung H, Jewa N, et al. MYC regulation of glutamine-proline regulatory axis is key in luminal B breast cancer. Br J Cancer, 2018, 118(2): 258-265.
8. Guo YF, Duan JJ, Wang J, et al. Inhibition of the ALDH18A1-MYCN positive feedback loop attenuates MYCN-amplified neuroblastoma growth. Sci Transl Med, 2020, 12(531): eaax8694.
9. Ye Z, Zhang H, Kong F, et al. Comprehensive analysis of alteration landscape and its clinical significance of mitochondrial energy metabolism pathway-related genes in lung cancers. Oxid Med Cell Longev, 2021, 2021: 9259297.
10. Kardos GR, Wastyk HC, Robertson GP. Disruption of proline synthesis in melanoma inhibits protein production mediated by the GCN2 pathway. Mol Cancer Res, 2015, 13(10): 1408-1420.
11. 马艳荣, 罗蕴之, 马福慧, 等. SRSF6 在大鼠胰岛细胞中结合的靶标及测序分析. 中华保健医学杂志, 2022, 24(4): 336-338.
12. David G, Reboutier D, Deschamps S, et al. The RNA-binding proteins CELF1 and ELAVL1 cooperatively control the alternative splicing of CD44. Biochem Biophys Res Commun, 2022, 626: 79-84.
13. Van Nostrand EL, Freese P, Pratt GA, et al. A large-scale binding and functional map of human RNA-binding proteins. Nature, 2020, 583(7818): 711-719.
14. Jonas K, Calin GA, Pichler M. RNA-binding proteins as important regulators of long non-coding RNAs in cancer. Int J Mol Sci, 2020, 21(8): 2969.
15. Li W, Deng X, Chen J. RNA-binding proteins in regulating mRNA stability and translation: roles and mechanisms in cancer. Semin Cancer Biol, 2022, 86(Pt 2): 664-677.
16. Li X, Liang QX, Lin JR, et al. Epitranscriptomic technologies and analyses. Sci China Life Sci, 2020, 63(4): 501-515.
17. Geng P, Qin W, Xu G. Proline metabolism in cancer. Amino Acids, 2021, 53(12): 1769-1777.
18. Shenoy A, Belugali Nataraj N, Perry G, et al. Proteomic patterns associated with response to breast cancer neoadjuvant treatment. Mol Syst Biol, 2020, 16(9): e9443.
19. Qin H, Ni H, Liu Y, et al. RNA-binding proteins in tumor progression. J Hematol Oncol, 2020, 13(1): 90.
20. Jiang F, Hedaya OM, Khor E, et al. RNA binding protein PRRC2B mediates translation of specific mRNAs and regulates cell cycle progression. Nucleic Acids Res, 2023, 51(11): 5831-5846.
21. Zhu Z, Chen D, Zhang W, et al. Modulation of alternative splicing induced by paclitaxel in human lung cancer. Cell Death Dis, 2018, 9(5): 491.
22. Castello A, Hentze MW, Preiss T. Metabolic enzymes enjoying new partnerships as RNA-binding proteins. Trends Endocrinol Metab, 2015, 26(12): 746-757.

West China Medical Journal

Binding target and sequencing analysis of aldehyde dehydrogenase 18 family member A1 in esophageal cancer cells

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