AccScience Publishing / GPD / Volume 2 / Issue 1 / DOI: 10.36922/gpd.305

Alkylation repair homolog 3-regulated esophageal squamous cell carcinoma associated long non-coding RNA 1 is required for maintaining the stemness of esophageal cancer

Yuanbo Cui1 Yanan Lou2 Pengju Lv1 Wei Cao1*
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1 Translational Medicine Center, Zhengzhou Central Hospital Affiliated to Zhengzhou University, Zhengzhou 450007, China
2 Department of Breast Surgery, Zhengzhou Central Hospital Affiliated to Zhengzhou University, Zhengzhou, 450007, China
Submitted: 28 December 2022 | Accepted: 21 February 2023 | Published: 13 March 2023
© 2023 by the Author(s). Licensee AccScience Publishing, Singapore. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution 4.0 International License ( )

N1-methyladenosine (m1A) RNA modification represents one of the essential post-transcriptional modifications in gene expression regulation. Long non-coding RNAs (lncRNAs) are involved in the development of malignant tumors, including esophageal cancer (ESCA). However, whether m1A can regulate that lncRNA in cancer cells remains unclear. ESCA cell lines TE1 and KYSE70 were used for functional experiments. The mRNA and protein levels were detected by quantitative reverse transcription polymerase chain reaction and Western blot, respectively. Colony formation and tumor sphere formation assays were used for evaluating ESCA stemness. The m1A modification on esophageal squamous cell carcinoma associated long non-coding RNA 1 (ESCCAL-1) transcript was examined by methylated RNA immunoprecipitation. In this study, we report that RNA m1A demethylase alkylation repair homolog 3 (ALKBH3)-mediated ESCCAL-1 is implicated in maintaining stem cell-like properties of ESCA. Clinically, ESCCAL-1 was up-regulated in ESCA and positively correlated with tumor stage. In addition, patients with higher ESCCAL-1 expression in tumors had shorter median survival. Functionally, the knockdown of ESCCAL-1 attenuated the stemness of ESCA cells as indicated by decreased sphere formation and colony formation capacities, while overexpression of ESCCAL-1 elicits the opposite biological effects. Moreover, ESCCAL-1 manipulation positively regulated both mRNA and protein levels of KLF4 and CD44, two stemness-related markers. Mechanistically, ALKBH3 upregulated ESCCAL-1 expression in an m1A demethylation-dependent manner. Notably, the downregulation of ALKBH3 mimicked the effects of ESCCAL-1 deficiency on ESCA stemness, and this phenomenon is significantly reversed by the enforced expression of ESCCAL-1. Our results revealed the role of m1A-mediated ESCCAL-1 in ESCA self-renewal, which expands the understanding of lncRNA post-transcriptional modification in cancer development.

Esophageal cancer
Medical Science and Technology Project of Henan Province
Key Project of Higher Education in Henan Province

Sung H, Ferlay J, Siegel RL, et al., 2021, Global cancer statistics 2020: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries. CA Cancer J Clin, 71(3): 209–249. 


Bray F, Ferlay J, Soerjomataram I, et al., 2018, Global cancer statistics 2018: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries. CA Cancer J Clin, 68(6): 394–424.


Smyth EC, Lagergren J, Fitzgerald RC, et al., 2017, Oesophageal cancer. Nat Rev Dis Primers, 3: 17048. 


Song Y, Li L, Ou Y, et al., 2014, Identification of genomic alterations in oesophageal squamous cell cancer. Nature, 509(7498): 91–95.


Cui Y, Chen H, Xi R, et al., 2020, Whole-genome sequencing of 508 patients identifies key molecular features associated with poor prognosis in esophageal squamous cell carcinoma. Cell Res, 30(10): 902–913.


Xi Y, Lin Y, Guo W, et al., 2022, Multi-omic characterization of genome-wide abnormal DNA methylation reveals diagnostic and prognostic markers for esophageal squamous-cell carcinoma. Signal Transduct Target Ther, 7(1): 53.


Slack FJ, Chinnaiyan AM, 2019, The role of non-coding RNAs in oncology. Cell, 179(5): 1033–1055.


Cao W, Lee H, Wu W, et al., 2020, Multi-faceted epigenetic dysregulation of gene expression promotes esophageal squamous cell carcinoma. Nat Commun, 11(1): 3675.


Liu J, Mayekar MK, Wu W, et al., 2020, Long non-coding RNA ESCCAL-1 promotes esophageal squamous cell carcinoma by down regulating the negative regulator of APOBEC3G. Cancer Lett, 493: 217–227. 


Cui Y, Yan M, Wu W, et al., 2022, ESCCAL-1 promotes cell-cycle progression by interacting with and stabilizing galectin-1 in esophageal squamous cell carcinoma. NPJ Precis Oncol, 6(1): 12.


Jin H, Huo C, Zhou T, et al., 2022, m1A RNA modification in gene expression regulation. Genes (Basel), 13(5): 910.


Chen Z, Qi M, Shen B, et al., 2019, Transfer RNA demethylase ALKBH3 promotes cancer progression via induction of tRNA-derived small RNAs. Nucleic Acids Res, 47(5): 2533–2545.


Wang Y, Wang J, Li X, et al., 2021, N1-methyladenosine methylation in tRNA drives liver tumourigenesis by regulating cholesterol metabolism. Nat Commun, 12(1): 6314.


Wu Y, Chen Z, Xie G, et al., 2022, RNA m1A methylation regulates glycolysis of cancer cells through modulating ATP5D. Proc Natl Acad Sci U S A, 119(28): e2119038119.


Lu Q, Wang H, Lei X, et al., 2022, LncRNA ALKBH3-AS1 enhances ALKBH3 mRNA stability to promote hepatocellular carcinoma cell proliferation and invasion. J Cell Mol Med, 26(20): 5292–5302.


Nallasamy P, Nimmakayala RK, Parte S, et al., 2022, Tumor microenvironment enriches the stemness features: The architectural event of therapy resistance and metastasis. Mol Cancer, 21(1): 225.


Chaudhary A, Raza SS, Haque R, 2023, Transcriptional factors targeting in cancer stem cells for tumor modulation. Semin Cancer Biol, 88: 123–137.


Wilkinson E, Cui YH, He YY, 2022, Roles of RNA modifications in diverse cellular functions. Front Cell Dev Biol, 10: 828683.


Wang Z, He J, Bach DH, et al., 2022, Induction of m6A methylation in adipocyte exosomal LncRNAs mediates myeloma drug resistance. J Exp Clin Cancer Res, 41(1): 4.


Cui L, Ma R, Cai J, et al., 2022, RNA modifications: Importance in immune cell biology and related diseases. Signal Transduct Target Ther, 7(1): 334.


Li J, Zhang H, Wang H, 2022, N1-methyladenosine modification in cancer biology: Current status and future perspectives. Comput Struct Biotechnol J, 20: 6578––6585.


Paul R, Dorsey JF, Fan Y, 2022, Cell plasticity, senescence, and quiescence in cancer stem cells: Biological and therapeutic implications. Pharmacol Ther, 231: 107985.


Du L, Cheng Q, Zheng H, et al., 2022, Targeting stemness of cancer stem cells to fight colorectal cancers. Semin Cancer Biol, 82: 150–161.


Liu C, Zhang Y, Gao J, et al., 2022, A highly potent small-molecule antagonist of exportin-1 selectively eliminates CD44+CD24-enriched breast cancer stem-like cells. Drug Resist Updat, 66: 100903. 


Ervin EH, French R, Chang CH, et al., 2022, Inside the stemness engine: Mechanistic links between deregulated transcription factors and stemness in cancer. Semin Cancer Biol, 87: 48–83.


Taheri M, Khoshbakht T, Jamali E, et al., 2021, Interaction between non-coding RNAs and androgen receptor with an especial focus on prostate cancer. Cells, 10(11): 3198.


Tortora F, Calin GA, Cimmino A, 2021, Effects of long non-coding RNAs on androgen signaling pathways in genitourinary malignancies. Mol Cell Endocrinol, 526: 111197.


Huang F, Chen H, Zhu X, et al., 2021, The oncogenomic function of androgen receptor in esophageal squamous cell carcinoma is directed by GATA3. Cell Res, 31(3): 362–365.


Zhao Y, Zhao Q, Kaboli PJ, et al., 2019, m1A regulated genes modulate PI3K/AKT/mTOR and ErbB pathways in gastrointestinal cancer. Transl Oncol, 12(10): 1323–1333.


Woo HH, Chambers SK, 2019, Human ALKBH3-induced m1A demethylation increases the CSF-1 mRNA stability in breast and ovarian cancer cells. Biochim Biophys Acta Gene Regul Mech, 1862(1): 35–46.

Conflict of interest
The authors declare that there are no competing interests.
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Gene & Protein in Disease, Electronic ISSN: 2811-003X Print ISSN: TBA, Published by AccScience Publishing