METTL16 promotes liver cancer stem cell self-renewal via controlling ribosome biogenesis and mRNA translation

Meilin Xue; Lei Dong; Honghai Zhang; Yangchan Li; Kangqiang Qiu; Zhicong Zhao; Min Gao; Li Han; Anthony K N Chan; Wei Li; Keith Leung; Kitty Wang; Sheela Pangeni Pokharel; Ying Qing; Wei Liu; Xueer Wang; Lili Ren; Hongjie Bi; Lu Yang; Chao Shen; Zhenhua Chen; Laleh Melstrom; Hongzhi Li; Nikolai Timchenko; Xiaolan Deng; Wendong Huang; Steven T Rosen; Jingyan Tian; Lin Xu; Jiajie Diao; Chun-Wei Chen; Jianjun Chen; Baiyong Shen; Hao Chen; Rui Su

doi:10.1186/s13045-024-01526-9

METTL16 promotes liver cancer stem cell self-renewal via controlling ribosome biogenesis and mRNA translation

J Hematol Oncol. 2024 Feb 1;17(1):7. doi: 10.1186/s13045-024-01526-9.

Authors

Meilin Xue^#^{1

2}, Lei Dong^#^{1

3}, Honghai Zhang^#¹, Yangchan Li^{1

4}, Kangqiang Qiu⁵, Zhicong Zhao^{1

6}, Min Gao¹, Li Han^{1

7}, Anthony K N Chan¹, Wei Li¹, Keith Leung¹, Kitty Wang¹, Sheela Pangeni Pokharel¹, Ying Qing¹, Wei Liu¹, Xueer Wang¹, Lili Ren¹, Hongjie Bi¹, Lu Yang¹, Chao Shen¹, Zhenhua Chen¹, Laleh Melstrom⁸, Hongzhi Li⁹, Nikolai Timchenko¹⁰, Xiaolan Deng¹, Wendong Huang^{11

12}, Steven T Rosen¹³, Jingyan Tian¹⁴, Lin Xu³, Jiajie Diao⁵, Chun-Wei Chen^{1

13}, Jianjun Chen^{1

13

15}, Baiyong Shen¹⁶, Hao Chen¹⁷, Rui Su^{18

19}

Affiliations

¹ Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA, 91016, USA.
² Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
³ Quantitative Biomedical Research Center, Peter O'Donnell Jr. School of Public Health, UT Southwestern Medical Center, Dallas, TX, 7539, USA.
⁴ Department of Radiation Oncology, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510080, Guangdong, China.
⁵ Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH, 45267, USA.
⁶ Department of Liver Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China.
⁷ School of Pharmacy, China Medical University, Shenyang, 110001, Liaoning, China.
⁸ Division of Surgical Oncology, Department of Surgery, Beckman Research Institute of City of Hope Comprehensive Cancer Center, Duarte, CA, 91010, USA.
⁹ Department of Molecular Medicine, City of Hope National Medical Center, Duarte, CA, 91016, USA.
¹⁰ Division of General and Thoracic Surgery, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA.
¹¹ Department of Diabetes Complications and Metabolism, Diabetes and Metabolism Research Institute, Beckman Research Institute of City of Hope, Duarte, CA, 91010, USA.
¹² Graduate School of Biological Science, City of Hope, Duarte, CA, 91010, USA.
¹³ City of Hope Comprehensive Cancer Center, City of Hope, Duarte, CA, 91010, USA.
¹⁴ State Key Laboratory of Medical Genomics, Clinical Trial Center, Shanghai Institute of Endocrine and Metabolic Diseases, Department of Endocrinology and Metabolism, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
¹⁵ Gehr Family Center for Leukemia Research, City of Hope, Duarte, CA, 91010, USA.
¹⁶ Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China. shenby@shsmu.edu.cn.
¹⁷ Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China. haochendr@126.com.
¹⁸ Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA, 91016, USA. rsu@coh.org.
¹⁹ City of Hope Comprehensive Cancer Center, City of Hope, Duarte, CA, 91010, USA. rsu@coh.org.

^# Contributed equally.

Abstract

Background: While liver cancer stem cells (CSCs) play a crucial role in hepatocellular carcinoma (HCC) initiation, progression, recurrence, and treatment resistance, the mechanism underlying liver CSC self-renewal remains elusive. We aim to characterize the role of Methyltransferase 16 (METTL16), a recently identified RNA N⁶-methyladenosine (m⁶A) methyltransferase, in HCC development/maintenance, CSC stemness, as well as normal hepatogenesis.

Methods: Liver-specific Mettl16 conditional KO (cKO) mice were generated to assess its role in HCC pathogenesis and normal hepatogenesis. Hydrodynamic tail-vein injection (HDTVi)-induced de novo hepatocarcinogenesis and xenograft models were utilized to determine the role of METTL16 in HCC initiation and progression. A limiting dilution assay was utilized to evaluate CSC frequency. Functionally essential targets were revealed via integrative analysis of multi-omics data, including RNA-seq, RNA immunoprecipitation (RIP)-seq, and ribosome profiling.

Results: METTL16 is highly expressed in liver CSCs and its depletion dramatically decreased CSC frequency in vitro and in vivo. Mettl16 KO significantly attenuated HCC initiation and progression, yet only slightly influenced normal hepatogenesis. Mechanistic studies, including high-throughput sequencing, unveiled METTL16 as a key regulator of ribosomal RNA (rRNA) maturation and mRNA translation and identified eukaryotic translation initiation factor 3 subunit a (eIF3a) transcript as a bona-fide target of METTL16 in HCC. In addition, the functionally essential regions of METTL16 were revealed by CRISPR gene tiling scan, which will pave the way for the development of potential inhibitor(s).

Conclusions: Our findings highlight the crucial oncogenic role of METTL16 in promoting HCC pathogenesis and enhancing liver CSC self-renewal through augmenting mRNA translation efficiency.

Keywords: Cancer stem cells; Hepatocellular carcinoma; METTL16; N6-methyladenosine; Ribosome biogenesis; Self-renewal; eIF3a; mRNA translation.

Publication types

Research Support, Non-U.S. Gov't
Research Support, N.I.H., Extramural

MeSH terms

Animals
Carcinoma, Hepatocellular* / genetics
Carcinoma, Hepatocellular* / pathology
Cell Line, Tumor
Cell Self Renewal / genetics
Humans
Liver Neoplasms* / genetics
Liver Neoplasms* / pathology
Methyltransferases / genetics
Methyltransferases / metabolism
Mice
Neoplastic Stem Cells* / pathology
Protein Biosynthesis
RNA
Ribosomes / metabolism

Substances

Methyltransferases
METTL16 protein, human
RNA

Abstract

Publication types

MeSH terms

Substances

Grants and funding