N6-Methyladenosine Reader YTHDF1 Promotes ARHGEF2 Translation and RhoA Signaling in Colorectal Cancer

Shiyan Wang; Shanshan Gao; Yong Zeng; Lin Zhu; Yulin Mo; Chi Chun Wong; Yi Bao; Peiran Su; Jianning Zhai; Lina Wang; Fraser Soares; Xin Xu; Huarong Chen; Kebria Hezaveh; Xinpei Ci; Aobo He; Tracy McGaha; Catherine O'Brien; Robert Rottapel; Wei Kang; Jianfeng Wu; Gang Zheng; Zongwei Cai; Jun Yu; Housheng Hansen He

doi:10.1053/j.gastro.2021.12.269

N6-Methyladenosine Reader YTHDF1 Promotes ARHGEF2 Translation and RhoA Signaling in Colorectal Cancer

Shiyan Wang, Shanshan Gao, Yong Zeng, Lin Zhu, Yulin Mo, Chi Chun Wong, Yi Bao, Peiran Su, Jianning Zhai, Lina Wang, Fraser Soares, Xin Xu, Huarong Chen, Kebria Hezaveh, Xinpei Ci, Aobo He, Tracy McGaha, Catherine O'Brien, Robert Rottapel, Wei KangJianfeng Wu, Gang Zheng, Zongwei Cai, Jun Yu^*, Housheng Hansen He^*

^*Corresponding author for this work

State Key Laboratory of Environmental and Biological Analysis

Research output: Contribution to journal › Journal article › peer-review

115 Citations (Scopus)

Abstract

Background & Aims: N6-methyladenosine (m⁶A) governs the fate of RNAs through m⁶A readers. Colorectal cancer (CRC) exhibits aberrant m⁶A modifications and expression of m⁶A regulators. However, how m⁶A readers interpret oncogenic m⁶A methylome to promote malignant transformation remains to be illustrated. Methods: YTH N6-methyladenosine RNA binding protein 1 (Ythdf1) knockout mouse was generated to determine the effect of Ythdf1 in CRC tumorigenesis in vivo. Multiomic analysis of RNA-sequencing, m⁶A methylated RNA immunoprecipitation sequencing, YTHDF1 RNA immunoprecipitation sequencing, and proteomics were performed to unravel targets of YTHDF1 in CRC. The therapeutic potential of targeting YTHDF1-m⁶A-Rho/Rac guanine nucleotide exchange factor 2 (ARHGEF2) was evaluated using small interfering RNA (siRNA) encapsulated by lipid nanoparticles (LNP). Results: DNA copy number gain of YTHDF1 is a frequent event in CRC and contributes to its overexpression. High expression of YTHDF1 is significantly associated with metastatic gene signature in patient tumors. Ythdf1 knockout in mice dampened tumor growth in an inflammatory CRC model. YTHDF1 promotes cell growth in CRC cell lines and primary organoids and lung and liver metastasis in vivo. Integrative multiomics analysis identified RhoA activator ARHGEF2 as a key downstream target of YTHDF1. YTHDF1 binds to m⁶A sites of ARHGEF2 messenger RNA, resulting in enhanced translation of ARHGEF2. Ectopic expression of ARHGEF2 restored impaired RhoA signaling, cell growth, and metastatic ability both in vitro and in vivo caused by YTHDF1 loss, verifying that ARHGEF2 is a key target of YTHDF1. Finally, ARHGEF2 siRNA delivered by LNP significantly suppressed tumor growth and metastasis in vivo. Conclusions: We identify a novel oncogenic epitranscriptome axis of YTHDF1-m⁶A-ARHGEF2, which regulates CRC tumorigenesis and metastasis. siRNA-delivering LNP drug validated the therapeutic potential of targeting this axis in CRC.

Original language	English
Pages (from-to)	1183-1196
Number of pages	14
Journal	Gastroenterology
Volume	162
Issue number	4
DOIs	https://doi.org/10.1053/j.gastro.2021.12.269
Publication status	Published - Apr 2022

Scopus Subject Areas

Gastroenterology
Hepatology

User-Defined Keywords

ARHGEF2
Colorectal Cancer
N6-Methyladenosine
Nanoparticle
YTHDF1
rhoA GTP-Binding Protein/genetics
Colorectal Neoplasms/pathology
Humans
Gene Expression Regulation, Neoplastic
Rho Guanine Nucleotide Exchange Factors/genetics
RNA-Binding Proteins/genetics
Nanoparticles
Adenosine/analogs & derivatives
Animals
Mice
RNA, Small Interfering
Liposomes
Carcinogenesis/genetics

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

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10.1053/j.gastro.2021.12.269

Cite this

Wang, S., Gao, S., Zeng, Y., Zhu, L., Mo, Y., Wong, C. C., Bao, Y., Su, P., Zhai, J., Wang, L., Soares, F., Xu, X., Chen, H., Hezaveh, K., Ci, X., He, A., McGaha, T., O'Brien, C., Rottapel, R., ... He, H. H. (2022). N6-Methyladenosine Reader YTHDF1 Promotes ARHGEF2 Translation and RhoA Signaling in Colorectal Cancer. Gastroenterology, 162(4), 1183-1196. https://doi.org/10.1053/j.gastro.2021.12.269

@article{4c2171e354314c589c6e5d6502db4338,

title = "N6-Methyladenosine Reader YTHDF1 Promotes ARHGEF2 Translation and RhoA Signaling in Colorectal Cancer",

abstract = "Background & Aims: N6-methyladenosine (m6A) governs the fate of RNAs through m6A readers. Colorectal cancer (CRC) exhibits aberrant m6A modifications and expression of m6A regulators. However, how m6A readers interpret oncogenic m6A methylome to promote malignant transformation remains to be illustrated. Methods: YTH N6-methyladenosine RNA binding protein 1 (Ythdf1) knockout mouse was generated to determine the effect of Ythdf1 in CRC tumorigenesis in vivo. Multiomic analysis of RNA-sequencing, m6A methylated RNA immunoprecipitation sequencing, YTHDF1 RNA immunoprecipitation sequencing, and proteomics were performed to unravel targets of YTHDF1 in CRC. The therapeutic potential of targeting YTHDF1-m6A-Rho/Rac guanine nucleotide exchange factor 2 (ARHGEF2) was evaluated using small interfering RNA (siRNA) encapsulated by lipid nanoparticles (LNP). Results: DNA copy number gain of YTHDF1 is a frequent event in CRC and contributes to its overexpression. High expression of YTHDF1 is significantly associated with metastatic gene signature in patient tumors. Ythdf1 knockout in mice dampened tumor growth in an inflammatory CRC model. YTHDF1 promotes cell growth in CRC cell lines and primary organoids and lung and liver metastasis in vivo. Integrative multiomics analysis identified RhoA activator ARHGEF2 as a key downstream target of YTHDF1. YTHDF1 binds to m6A sites of ARHGEF2 messenger RNA, resulting in enhanced translation of ARHGEF2. Ectopic expression of ARHGEF2 restored impaired RhoA signaling, cell growth, and metastatic ability both in vitro and in vivo caused by YTHDF1 loss, verifying that ARHGEF2 is a key target of YTHDF1. Finally, ARHGEF2 siRNA delivered by LNP significantly suppressed tumor growth and metastasis in vivo. Conclusions: We identify a novel oncogenic epitranscriptome axis of YTHDF1-m6A-ARHGEF2, which regulates CRC tumorigenesis and metastasis. siRNA-delivering LNP drug validated the therapeutic potential of targeting this axis in CRC.",

keywords = "ARHGEF2, Colorectal Cancer, N6-Methyladenosine, Nanoparticle, YTHDF1, rhoA GTP-Binding Protein/genetics, Colorectal Neoplasms/pathology, Humans, Gene Expression Regulation, Neoplastic, Rho Guanine Nucleotide Exchange Factors/genetics, RNA-Binding Proteins/genetics, Nanoparticles, Adenosine/analogs & derivatives, Animals, Mice, RNA, Small Interfering, Liposomes, Carcinogenesis/genetics",

author = "Shiyan Wang and Shanshan Gao and Yong Zeng and Lin Zhu and Yulin Mo and Wong, {Chi Chun} and Yi Bao and Peiran Su and Jianning Zhai and Lina Wang and Fraser Soares and Xin Xu and Huarong Chen and Kebria Hezaveh and Xinpei Ci and Aobo He and Tracy McGaha and Catherine O'Brien and Robert Rottapel and Wei Kang and Jianfeng Wu and Gang Zheng and Zongwei Cai and Jun Yu and He, {Housheng Hansen}",

note = "Funding Information: Funding This work was supported by the Princess Margaret Cancer Foundation (886012001223 to Housheng Hansen He), Canada Foundation for Innovation and Ontario Research Fund (CFI32372 to Housheng Hansen He), Natural Sciences and Engineering Research Council of Canada discovery grant (498706 to Housheng Hansen He), Canadian Institutes of Health Research (CIHR) operating grants (142246, 152863, 152864 and 159567 to Housheng Hansen He), Terry Fox New Frontiers Program Project Grant (1090 P3 to Housheng Hansen He), Research Grants Council Collaborative Research Fund Hong Kong (C4039-19GF) and Research Grants Council General Research Fund (14110819). Housheng Hansen He was supported by Ontario Ministry of Research, Innovation and Science Early Researcher Award and CIHR New Investigator Award. Publisher Copyright: {\textcopyright} 2022 The Authors Copyright {\textcopyright} 2022 The Authors. Published by Elsevier Inc. All rights reserved.",

year = "2022",

month = apr,

doi = "10.1053/j.gastro.2021.12.269",

language = "English",

volume = "162",

pages = "1183--1196",

journal = "Gastroenterology",

issn = "0016-5085",

publisher = "W.B. Saunders Ltd",

number = "4",

}

Wang, S, Gao, S, Zeng, Y, Zhu, L, Mo, Y, Wong, CC, Bao, Y, Su, P, Zhai, J, Wang, L, Soares, F, Xu, X, Chen, H, Hezaveh, K, Ci, X, He, A, McGaha, T, O'Brien, C, Rottapel, R, Kang, W, Wu, J, Zheng, G, Cai, Z, Yu, J & He, HH 2022, 'N6-Methyladenosine Reader YTHDF1 Promotes ARHGEF2 Translation and RhoA Signaling in Colorectal Cancer', Gastroenterology, vol. 162, no. 4, pp. 1183-1196. https://doi.org/10.1053/j.gastro.2021.12.269

TY - JOUR

T1 - N6-Methyladenosine Reader YTHDF1 Promotes ARHGEF2 Translation and RhoA Signaling in Colorectal Cancer

AU - Wang, Shiyan

AU - Gao, Shanshan

AU - Zeng, Yong

AU - Zhu, Lin

AU - Mo, Yulin

AU - Wong, Chi Chun

AU - Bao, Yi

AU - Su, Peiran

AU - Zhai, Jianning

AU - Wang, Lina

AU - Soares, Fraser

AU - Xu, Xin

AU - Chen, Huarong

AU - Hezaveh, Kebria

AU - Ci, Xinpei

AU - He, Aobo

AU - McGaha, Tracy

AU - O'Brien, Catherine

AU - Rottapel, Robert

AU - Kang, Wei

AU - Wu, Jianfeng

AU - Zheng, Gang

AU - Cai, Zongwei

AU - Yu, Jun

AU - He, Housheng Hansen

N1 - Funding Information: Funding This work was supported by the Princess Margaret Cancer Foundation (886012001223 to Housheng Hansen He), Canada Foundation for Innovation and Ontario Research Fund (CFI32372 to Housheng Hansen He), Natural Sciences and Engineering Research Council of Canada discovery grant (498706 to Housheng Hansen He), Canadian Institutes of Health Research (CIHR) operating grants (142246, 152863, 152864 and 159567 to Housheng Hansen He), Terry Fox New Frontiers Program Project Grant (1090 P3 to Housheng Hansen He), Research Grants Council Collaborative Research Fund Hong Kong (C4039-19GF) and Research Grants Council General Research Fund (14110819). Housheng Hansen He was supported by Ontario Ministry of Research, Innovation and Science Early Researcher Award and CIHR New Investigator Award. Publisher Copyright: © 2022 The Authors Copyright © 2022 The Authors. Published by Elsevier Inc. All rights reserved.

PY - 2022/4

Y1 - 2022/4

N2 - Background & Aims: N6-methyladenosine (m6A) governs the fate of RNAs through m6A readers. Colorectal cancer (CRC) exhibits aberrant m6A modifications and expression of m6A regulators. However, how m6A readers interpret oncogenic m6A methylome to promote malignant transformation remains to be illustrated. Methods: YTH N6-methyladenosine RNA binding protein 1 (Ythdf1) knockout mouse was generated to determine the effect of Ythdf1 in CRC tumorigenesis in vivo. Multiomic analysis of RNA-sequencing, m6A methylated RNA immunoprecipitation sequencing, YTHDF1 RNA immunoprecipitation sequencing, and proteomics were performed to unravel targets of YTHDF1 in CRC. The therapeutic potential of targeting YTHDF1-m6A-Rho/Rac guanine nucleotide exchange factor 2 (ARHGEF2) was evaluated using small interfering RNA (siRNA) encapsulated by lipid nanoparticles (LNP). Results: DNA copy number gain of YTHDF1 is a frequent event in CRC and contributes to its overexpression. High expression of YTHDF1 is significantly associated with metastatic gene signature in patient tumors. Ythdf1 knockout in mice dampened tumor growth in an inflammatory CRC model. YTHDF1 promotes cell growth in CRC cell lines and primary organoids and lung and liver metastasis in vivo. Integrative multiomics analysis identified RhoA activator ARHGEF2 as a key downstream target of YTHDF1. YTHDF1 binds to m6A sites of ARHGEF2 messenger RNA, resulting in enhanced translation of ARHGEF2. Ectopic expression of ARHGEF2 restored impaired RhoA signaling, cell growth, and metastatic ability both in vitro and in vivo caused by YTHDF1 loss, verifying that ARHGEF2 is a key target of YTHDF1. Finally, ARHGEF2 siRNA delivered by LNP significantly suppressed tumor growth and metastasis in vivo. Conclusions: We identify a novel oncogenic epitranscriptome axis of YTHDF1-m6A-ARHGEF2, which regulates CRC tumorigenesis and metastasis. siRNA-delivering LNP drug validated the therapeutic potential of targeting this axis in CRC.

AB - Background & Aims: N6-methyladenosine (m6A) governs the fate of RNAs through m6A readers. Colorectal cancer (CRC) exhibits aberrant m6A modifications and expression of m6A regulators. However, how m6A readers interpret oncogenic m6A methylome to promote malignant transformation remains to be illustrated. Methods: YTH N6-methyladenosine RNA binding protein 1 (Ythdf1) knockout mouse was generated to determine the effect of Ythdf1 in CRC tumorigenesis in vivo. Multiomic analysis of RNA-sequencing, m6A methylated RNA immunoprecipitation sequencing, YTHDF1 RNA immunoprecipitation sequencing, and proteomics were performed to unravel targets of YTHDF1 in CRC. The therapeutic potential of targeting YTHDF1-m6A-Rho/Rac guanine nucleotide exchange factor 2 (ARHGEF2) was evaluated using small interfering RNA (siRNA) encapsulated by lipid nanoparticles (LNP). Results: DNA copy number gain of YTHDF1 is a frequent event in CRC and contributes to its overexpression. High expression of YTHDF1 is significantly associated with metastatic gene signature in patient tumors. Ythdf1 knockout in mice dampened tumor growth in an inflammatory CRC model. YTHDF1 promotes cell growth in CRC cell lines and primary organoids and lung and liver metastasis in vivo. Integrative multiomics analysis identified RhoA activator ARHGEF2 as a key downstream target of YTHDF1. YTHDF1 binds to m6A sites of ARHGEF2 messenger RNA, resulting in enhanced translation of ARHGEF2. Ectopic expression of ARHGEF2 restored impaired RhoA signaling, cell growth, and metastatic ability both in vitro and in vivo caused by YTHDF1 loss, verifying that ARHGEF2 is a key target of YTHDF1. Finally, ARHGEF2 siRNA delivered by LNP significantly suppressed tumor growth and metastasis in vivo. Conclusions: We identify a novel oncogenic epitranscriptome axis of YTHDF1-m6A-ARHGEF2, which regulates CRC tumorigenesis and metastasis. siRNA-delivering LNP drug validated the therapeutic potential of targeting this axis in CRC.

KW - ARHGEF2

KW - Colorectal Cancer

KW - N6-Methyladenosine

KW - Nanoparticle

KW - YTHDF1

KW - rhoA GTP-Binding Protein/genetics

KW - Colorectal Neoplasms/pathology

KW - Humans

KW - Gene Expression Regulation, Neoplastic

KW - Rho Guanine Nucleotide Exchange Factors/genetics

KW - RNA-Binding Proteins/genetics

KW - Nanoparticles

KW - Adenosine/analogs & derivatives

KW - Animals

KW - Mice

KW - RNA, Small Interfering

KW - Liposomes

KW - Carcinogenesis/genetics

UR - http://www.scopus.com/inward/record.url?scp=85124646966&partnerID=8YFLogxK

U2 - 10.1053/j.gastro.2021.12.269

DO - 10.1053/j.gastro.2021.12.269

M3 - Journal article

C2 - 34968454

AN - SCOPUS:85124646966

SN - 0016-5085

VL - 162

SP - 1183

EP - 1196

JO - Gastroenterology

JF - Gastroenterology

IS - 4

ER -

N6-Methyladenosine Reader YTHDF1 Promotes ARHGEF2 Translation and RhoA Signaling in Colorectal Cancer

Abstract

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