A Pan-cancer Analysis of the Expression and Clinical Relevance of Small Nucleolar RNAs in Human Cancer

Jing Gong; Yajuan Li; Chun-Jie Liu; Yu Xiang; Chunlai Li; Youqiong Ye; Zhao Zhang; David H Hawke; Peter K Park; Lixia Diao; John A Putkey; Liuqing Yang; An-Yuan Guo; Chunru Lin; Leng Han

doi:10.1016/j.celrep.2017.10.070

A Pan-cancer Analysis of the Expression and Clinical Relevance of Small Nucleolar RNAs in Human Cancer

Cell Rep. 2017 Nov 14;21(7):1968-1981. doi: 10.1016/j.celrep.2017.10.070.

Authors

Jing Gong¹, Yajuan Li², Chun-Jie Liu³, Yu Xiang⁴, Chunlai Li², Youqiong Ye⁴, Zhao Zhang⁴, David H Hawke⁵, Peter K Park², Lixia Diao⁶, John A Putkey⁴, Liuqing Yang⁷, An-Yuan Guo⁸, Chunru Lin⁹, Leng Han¹⁰

Affiliations

¹ Department of Biochemistry and Molecular Biology, McGovern Medical School at The University of Texas Health Science Center at Houston, Houston, TX 77030, USA; Department of Epidemiology and Biostatistics, Key Laboratory of Environmental Health of Ministry of Education, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, PRC.
² Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
³ Department of Biochemistry and Molecular Biology, McGovern Medical School at The University of Texas Health Science Center at Houston, Houston, TX 77030, USA; Department of Bioinformatics and Systems Biology, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, PRC.
⁴ Department of Biochemistry and Molecular Biology, McGovern Medical School at The University of Texas Health Science Center at Houston, Houston, TX 77030, USA.
⁵ Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
⁶ Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
⁷ Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; The Graduate School of Biomedical Sciences, The University of Texas MD Anderson Cancer Center UTHealth, Houston, TX 77030, USA; Center for RNA Interference and Non-Coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
⁸ Department of Bioinformatics and Systems Biology, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, PRC. Electronic address: guoay@mail.hust.edu.cn.
⁹ Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; The Graduate School of Biomedical Sciences, The University of Texas MD Anderson Cancer Center UTHealth, Houston, TX 77030, USA. Electronic address: clin2@mdanderson.org.
¹⁰ Department of Biochemistry and Molecular Biology, McGovern Medical School at The University of Texas Health Science Center at Houston, Houston, TX 77030, USA; The Graduate School of Biomedical Sciences, The University of Texas MD Anderson Cancer Center UTHealth, Houston, TX 77030, USA. Electronic address: leng.han@uth.tmc.edu.

PMID: 29141226
DOI: 10.1016/j.celrep.2017.10.070

Abstract

Increasing evidence has demonstrated that small nucleolar RNAs (snoRNAs) play important roles in tumorigenesis. We systematically investigated the expression landscape and clinical relevance of snoRNAs in >10,000 samples across 31 cancer types from The Cancer Genome Atlas. We observed overall elevated expression of snoRNAs and their ribonucleoproteins in multiple cancer types. We showed complex regulation of snoRNA expression by their host genes, copy number variation, and DNA methylation. Unsupervised clustering revealed that the snoRNA expression subtype is highly concordant with other molecular/clinical subtypes. We further identified 46 clinically relevant snoRNAs and experimentally demonstrated functional roles of SNORD46 in promoting cell proliferation, migration, and invasion. We developed a user-friendly data portal, SNORic, to benefit the research community. Our study highlights the significant roles of snoRNAs in the development and implementation of biomarkers or therapeutic targets for cancer and provides a valuable resource for cancer research.

Keywords: clinical relevance; data portal; pan-cancer; small nucleolar RNA; snoRNA.

MeSH terms

Biomarkers, Tumor / genetics*
Biomarkers, Tumor / metabolism
DNA Methylation
Gene Dosage
Gene Expression Regulation, Neoplastic*
Humans
Neoplasms / genetics*
Neoplasms / metabolism
Neoplasms / pathology
RNA, Small Nucleolar / genetics*
RNA, Small Nucleolar / metabolism
Software

Substances

Biomarkers, Tumor
RNA, Small Nucleolar

Abstract

MeSH terms

Substances

Grants and funding