Using sno-lncRNAs as potential markers for Prader-Willi syndrome diagnosis

Jiu-Ru Sun; Liang-Zhong Yang; Yang-Li Dai; Huang Wu; Siqi Li; Yi-Feng Xu; Youkui Huang; Hao Wu; Zheng Shen; Chaochun Zou; Ling-Ling Chen

doi:10.1080/15476286.2023.2230406

Using sno-lncRNAs as potential markers for Prader-Willi syndrome diagnosis

RNA Biol. 2023 Jan;20(1):419-430. doi: 10.1080/15476286.2023.2230406.

Authors

Jiu-Ru Sun¹, Liang-Zhong Yang², Yang-Li Dai³, Huang Wu^{2

4}, Siqi Li², Yi-Feng Xu², Youkui Huang², Hao Wu², Zheng Shen³, Chaochun Zou³, Ling-Ling Chen^{1

2

5}

Affiliations

¹ Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China.
² State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Shanghai, China.
³ Department of Endocrinology, Children's Hospital, Zhejiang University School of Medicine, Hangzhou, China.
⁴ Department of Blood Transfusion, Daping Hospital ArmyMedical University, Chongqing, China.
⁵ New Cornerstone Science Laboratory, Shenzhen, China.

Abstract

The genetic disorder Prader-Willi syndrome (PWS) is mainly caused by the loss of multiple paternally expressed genes in chromosome 15q11-q13 (the PWS region). Early diagnosis of PWS is essential for timely treatment, leading to effectively easing some clinical symptoms. Molecular approaches for PWS diagnosis at the DNA level are available, but the diagnosis of PWS at the RNA level has been limited. Here, we show that a cluster of paternally transcribed snoRNA-ended long noncoding RNAs (sno-lncRNAs, sno-lncRNA1-5) derived from the SNORD116 locus in the PWS region can serve as diagnostic markers. In particular, quantification analysis has revealed that 6,000 copies of sno-lncRNA3 are present in 1 μL whole blood samples from non-PWS individuals. sno-lncRNA3 is absent in all examined whole blood samples of 8 PWS individuals compared to 42 non-PWS individuals and dried blood samples of 35 PWS individuals compared to 24 non-PWS individuals. Further developing a new CRISPR-MhdCas13c system for RNA detection with a sensitivity of 10 molecules per μL has ensured sno-lncRNA3 detection in non-PWS, but not PWS individuals. Together, we suggest that the absence of sno-lncRNA3 represents a potential marker for PWS diagnosis that can be detected by both RT-qPCR and CRISPR-MhdCas13c systems with only microlitre amount of blood samples. Such an RNA-based sensitive and convenient approach may facilitate the early detection of PWS.

Keywords: CRISPR-Mhdcas13c; Prader-Willi syndrome; RNA detection; Sno-lncRNA3; Sno-lncRNAs; diagnostic marker; dried blood spot; whole blood samples.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Humans
Prader-Willi Syndrome* / diagnosis
Prader-Willi Syndrome* / genetics
RNA, Long Noncoding* / genetics
RNA, Small Nucleolar / genetics

Substances

RNA, Long Noncoding
RNA, Small Nucleolar

Grants and funding

The work was supported by the the Key R & D Projects of Zhejiang Provincial Science and Technology Agency [2021C03094]; the National Natural Science Foundation of China (NSFC) [31830108]; the National Natural Science Foundation of China (NSFC) [31725009]; the HHMI International Programme [55008728]; the National Key R&D Programme of China [2021YFA1100203]; the Centre for Excellence in Molecular Cell Science (CEMCS) [2020DF03]; the CAS Project for Young Scientists in Basic Research [YSBR-009].