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Genome-Wide Sequencing Reveals Small Nucleolar RNAs Downregulated in Cerebral Cavernous Malformations

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Abstract

Cerebral cavernous malformations (CCM) are vascular malformations associated with abnormally dilated blood vessels and leaky capillaries that often result in hemorrhages. Despite recent advances, precise understanding of the cellular and molecular mechanism leading to the pathogenesis of CCM remains elusive. Emerging evidence indicates that small nucleolar RNAs (snoRNAs), belonging to the class of non-coding RNAs, may play a significant role as diagnostic markers in human diseases. However, there is no report till date that studied the role of snoRNAs in CCM biology. The objective of the current study was to identify snoRNAs associated with CCM pathogenesis. Using genome-wide small RNA sequencing, we identified a total of 271 snoRNAs reliably expressed in CCM. By applying additional statistical stringency, three snoRNAs (SNORD115-32, SNORD114-22, and SNORD113-3) were found to be significantly downregulated in CCM patient tissue samples (n = 3) as compared to healthy brains (n = 3). Deregulation of the selected snoRNAs was further validated by qRT-PCR. Further, cellular localization via in situ hybridization also confirmed robust reduction in the expression of SNORD115-32 and SNORD114-22 in CCM tissues as compared to the healthy controls. By applying high-throughput sequencing and cellular localization analyses, we report here for the first time the genome-wide expression profile of snoRNAs in CCM tissues and a robust downregulation of candidate snoRNAs in CCM conditions. Future studies should warrant the screening in large CCM patient cohorts and will be helpful in the development of potential biomarkers and improved clinical diagnosis.

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Acknowledgements

We thank the Research Core Unit Transcriptomics (RCUT) of the Medical School of Hannover for their technical assistance and support with regard to total RNA isolation and quality control.

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Authors and Affiliations

  1. International Neuroscience Institute, Rudolf-Pichlmayr-Strasse 4, 30625, Hannover, Germany

    Souvik Kar, Amir Samii & Helmut Bertalanffy

  2. Pharmacology Institute, Medical Faculty Heidelberg, Heidelberg University, Heidelberg, Germany

    Kiran Kumar Bali

  3. Molecular Medicine Partnership Unit with European Molecular Biology Laboratory, Heidelberg, Germany

    Kiran Kumar Bali

  4. Department of Kidney, Liver and Metabolic Diseases, Children’s Hospital, Hannover Medical School, Hannover, Germany

    Arpita Baisantry

  5. Genome Analytics Research Group, Helmholtz Centre for Infection Research, Brunswick, Germany

    Robert Geffers

  6. Department of Neuropathology and Neurosurgery, Hannover Medical School, Hannover, Germany

    Christian Hartmann

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  1. Souvik Kar
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  2. Kiran Kumar Bali
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  4. Robert Geffers
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Contributions

SK and HB conceived and designed the study; SK, KKB, and AB performed the experiments; SK and KKB contributed to the data interpretation and analysis; RG carried out the NGS sequencing; CH helped in the in situ hybridization staining analysis; HB provided the clinical tissue samples from 3 CCM patients; SK wrote the manuscript; AS, HB, and CH critically revised the article. All authors approved the manuscript.

Corresponding author

Correspondence to Souvik Kar.

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All authors declare that they have no conflict of interest.

Ethical Approval

All procedures performed in studies involving human participants were in accordance with the ethical standards of the responsible committee (institutional and national) and with the 1964 Helsinki declaration and its later amendments. This study was approved by the local ethical committee at the Hannover Medical School (Approval Number 6960).

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Informed consent was obtained from all individual participants included in the study.

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10571_2018_602_MOESM1_ESM.xlsx

Additional file 1: Table S1 List of 120 expressed snoRNAs in CCM (p < 0.05, t-test). Supplementary material 1 (XLSX 17 KB)

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Kar, S., Bali, K.K., Baisantry, A. et al. Genome-Wide Sequencing Reveals Small Nucleolar RNAs Downregulated in Cerebral Cavernous Malformations. Cell Mol Neurobiol 38, 1369–1382 (2018). https://doi.org/10.1007/s10571-018-0602-9

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