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Annotating function to differentially expressed LincRNAs in myelodysplastic syndrome using a network-based method.

Keqin Liu1, Dominik Beck2,3, Julie A I Thoms2

  • 1Department of Radiology, Center for Bioinformatics and Systems Biology, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA.

Bioinformatics (Oxford, England)
|May 5, 2017
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Summary
This summary is machine-generated.

Aberrantly expressed long non-coding RNAs (lncRNAs) are involved in Myelodysplastic syndromes (MDS). A novel network-based method (NLCFA) prioritizes these lncRNAs for further study in various diseases.

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Area of Science:

  • Molecular Biology
  • Genomics
  • Bioinformatics

Background:

  • Long non-coding RNAs (lncRNAs) play crucial roles in biological functions, but their roles in most diseases remain largely unexplored.
  • The rapid discovery of novel lncRNAs necessitates methods to understand their disease-specific functions.
  • Integrating lncRNA, mRNA, and miRNA interactions is key to deciphering complex cellular signaling networks.

Purpose of the Study:

  • To develop and apply a novel network-based computational method (NLCFA) for elucidating lncRNA function in human diseases.
  • To identify and prioritize aberrantly expressed lncRNAs in Myelodysplastic syndromes (MDS).
  • To investigate the involvement of lncRNAs in cancer-associated signaling pathways within MDS.

Main Methods:

  • Developed the Network-based Long non-coding RNA Functionality Assessment (NLCFA) method.
  • Integrated lncRNA, protein-coding gene, and miRNA expression data.
  • Incorporated target gene associations and protein-protein interaction networks.
  • Generated lncRNA expression profiles from hematopoietic stem and progenitor cells (HSPCs) of MDS patients and healthy donors.

Main Results:

  • Identified and reported, for the first time, aberrantly expressed lncRNAs in Myelodysplastic syndromes (MDS).
  • Utilized the NLCFA method to prioritize biologically relevant lncRNAs in MDS.
  • Demonstrated that aberrant lncRNA levels are associated with network modules controlling cancer-related signaling pathways and cellular processes.

Conclusions:

  • Aberrant long non-coding RNAs (lncRNAs) are significantly involved in Myelodysplastic syndromes (MDS) pathogenesis.
  • The developed NLCFA method effectively prioritizes disease-associated lncRNAs for functional studies.
  • This approach is applicable for prioritizing lncRNAs in other diseases and biological contexts.