A network-based approach reveals long non-coding RNAs associated with disease activity in lupus nephritis: key pathways for flare and potential biomarkers to be used as liquid biopsies

George Sentis; Catherine Loukogiannaki; Nikos Malissovas; Dionysis Nikolopoulos; Theodora Manolakou; Sofia Flouda; Maria Grigoriou; Aggelos Banos; Dimitrios T Boumpas; Anastasia Filia

doi:10.3389/fimmu.2023.1203848

A network-based approach reveals long non-coding RNAs associated with disease activity in lupus nephritis: key pathways for flare and potential biomarkers to be used as liquid biopsies

Front Immunol. 2023 Jul 5:14:1203848. doi: 10.3389/fimmu.2023.1203848. eCollection 2023.

Authors

Affiliations

¹ Laboratory of Autoimmunity and Inflammation, Center of Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation Academy of Athens, Athens, Greece.
² 4th Department of Internal Medicine, Attikon University Hospital, National and Kapodistrian University of Athens Medical School, Athens, Greece.
³ 1st Department of Internal Medicine, University Hospital of Alexandroupolis, Democritus University of Thrace, Alexandroupolis, Greece.

Abstract

Objective: A blood-based biomarker is needed to assess lupus nephritis (LN) disease activity, minimizing the need for invasive kidney biopsies. Long non-coding RNAs (lncRNAs) are known to regulate gene expression, appear to be stable in human plasma, and can serve as non-invasive biomarkers.

Methods: Transcriptomic data of whole blood samples from 74 LN patients and 20 healthy subjects (HC) were analyzed to identify differentially expressed (DE) lncRNAs associated with quiescent disease and flares. Weighted gene co-expression network analysis (WGCNA) was performed to uncover lncRNAs with a central role (hub lncRNAs) in regulating key biological processes that drive LN disease activity. The association of hub lncRNAs with disease activity was validated using RT-qPCR on an independent cohort of 15 LN patients and 9 HC. cis- and trans-targets of validated lncRNAs were explored in silico to examine potential mechanisms of their action.

Results: There were 444 DE lncRNAs associated with quiescent disease and 6 DE lncRNAs associated with flares (FDR <0.05). WGCNA highlighted IFN signaling and B-cell activity/adaptive immunity as the most significant processes contributing to nephritis activity. Four disease-activity-associated lncRNAs, namely, NRIR, KLHDC7B-DT, MIR600HG, and FAM30A, were detected as hub genes and validated in an independent cohort. NRIR and KLHDC7B-DT emerged as potential key regulators of IFN-mediated processes. Network analysis suggests that FAM30A and MIR600HG are likely to play a central role in the regulation of B-cells in LN through cis-regulation effects and a competing endogenous RNA mechanism affecting immunoglobulin gene expression and the IFN-λ pathway.

Conclusions: The expression of lncRNAs NRIR, KLHDC7B-DT, FAM30A, and MIR600HG were associated with disease activity and could be further explored as blood-based biomarkers and potential liquid biopsy on LN.

Keywords: RNA-sequencing; SLEDAI-2K; WGCNA; blood-based biomarker; ceRNA; disease activity; long non-coding RNAs; lupus nephritis.

Publication types

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

MeSH terms

Biomarkers
Gene Expression Profiling
Humans
Liquid Biopsy
Lupus Nephritis* / diagnosis
Lupus Nephritis* / genetics
RNA, Long Noncoding*

Substances

RNA, Long Noncoding
Biomarkers

Grants and funding

This work was supported by a research grant from the State Scholarships Foundation (IKY - MIS-5033021) to AF and research grants from the EU (SYSCID grant agreement number 733100) and European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (GAN:742390) to DB. Computational time was granted from the National Infrastructures for Research and Technology S.A. (GRNET S.A.) in the National HPC facility - ARIS - under project ID pr011006_taskp-BIOSLE.