Not a Messenger, but Lots to Say: New Insights on Long Noncoding RNAs in the Kidney

Over the past two decades, research utilizing transcriptomics, proteomics, and metabolomics has allowed investigators to look into snapshots of mRNA, protein, and metabolite levels in cells and tissues. These practices have been optimized to look even at a single cell or single nucleus. Further advancements have inspired circadian collections—samples collected every few hours over the course of days—to undergo multi‐omics analysis to look at changes in mRNA, protein, and metabolite levels over the course of the day [1, 2]. Even further is a recent publication in Acta Physiologica by Wigger et al. which utilized multi‐omics to investigate the time‐of‐day differences in expression of renal long noncoding RNAs (lncRNAs, Figure 1) [3].

FIGURE 1.

Wigger et al. asked the experimental questions, “How does renal lncRNA expression change throughout the day?” and “How does renal lncRNA expression change when the kidney circadian clock is broken?” Image generated using BioRender (Biorender.com).

LncRNAs are as their name describes, long RNA sequences (≥ 200 nucleotides) which are transcribed, but do not code for a protein to be produced. Although they do not code for protein, they can take on many roles in the cell, such as acting as “decoys” to sequester transcription factors or miRNA, “guides” which lead nucleic acids or proteins to specified targets, “scaffolds” to provide structure within complexes, and intracellular “signals” that are influenced by external stimuli [4]. They have also been shown to play a role in disease states in tissues such as the kidney [4]. However, as many lncRNAs remain unannotated in online databases, they can often go overlooked or be thrown out when analyzing transcriptomics data. Additionally, many transcriptomics studies are based on tissues or cells collected at only one time of day, sometimes undefined in the methods.

Wigger et al. is the first study to investigate time‐of‐day influence on lncRNA in the kidney through transcriptomics, doing so in male mice from bulk and single‐nucleus RNA‐Seq data sets [3]. The single‐nucleus RNA‐Seq dataset was mapped to specific kidney cell types and found that lncRNA was cell‐type specific and as reliable as standard mRNA markers to differentiate cell types. Additionally, they looked at how lncRNA expression and rhythms changed in male mice with a conditional kidney tubule specific KO of BMAL1 (cKOt), a protein within the molecular circadian clock which is responsible for regulating the time of transcription of nearly half of the genome. The datasets analyzed were collected at two timepoints (4 h (ZT4) and 16 h (ZT16) after lights‐on) and the influence of the molecular circadian clock was investigated by comparing reads from control kidneys to those from cKOt mice. Between these data sets, 5.1% of lncRNAs were differentially expressed between control and cKOt at ZT4 and 10.8% were differentially expressed at ZT16, suggesting a time‐of‐day influence and circadian regulation of renal lncRNAs, notably in the renal epithelia. To determine if the lncRNAs had a circadian rhythm of expression, they reanalyzed their previously published bulk RNASeq dataset from circadian collections of control and cKOt kidneys (4‐h increments over 24 h) [5]. Interestingly, 16.8% of lncRNAs were rhythmic in control kidneys and 15.7% were rhythmic in cKOt kidneys. The majority of transcripts (62.1%) retained the same circadian rhythmicity regardless of cKOt, but 21.1% lost rhythmicity, and 15.3% gained rhythmicity in cKOt kidneys. The authors speculate that lncRNAs that retained their rhythms despite cKOt of BMAL1 may have their expression regulated by hormonal synchronization, triggered by the functional molecular circadian clock outside of the kidney tubule. This study establishes renal lncRNAs as having cell‐specific and time‐of‐day specific expression patterns, some of which being dependent on the renal molecular circadian clock mechanism.

While this publication identifies roles for the molecular circadian clock in the expression of lncRNAs in the kidney, many previous publications have identified roles for lncRNAs in kidney‐associated diseases. For example, Douma et al. identified that lncRNA Edn1‐AS has a circadian rhythm of expression in human proximal tubule cells, and a later study found renal Edn1‐AS to be overexpressed in a rodent model of salt‐sensitive hypertension [6, 7]. Analysis of RNA‐Seq from renal carcinomas and adjacent normal tissue identified the lncRNA OIP5‐AS1 as being highly expressed in renal clear cell carcinoma patients with lower survival probabilities [8]. Interestingly, both of these lncRNAs are transcribed from the antisense strand of coding mRNAs, one antisense to the Edn1 gene, which codes for the vasoactive peptide hormone endothelin‐1, and the other antisense to OIP5, which codes for a protein required for chromatin organization during the cell cycle and often upregulated in different cancers. Single‐cell RNA‐Seq identified lncPTEC to be associated with diabetic kidney disease, as its upregulation correlated with increased albuminuria in patients [9]. In vitro and in vivo, it also worsened renal fibrosis and mitochondrial oxidative stress [9]. The lncRNA KCNQ10T1 was found to be upregulated in the serum of chronic kidney disease patients, identifying it as a potential biomarker for diagnosis of chronic kidney disease [10]. These recent studies link overexpression of specific lncRNAs to numerous renal diseases and suggest potential roles for them in disease progression or their potential for use in diagnosis and prognosis.

Overall, this recent innovative study by Wigger et al. and other studies looking at lncRNAs in transcriptomic data are paving the way for future discoveries in the importance of lncRNAs in kidney diseases and renal function. While analyzing your transcriptomics data, don't be so quick to exclude the lncRNAs. They might not code for protein, but they could be hiding important messages that are relevant for your research.

Conflicts of Interest

The author declares no conflicts of interest.

Linked Articles

This article is linked to Wigger et al. papers. To view this article, visit https://doi.org/10.1111/apha.70273.

Data Availability Statement

The author has nothing to report.