Single cell analysis reveals the involvement of the long non-coding RNA Pvt1 in the modulation of muscle atrophy and mitochondrial network

Abstract

Long non-coding RNAs (lncRNAs) are emerging as important players in the regulation of several aspects of cellular biology. For a better comprehension of their function, it is fundamental to determine their tissue or cell specificity and to identify their subcellular localization. In fact, the activity of lncRNAs may vary according to cell and tissue specificity and subcellular compartmentalization. Myofibers are the smallest complete contractile system of skeletal muscle influencing its contraction velocity and metabolism. How lncRNAs are expressed in different myofibers, participate in metabolism regulation and muscle atrophy or how they are compartmentalized within a single myofiber is still unknown. We compiled a comprehensive catalog of lncRNAs expressed in skeletal muscle, associating the fiber-type specificity and subcellular location to each of them, and demonstrating that many lncRNAs can be involved in the biological processes de-regulated during muscle atrophy. We demonstrated that the lncRNA Pvt1, activated early during muscle atrophy, impacts mitochondrial respiration and morphology and affects mito/autophagy, apoptosis and myofiber size in vivo . This work corroborates the importance of lncRNAs in the regulation of metabolism and neuromuscular pathologies and offers a valuable resource to study the metabolism in single cells characterized by pronounced plasticity.

A Single Cell but Many Different Transcripts: A Journey into the World of Long Non-Coding RNAs

“…We functionally discussed the involvement of the lncRNA Pvt1 in the modulation of muscle atrophy and mitochondrial network. Our findings suggested that Pvt1 can modulate the expression of c-Myc, which in turn regulates Bcl-2, having an effect on autophagy and apoptosis that are strictly linked to the conformation of the mitochondrial network [114].…”

“…We revealed that cells with different metabolic properties express different lncRNAs. Moreover, we revealed that some differentially expressed lncRNAs localize differently in cellular compartments according to cell metabolism and lncRNA isoform [114]. This last result suggests that the same lncRNA could have different roles in different cells and that the same might be true for different isoforms of the same lncRNA.…”

“…The analysis of lncRNAs requires a deeper mechanistic exploration of their cellular expression, subcellular localization, interacting partners to interpret their function in cell reprogramming and several other biological contexts. We and other researchers demonstrated the importance of using a single-cell approach to evidence the function of specific ncRNAs [113,114,212]. This result is related to the cell-specific expression of ncRNAs not detectable analyzing RNA expression using whole tissues or a heterogeneous cell population.…”

“…Several methods have been established to isolate single cells, each with particular benefits and drawbacks. The micropipette isolation method consists in diluting the cells to a very low concentration and seeding them into a tube [113,114] or 96 well plate [115] ( Figure 3A). This technique does not require sophisticated platforms but is laborious and not very efficient.…”

“…MONOCL is a database designed to retrieve annotations, expression profiles and functional enrichment results of lncRNAs expressed in lung. It has been demonstrated that lncRNAs impact on patient prognosis [198] and influence pathological conditions [114]. For these reasons, it is important to catalog lncRNAs linking their involvement with pathologies such as cancer.…”