title: Transcriptomics profiling to study the role of noncoding RNAs in muscle ageing and its modulation by calorie restriction
Creators: name: Altab, Gulam
Publisher: name: University of Liverpool Repository
Year: 2024

description: The ageing of skeletal muscles, known as sarcopenia, is characterised by a decline in muscle mass,
strength, and function. The specific mechanisms behind this process are not yet fully understood, but
it significantly impacts the quality of life for older adults and can contribute to long-term hospitalisation. Therefore, it is essential to investigate in detail the mechanisms of muscle ageing.

Caloric restriction (CR) has been shown to extend the lifespan and health span of rodents and has
similar beneficial effects on human health. Moreover, it can improve health span by reducing the
incidence and delaying the onset of age-related diseases, including sarcopenia. Non-coding RNAs
(ncRNAs), including microRNAs (miRNAs) and long non-coding RNA (lncRNAs), play a vital role in
myogenesis. Studies have shown that ncRNAs are differentially expressed in skeletal muscle with age
and may play a role in the ageing process. However, there is a lack of research exploring the effects of
CR on ncRNAs and transcriptomics in the context of muscle ageing in rodents. Additionally, the precise
mechanisms through which CR slows the process of muscle ageing require further investigation. Therefore, the objective of this thesis is to utilise RNA-sequencing techniques to explore the role of
transcriptomics and ncRNA changes in skeletal muscle ageing and their alteration by caloric restriction.

In chapter 3, we have examined alterations in gene expression via RNA-seq data among young, aged,
and aged rats under CR. Through a transcriptomic perspective, we have discovered various genes that
were previously unknown in the ageing of muscles and their response to CR. Additionally, we have
found evidence suggesting that inflammation may play a significant role in muscle ageing, and CR
could substantially suppress this phenomenon, which is consistent with earlier reports. Thirdly, our
analysis suggests that circadian regulation may have a more substantial impact on muscle ageing than
previously understood, it could be one of the key mechanisms through which CR exerts its beneficial
effects on skeletal muscle during the ageing process. We have also identified several top genes that
may play a crucial role in muscle ageing and CR. Furthermore, by utilising co-expression analysis and
PPI network analysis, we have identified key genes that could serve as important regulators of muscle
ageing, as well as some of the key genes through which CR may work.

In chapter 4, we explored alterations in microRNAs using small RNA-seq data from young, old, and old
CR skeletal muscle. Our findings unveiled new miRNAs involved in muscle ageing and sensitive to CR.
We observed that upregulated miRNAs in old muscle were linked to vital pathways for muscle mass,
function, and homeostasis, such as AMPK signalling, insulin resistance, and autophagy signalling.
Interestingly, our results suggest that by downregulating specific miRNAs, complement and
coagulation cascade upregulation may occur, which could explain the persistent inflammation seen
with ageing. CR was found to restore many miRNAs to a younger expression level, thereby protecting
signalling pathways from disruption in ageing muscle. Moreover, we identified that miRNA-96-5p
expression is adversely linked with age and affects myogenesis, mitochondrial function and
biogenesis, and autophagy. Hence, controlling miR-96-5p through CR may help in restoring or
protecting against age-related disruptions in myogenesis, mitochondrial function, and autophagy.

In chapter 5 of this thesis, we presented the changes in lncRNA expression linked to ageing in skeletal
muscle and under CR. We also discovered over 2000 new lncRNAs in rat skeletal muscle. Overall, 78
lncRNAs showed differential expression in old muscle, and 103 lncRNAs in old CR muscle compared to
young muscle, indicating the profound impact of CR on lncRNA expression. CR helped to normalise a
significant number of age-associated dysregulated lncRNAs in old muscle. Our findings suggest that
age-associated lncRNAs may have a role in skeletal muscle contraction, musculoskeletal movement,
TNF signalling, and regeneration. CR-affected lncRNAs may contribute to carbohydrate metabolic processes, circadian rhythm, and signalling pathways such as TNF signalling, MAPK family signalling,
and chaperone mediated autophagy. The lncRNAs discovered in this research may help in selecting
previously unknown lncRNAs for future functional investigations in ageing or to understand the
mechanism of CR.

In conclusion, these findings offer a direction for additional therapeutic exploration into ncRNA targets
designed to impede the deterioration of skeletal muscle mass and function during the ageing process.
Furthermore, these studies have identified specific sets of significant genes that may have an impact
on the ageing process and CR. The outcomes of this study reveal insights into how transcriptomics and
ncRNAs affect the ageing of muscles, as well as the mechanisms of calorie restriction. Overall, the
findings presented in this thesis provide valuable resource for forthcoming research endeavours.