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INNOSC Theranostics and
Pharmacological Sciences Transcriptome-based RNA sequencing

scale studies, RNA-seq can be relatively expensive. The Funding
processing of RNA-seq data is a delicate process and thus
requires the use of specific visualization tools as well as None.
extensive knowledge in the field of molecular and cell Conflict of interest
biology. Other limitations include specimen factors such
as RNA degradation and sequencing errors. As mentioned The authors declare they have no competing interests.
earlier, RA is a heterogeneous disease and RNA-seq may
not be an ideal method to detect upfold changes of genes Author contributions
in different cellularity of the joint. Conceptualization: Rideb Chakraborty, Naureen Afrose

RNA-seq has led to significant advances in our Writing – original draft: Bijoy Jana, Sandip Koner, Surya
understanding of RA pathogenesis. It has provided novel Kanta Maiti
genes of RA that are involved in immune cell activation, Writing – review & editing: Rideb Chakraborty, Naureen
inflammation, and destruction of joints. RNA-seq has Afrose, Pratibha Bhowmick, Mithun Bhowmick
played some roles in the function of immune cells involved
in RA, including Th17 cells, different T regulatory cells, Ethics approval and consent to participate
and macrophages. It has provided tremendous insights into Not applicable.
novel regulatory RNA molecules, including lncRNAs and
miRNAs involved in the pathogenesis of RA. Some of the Consent for publication
genes involved in immune cell signaling and inflammation Not applicable.
have been proposed as therapeutic targets for RA using
RNA-seq technology. Availability of data
9. Conclusion Not applicable.

The use of next-generation RNA-seq has completely changed References
our knowledge of the intricate transcriptome landscape
associated with RA. This review examined the use of 1. Vlachogiannis NI, Gatsiou A, Silvestris DA, et al. Increased
RNA-seq in analyzing the pathophysiology of RA, ranging adenosine-to-inosine RNA editing in rheumatoid arthritis.
J Autoimmun. 2020;106:102329.
from defining dysregulated pathways and gene expression
patterns to discovering novel biomarkers. Important doi: 10.1016/j.jaut.2019.102329
discoveries include the identification of alternative splicing 2. Shchetynsky K, Protsyuk D, Ronninger M, Diaz-Gallo LM,
events, DEGs linked to RA pathophysiology, and the Klareskog L, Padyukov L. Gene-gene interaction and RNA
potential use of lncRNAs and circular RNAs as diagnostic splicing profiles of MAP2K4 gene in rheumatoid arthritis.
tools. The complex regulatory networks and signaling Clin Immunol. 2015l;158(1):19-28.
pathways involved in RA have also been clarified using doi: 10.1016/j.clim.2015.02.011
RNA-seq. Researchers can obtain a more comprehensive
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combining multiomics data. These findings are extremely coding RNAs in immunoregulation and autoimmunity:
promising for the development of tailored treatment Technological advances and critical limitations.
J Autoimmun. 2023;134:102982.
approaches, improvement of diagnostic capabilities, and
eventually, the discovery of novel therapeutic targets for 4. Ding Q, Hu W, Wang R, et al. Signaling pathways in
individuals with RA. Prospective avenues for investigation rheumatoid arthritis: Implications for targeted therapy.
may focus on overcoming constraints such as data analysis Signal Transduct Target Ther. 2023;8(1):68.
obstacles and integrating spatial transcriptomics data doi: 10.1038/s41392-023-01331-9
to comprehend cellular heterogeneity in the combined 5. Roszkowski L, Ciechomska M. Tuning monocytes and
microenvironment. Certainly, additional research into the macrophages for personalized therapy and diagnostic
potential of RNA-seq will result in important discoveries in challenge in rheumatoid arthritis. Cells. 2021;10(8):1860.
the field of RA research, providing better patient outcomes.
doi: 10.3390/cells10081860
Acknowledgments 6. Abbasi M, Mousavi MJ, Jamalzehi S, et al. Strategies toward
The authors are grateful to the Department of rheumatoid arthritis therapy; the old and the new. J Cell
Pharmaceutical Sciences for providing them with the Physiol. 2019;234(7):10018-10031.
required facilities to carry out this review work. doi: 10.1002/jcp.27860

Volume 8 Issue 1 (2025) 27 doi: 10.36922/itps.4449