Senescent Fibroblasts in IPF Linked to NUDT21 Deficiency

A study published in Aging Cell details new research suggesting that alternative polyadenylation (APA), regulated by the RNA-binding protein Nudix Hydrolase 21 (NUDT21), plays a central role in fibroblast senescence and the progression of idiopathic pulmonary fibrosis (IPF).¹ Researchers identified NUDT21, also known as CFIm25, as a key regulator of senescence-associated pathways in fibroblasts, observing that NUDT21 was significantly decreased in aged and fibrotic lungs, particularly within the fibrotic foci of IPF, which are rich in senescent myofibroblasts and collagen.

IPF is a chronic, progressive, and irreversible scarring of the lungs that disproportionately affects older adults, with a median age of diagnosis around 66 years and a median survival of 3 to 5 years after diagnosis. Existing therapies, pirfenidone and nintedanib, slow disease progression but do not reverse fibrosis. The present study aimed to explain the mechanistic ties between aging, fibroblast senescence, and aberrant gene regulation that may underpin poor clinical outcomes in older patients.

Researchers identified NUDT21, also known as CFIm25, as a key regulator of senescence-associated pathways in fibroblasts. | Image credit: Vitalii Vodolazskyi - stock.adobe.com

Fibroblasts are key effector cells in the fibroproliferative response, and their senescence, or permanent cell cycle arrest, is known to worsen with age, contributing to a pro-inflammatory state called the senescence-associated secretory phenotype (SASP). However, the precise mechanisms driving this process at the post-transcriptional level have been poorly understood.

The study highlights the crucial role of NUDT21, stating, "We recently discovered that Nudix Hydrolase 21 (NUDT21, also named CFIm25), an RNA-binding protein, plays a critical role in regulating the expression of SASP factors through alternative polyadenylation (APA)." APA is a post-transcriptional mechanism that enables a single gene to produce different transcript isoforms by utilizing alternative polyadenylation sites, resulting in mRNAs with distinct 3′ untranslated region (UTR) lengths. This process can affect transcript stability and protein translation. The investigators report that "NUDT21 knockdown in normal lung fibroblasts promoted the 3′ UTR shortening of several STAT3 signaling components and enhanced STAT3 phosphorylation and the expression of several SASPs, including interleukins, collagens, and matrix metalloproteinases (MMPs)." This mechanistic link between APA regulation and SASP factors highlights a novel driver of fibrosis.

The research team found that NUDT21 was significantly downregulated in both aging and fibrotic human and mouse lungs. Western blot data from 20 normal human lungs demonstrated a negative correlation between NUDT21 expression and age. In IPF tissue, dual immunostaining confirmed NUDT21 downregulation specifically in α-SMA–positive myofibroblasts. Fibroblasts isolated from IPF patients also displayed reduced NUDT21 and increased levels of P16 and fibronectin. In a repetitive bleomycin-induced pulmonary fibrosis model in mice, NUDT21 protein levels were reduced in isolated lungs and fibroblasts. Old mice (18 months) also demonstrated decreased NUDT21 expression in association with elevated collagen I, p53, and p16. These findings confirm that loss of NUDT21 is a consistent feature of fibrotic and aging lungs across species.

RNA-sequencing analysis of NUDT21-depleted fibroblasts identified widespread transcriptomic changes. The authors noted that, "808 genes with shortened 3′ UTR and only 29 genes with lengthened 3′ UTR" were detected. Importantly, several of these were linked to increased activation of the STAT3 signaling pathway, a pathway known to drive fibrosis and cellular senescence. The study findings also showed that phosphorylated STAT3 (Y705) was significantly elevated not only in fibroblasts after NUDT21 silencing but also in primary IPF fibroblasts.

Downstream effects included broader fibroblast senescence and mitochondrial dysfunction. A significant increase in the number of p-H2A.X foci was observed, signaling DNA damage, along with elevated β-galactosidase activity, a hallmark of senescence. Mitochondrial stress testing revealed "oxygen consumption rate was significantly increased in NUDT21-depleted cells," echoing other findings that aging cells display heightened oxidative respiration. ROS assays confirmed that a significantly higher proportion of DCFDA-high fibroblasts were present in NUDT21-deficient cells, linking NUDT21 loss not only to senescence but also to oxidative stress.

To test whether restoring NUDT21 expression could mitigate these effects, investigators overexpressed NUDT21 in fibroblasts. This intervention reversed multiple senescence features, lowering SASP gene expression and reducing STAT3 activation. These results suggest that "NUDT21 downregulation plays a critical role in the pathogenesis of IPF during aging by promoting fibroblast senescence and SASP release, positioning NUDT21 as a potential therapeutic target for addressing aging-associated pulmonary fibrosis."

References

1. Huang J, Gacha-Garay MJ, Wang Y, et al. Alternative polyadenylation contributes to fibroblast senescence in pulmonary fibrosis. Aging Cell. Published online July 30, 2025. doi:10.1111/acel.70179

2. Ley B, Collard HR, King TE Jr. Clinical course and prediction of survival in idiopathic pulmonary fibrosis. Am J Respir Crit Care Med. 2011;183(4):431-40. doi:10.1164/rccm.201006-0894CI