Genome‐Wide Occupancy Profiling Reveals Critical Roles of FoxO1 in Regulating Extracellular Matrix and Circadian Rhythm Genes in Human Chondrocytes

Abstract

Objective Osteoarthritis (OA) is the most common age‐related joint disease. With aging and in OA, the expression of FoxO transcription factors is reduced, diminishing their chondroprotective actions. In order to elucidate the molecular mechanisms by which FoxO1 protects chondrocytes, we sought to identify the genome‐wide occupancy profile of FoxO1. Methods We performed FoxO1 chromatin immunoprecipitation followed by high‐throughput sequencing (ChIP‐Seq) on human primary chondrocytes. ChIP‐Seq data were integrated with RNA sequencing (RNA‐Seq) data sets. Bioinformatics results were confirmed in primary chondrocytes that were treated with a FoxO1 inhibitor. Results Analysis of FoxO1 ChIP‐Seq on human primary chondrocytes showed that pathways implicated in OA pathogenesis are mainly regulated by FoxO1 binding to tissue‐specific enhancers with suboptimal binding sites (20% of the peaks), while more ubiquitous FoxO1 pathways are regulated at the promoter level through interaction with its canonical binding motif (7% of the peaks). Integrating FoxO1 occupancy data with RNA‐Seq data comparing OA and healthy human cartilage revealed 428 putative FoxO1 target genes that are dysregulated in OA. Pathway analysis showed enrichment for genes belonging to the senescence pathway (logP = −6.73), extracellular matrix (ECM) pathway (logP = −12.97), and circadian clock pathway (logP = −6.30), which suggests that FoxO1 dysregulation plays an important role in their abnormal expression in OA. Using an inhibitor of FoxO1, we confirmed that FoxO1 regulates these pathways in cultured human chondrocytes. Conclusion FoxO1 regulates ubiquitous and cartilage‐specific genes in chondrocytes by using different mechanisms. The FoxO1 transcriptional network is a key player in regulating homeostasis, ECM, and circadian clock genes and plays an important role in the abnormal expression of these pathways observed in OA pathogenesis.

Cross-Talking Pathways of Forkhead Box O1 (FOXO1) Are Involved in the Pathogenesis of Alzheimer’s Disease and Huntington’s Disease

“…Expression of collagen, a major component of ECM, is substantially upregulated in the subclinical and clinical phases of AD, which is associated with increased A β deposition [ 100 ]. In addition, our enrichment analysis has clarified that FOXO1 is associated with the regulation of ECM-receptor interaction pathway, in line with evidence of osteoarthritis for the involvement of aberrant FOXO1 expression in ECM-receptor interaction pathway [ 101 ].…”

DL-3-N-Butylphthalide Promotes Cartilage Extracellular Matrix Synthesis and Inhibits Osteoarthritis Development by Regulating FoxO3a

“…FoxO transcription factors could regulate various cellular processes, including cell cycle regulation, redox balance, autophagy, apoptosis, metabolism, and repair of DNA damage [ 29 , 33 , 34 ]. FoxO is an important regulator of cartilage homeostasis and involved in the formation, development, and maturation of cartilage [ 35 , 36 ]. Akasaki et al found the various expressions of FoxO in the cartilage of mice of different ages and different months [ 32 ].…”

In vitro effects of nutraceutical treatment on human osteoarthritic chondrocytes of females of different age and weight groups

“…It regulates the gene expression of ACAN and COL2A1 ( Fig. 6(b) ) ( 50 ) . TNFAIP6 is an anti-inflammatory protein that is induced by TNF-α cytokine.…”