Use of cellular free nucleic acids for diagnosis and treatment of inflammatory bowel disease
Year: 2025
Type: article
Abstract: To the Editor: Inflammatory bowel disease (IBD) is a chronic inflammatory condition with unclear causes, comprising ulcerative colitis (UC) and Crohn’s disease (CD). The disease alternates between active and remission phases, complicating monitoring and management. Current clinical biomarkers have limitations in specificity and predictability. Cellular free nucleic acids (cfNAs), as a non-invasive diagnostic tool, offer significant potential in diagnosis and precision medicine. CfNAs, including DNA and RNA, are found in extracellular fluids like plasma, cerebrospinal fluid, saliva, urine, and feces. In conditions such as pregnancy, cancer, liver damage, and IBD, apoptotic cells and damaged tissues release cfNAs. Additionally, pathogens, especially bacteria, release cfNAs when broken down by phagocytic cells. CfNAs in body fluids exist mainly as free-floating, protein-bound, or encapsulated within extracellular vesicles. Free-floating cfNAs degrade quickly due to nucleases and have a short half-life. Methylation improves their stability, extending their presence in body fluids. Proteins can also bind to cfNAs, forming stable complexes that protect against degradation without affecting their biological activity. Extracellular vesicles, particularly exosomes (Exo), are notable for their small size, low clearance rate, high biocompatibility, and low immunogenicity. Exo facilitate immune evasion and targeted drug delivery, reducing side effects. In any form, cfNAs are crucial for physiological functions. The levels of cfNAs in the body are closely associated with the activity of IBD, offering a novel perspective for early diagnosis, efficacy monitoring, and prognosis assessment of the disease. CfNAs participate in various biological activities in the gastrointestinal tract primarily through paracrine mechanisms. In the presence of inflammatory or infectious factors, the intestines of IBD patients remain in a continuous inflammatory state, resulting in the shedding of numerous damaged or dead cells from the intestinal wall, which releases substantial amounts of cfNAs. The cfNAs that are not excreted with feces can modulate immune and inflammatory signals through various pathways, thus contributing to the progression of IBD. Notably, the levels of cfNAs in the blood, intestinal lavage fluid, and feces of patients are significantly elevated and positively correlated with inflammatory factors, biomarkers, clinical symptoms, and disease activity. Patients with IBD face an increased risk of developing colon cancer. Compared to individuals with IBD, cells undergoing carcinogenesis release a greater quantity of cfNAs, and the methylation levels of cfNAs exhibit a gradient decrease from colitis to colon cancer, indicating that alterations in cfNAs and their methylation levels may serve as indicators during the transition from colitis to colon cancer. Long et al[1] conducted whole-genome sequencing on 169 cfNAs samples derived from colorectal cancer tumor tissue and confirmed the hypomethylation of differentially methylated regions (DMRs) in the tissue, identifying a set of DMRs with potential diagnostic relevance in cfNAs. These DMRs are anticipated to serve as biomarkers for the detection of colon cancer. IBD is not limited to adults; about 30% of patients receive their diagnosis during childhood. However, children face a higher risk of complications associated with colonoscopy compared to adults, and they often exhibit poor compliance. Additionally, some patients may present atypical endoscopic findings, all of which can potentially delay diagnosis and increase the risk of extraintestinal complications and colorectal cancer, adversely affecting normal growth, development, and daily life in children. Studies have indicated that children with UC have 1.47 times higher levels of circulating cfNAs compared to those with CD.[2] Furthermore, after glucocorticoid therapy, the levels of certain cfNAs in children increase, suggesting that glucocorticoids may directly regulate cfNA expression, thereby contributing to the pathogenesis of IBD. Variations in the levels of specific cfNA subtypes before and after treatment may assist in understanding treatment effectiveness.[3] In summary, cfNAs exhibit significant potential in differentiating UC from CD and are beneficial for evaluating therapeutic effects. In addition to the diagnostic advantages mentioned, cfNAs offer new avenues for innovative therapies for IBD. Exo derived from macrophages (Mφ) retain the molecular characteristics of Mφ and can participate in the body’s immune responses. Mφ can polarize into pro-inflammatory (M1) or anti-inflammatory (M2) states during infections and immune system dysregulation. Exo derived from M1 state Mφ differentially express membrane tumor necrosis factor (TNF) on their surfaces, triggering glycolysis through the TNF receptor (TNFR)2/NF-κB pathway and contributing to the inflammatory process. The effectiveness of anti-TNF drugs in alleviating intestinal inflammation in clinical IBD patients is notable. Targeted delivery of anti-TNF drugs can efficiently neutralize TNF in the areas of intestinal lesions, enhancing local therapeutic effects and minimizing damage to normal cells. Furthermore, these drugs play a positive regulatory role in immunosuppression, which can exacerbate dysfunction in the intestinal mucosal barrier and disrupt intestinal microbiota by inhibiting the specifically expressed glycoprotein TMIGD1 (transmembrane and immunoglobulin domain-containing protein 1) on intestinal epithelial cells (IECs). Therefore, silencing M1 state-derived Exo and supplementing TMIGD1 may represent new therapeutic targets for IBD. Exo derived from plants, such as ginseng, can also decrease the release of pro-inflammatory factors by inhibiting the NF-κB pathway, enhance the polarization of Mφ toward the M2 state, and promote the production of interleukin (IL)-10.[4] Plant-derived Exo are generally purer and more readily obtainable than those from human cells. However, differences exist in the survival conditions between plant cells and human cells, and the targeted delivery capabilities, effective transformation, and long-term survival of plant-derived Exo within the human body require further validation. Mesenchymal stem cells (MSCs) possess the ability to differentiate into blood cells, adipocytes, and other cell types under specific conditions, contributing to various physiological and pathological processes such as cell survival, immune regulation, and tissue repair through paracrine pathways. Exosomes derived from MSCs (MSCs-Exo) serve as drug delivery vehicles, minimizing the potential side effects associated with the injection of live cells, thus providing clinical advantages over MSCs. However, clinical research on this application remains relatively limited. In a study involving the local injection of MSCs-Exo into five IBD patients with refractory anal fistulas, no systemic or local adverse reactions were observed after six months, and three patients achieved complete healing, indicating that exosome therapy is a viable approach.[5] Patients with IBD experience a dysbiosis in gut microbiota, characterized by an increased abundance of various pathogenic bacteria that produce specific Exo, which intensify inflammation. Fusobacterium nucleatum (Fn), a Gram-negative bacillus, is found to be enriched in the colonic tissue of individuals with UC. Limited research has been conducted on this bacterium in the intestines of patients with CD. Fn can directly invade the intestinal mucosa, significantly modifying the Exo derived from infected IECs, referred to as Fn-Exo. The levels of cfNAs in Fn-Exo and those derived from uninfected IECs (Con-Exo) have been sequenced and compared, revealing that several subtypes of cfNAs were significantly elevated in the Fn-Exo group. Through the TIMELESS axis, these cfNAs activate the ataxia telangiectasia mutated and Rad3-related kinase (ATM/ATR)/p53 pathway, thereby promoting cellular senescence and colon inflammation. Transmission of Fn-Exo to uninfected IECs resulted in exacerbated barrier dysfunction and increased inflammation. Consequently, targeting the TIMELESS axis or the ATM/ATR/p53 pathway may present a promising approach for treating UC caused by Fn. Exo derived from plants, such as ginseng, can also mitigate the release of pro-inflammatory factors by inhibiting the NF-κB pathway, enhancing macrophage polarization toward the M2 phenotype, and promoting IL-10 production.[4] Plant-derived Exo are generally purer and more readily obtainable than those derived from mammalian cells. Nonetheless, differences in the survival conditions of plant and mammalian cells, as well as their capacity for targeted delivery, effective transformation, and long-term survival within the human body, require further investigation. Exo can provide therapeutic benefits through various treatments. UC is associated with excessive reactive oxygen species (ROS) and DNA damage. MSCs exhibit enhanced activity and migration ability under hypoxia (HP) conditions. Therefore, MSC-derived Exo treated under hypoxic conditions can reduce ROS production and DNA damage in IECs while inhibiting mTOR signaling by promoting HP-inducible factor-1α, alleviating inflammation. MSC-derived Exo preconditioned under HP are more effective for drug delivery. Intravenous administration is commonly used, improving symptoms but increasing risks of adverse reactions. Oral administration faces challenges from degradation by gastric acid, but the colon offers favorable conditions, including low enzyme concentrations and long retention time, making it ideal for targeted drug delivery. Optimizing delivery methods enhances Exo bioavailability and reduces potential side effects. CfNAs play a crucial role in the initiation and progression of IBD, providing distinct diagnostic benefits related to disease severity, age of onset, and complications. They can serve as direct therapeutic agents or carriers for IBD medications to enable targeted therapy. The potential of cfNAs as a novel therapeutic target for diagnosing and treating IBD is considerable. Nevertheless, substantial clinical samples are required to confirm their efficacy. Future investigations should prioritize larger-scale prospective cohort studies and more precise quantification and sequencing of nucleic acids to establish a comprehensive cfNA database. This database would not only enhance diagnostic clarity but also facilitate faster and more accurate monitoring of disease dynamics. It is anticipated that cfNAs could be utilized for interventions in IBD patients of varying ages, types, and stages, thereby enabling personalized treatment and significantly improving patient prognosis. Funding This study was supported by the National Natural Science Foundation of China (No. 82260115).
Source: Chinese Medical Journal
Authors: Jing Ai, Xiaoyan Duan, Rui Wang, Ping Chen
Institution: Inner Mongolia Medical University
Language: English
Topic: Inflammatory Bowel Disease
Subfield: Genetics
Domain: Life Sciences
Open Access status: gold
Estimated APC paid: $2,000
OpenAlex ID: W4409846211