Predicting major-histocompatibility complex class II (MHC-II) restricted epitopes is challenging; however, AlphaFold (AF) may provide a structure-based pan-prediction solution. In this study, we have established the new tool AlphaFold-prediction (AF-pred) with a clear standard for quantitative prediction results of MHC-II-restricted epitopes. We validated AF-pred using MHC-II molecules from humans, pigs, cattle, and bats, with this validation including large-scale in silico analyses with known immunopeptidome datasets, as well as in vitro binding assays and crystallographic characterization of newly predicted epitopes. When compared to sequence-based tools heavily trained with the human immunopeptidome, AF-pred demonstrates advantages in the prediction of cross-species MHC-II binding patterns. Using unreported bat MHC-II structures, we analyzed the prediction capability, logic, and limitations of AF-pred. In addition, we explored the impact of the AF algorithm iterations on the prediction of MHC-II-restricted epitopes. These results demonstrate that AF-pred is capable of cross-species prediction of MHC-II-restricted epitopes, which is conducive to the development of novel T-cell epitope vaccines and the advancement of the "One Health" initiative.

Radiation-induced lung injury (RILI) is a common complication of radiotherapy. Berberine, a natural compound used in traditional Chinese medicine, has been associated with reduced RILI incidence, but its mechanism remains unclear. In a mouse model of thoracic irradiation, researchers found that berberine reshaped the gut microbiota and increased beneficial microbial metabolites, which were linked to reduced lung inflammation and tissue injury. The findings highlight the gut–lung axis as an important regulator of radiation responses and suggest new opportunities to improve the safety of radiotherapy.

For people who have recovered from diagnoses characterised by persistent fatigue, a new understanding of symptoms seems to have been key to recovery. This is the conclusion of a study from Linköping University, Sweden. The researchers have identified common steps and turning points in patients’ stories, which can contribute to new ways of understanding and rehabilitating these conditions.

Dental pulp regeneration remains a major clinical challenge. Researchers have discovered that SMAD7 directly forms a transcriptional complex with β-catenin in human dental pulp stem cells, activating Wnt signaling and promoting regenerative gene expression. By redefining SMAD7’s role from inhibitor to signaling mediator, the study clarifies a molecular mechanism controlling stem cell-driven repair. The findings suggest new strategies for biologically based dental therapies aimed at preserving tooth vitality and improving long-term clinical outcomes.

Dental pulp injury caused by trauma or deep caries often leads to inflammation, tissue necrosis, and eventual loss of tooth vitality. In severe cases, bacterial invasion and sustained immune responses further compromise the pulp’s microenvironment, disrupting its natural capacity for repair. Although regenerative endodontic approaches aim to restore living tissue, predictable biological repair remains difficult to achieve. Central to successful regeneration is the precise regulation of stem cell signaling pathways that coordinate cellular proliferation, differentiation, and matrix remodeling. Among these, Wnt/β-catenin signaling plays a fundamental role in stem cell proliferation, differentiation, and tissue repair. However, the upstream molecular mechanisms governing this pathway in human dental pulp stem cells have remained incompletely understood. 

 

To address this question, researchers investigated the function of SMAD7, a protein traditionally regarded as a negative regulator of transforming growth factor-beta (TGF-β) signaling and often associated with inhibitory cellular responses. Using human dental pulp stem cells (hDPSCs), the team applied immunofluorescent staining, gene silencing techniques, nuclear protein quantification, and western blot analysis to examine intracellular signaling dynamics in detail. Their experiments revealed that SMAD7 directly interacts with β-catenin inside the nucleus, forming a transcriptional complex that enhances Wnt pathway activation. Mechanistically, phosphorylated SMAD2/3 (P-SMAD2/3), activated downstream of TGF-β signaling, can bind and “capture” β-catenin, thereby limiting β-catenin nuclear availability and suppressing Wnt/β-catenin signaling activation. In this context, SMAD7 functions as a critical mediator that restrains TGF-β–SMAD2/3 signaling and preserves β-catenin activity: loss of SMAD7 leads to increased P-SMAD2/3 accumulation, which sequesters β-catenin and weakens Wnt pathway output. These findings were published on January 6, 2026 of the journal International Journal of Oral Science.

 

The research was led by Dr. Tian Chen, postdoctoral researcher from the Department of Orthodontics at West China Hospital of Stomatology, Sichuan University, Chengdu, China.

 

At the mechanistic level, the study overturns the long-standing assumption that SMAD7 functions solely as an inhibitory signaling molecule. Instead, the findings demonstrate that SMAD7 can act as a direct transcriptional mediator of Wnt/β-catenin signaling. By forming a nuclear complex with β-catenin, SMAD7 promotes activation of genes associated with stem cell proliferation and regenerative differentiation. “We were surprised to observe SMAD7 functioning as a positive regulator within the nucleus,” said Dr. Chen. “This direct partnership with β-catenin provides a clearer explanation for how Wnt signaling is amplified during dental pulp regeneration.”

 

Beyond clarifying a molecular mechanism, the study highlights important translational opportunities. In the short term, targeting the SMAD7–β-catenin interaction could improve regenerative endodontic procedures by enhancing natural pulp healing responses. Biomaterials or small-molecule modulators designed to optimize this signaling axis may help preserve tooth vitality and reduce reliance on conventional root canal treatment. Such advances could directly improve patient outcomes by supporting biological repair instead of artificial replacement.

 

Over the longer term, the implications extend beyond dentistry. Wnt/β-catenin signaling is central to bone biology, craniofacial development, and broader tissue engineering applications. Identifying SMAD7 as a direct transcriptional partner of β-catenin opens avenues for interdisciplinary collaboration in regenerative medicine and stem cell-based therapeutics. Over the next decade, refined control of this pathway may contribute to precision strategies that guide tissue repair in oral and skeletal systems. “Our motivation comes from clinical challenges we see every day,” Dr. Chen added. “Understanding these molecular interactions brings us closer to therapies that regenerate living tissue and transform restorative care.”

 

 

Reference

Titles of original paper: SMAD7 regulates the canonical Wnt signaling through TGF-β cascade crosstalk and SMAD7/β-CATENIN transcription factor complex formation during tooth regeneration

Journal: International journal of oral science

DOI: https://doi.org/10.1038/s41368-025-00393-5

 

 

About Dr. Tian Chen

Dr. Tian Chen is a postdoctoral researcher in the Department of Orthodontics at West China Hospital of Stomatology, Sichuan University, Chengdu, China. Her research centers on tooth and craniofacial development, stem cell biology, molecular signaling, and regenerative strategies for oral tissues. From 2017 to 2022, she conducted her Joint PhD training and postdoctoral research at the Department of Cell and Molecular Biology at Tulane University, New Orleans, USA, where she strengthened her expertise in translational biomedical research and became proficient in the construction of various transgenic mouse models. Skilled in chromatography and advanced cellular signaling analysis, she integrates molecular techniques with regenerative applications. Dr. Chen has authored 22 publications and received 474 citations, reflecting her growing academic impact.

Radiomics extracts quantitative data from medical images, but its role in predicting deterioration after traumatic brain injury (TBI) remains uncertain. Now, researchers have analyzed pre-evacuation computed tomography scans from patients with TBI who underwent hematoma evacuation and developed a machine learning model predicting the need for secondary decompressive craniectomy. The model showed stronger predictive performance than clinical data alone, suggesting that the imaging biomarkers may help identify high-risk patients and guide interventions strategies.

The single-stranded DNA molecules developed by researchers using the SELEX technology could transform blood testing for Alzheimer's biomarkers. These synthetic aptamers target neurofilament light chain (NfL), a structural protein component of nerve cells, that is released into the bloodstream upon neuronal injury. These aptamers exhibit binding strength and selectivity comparable to anti-NfL antibodies used in current tests, while being more economical to produce and reliable, opening the door to affordable, diagnostic biosensors.

A research team led by Professor Nicholas X. Fang from the Department of Mechanical Engineering from the Faculty of Engineering at The University of Hong Kong (HKU) have developed a world-leading innovation known as “SonoMeta”. This artificial intelligence (AI)-powered MetaLens effectively addresses a longstanding challenge in the medical field, bringing revolutionary advancements in cardiology, pulmonary medicine, and emergency care.