Accumulation of NCOA1 dependent on HERC3 deficiency transactivates matrix metallopeptidases and promotes extracellular matrix degradation in intervertebral disc degeneration

scPRINT: pre-training on 50 million cells allows robust gene network predictions

A cell is governed by the interaction of myriads of macromolecules. Inferring such a network of interactions has remained an elusive milestone in cellular biology. Building on recent advances in large foundation models and their ability to learn without supervision, we present scPRINT, a large cell model for the inference of gene networks pre-trained on more than 50 million cells from the cellxgene database. Using innovative pretraining tasks and model architecture, scPRINT pushes large transformer models towards more interpretability and usability when uncovering the complex biology of the cell. Based on our atlas-level benchmarks, scPRINT demonstrates superior performance in gene network inference to the state of the art, as well as competitive zero-shot abilities in denoising, batch effect correction, and cell label prediction. On an atlas of benign prostatic hyperplasia, scPRINT highlights the profound connections between ion exchange, senescence, and chronic inflammation.

Innovating intervertebral disc degeneration therapy: Harnessing the power of extracellular vesicles

Intervertebral disc degeneration is the leading cause of low back pain, imposing significant burdens on patients, societies, and economies. Advancements in regenerative medicine have spotlighted extracellular vesicles as promising nanoparticles for intervertebral disc degeneration treatment. Extracellular vesicles retain the potential of cell therapy and serve as carriers to deliver their cargo to target cells, thereby regulating cell activity. This review summarizes the biogenesis and molecular composition of extracellular vesicles and explores their therapeutic roles in intervertebral disc degeneration treatment through various mechanisms. These mechanisms include mitigating cell loss and senescence, delaying extracellular matrix degeneration, and modulating the inflammatory microenvironment. Additionally, it highlights recent efforts in engineering extracellular vesicles to enhance their targeting and therapeutic efficacy. The integration of extracellular vesicle-based acellular therapy is anticipated to drive significant advancements in disc regenerative medicine.

The translational potential of this article

Existing clinical treatment strategies often fail to effectively address the challenges associated with regenerating degenerated intervertebral discs. As a new regenerative medicine strategy, the extracellular vesicle strategy avoids the risks associated with cell transplantation and shows great promise in treating intervertebral disc degeneration by carrying therapeutic cargo. This review comprehensively examines the latest research, underlying mechanisms, and therapeutic potential of extracellular vesicles, offering a promising new strategy for intervertebral disc degeneration treatment.

Network pharmacology and experimental validation to explore the pharmacological mechanism of saw palmetto and its core ingredients in benign prostatic hyperplasia treatment

Benign prostatic hyperplasia (BPH) is a prevalent urological condition that predominantly affects the geriatric male population, resulting in lower urinary tract symptoms. Saw palmetto is a traditional Chinese medicine for treating BPH. This study aimed to investigate the potential therapeutic mechanisms of saw palmetto in BPH treatment. The active ingredients and potential targets of saw palmetto were obtained through the TCMSP database. BPH-related targets were retrieved from the GeneCards database. PPI, GO, and KEEG analyses were performed to predict the potential therapeutic mechanism. The active ingredient-common target and common target-pathway networks were constructed by Cytoscape software. Molecular docking and cellular experiments were carried out to further validate the potential mechanism. We obtained 13 active components in saw palmetto and 56 common targets in BPH treatment. KEEG analysis showed that the estrogen signaling pathway was the most enriched and exhibited a close association with BPH. PPI analysis, along with ingredient-target and target-pathway network analyses, indicated that stigmasterol was the core ingredient and PGR, NCOA1, and NCOA2 were identified as the hub genes mediating the effects of saw palmetto against BPH. In addition, molecular docking showed that stigmasterol had strong binding to PGR, NCOA1, and NCOA2. Cellular experiments revealed that stigmasterol significantly increased the percentage of BPH-1 cells in the G0/G1 phase and inhibited cell viability and division. Furthermore, it notably reduced the expression of PGR, NCOA1, and NCOA2. Saw palmetto might inhibit cell viability and division by suppressing the expression of PGR, NCOA1, and NCOA2, thereby playing a therapeutic role in treating BPH.

PNSC5325 prevents acute respiratory distress syndrome by alleviating inflammation and inhibiting extracellular matrix degradation of alveolar macrophages

BACKGROUND

Acute respiratory distress syndrome (ARDS) is characterized by severe inflammation and significant extracellular matrix (ECM) degradation in the lungs. Our prior research identified the CtBP2-p300-NF-κB (C-terminal-binding protein 2-histone acetyltransferase p300-nuclear factor kappa B) transcriptional complex as critical in ARDS by activating pro-inflammatory cytokine genes.

METHODS

An ARDS mouse model was established using intratracheal instillation of lipopolysaccharide (LPS). Small molecules that inhibit the CtBP2-p300 interaction were identified through AlphaScreen. RNA sequencing (RNA-Seq) was conducted to determine differential gene expression. Immunoprecipitation and co-immunoprecipitation analyzed protein interactions. Reverse transcription-quantitative polymerase chain reaction (RT-qPCR) and immunoblotting detected gene and protein expression. Histological staining evaluated tissue damage.

RESULTS

Through AlphaScreen, two natural compounds, PNSC2477 and PNSC5325, were identified for their ability to inhibit the CtBP2-p300 interaction. While PNSC2477 demonstrated toxicity and was deemed unsuitable for further research, PNSC5325 exhibited minimal toxicity. PNSC5325 effectively inhibited the CtBP2-p300 interaction and reduced pro-inflammatory cytokine gene expression. RNA-Seq analysis of PNSC5325-treated cells indicated significant suppression of pro-inflammatory cytokine genes and matrix metalloproteinases (MMPs). Further molecular studies revealed that the CtBP2-p300 complex, in conjunction with activator protein 1 (AP1), activates MMP expression. PNSC5325 simultaneously suppressed both pro-inflammatory cytokines and MMPs by targeting the CtBP2-p300 complex. In LPS-injected mice, PNSC5325 administration significantly reduced ARDS incidence by inhibiting inflammatory and MMP genes.

CONCLUSION

These findings suggest that PNSC5325 protects against ARDS by inhibiting key inflammatory and ECM degradation pathways, highlighting its potential as a novel therapeutic agent for ARDS and paving the way for further clinical investigations.

YTHDF2-dependent m6A modification of FOXO3 mRNA mediates TIMP1 expression and contributes to intervertebral disc degeneration following ROS stimulation

The accumulation of reactive oxygen species (ROS) significantly contributes to intervertebral disc degeneration (IDD), but the mechanisms behind this phenomenon remain unclear. This study revealed elevated ROS levels in the intervertebral discs (IVDs) of aged mice compared to those of younger mice. The local application of hydrogen peroxide (H2O2) near lumbar discs also induced ROS accumulation and IDD. Isobaric tags for relative and absolute quantitation (iTRAQ) analysis of discs from aged and H2O2-injected mice showed increased levels of YTH N6-methyladenosine RNA binding protein F2 (YTHDF2) and matrix metallopeptidase 1/3/7/9 (MMP1/3/7/9), along with decreased levels of forkhead box O3 (FOXO3) and TIMP1 (tissue inhibitor of metalloproteinases 1). Our experiments indicated that in nucleus pulposus (NP) cells and young mouse IVDs that were not exposed to ROS, FOXO3 recruited histone acetyltransferase CBP (CREB binding protein) and mediator complex subunit 1 (Med1) to activate TIMP1 expression, which inhibited MMP activity and prevented disc degeneration. However, ROS exposure activated YTHDF2 and promoted the degradation of m6A-modified FOXO3 mRNA, impairing FOXO3's ability to activate TIMP1. This degradation exacerbated MMP activity and contributed to the degradation of the IVD extracellular matrix. Notably, administration of the YTHDF2 inhibitor DC-Y13-27 in older and H2O2-treated mice significantly enhanced FOXO3 and TIMP1 expression, reduced MMP activity, and mitigated IVD degeneration. Together, this study uncovers a novel ROS-regulated pathway in IDD, centered on the YTHDF2/FOXO3/TIMP1/MMPs axis, suggesting that targeting YTHDF2 may represent a promising therapeutic strategy for combating the progression of IDD.

A novel spherical GelMA-HAMA hydrogel encapsulating APET×2 polypeptide and CFIm25-targeting sgRNA for immune microenvironment modulation and nucleus pulposus regeneration in intervertebral discs

METHODS

Single-cell transcriptomics and high-throughput transcriptomics were used to screen factors significantly correlated with intervertebral disc degeneration (IDD). Expression changes of CFIm25 were determined via RT-qPCR and Western blot. NP cells were isolated from mouse intervertebral discs and induced to degrade with TNF-α and IL-1β. CFIm25 was knocked out using CRISPR-Cas9, and CFIm25 knockout and overexpressing nucleus pulposus (NP) cell lines were generated through lentiviral transfection. Proteoglycan expression, protein expression, inflammatory factor expression, cell viability, proliferation, migration, gene expression, and protein expression were analyzed using various assays (alcian blue staining, immunofluorescence, ELISA, CCK-8, EDU labeling, transwell migration, scratch assay, RT-qPCR, Western blot). The GelMA-HAMA hydrogel loaded with APET×2 polypeptide and sgRNA was designed, and its effects on NP regeneration were assessed through in vitro and mouse model experiments. The progression of IDD in mice was evaluated using X-ray, H&E staining, and Safranin O-Fast Green staining. Immunohistochemistry was performed to determine protein expression in NP tissue. Proteomic analysis combined with in vitro and in vivo experiments was conducted to elucidate the mechanisms of hydrogel action.

RESULTS

CFIm25 was upregulated in IDD NP tissue and significantly correlated with disease progression. Inhibition of CFIm25 improved NP cell degeneration, enhanced cell proliferation, and migration. The hydrogel effectively knocked down CFIm25 expression, improved NP cell degeneration, promoted cell proliferation and migration, and mitigated IDD progression in a mouse model. The hydrogel inhibited inflammatory factor expression (IL-6, iNOS, IL-1β, TNF-α) by targeting the p38/NF-κB signaling pathway, increased collagen COLII and proteoglycan Aggrecan expression, and suppressed NP degeneration-related factors (COX-2, MMP-3).

CONCLUSION

The study highlighted the crucial role of CFIm25 in IDD and introduced a promising therapeutic strategy using a porous spherical GelMA-HAMA hydrogel loaded with APET×2 polypeptide and sgRNA. This innovative approach offers new possibilities for treating degenerated intervertebral discs.

Progress in the study of molecular mechanisms of intervertebral disc degeneration

Degenerative intervertebral disc disease (IVDD) is one of the main spinal surgery, conditions, which markedly increases the incidence of low back pain and deteriorates the patient's quality of life, and it imposes significant social and economic burdens. The molecular pathology of IVDD is highly complex and multilateral however still not ompletely understood. New findings indicate that IVDD is closely associated with inflammation, oxidative stress, cell injury and extracellular matrix metabolismdysregulation. Symptomatic management is the main therapeutic approach adopted for IVDD, but it fails to address the basic pathological changes and the causes of the disease. However, research is still focusing on molecular aspects in terms of gene expression, growth factors and cell signaling pathways in an attempt to identify specific molecular targets for IVDD treatment. The paper summarizes the most recent achievements in molecularunderstanding of the pathogenesis of IVDD and gives evidence-based recommendations for clinical practice.

Visualizing the bibliometrics of the inflammatory mechanisms in intervertebral disc degeneration

OBJECTIVE

Intervertebral disc degeneration (IVDD) constitutes a crucial pathological foundation for spinal degenerative diseases (SDD) and stands as a primary contributor to both low back pain (LBP) and disability. The progression of IVDD is linked to structural and functional alterations in tissues, where an imbalance in the inflammatory microenvironment can induce extracellular matrix (ECM) degradation, senescence, and apoptosis. This imbalance is a key pathomechanism in the disease's development, gaining considerable attention in recent years. This study aims to conduct a bibliometric analysis of publications pertaining to the inflammatory mechanisms of IVDD to quantitatively assess current research hotspots and directions.

METHODS

In this study, we queried the Web of Science Core Collection (WOSCC) database covering the period from January 1, 2001, to November 7, 2023. Content in this area was analyzed and visualized using software such as Citespace, Vosviewer, and the bibliometrix package.

RESULTS

Findings indicate a consistent annual increase in the number of publications, highlighting the widespread attention garnered by research on the inflammatory mechanisms of IVDD. In terms of journal research, Spine emerged with the highest number of publications, along with significantly elevated total citations and average citations compared to other journals. Regarding country analysis, China led in the number of publications, while the USA claimed the highest number of citations and total link strength. Institutional analysis revealed Sun Yat-sen University as having the highest number of publications and total link strength, with Thomas Jefferson University securing the highest total citations. Author analysis identified Ohtori, S. with the highest number of publications, Risbud, M.V. with the highest number of citations, and Inoue, G. with the highest total link strength, all of whom have made significant contributions to the field's development. Citation and co-citation analyses indicated that highly cited documents primarily focused on classical studies exploring inflammatory mechanisms in IVDD pathogenesis. Keyword analysis showcased the ongoing research hotspot as the further investigation of mechanisms and treatment studies. Recent years have seen a shift towards exploring pyroptosis, necrotic apoptosis, autophagy, ferroptosis, oxidative stress, and bacterial infection, among other mechanisms. In terms of treatment, alongside traditional monomer, drug, and compound therapies for IVDD, research is increasingly concentrating on stem cell therapy, exosomes, hydrogels, and scaffolds.

CONCLUSION

This bibliometric analysis of research on inflammatory mechanisms in IVDD provides insights into the current status, hotspots, and potential future trends. These findings can serve as a valuable reference and guide for researchers in the field.