Single-Cell Integration Analysis of Heterotopic Ossification and Fibrocartilage Developmental Lineage: Endoplasmic Reticulum Stress Effector Xbp1 Transcriptionally Regulates the Notch Signaling Pathway to Mediate Fibrocartilage Differentiation

Single-cell atlas of endothelial cells in atherosclerosis: identifying C1 CXCL12+ ECs as key proliferative drivers for immunological precision therapeutics in atherosclerosis

Background

Atherosclerosis (AS) is a chronic inflammatory disease characterized by endothelial dysfunction, monocyte infiltration, smooth muscle proliferation, and extracellular matrix accumulation. Endothelial cell (EC) dysfunction plays a pivotal role in the initiation and progression of AS. Despite progress in traditional research methods, the complexity of cellular heterogeneity within the disease remains poorly understood, necessitating a more refined approach for uncovering disease mechanisms.

Methods

In this study, we employed single-cell RNA sequencing (scRNA-seq) to map the endothelial cell landscape in AS comprehensively. By analyzing cellular heterogeneity, differentiation trajectories, and functional states, we identified critical endothelial subpopulations and their roles in the progression of AS. Functional enrichment and differentiation analyses were conducted, and the findings were validated through in vitro experiments.

Results

The single-cell analysis revealed distinct EC subpopulations with unique contributions to AS progression. Among these, C1 CXCL12+ ECs emerged as a key subpopulation associated with endothelial differentiation, vascular remodeling, and inflammation. These cells demonstrated high proliferative potential and were enriched in pathways related to endothelial migration and repair. Through CCK-8, Transwell assay, EdU staining and angiogenesis ability, we found that knockdown of FOXM1 in C1 CXCL12+ ECs resulted in decreased proliferation, migration and invasion. Thus, it affects the progression of AS.

Conclusion

This study provides a detailed single-cell atlas of endothelial cells in AS, identifying critical subpopulations, regulatory pathways, and key factors driving disease progression. The application of single-cell technologies paves the way for advancing our understanding of cardiovascular diseases and offers significant potential for developing personalized therapeutic strategies in immunology and precision medicine.

Decoding multiple myeloma: single-cell insights into tumor heterogeneity, immune dynamics, and disease progression

Background

Multiple myeloma (MM) is a biologically heterogeneous malignancy of clonal plasma cells, often progressing from MGUS or smoldering MM. It causes anemia, bone lesions, and immune dysfunction due to abnormal plasma cell expansion in the bone marrow. Neuroinflammatory and neurotrophic factors may influence MM progression by affecting immune cells and the bone marrow niche. Growing evidence points to a role for neuroimmune regulation in tumor immunity. Despite therapeutic progress, disease heterogeneity and resistance highlight the need for new strategies targeting the tumor microenvironment and neuroimmune axis.

Methods

This investigation exploited single-cell RNA sequencing (scRNA-seq) to analyze MM and high-risk smoldering multiple myeloma (SMMh) samples, identifying 11 distinct cell types. We examined their transcriptional signatures, stemness, proliferative properties, and metabolic pathways, with particular attention to neuroimmune interactions in the tumor microenvironment. Using trajectory inference tools such as CytoTRACE, Monocle2, and Slingshot, we traced the differentiation paths of MM cell subpopulations and identified key signaling pathways that may influence immune responses and tumor progression.

Results

The analysis identified four distinct subpopulations of myeloma cells, with the C0 IGLC3+ myeloma cells representing the least differentiated and most proliferative subset. These cells played a critical role in MM progression and may contribute to immune evasion mechanisms. Additionally, receptor-ligand interactions within the tumor microenvironment were identified, which may be influenced by neuroinflammatory and neurotrophic factors. These findings suggest that the nervous system and immune modulation significantly affect tumor biology, highlighting potential therapeutic targets that could be exploited to overcome resistance to conventional therapies.

Conclusion

This single-cell analysis provided new insights into the cellular diversity and differentiation trajectories in MM, offering a deeper understanding of the complex neuroimmune interactions that drive tumor progression and resistance. By incorporating the role of neuroinflammation and immune modulation, our study suggested novel therapeutic strategies targeting the neuroimmune axis in oncology, ultimately contributing to the development of more effective, personalized treatment approaches for MM.

The Potential Role of C4 MYH11+ Fibroblasts and the MDK-SDC2 Ligand-Receptor Pair in Lung Adenocarcinoma: Implications for Prognosis and Therapeutic Strategies

BACKGROUND

Lung adenocarcinoma (LUAD) posed a significant threat to global human health. This study employed single-cell RNA sequencing (scRNA-seq) to analyze transcriptomic data from nine LUAD patients at different stages of tumor infiltration, aiming to elucidate the tumor microenvironment and key biological processes of LUAD.

METHODS

In this study, we processed the scRNA-seq data using the Seurat package and sequentially applied principal component analysis followed by the Harmony package to effectively correct for batch effects, identifying 105,725 high-quality cells. Through cell clustering and gene expression profiling, we identified critical cell subpopulations and gene expression patterns in LUAD patients.

RESULTS

Our analysis revealed that the C4 MYH11+ Fibroblasts subtype was primarily involved in biological processes related to muscle function. Further investigations uncovered the MDK-SDC2 ligand-receptor pair as a critical regulator of tumor cell invasion, proliferation, and migration, driving LUAD progression. Additionally, we developed a gene-based prognostic model that effectively predicted patient survival, providing valuable clinical insights.

CONCLUSION

This study provided a comprehensive atlas of the LUAD tumor microenvironment, highlighted the role of the C4 MYH11+ Fibroblasts in tumor progression. It also proposed the MDK-SDC2 ligand-receptor pair as a novel mechanism, addressing a significant gap in this area of research. And presented a gene-based prognostic model as a novel perspective for research into immunotherapy and drug sensitivity in LUAD.

Elevation of Plasma IL-15 and RANTES as Potential Biomarkers of Healing in Chronic Venous Ulcerations: A Pilot Study

Chronic wounds present a large burden to our healthcare system and are typically marked by a failure to transition out of the inflammatory phase of wound healing. Venous leg ulcers (VLUs) represent the largest portion of chronic wounds. A pilot study of eleven (11) patients with VLUs seen over a 12-week period was undertaken utilizing RNA sequencing of wound biopsies and plasma cytokine levels to determine if biomarkers could be identified that would distinguish between wounds which heal versus those that do not. Chronic wounds were found to have increased expression of genes relating to epithelial-to-mesenchymal transition (EMT), cartilage and bone formation, and regulation of apical junction. Plasma cytokine levels showed predictive potential for IL-15 and RANTES, which were found to increase over time in patients with healed wounds. Further research is needed to validate these biomarkers as well as additional study of other chronic wound models, such as diabetic foot ulcers (DFUs).

Single-cell RNA sequencing revealed PPARG promoted osteosarcoma progression: based on osteoclast proliferation

Background

Osteosarcoma (OS) is one of the most common primary malignant bone tumors, primarily originating from mesenchymal tissue. It is notorious for its high invasiveness, high disability rate, high mortality rate, and poor prognosis. In most primary and metastatic malignant tumors, bone destruction can promote cancer progression, which is closely related to osteoclast activation and the imbalance between osteoblasts and osteoclasts. A large number of studies confirmed that osteoclasts are an important part of OS, which play an active role in destroying bone homeostasis and promoting the progress of OS. Therefore, we conducted a detailed study of osteoclasts at the single cell level, aiming to find new OS therapeutic targets to prevent tumor progression and local spread.

Methods

We analyzed the single-cell sequencing data of OS patients and usedMonocle2, Cytotrace, and Slingshot software to analyze the pseudo-sequential trajectory during OS progression. CellChat was used to reveal the communication between cells. PySCENIC was used to identify active transcription factors in osteoclasts. Finally, we further demonstrated the results by RT-qPCR analysis, CCK-8 assay, wound healing assay, Transwell assay, etc.

Results

Through the analysis of single-cell sequencing data in OS, we identified a highly specific subgroup, C2MKI67+ Osteoclast. The key signaling pathway APP and the top 1 transcription factor PPARG in this subgroup played essential roles in osteoclast proliferation and differentiation. Given the pivotal role of osteoclasts in OS progression, we speculated that these signaling pathways and transcription factors could emerge as novel therapeutic targets, offering innovative strategies for OS treatment.

Conclusion

This study enhanced our understanding of OS and osteoclasts through scRNA-seq. Furthermore, we discovered that PPARG amplifies osteoclast activation and proliferation, resulting in excessive bone resorption and degradation of the bone matrix, thereby creating a favorable environment for tumor cell proliferation and growth. By innovatively targeting PPARG, it affected osteoclast proliferation and thus affected tumor progression; this work offered new insights and directions for the clinical treatment of OS patients.

Cross-disease transcriptomic analysis reveals DOK3 and PAPOLA as therapeutic targets for neuroinflammatory and tumorigenic processes

Objective

Subarachnoid hemorrhage (SAH) and tumorigenesis share numerous biological complexities; nevertheless, the specific gene expression profiles and underlying mechanisms remain poorly understood. This study aims to identify differentially expressed genes (DEGs) that could serve as biomarkers for diagnosis and prognosis.

Methods

Gene expression datasets (GSE122063, GSE13353, GSE161870) were analyzed using machine learning algorithms and logistic regression to identify DEGs associated with both SAH and tumorigenesis. Lasso regression and receiver operating characteristic (ROC) curve analysis were employed to evaluate the classification accuracy of these genes. Validation of critical DEGs was performed through pan-cancer analysis and experimental studies, focusing on the role of DOK3 in modulating inflammation and oxidative stress in U251MG glioblastoma and BV2 microglia cells.

Results

Fifteen common DEGs were identified, with DOK3 and PAPOLA highlighted as crucial genes implicated in SAH and neurodegenerative processes. Experimental validation demonstrated that DOK3 overexpression significantly reduced pro-inflammatory cytokine levels and oxidative stress markers while enhancing antioxidant enzyme activity. Additionally, DOK3 influenced tumorigenic processes such as apoptosis, cell cycle regulation, and proliferation, effectively mitigating LPS-induced cytotoxicity and inflammation in BV2 microglial cells.

Conclusions

DOK3 and PAPOLA play critical roles in both SAH and related neurodegeneration, presenting themselves as potential prognostic biomarkers and therapeutic targets. Notably, DOK3 exhibits potential as an antitumor agent with anti-inflammatory and antioxidative properties, offering therapeutic benefits for both cancer and neuroinflammatory conditions.

The role of miRNAs as biomarkers in heterotopic ossification

Fibrodysplasia ossificans progressiva and progressive osseous heteroplasia are genetic forms of heterotopic ossification (HO). Fibrodysplasia ossificans progressiva is caused by ACVR1 gene mutations, while progressive osseous heteroplasia is caused by GNAS gene mutations. Nongenetic HO typically occurs after trauma or surgery, with an occurrence rate of 20-60%. It can also be observed in conditions such as diffuse idiopathic skeletal hyperostosis, spinal ligament ossification, ankylosing spondylitis, and skeletal fluorosis. The exact cause of nongenetic HO is not entirely clear. More than 100 types of miRNAs have been identified as being linked to the development of HO. Some miRNAs are promising potential biomarkers for traumatic HO and ossification of the posterior longitudinal ligament. These findings further emphasize the significant role miRNAs play in the pathogenesis and progression of bone disorders. Repeated investigations into the function of a specific miRNA are infrequent and yield inconsistent results, possibly because of variable experimental conditions. It is hypothesized that miRNAs can enhance osteogenesis for the management of fractures and bone defects. However, further research is required to validate this hypothesis.

Angiogenesis in heterotopic ossification: From mechanisms to clinical significance

Heterotopic ossification (HO) refers to the formation of pathologic bone in nonskeletal tissues (including muscles, tendons or other soft tissues). HO typically occurs after a severe injury and can occur in any part of the body. HO lesions are highly vascularized. Angiogenesis, which is the formation of new blood vessels, plays an important role in the pathophysiology of HO. Surgical resection is considered an effective treatment for HO. However, it is difficult to completely remove new vessels, which can lead to the recurrence of HO and is often accompanied by significant problems such as intraoperative hemorrhage, demonstrating the important role of angiogenesis in HO. Here, we broadly summarize the current understanding of how angiogenesis contributes to HO; in particular, we focus on new insights into the cellular and signaling mechanisms underlying HO angiogenesis. We also review the development and current challenges associated with antiangiogenic therapy for HO.

Metabolic Syndrome and Tendon Disease: A Comprehensive Review

Metabolic syndrome (MS) is a multifaceted pathological condition characterized by the atypical accumulation of various metabolic components such as central obesity or excess weight, hyperlipidemia, low-density lipoprotein (LDL), hypertension, and insulin resistance. Recently, MS has been recognized as a notable contributor to heart and circulatory diseases. In addition, with increasing research, the impact of MS on tendon repair and disease has gradually emerged. Recent studies have investigated the relationship between tendon healing and diseases such as diabetes, dyslipidemia, obesity, and other metabolic disorders. However, diabetes mellitus (DM), hypercholesterolemia, obesity, and various metabolic disorders often coexist and together constitute MS. At present, insulin resistance is considered the major pathological mechanism underlying MS, central obesity is regarded as the predominant factor responsible for it, and dyslipidemia and other metabolic diseases are known as secondary contributors to MS. This review aims to evaluate the current literature regarding the impact of various pathological conditions in MS on tendon recovery and illness, and to present a comprehensive overview of the effects of MS on tendon recovery and diseases, along with the accompanying molecular mechanisms.

Exercise potentially prevents colorectal cancer liver metastases by suppressing tumor epithelial cell stemness via RPS4X downregulation

BACKGROUND

Colorectal cancer (CRC) is the third most prevalent tumor globally. The liver is the most common site for CRC metastasis, and the involvement of the liver is a common cause of death in patients with late-stage CRC. Consequently, mitigating CRC liver metastasis (CRLM) is key to improving CRC prognosis and increasing survival. Exercise has been shown to be an effective method of improving the prognosis of many tumor types. However, the ability of exercise to inhibit CRLM is yet to be thoroughly investigated.

METHODS

The GSE157600 and GSE97084 datasets were used for analysis. A pan-cancer dataset which was uniformly normalized was downloaded and analyzed from the UCSC database: TCGA, TARGET, GTEx (PANCAN, n = 19,131, G = 60,499). Several advanced bioinformatics analyses were conducted, including single-cell sequencing analysis, correlation algorithm, and prognostic screen. CRC tumor microarray (TMA) as well as cell/animal experiments are used to further validate the results of the analysis.

RESULTS

The greatest variability was found in epithelial cells from the tumor group. RPS4X was generally upregulated in all types of CRC, while exercise downregulated RPS4X expression. A lowered expression of RPS4X may prolong tumor survival and reduce CRC metastasis. RPS4X and tumor stemness marker-CD44 were highly positively correlated and knockdown of RPS4X expression reduced tumor stemness both in vitro and in vivo.

CONCLUSION

RPS4X upregulation may enhance CRC stemness and increase the odds of metastasis. Exercise may reduce CRC metastasis through the regulation of RPS4X.

Translational studies of exosomes in sports medicine - a mini-review

This review in sports medicine focuses on the critical role of exosomes in managing chronic conditions and enhancing athletic performance. Exosomes, small vesicles produced by various cells, are essential for cellular communication and transporting molecules like proteins and nucleic acids. Originating from the endoplasmic reticulum, they play a vital role in modulating inflammation and tissue repair. Their significance in sports medicine is increasingly recognized, particularly in healing athletic injuries, improving articular cartilage lesions, and osteoarthritic conditions by modulating cellular behavior and aiding tissue regeneration. Investigations also highlight their potential in boosting athletic performance, especially through myocytes-derived exosomes that may enhance adaptability to physical training. Emphasizing a multidisciplinary approach, this review underlines the need to thoroughly understand exosome biology, including their pathways and classifications, to fully exploit their therapeutic potential. It outlines future directions in sports medicine, focusing on personalized treatments, clinical evaluations, and embracing technological advancements. This research represents a frontier in using exosomes to improve athletes' health and performance capabilities.

Single-cell transcriptome sequencing reveals aberrantly activated inter-tumor cell signaling pathways in the development of clear cell renal cell carcinoma

BACKGROUND

Aberrant intracellular or intercellular signaling pathways are important mechanisms that contribute to the development and progression of cancer. However, the intercellular communication associated with the development of ccRCC is currently unknown. The purpose of this study was to examine the aberrant tumor cell-to-cell communication signals during the development of ccRCC.

METHODS

We conducted an analysis on the scRNA-seq data of 6 ccRCC and 6 normal kidney tissues. This analysis included sub clustering, CNV analysis, single-cell trajectory analysis, cell-cell communication analysis, and transcription factor analysis. Moreover, we performed validation tests on clinical samples using multiplex immunofluorescence.

RESULTS

This study identified eleven aberrantly activated intercellular signaling pathways in tumor clusters from ccRCC samples. Among these, two of the majors signaling molecules, MIF and SPP1, were mainly secreted by a subpopulation of cancer stem cells. This subpopulation demonstrated high expression levels of the cancer stem cell markers POU5F1 and CD44 (POU5F1hiCD44hiE.T), with the transcription factor POU5F1 regulating the expression of SPP1. Further research demonstrated that SPP1 binds to integrin receptors on the surface of target cells and promotes ccRCC development and progression by activating potential signaling mechanisms such as ILK and JAK/STAT.

CONCLUSION

Aberrantly activated tumor intercellular signaling pathways promote the development and progression of ccRCC. The cancer stem cell subpopulation (POU5F1hiCD44hiE.T) promotes malignant transformation and the development of a malignant phenotype by releasing aberrant signaling molecules and interacting with other tumor cells.

Erxian Decoction-induced serum exosomes slowed bone marrow mesenchymal stem cell senescence through mitophagy

OBJECTIVE

Erxian Decoction (EXD) is traditionally employed in the treatment of menopausal syndromes, although its underlying mechanisms remain largely undefined. Given that the senescence of bone marrow mesenchymal stem cells (BMSCs) is intertwined with organismal aging and associated diseases, this study endeavored to elucidate the influence of EXD on aging BMSCs and uncover the mechanisms through which EXD impedes BMSC senescence.

METHODS

Initially, we probed the anti-senescent mechanisms of EXD on BMSCs via network pharmacology. We subsequently isolated and identified exosomes from the serum of EXD-fed rats (EXD-Exos) and administered these to H2 O2 -induced aging BMSC. Assays were conducted to assess BMSC senescence indicators and markers pertinent to mitochondrial autophagy. Treatments with mitophagy inhibitors and activators were then employed to substantiate our findings.

RESULTS

Protein-protein interaction (PPI) network analyses spotlighted AKT1, TP53, TNF, JUN, VEGFA, IL6, CASP3 and EGFR as focal targets. Gene Ontology and Kyoto Encylcopedia of Genes and Genomes pathway analyses underscored oxidative stress, mitophagy and cell proliferation as pivotal processes. Our cellular assays ascertained that EXD-Exos mitigated H2 O2 -induced senescence phenotypes in BMSCs. Moreover, EXD-Exos ameliorated disrupted mitophagy in BMSCs, as evidenced by enhanced cellular membrane potential and diminished reactive oxygen species levels. Intriguingly, EXD-Exos also preserved the osteogenic differentiation potential of BMSCs while curtailing their adipogenic propensity.

CONCLUSION

Our findings compellingly suggest that EXD counteracts BMSC senescence by fostering mitophagy.

Mechanical regulation of the Notch signaling pathway

The mechanical regulation of Notch signaling is an emerging area of interest in cell biology. Notch is essential in many physiological processes in which mechanical stress plays an important role. This review provides an overview of the mechanoregulation of Notch signaling in multiple steps of the pathway. First, we discuss the current knowledge on the direct mechanoregulation of Notch receptor maturation and localization to the membrane and the effect of mechanical stress on the Notch components. Next, we explore how ligand-receptor interactions and membrane dynamics are possible subjects to mechano-regulation, emphasizing the role of cytoskeletal interactions, membrane stiffness, and endocytic complex formation. We further delve into the necessity of tension generation for negative regulatory region (NRR) domain unfolding, facilitated by ligand endocytosis and other microforces. Additionally, we examine the indirect mechano-regulation of S2 and S3 cleavages. Finally, we discuss the mechanoregulation of the Notch intracellular domain (NICD) trafficking and nuclear entry and the impact of mechanical stress on heterochromatin dynamics and nuclear NICD interactions. This review aims to draw attention to the intricate interplay between mechanical cues and Notch signaling regulation, offering novel insights into the multifaceted nature of cellular mechanobiology.

Single-cell RNA sequencing in orthopedic research

Although previous RNA sequencing methods have been widely used in orthopedic research and have provided ideas for therapeutic strategies, the specific mechanisms of some orthopedic disorders, including osteoarthritis, lumbar disc herniation, rheumatoid arthritis, fractures, tendon injuries, spinal cord injury, heterotopic ossification, and osteosarcoma, require further elucidation. The emergence of the single-cell RNA sequencing (scRNA-seq) technique has introduced a new era of research on these topics, as this method provides information regarding cellular heterogeneity, new cell subtypes, functions of novel subclusters, potential molecular mechanisms, cell-fate transitions, and cell‒cell interactions that are involved in the development of orthopedic diseases. Here, we summarize the cell subpopulations, genes, and underlying mechanisms involved in the development of orthopedic diseases identified by scRNA-seq, improving our understanding of the pathology of these diseases and providing new insights into therapeutic approaches.

Analysis of co-expression gene network associated with intracranial aneurysm and type 2 diabetes mellitus

To screen for common target genes in intracranial aneurysms (IA) and type 2 diabetes mellitus (T2DM), construct a common transcriptional regulatory network to predict clusters of candidate genes involved in the pathogenesis of T2DM and IA, and identify the common neurovascular markers and pathways in T2DM causing IA. Microarray datasets (GSE55650, GSE25462, GSE26969, GSE75436, and GSE13353) from the GEO database were analyzed in this research. Screening of the IA and the T2DM datasets yielded a total of 126 DEGs, among which 78 were upregulated and 138 were downregulated. Functional enrichment analysis revealed that these DEGs were enriched for a total of 68 GO pathways, including extracellular matrix composition, coagulation regulation, hemostasis regulation, and collagen fiber composition pathways. We also constructed transcriptional regulatory networks, and identified key transcription factors involved in both the conditions. Univariate logistic regression analysis showed that ARNTL2 and STAT1 were significantly associated with the development of T2DM and IA, acting as the common neurovascular markers for both the diseases. In cellular experiments, hyperglycemic microenvironments exhibited upregulated STAT1 expression. STAT1 may be involved in the pathogenesis of IA in T2DM patients. Being the common neurovascular markers, STAT1 may acts as novel therapeutic targets for the treatment of IA and T2DM.

Exercise-induced IL-15 acted as a positive prognostic implication and tumor-suppressed role in pan-cancer

Objective: Exercise can produce a large number of cytokines that may benefit cancer patients, including Interleukin 15 (IL-15). IL-15 is a cytokine that has multiple functions in regulating the adaptive and innate immune systems and tumorigenesis of lung and breast cancers. However, the roles of IL-15 in other types of cancer remain unknown. In this article, we try to systematically analyze if IL-15 is a potential molecular biomarker for predicting patient prognosis in pan-cancer and its connection with anti-cancer effects of exercise. Methods: The expression of IL-15 was detected by The Cancer Genome Atlas (TCGA) database, Human protein Atlas (HPA), and Genotype Tissue-Expression (GTEX) database. Analysis of IL-15 genomic alterations and protein expression in human organic tissues was analyzed by the cBioPortal database and HPA. The correlations between IL-15 expression and survival outcomes, clinical features, immune-associated cell infiltration, and ferroptosis/cuproptosis were analyzed using the TCGA, ESTIMATE algorithm, and TIMER databases. Gene Set Enrichment Analysis (GSEA) was performed to evaluate the biological functions of IL-15 in pan-cancer. Results: The differential analysis suggested that the level of IL-15 mRNA expression was significantly downregulated in 12 tumor types compared with normal tissues, which is similar to the protein expression in most cancer types. The high expression of IL-15 could predict the positive survival outcome of patients with LUAD (lung adenocarcinoma), COAD (colon adenocarcinoma), COADREAD (colon and rectum adenocarcinoma), ESCA (esophageal carcinoma), SKCM (skin cutaneous melanoma), UCS (uterine carcinosarcoma), and READ (rectum adenocarcinoma). Moreover, amplification was found to be the most frequent mutation type of IL-15 genomic. Furthermore, the expression of IL-15 was correlated to the infiltration levels of various immune-associated cells in pan-cancer assessed by the ESTIMATE algorithm and TIMER database. In addition, IL-15 is positively correlated with ferroptosis/cuproptosis-related genes (ACSL4 and LIPT1) in pan-cancer. Levels of IL-15 were reported to be elevated in humans for 10-120 min following an acute exercise. Therefore, we hypothesized that the better prognosis of pan-cancer patients with regular exercise may be achieved by regulating level of IL-15. Conclusion: Our results demonstrated that IL-15 is a potential molecular biomarker for predicting patient prognosis, immunoreaction, and ferroptosis/cuproptosis in pan-cancer and partly explained the anti-cancer effects of exercise.

Based on Network Pharmacology and Molecular Dynamics Simulations, Baicalein, an Active Ingredient of Yiqi Qingre Ziyin Method, Potentially Protects Patients With Atrophic Rhinitis From Cognitive Impairment

Cognition may be improved by the active ingredients of the Yiqi Qingre Ziyin method in patients with atrophic rhinitis (AR). This study aimed to identify potential targets of the Yiqi Qingre Ziyin method for the treatment of patients with cognitive impairment. Nasal mucosal tissue samples from patients with AR were subjected to proteomic assays, and differentially expressed proteins were obtained. To explore the mechanism of AR leading to mild cognitive impairment (MCI), a differential analysis of AR related differential proteins in the MCI related GSE140831 dataset was performed. Most AR-related differential proteins are also differentially expressed in peripheral blood tissues of MCI, have similar biological functions and are enriched in similar pathways. These co-expressed differential factors in AR and MCI are known as common differential proteins of AR and MCI (CDPAM). Based on the analysis and validation of the random forest, support vector machine and neural network models, CDPAM acted as a diagnostic marker for MCI risk. Cytochrome C (CYCS) was significantly upregulated in the peripheral blood of patients with MCI. The active ingredients in the Yiqi Qingre Ziqin method were obtained and targeted 137 proteins. Among these targeted proteins, CYCS belong to the CDPAM set. Molecular docking and molecular dynamics analysis revealed that baicalein, an active ingredient in the Yiqi Qingre Ziyin method, stably targeted the CYCS protein. Results of the enrichment analysis revealed that the up-regulation of CYCS expression may have a defensive effect on the cells to resist foreign stimuli. Therefore, baicalein, an active ingredient in the Yiqi Qingre Ziyin method, may prevent the development and progression of MCI by targeting the CYCS protein.

MicroRNAs Promote the Progression of Sepsis-Induced Cardiomyopathy and Neurovascular Dysfunction Through Upregulation of NF-kappaB Signaling Pathway-Associated HDAC7/ACTN4

Introduction

The objective of this study was to determine the NF-kappaB pathway, hub genes, and transcription factors (TFs) in monocytes implicated in the progression of neurovascular-related sepsis-induced cardiomyopathy (SIC) as well as potential miRNAs with regulatory functions.

Methods

: Sepsis-induced cardiomyopathy—and heart failure (HF)-related differentially expressed genes (DEGs) between SIC and HF groups were identified separately by differential analysis. In addition, DEGs and differentially expressed miRNAs (DEmiRNAs) in monocytes between sepsis and the HC group were identified. Then, common DEGs in SIC, HF, and monocyte groups were identified by intersection analysis. Based on the functional pathways enriched by these DEGs, genes related to the NF-kB-inducing kinase (NIK)/NF-kappaB signaling pathway were selected for further intersection analysis to obtain hub genes. These common DEGs, together with sepsis-related DEmiRNAs, were used to construct a molecular interplay network and to identify core TFs in the network.

Results

: A total of 153 upregulated genes and 25 downregulated genes were obtained from SIC-, HF-, and monocyte-related DEGs. Functional pathway analysis revealed that the upregulated genes were enriched in NF-κB signaling pathway. A total of eight genes associated with NF-κB signaling pathway were then further identified from the 178 DEGs. In combination with sepsis-related DEmiRNAs, HDAC7/ACTN4 was identified as a key transcriptional regulatory pair in the progression of SIC and in monocyte regulation. hsa-miR-23a-3p, hsa-miR-3175, and hsa-miR-23b-3p can regulate the progression of SIC through the regulation of HDAC7/ACTN4. Finally, gene set enrichment analysis (GSEA) suggested that HDAC7/ACTN4 may be associated with apoptosis in addition to the inflammatory response.

Conclusion

: hsa-miR-23a-3p, hsa-miR-3175, and hsa-miR-23b-3p are involved in SIC progression by regulating NF-κB signaling signaling pathway-related HDAC7/ACTN4 in monocytes and cardiac tissue cells. These mechanisms may contribute to sepsis-induced neurovascular damage.

Role of Ultrasound Imaging in the Prediction of TRIM67 in Brain Metastases From Breast Cancer

Objectives

Ultrasound (US) imaging is a relatively novel strategy to monitor the activity of the blood–brain barrier, which can facilitate the diagnosis and treatment of neurovascular-related metastatic tumors. The purpose of this study was to investigate the clinical significance of applying a combination of US imaging outcomes and the associated genes. This was performed to construct line drawings to facilitate the prediction of brain metastases arising from breast cancer.

Methods

The RNA transcript data from The Cancer Genome Atlas (TCGA) database was obtained for breast cancer, and the differentially expressed genes (DEGs) associated with tumor and brain tumor metastases were identified. Subsequently, key genes associated with survival prognosis were subsequently identified from the DEGs.

Results

Tripartite motif-containing protein 67 (TRIM67) was identified and the differential; in addition, the survival analyses of the TCGA database revealed that it was associated with brain tumor metastases and overall survival prognosis. Applying independent clinical cohort data, US-related features (microcalcification and lymph node metastasis) were associated with breast cancer tumor metastasis. Furthermore, ultrasonographic findings of microcalcifications showed correlations with TRIM67 expression. The study results revealed that six variables [stage, TRIM67, tumor size, regional lymph node staging (N), age, and HER2 status] were suitable predictors of tumor metastasis by applying support vector machine–recursive feature elimination. Among these, US-predicted tumor size correlated with tumor size classification, whereas US-predicted lymph node metastasis correlated with tumor N classification. The TRIM67 upregulation was accompanied by upregulation of the integrated breast cancer pathway; however, it leads to the downregulation of the miRNA targets in ECM and membrane receptors and the miRNAs involved in DNA damage response pathways.

Conclusions

The TRIM67 is a risk factor associated with brain metastases from breast cancer and it is considered a prognostic survival factor. The nomogram constructed from six variables—stage, TRIM67, tumor size, N, age, HER2 status—is an appropriate predictor to estimate the occurrence of breast cancer metastasis.

Intracranial Aneurysms Induced by RUNX1 Through Regulation of NFKB1 in Patients With Hypertension-An Integrated Analysis Based on Multiple Datasets and Algorithms

Objective

The purpose of this study was to identify potential therapeutic targets by examining the hub genes contributing to progression of intracranial aneurysm (IA) in patients with hypertension.

Methods

The bulk RNA sequencing (RNA-seq) datasets of hypertension and IA were obtained from the Gene Expression Omnibus (www.ncbi.nlm.nih.gov/geo) database. These data were then used to calculate disease-related differentially expressed genes (DEGs) at the individual level. An scRNA-seq dataset of patients with abdominal aortic aneurysms (AAA) was used to analyze monocyte/macrophage-related DEGs. On the basis of the DEG data related to monocytes and macrophages, a TF-genes network has been developed. Hub genes and core sub-networks have also been identified. Furthermore, the key genes have been validated in an external cohort.

Results

From combined monocyte and macrophage-derived DEGs from abdominal aortic aneurysms, five hub DEGs were detected, including IFI30, SERPINE1, HMOX1, IL24, and RUNX1. A total of 57 genes were found in the IA bulk RNA-seq dataset. A support vector machine-recursive feature elimination algorithm (SVM-RFE) was applied to further screen the seven genes (RPS4Y1, DDX3Y, RUNX1, CLEC10A, PLAC8, SLA, and LILRB3). RUNX1 was the hub gene that regulated NFKB1 in the monocyte/macrophage-related network. And RUNX1 is implicated in IA progression by regulating hematopoietic stem cell differentiation and abnormal platelet production, according to gene set enrichment analysis.

Conclusion

Among patients with hypertension, RUNX1 in monocytes and macrophages was associated with a higher risk of IA through its regulation of NFKB1.

Single-Cell Analysis Reveals the Role of the Neuropeptide Receptor FPR2 in Monocytes in Kawasaki Disease: A Bioinformatic Study

Exploring the role of neuropeptides in the communication between monocyte subtypes facilitates an investigation of the pathogenesis of Kawasaki disease (KD). We investigated the patterns of interaction between neuropeptide-associated ligands and receptors in monocyte subpopulations in KD patients. Single-cell analysis was employed for the identification of cell subpopulations in KD patients, and monocytes were classified into 3 subpopulations: classical monocytes (CMs), intermediate monocytes (IMs), and nonclassical monocytes (NCMs). Cell-cell communication and differential analyses were used to identify ligand-receptor interactions in monocytes. Five neuropeptide-related genes (SORL1, TNF, SORT1, FPR2, and ANXA1) were involved in cell-cell interactions, wherein FPR2, a neuropeptide receptor, was significantly highly expressed in KD. Weighted gene coexpression network analysis revealed a significant correlation between the yellow module and FPR2 (p < 0.001, CC = 0.43). Using the genes in the yellow module, we constructed a PPI network to assess the possible functions of the FPR2-associated gene network. Gene set enrichment analysis showed that increased FPR2 levels may be involved in immune system regulation. FPR2 in CMs mediates the control of inflammation in KD. The findings of this study may provide a novel target for the clinical treatment of KD.

miR-17-5p/HOXA7 Is a Potential Driver for Brain Metastasis of Lung Adenocarcinoma Related to Ferroptosis Revealed by Bioinformatic Analysis

Objectives

Present study aims to identify the essential mRNAs responsible for the development of brain neurovascular-related metastases (BNM) among lung adenocarcinoma (LUAD) patients. Further, we attempted to predict brain metastases more accurately and prevent their development in LUAD patients.

Methods

Transcriptome data analysis was used to identify differentially expressed mRNAs (DEMs) associated with brain metastasis, and thereby the ferroptosis index (FPI) is calculated using a computational model. Meanwhile, the DEmRNAs linked with FPI, and brain metastasis were derived by the intersection of these two groups of DEMs. We also constructed a ceRNA network containing these DEmRNAs, identifying the HCP5 /hsa-miR-17-5p/HOXA7 axis for analysis. Further, a clinical cohort was employed to validate the regulatory roles of molecules involved in the ceRNA regulatory axis.

Results

Here we report the development of a ceRNA network based on BNM-associated DEMs and FPI-associated DEmRNAs which includes three core miRNAs (hsa-miR-338-3p, hsa-miR-429, and hsa-miR-17-5p), three mRNAs (HOXA7, TBX5, and TCF21), and five lncRNAs (HCP5, LINC00460, TP53TG1). Using gene set enrichment analysis (GSEA) and survival analysis, the potential axis of HCP5 /hsa-miR-17-5p/HOXA7 was further investigated. It is found that HOXA7 and ferroptosis index are positively correlated while inhibiting tumor brain metastasis. It may be that HCP5 binds competitively with miR-17-5p and upregulates HOXA7 to increase iron death limiting brain cancer metastases.

Conclusions

The expression of both HOXA7 and HCP5 is positively correlated with FPI, indicating a possible link between ferroptosis and BNM. According to the results of our study, the ferroptosis-related ceRNA HCP5 /hsa-miR-17-5p/HOXA7 axis may contribute to the development of BNM in LUAD patients.

Potential Mechanism Underlying Exercise Upregulated Circulating Blood Exosome miR-215-5p to Prevent Necroptosis of Neuronal Cells and a Model for Early Diagnosis of Alzheimer's Disease

Exercise is crucial for preventing Alzheimer's disease (AD), although the exact underlying mechanism remains unclear. The construction of an accurate AD risk prediction model is beneficial as it can provide a theoretical basis for preventive exercise prescription. In recent years, necroptosis has been confirmed as an important manifestation of AD, and exercise is known to inhibit necroptosis of neuronal cells. In this study, we extracted 67 necroptosis-related genes and 32 necroptosis-related lncRNAs and screened for key predictive AD risk genes through a random forest analysis. Based on the neural network Prediction model, we constructed a new logistic regression-based AD risk prediction model in order to provide a visual basis for the formulation of exercise prescription. The prediction model had an area under the curve (AUC) value of 0.979, indicative of strong predictive power and a robust clinical application prospect. In the exercise group, the expression of exosomal miR-215-5p was found to be upregulated; miR-215-5p could potentially inhibit the expressions of IDH1, BCL2L11, and SIRT1. The single-cell SCENIC assay was used to identify key transcriptional regulators in skeletal muscle. Among them, CEBPB and GATA6 were identified as putative transcriptional regulators of miR-215. After "skeletal muscle removal of load," the expressions of CEBPB and GATA6 increased substantially, which in turn led to the elevation of miR-215 expression, thereby suggesting a putative mechanism for negative feedback regulation of exosomal homeostasis.

Single-Cell Transcriptome Analysis Reveals the Importance of IRF1/FSTL1 in Synovial Fibroblast Subsets for the Development of Rheumatoid Arthritis

Objectives

This study aimed to investigate the potential role of synovial fibroblasts (SFs) in the development of rheumatoid arthritis (RA) to identify potential molecular targets and provide a theoretical basis for the treatment of RA.

Methods

GSE109449, a fibroblast transcriptome dataset of synovial tissue from RA and osteoarthritis (OA), were obtained from the GEO database. After standard cell quality control, this single-cell transcriptome data was used to perform routine single-cell analysis processes. After completing dimensionality reduction, clustering, and cell subset identification of fibroblasts, the SCENIC analysis helped calculate the significant gene regulatory networks in fibroblasts and their subsets. From these computed gene regulatory networks, the regulon in which follistatin-like protein 1 (FSTL1) resides was extracted and used to analyze the transcriptional regulatory status of fibroblasts. Finally, the gene set enrichment analysis (GSEA) was used to calculate the respective enriched gene sets of IRF1 and FSTL1.

Results

Three SF subgroups were identified from the single-cell transcriptome analysis; SF subset 3 was more abundant in RA than in OA (p < 0.001). From the SCENIC analysis, we obtained 269 regulons and the corresponding gene regulatory networks in SF from the RA datasets. Next, we screened and obtained a regulon-containing FSTL1, where IRF1 was the major transcription factor. The top five regulons in SF subset 3 were TWIST1, MECOM, KLF6, MAFB, and RUNX1. Among the 3 SF subsets, IRF1 regulon was ranked the highest in SF subset 3. Differential analysis of pseudobulk RNA-seq showed that IRF1 was up-regulated in RA compared to OA. Between the three SF subgroups, IRF1 and FSTL1 expression was more up-regulated in SF subset 3 compared to the other two subgroups.

Conclusions

IRF1 was found to regulate the invasiveness of SFs by regulating FSTL1, which may influence the disease progression of RA.

Exercise Modifies the Transcriptional Regulatory Features of Monocytes in Alzheimer's Patients: A Multi-Omics Integration Analysis Based on Single Cell Technology

Monocytes have been reported to be important mediators of the protective effect of exercise against the development of Alzheimer's disease (AD). This study aims explored the mechanism by which monocytes achieve this. Using single cell transcriptome analysis, results showed that CD14 + and CD16 + monocytes interacted with other cells in the circulating blood. TNF, CCR1, APP, and AREG, the key ligand-receptor-related genes, were found to be differentially expressed between exercise-treated and AD patients. The SCENIC analysis was performed to identify individual clusters of the key transcription factors (TFs). Nine clusters (M1-M9) were obtained from the co-expression network. Among the identified TFs, MAFB, HES4, and FOSL1 were found to be differentially expressed in AD. Moreover, the M4 cluster to which MAFB, HES4, and FOSL1 belonged was defined as the signature cluster for AD phenotype. Differential analysis by bulkRNA-seq revealed that the expression of TNF, CCR1, and APP were all upregulated after exercise (p < 0.05). And ATF3, MAFB, HES4, and KLF4 that were identified in M4 clusters may be the TFs that regulate TNF, CCR1, and APP in exercise prescription. After that, APP, CCR1, TNF, ATF3, KLF4, HES4, and MAFB formed a regulatory network in the ERADMT gene set, and all of them were mechanistically linked. The ERADMT gene set has been found to be a potential risk marker for the development of AD and can be used as an indicator of compliance to exercise therapy in AD patients. Using single-cell integration analysis, a network of exercise-regulating TFs in monocytes was constructed for AD disease. The constructed network reveals the mechanism by which exercise regulated monocytes to confer therapeutic benefits against AD and its complications. However, this study, as a bioinformatic research, requires further experimental validation.

hsa-miR-518-5p/hsa-miR-3135b Regulates the REL/SOD2 Pathway in Ischemic Cerebral Infarction

Objectives

Ischemic cerebral infarction (ICI) is a fatal neurovascular disorder. A bioinformatics approach based on single-cell and bulk RNA-seq analyses was applied to investigate the pathways and genes involved in ICI and study the expression profile of these genes.

Methods

First, the aberrantly regulated “small-molecule ribonucleic acids” [microRNA (miRNAs)] and messenger RNAs (mRNAs) were analyzed using transcriptome data from the ischemic brain infarction dataset of the Gene Expression Omnibus (GEO) database. In mouse cerebrovascular monocytes, the single-cell regulatory network inference and clustering (SCENIC) workflow was used to identify key transcription factors (TFs). Then, the two miRNA-TF-mRNA interaction networks were constructed. Moreover, the molecular complex detection (MCODE) extracted the core sub-networks and identified the important TFs within these sub-networks. Finally, whole blood samples were collected for validation of the expression of critical molecules in ICI.

Results

We identified four cell types and 266 regulons in mouse cerebrovascular monocytes using SCENIC analysis. Moreover, 112 differently expressed miRNAs and 3,780 differentially expressed mRNAs were identified. We discovered potential biomarkers in ICI by building a miRNA-TF-mRNA interaction network. The hsa-miR-518-5p/hsa-miR-3135b/REL/SOD2 was found to play a potential role in ICI progression. The expression of REL and superoxide dismutase 2 (SOD2) was significantly elevated in the ICI group in the clinical cohort (P &lt; 0.05). Furthermore, a REL expression was elevated in endothelial cells and fibroblasts at the single-cell level, indicating that REL is a cell-specific regulon. Functional enrichment analyses revealed that REL is primarily engaged in neurotransmitter activity and oxidative phosphorylation.

Conclusions

Our research uncovered novel biomarkers for ICI of neurovascular disease. The hsa-miR-518-5p/hsa-miR-3135b may regulate the REL/SOD2 pathway in ICI progression.

The Neuronal Transcription Factor Creb3l1 Potential Upregulates Ntrk2 in the Hypertensive Microenvironment to Promote Vascular Smooth Muscle Cell-Neuron Interaction and Prevent Neurons from Ferroptosis: A Bioinformatic Research of scRNA-seq Data

Background

There is still a lack of knowledge regarding the association between hypertension and ferroptosis. A single-cell approach was used to study the changes in neuropeptide expression as they might contribute to the mechanisms leading to ferroptosis in a hypertensive microenvironment.

Methods

We analyzed 11798 cells from the SHR group and 12589 cells from the WKY group of mouse arterial cells. CellPhoneDB was used for cell communication analysis, and the SCENIC method was used to identify key transcription factors in neurons. The correlation between Ntrk2 and ferroptosis-related genes was further analyzed and validated via quantitative polymerase chain reaction.

Results

The arterial cells were clustered into six cell types. Ligand-receptor analysis suggested that Ngf, Ntf3, Cxcr4, and Ntrk2 were key neuropeptide-related genes involved in the communication between vascular smooth muscle cells and neural cells. In the hypertensive microenvironment, the neuronal transcription factor Creb3l1 appears to play a key role in the upregulation of Ntrk2 to promote the interaction between neurons and vascular smooth muscle cells. An association between Ntrk2 and the ferroptosis death inhibitor Gpx4 was suggested. RT-qPCR experiments confirmed that Ntrk2 downregulation in neural cells was followed by downregulated expression of Gpx4.

Conclusions

Creb3l1, a key transcription factor in vascular neurons, may upregulate Ntrk2 to promote vascular smooth muscle cell-neuron interaction and thereby potentially prevent ferroptosis in neurons.

A Hyperglycemic Microenvironment Inhibits Tendon-to-Bone Healing through the let-7b-5p/CFTR Pathway

Background

Tendon-to-bone healing is a difficult process in treatment of rotator cuff tear (RCT). In addition, diabetes is an important risk factor for poor tendon-to-bone healing. Therefore, we investigated the specific mechanisms through which diabetes affects tendon-to-bone healing by regulating the Cystic Fibrosis Transmembrane Conductance Regulator (CFTR).

Methods

Tendon-derived stem cells (TDSCs) were extracted from rats after which their proliferative capacities were evaluated by the MTT assay. The expression levels of CFTR and tendon-related markers were determined by qRT-PCR. Then, bioinformatics analyses and dual luciferase reporter gene assays were used to identify miRNAs with the ability to bind CFTR mRNA. Finally, CFTR was overexpressed in TDSCs to validate the specific mechanisms through which the high glucose microenvironment inhibits tendon-to-bone healing.

Results

The high glucose microenvironment downregulated mRNA expression levels of tendon-related markers and CFTR in TDSCs cultured with different glucose concentrations. Additionally, bioinformatics analyses revealed that let-7b-5p may be regulated by the high glucose microenvironment and can regulate CFTR levels. Moreover, a dual luciferase reporter gene assay was used to confirm that let-7b-5p targets and binds CFTR mRNA. Additional experiments also confirmed that overexpressed CFTR effectively reversed the negative effects of the hyperglycaemic microenvironment and upregulation of let-7b-5p on TDSC proliferation and differentiation. These findings imply that the hyperglycemic microenvironment inhibits CFTR transcription and, consequently, proliferation and differentiation of TDSCs in vitro by upregulating let-7b-5p.

Conclusions

A hyperglycemic microenvironment inhibits TDSC proliferation in vitro via the let-7b-5p/CFTR pathway, and this is a potential mechanism in diabetes-induced poor tendon-to-bone healing.

Transcription Factors Leading to High Expression of Neuropeptide L1CAM in Brain Metastases from Lung Adenocarcinoma and Clinical Prognostic Analysis

Background

There is a lack of understanding of the development of metastasis in lung adenocarcinoma (LUAD). This study is aimed at exploring the upstream regulatory transcription factors of L1 cell adhesion molecule (L1CAM) and to construct a prognostic model to predict the risk of brain metastasis in LUAD.

Methods

Differences in gene expression between LUAD and brain metastatic LUAD were analyzed using the Wilcoxon rank-sum test. The GRNdb (http://www.grndb.com) was used to reveal the upstream regulatory transcription factors of L1CAM in LUAD. Single-cell expression profile data (GSE131907) were obtained from the transcriptome data of 10 metastatic brain tissue samples. LUAD prognostic nomogram prediction models were constructed based on the identified significant transcription factors and L1CAM.

Results

Survival analysis suggested that high L1CAM expression was negatively significantly associated with overall survival, disease-specific survival, and prognosis in the progression-free interval (p < 0.05). The box plot indicates that high expression of L1CAM was associated with distant metastases in LUAD, while ROC curves suggested that high expression of L1CAM was associated with poor prognosis. FOSL2, HOXA9, IRF4, IKZF1, STAT1, FLI1, ETS1, E2F7, and ADARB1 are potential upstream transcriptional regulators of L1CAM. Single-cell data analysis revealed that the expression of L1CAM was found significantly and positively correlated with the expression of ETS1, FOSL2, and STAT1 in brain metastases. L1CAM, ETS1, FOSL2, and STAT1 were used to construct the LUAD prognostic nomogram prediction model, and the ROC curves suggest that the constructed nomogram possesses good predictive power.

Conclusion

By bioinformatics methods, ETS1, FOSL2, and STAT1 were identified as potential transcriptional regulators of L1CAM in this study. This will help to facilitate the early identification of patients at high risk of metastasis.