Search

Background: Ovarian cancer (OC) is one of the most prevalent gynecologic malignancies and exhibites the highest fatality rate among all gynecologic malignancies. The absence of an early diagnostic biomarker and therapeutic target contributes to an overall 5-year survival rate ranging from 30 to 50%. Plectin (PLEC), a 500 kDa scaffolding protein, has gained prominence in recent years due to its pivotal role in various cellular biological functions such as cell morphology, migration and adhesion, while the accurate role of PLEC in OC remains elusive. Results: In this study, our findings demonstrate that PLEC exerts a positive influence on the progression of OC, encompassing cellular proliferation, migration, invasion, and adhesion both in vitro and in vivo. Conclusions: The results providing new insights for the diagnosis and treatment in OC. [ABSTRACT FROM AUTHOR]

Hepatocellular carcinoma (HCC) is the fourth leading cause of cancer-related death worldwide, with approximately 800,000 deaths worldwide each year. Owing to the atypical early symptoms and characteristics of HCC, over 80% of HCC patients cannot receive curative treatment. The treatment of HCC is facing a bottleneck, and new treatment methods are urgently needed. Since the pathogenesis of HCC is not yet clear, identifying the molecular mechanisms and therapeutic targets related to it is crucial. Centromeres are considered special deoxyribonucleic acid (DNA) sequences with highly repetitive sequences that are physically connected to the spindle during cell division, ensuring equal division of genetic material between daughter cells. The numerous proteins that aggregate on this sequence during cell division are called centromere proteins (CENPs). Currently, numerous studies have shown that CENPs are abnormally expressed in tumor cells and are associated with patient prognosis. The abnormal expression of CENPs is a key cause of chromosomal instability. Furthermore, chromosomal instability is a common characteristic of the majority of tumors. Chromosomal instability can lead to uncontrolled and sustained division and proliferation of malignant tumors. Therapeutic plans targeting CENPs play important roles in the treatment of HCC. For example, small ribonucleic acid (RNA) can silence CENP expression and prevent the occurrence and development of liver cancer. In recent years, studies of HCC-targeting CENPs have gradually increased but are still relatively novel, requiring further systematic elaboration. In this review, we provide a detailed introduction to the characteristics of CENPs and discuss their roles in HCC. In addition, we discuss their application prospects in future clinical practice. [ABSTRACT FROM AUTHOR]

The mitochondrial serine β-lactamase-like protein LACTB has emerged as a critical regulator in cancer biology, distinguished by its unique structural and functional attributes. Defined by its conserved penicillin-binding proteins and β-lactamases (PBP-βLs) domain and SXXK catalytic motif, LACTB demonstrates properties distinct from its prokaryotic homologs, including the ability to polymerize into filaments. These structural characteristics enable LACTB to modulate mitochondrial organization and enzymatic activity, influencing lipid metabolism and indirectly affecting cellular proliferation. Importantly, the expression and functional roles of LACTB exhibit cancer-type-specific variation, underscoring its dual function as both a tumor suppressor and an oncogene. Decreased LACTB expression is associated with poor clinical outcomes in cancers such as breast cancer, lung cancer, and colorectal cancer, while specific mutations and regulatory mechanisms have been linked to its oncogenic activity in osteosarcoma and pancreatic adenocarcinoma. Mechanistically, LACTB regulates key processes in cancer progression, including mitochondrial dynamics, epithelial–mesenchymal transition (EMT), and cell death pathways. This duality highlights LACTB as a promising therapeutic target and underscores its relevance in advancing precision oncology strategies. This review provides a comprehensive analysis of expression level, structure–function relationships, and the diverse roles of LACTB in oncogenesis, underscoring its promise as a focal point for precision cancer therapies. [ABSTRACT FROM AUTHOR]

Nuclear receptors (NRs) are ligand-activated transcription factors that regulate a broad array of biological processes, including inflammation, lipid metabolism, cell proliferation, and apoptosis. Among the diverse family of NRs, peroxisome proliferator-activated receptors (PPARs), estrogen receptor (ER), liver X receptor (LXR), farnesoid X receptor (FXR), retinoid X receptor (RXR), and aryl hydrocarbon receptor (AhR) have garnered significant attention for their roles in neurodegenerative diseases, particularly Alzheimer's disease (AD). NRs influence the pathophysiology of AD through mechanisms such as modulation of amyloid-beta (Aβ) deposition, regulation of inflammatory pathways, and improvement of neuronal function. However, the dual role of NRs in AD progression, where some receptors may exacerbate the disease while others offer therapeutic potential, presents a critical challenge for their application in AD treatment. This review explores the functional diversity of NRs, highlighting their involvement in AD-related processes and discussing the therapeutic prospects of NR-targeting strategies. Furthermore, the key challenges, including the necessity for the precise identification of beneficial NRs, detailed structural analysis through molecular dynamics simulations, and further investigation of NR mechanisms in AD, such as tau pathology and autophagy, are also discussed. Collectively, continued research is essential to clarify the role of NRs in AD, ultimately facilitating their potential use in the diagnosis, prevention, and treatment of AD. [ABSTRACT FROM AUTHOR]

Alzheimer's disease (AD) is a major neurodegenerative dementia, with its complex pathophysiology challenging current treatments. Recent advancements have shifted the focus from the traditionally dominant amyloid hypothesis toward a multifactorial understanding of the disease. Emerging evidence suggests that while amyloid-beta (A β) accumulation is central to AD, it may not be the primary driver but rather part of a broader pathogenic process. Novel hypotheses have been proposed, including the role of tau protein abnormalities, mitochondrial dysfunction, and chronic neuroinflammation. Additionally, the gut–brain axis and epigenetic modifications have gained attention as potential contributors to AD progression. The limitations of existing therapies underscore the need for innovative strategies. This study explores the integration of machine learning (ML) in drug discovery to accelerate the identification of novel targets and drug candidates. ML offers the ability to navigate AD's complexity, enabling rapid analysis of extensive datasets and optimizing clinical trial design. The synergy between these themes presents a promising future for more effective AD treatments. [ABSTRACT FROM AUTHOR]

Gene‒gene interactions play pivotal roles in disease pathogenesis and are fundamental in the development of targeted therapeutics, particularly through the elucidation of oncogenic gene drivers in cancer. The systematic analysis of pathways and gene interactions is critical in the drug discovery process for various cancer subtypes. SPAG5, known for its role in spindle formation during cell division, has been identified as an oncogene in several cancers, although its specific impact on AML remains underexplored. This study leverages a high-throughput swarm-based deep neural network (SDNN) and transcriptomic data—an approach that enhances predictive accuracy and robustness through collective intelligence—to augment, model, and enhance the understanding of the TP53 pathway in AML cohorts. Our integrative systems biology approach identified SPAG5 as a uniquely downregulated driver in adult AML, underscoring its potential as a novel therapeutic target. The interaction of SPAG5 with key hub genes such as MDM2 and CDK1 not only reinforces its role in tumour suppression through negative regulation but also highlights its potential in moderating the phenotypic and genomic alterations associated with AML progression. This study of the role and interaction dynamics of SPAG5 sets the stage for future research aimed at developing targeted and personalized treatment approaches for AML, utilizing the capabilities of genetic interventions. [ABSTRACT FROM AUTHOR]

Colorectal cancer (CRC) is the third most common cancer globally, with limited effective biomarkers and sensitive therapeutic targets. An increasing number of studies have highlighted the critical role of tumor microenvironment (TME) imbalances, particularly immune escape due to impaired chemokine-mediated trafficking, in tumorigenesis and progression. Notably, CC chemokines (CCLs) have been shown to either promote or inhibit angiogenesis, metastasis, and immune responses in tumors, thereby influencing cancer development and patient outcomes. However, the diagnostic and prognostic significance of CCLs in CRC remains unclear. In this study, multiple online tools for bioinformatics analyses were utilized. The findings revealed that the mRNA expression levels of CCL3, CCL4, and CCL26 were significantly elevated in CRC tissues compared to normal tissues, whereas CCL2, CCL5, CCL11, CCL21, and CCL28 mRNA levels were markedly downregulated. Additionally, dysregulation of CCL4, CCL5, and CCL21 was strongly associated with clinical staging, and elevated levels of CCL4, CCL11, and CCL28 were linked to significantly prolonged survival in CRC patients. Functional enrichment analysis indicated that the cellular roles of CCLs were predominantly associated with the chemokine, Wnt, and Toll-like receptor signaling pathways, as well as protein kinase activity. Furthermore, transcriptional regulation of most CCLs involved RELA and NFKB1. Key downstream targets included members of the SRC family of tyrosine kinases (HCK, LYN, and LCK), serine/threonine kinases (ATR and ATM), and others such as CSNK1G2, NEK2, and CDK2. Moreover, CCLs (CCL2, CCL3, CCL4, CCL5, CCL11, CCL21, and CCL28) exhibited strong correlations with major infiltration-related immune cells, including B cells, CD8+ T cells, CD4+ T cells, macrophages, neutrophils, and dendritic cells. In conclusion, our study provides novel insights into the potential utility of CCLs as biomarkers and therapeutic targets for CRC prevention and immunotherapy. [ABSTRACT FROM AUTHOR]

Background: To investigate the role of the translocase of the outer mitochondrial membrane 40 (TOM40) in oral squamous cell carcinoma (OSCC) with the aim of identifying new biomarkers or potential therapeutic targets. Methods: TOM40 expression level in OSCC was evaluated using datasets downloaded from The Cancer Genome Atlas (TCGA), as well as clinical data. The correlation between TOM40 expression level and the clinicopathological parameters and survival were analyzed in TCGA. The signaling pathways associated with TOM40 were identified through gene set enrichment analysis. A network of genes co-expressed with TOM40 was constructed and functionally annotated by gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses. The immune infiltration pattern in OSCC was analyzed in the TCGA-OSCC cohort using the CIBERSORT algorithm. Clinically significant factors of OSCC were screened through the expression levels of TOM40 and a clinically relevant nomogram was constructed. The TCGA-OSCC cohort was divided into the TOM40high and TOM40low groups and the correlation between TOM40 expression level and the sensitivity to frequently used chemotherapeutic drugs was evaluated. CCK-8 and colony formation assays were applied to determine the cell growth. Results: TOM40 was highly expressed in OSCC tissues and correlated negatively with the overall survival (P < 0.05). Patients with high TOM40 expression level showed worse prognosis. Furthermore, GO and KEGG enrichment analyses of the differentially expressed genes related to TOM40 showed that these genes are mainly associated with immunity and tumorigenesis. Immunological infiltration analysis has found that the expression levels of TOM40 are correlated with the proportions of several immune cells. Moreover, we found that TOM40 knockdown inhibited cell growth in OSCC cell lines. Conclusions: Our results uncovered that TOM40 is a reliable prognostic marker and therapeutic target in OSCC. [ABSTRACT FROM AUTHOR]

Background: Enterobacter cloacae is increasingly prevalent and resistant to multiple antibiotics, making it a significant pathogen in healthcare settings with high mortality rates. However, its pathogenic mechanisms are not fully understood. Results: In this study, we explored the role of nagZ in regulating the virulence of E. cloacae and its potential as a therapeutic target. Our research showed that pathogenic strains of E. cloacae express higher levels of nagZ than colonizing strains, particularly in simulated infection environments. Deleting nagZ significantly reduced E. cloacae virulence in various infection models, including Galleria mellonella larvae, mice, and RAW264.7 cells. Moreover, nagZ knockout decreased the bacterium's ability to induce inflammatory factor levels, while complementing nagZ in knockout strains partially rescued this ability. Importantly, the absence of nagZ also enhanced the antibacterial efficacy of ceftazidime against E. cloacae. Conclusions: These findings underscore the crucial role of nagZ in E. cloacae pathogenesis and highlight its potential as a novel therapeutic target for treating infections caused by this pathogen. [ABSTRACT FROM AUTHOR]

The current mortality rates for breast cancer underscore the need for better prognostic tools; moreover, LIM and calponin homology domain 1 (LIMCH1), which is a protein with dual roles in cancer, is a promising candidate for investigation. This study employed an integrative approach combining bioinformatics analysis of The Cancer Genome Atlas (TCGA) cohort and clinical immunohistochemistry (IHC) cohort data. We analysed LIMCH1 expression patterns, its associations with clinicopathological features and prognosis, and its impact on the tumour immune microenvironment (TIME). Functional annotations and single-cell RNA sequencing (scRNA-seq) data were used to explore the underlying molecular mechanisms. Our analysis revealed that high LIMCH1 expression in breast cancer patients was significantly associated with unfavourable clinical outcomes and served as an independent prognostic indicator. The functional annotations revealed pathways related to carcinogenesis and metabolic reconfiguration, thus suggesting the role of LIMCH1 in tumour progression. Additionally, LIMCH1 expression was correlated with an immunosuppressive TIME characterized by increased numbers of M2 macrophages and reduced numbers of CD8 + T cells and NK cells. Finally, we developed a nomogram incorporating LIMCH1 expression for predicting overall survival rates, thus providing a clinically applicable tool. Our research elucidates the diverse functions of LIMCH1 in the pathogenesis of breast cancer, thus highlighting its potential utility as both a prognostic indicator and a therapeutic intervention. [ABSTRACT FROM AUTHOR]

Purpose: This study aims to elucidate the role of pituitary adenylate cyclase-activating polypeptide (PACAP) in Hunner-type Interstitial Cystitis (HIC) and evaluate its potential as a therapeutic target. Methods: Bladder tissue samples were obtained from HIC patients and normal bladder tissue from bladder cancer patients. PACAP expression was assessed through immunohistochemistry. An in vitro HIC model was established using LPS-induced SV-HUC1 cells. PACAP knockdown was performed using siRNA. The expression of inflammatory markers (IL-6, IL-1β, TNF-α) and fibrotic markers (fibronectin 1, TGF-β1, collagen I) was evaluated via qPCR, Western blot, and ELISA. Cell migration and proliferation were analyzed using wound healing and CCK-8 assays. Transcriptomic profiling was conducted to identify differentially expressed genes (DEGs) and explore their functional significance. Results: PACAP expression was significantly elevated in the bladder tissues of HIC patients. LPS stimulation of SV-HUC1 cells induced PACAP expression alongside increased levels of inflammatory cytokines, validating the inflammatory model. PACAP knockdown markedly suppressed IL-6, IL-1β, and TNF-α expression and attenuated LPS-induced fibrosis by reducing fibronectin 1, TGF-β1, and collagen I levels. Additionally, PACAP knockdown inhibited LPS-induced cell migration and proliferation, as evidenced by wound healing and CCK-8 assays. Transcriptomic analysis revealed distinct molecular alterations in HIC tissues, including PACAP upregulation, implicating it in HIC pathogenesis. Conclusion: PACAP plays a pivotal role in the inflammatory and fibrotic pathways of HIC. PACAP knockdown alleviates LPS-induced pathological responses, highlighting its potential as a novel therapeutic target. Further research is warranted to investigate PACAP's precise mechanisms in HIC and its translational application in clinical settings. [ABSTRACT FROM AUTHOR]

Background: Thoracotomy is a common treatment for non-small cell lung cancer (NSCLC). However, the significant trauma from this procedure can limit patients' postoperative prognosis. Therefore, it's crucial to find an easily detected indicator that can predict the prognosis of NSCLC patients undergoing thoracotomy. FAM83A-AS1 was hypothesized as a predictor for the therapeutic effectiveness of thoracotomy. We evaluated its correlation with patient outcomes and its significance in predicting postoperative prognosis, with the aim of providing a reference to improve postoperative prognosis of thoracotomy. Materials and methods: The study enrolled patients with NSCLC who underwent thoracotomy, and tissue samples were collected during surgery. Blood samples were collected preoperatively and three days postoperatively. PCR was used to analyze plasma FAM83A-AS1 levels. The significance of these levels in the patients' postoperative prognosis was evaluated via logistic regression and ROC analyses, with a follow-up period of six months. Results: FAM83A-AS1 was significantly upregulated in NSCLC and correlated with severe progression in patients. Thoracotomy suppressed FAM83A-AS1 expression and reduced CA50, CEA, and CYFRA21-1 levels. Postoperative plasma levels of FAM83A-AS1 positively correlated with CA50, CEA, and CYFRA21-1. Patients with worse prognoses had higher plasma FAM83A-AS1 levels. FAM83A-AS1 was identified as a risk factor for poor postoperative outcomes in NSCLC patients undergoing thoracotomy and could be used to identify patients at risk of worse prognosis. Conclusion: An increase in FAM83A-AS1 in NSCL indicates severe disease development and can serve as a biomarker associated with thoracotomy, predicting a poor prognosis. It provides a potential indicator for patient outcomes. [ABSTRACT FROM AUTHOR]

Objective To explore the relationship between PANoptosis and hepatic ischemia-reperfusion injury (HIRI), and to screen the key genes of PANoptosis in HIRI. Methods PANoptosis-related differentially expressed genes (PDG) were obtained through the Gene Expression Omnibus database and GeneCards database. Gene ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and Gene Set Enrichment Analysis (GSEA) were used to explore the biological pathways related to PDG. A protein-protein interaction network was constructed. Key genes were selected, and their diagnostic value was assessed and validated in the HIRI mice. Immune cell infiltration analysis was performed based on the cell-type identification by estimating relative subsets of RNA transcripts. Results A total of 16 PDG were identified. GO analysis showed that PDG were closely related to cellular metabolism. KEGG analysis indicated that PDG were mainly enriched in cellular death pathways such as apoptosis and immune-related signaling pathways such as the tumor necrosis factor signaling pathway. GSEA results showed that key genes were mainly enriched in immune-related signaling pathways such as the mitogen-activated protein kinase (MAPK) signaling pathway. Two key genes, DFFB and TNFSF10, were identified with high accuracy in diagnosing HIRI, with areas under the curve of 0.964 and 1.000, respectively. Immune infiltration analysis showed that the control group had more infiltration of resting natural killer cells, M2 macrophages, etc., while the HIRI group had more infiltration of M0 macrophages, neutrophils, and naive B cells. Real-time quantitative polymerase chain reaction results showed that compared with the Sham group, the relative expression of DFFB messenger RNA in liver tissue of HIRI group mice increased, and the relative expression of TNFSF10 messenger RNA decreased. Cibersort analysis showed that the infiltration abundance of naive B cells was positively correlated with DFFB expression (r=0.70, P=0.035), and the infiltration abundance of M2 macrophages was positively correlated with TNFSF10 expression (r=0.68, P=0.045). Conclusions PANoptosis-related genes DFFB and TNFSF10 may be potential biomarkers and therapeutic targets for HIRI. [ABSTRACT FROM AUTHOR]

Purpose: Colorectal cancer (CRC) is a leading cause of cancer-related mortality worldwide. The Fat mass and obesity-associated protein (FTO), a genetic variant associated with obesity, significantly impact the energetic metabolism of mechanical tumors. However, research on the function of FTO in CRC is scarce. Methods: Bioinformatics analysis of TCGA and UALCAN databases was conducted to examine FTO expression in CRC. Immunohistochemistry was used to assess FTO and PKM2 protein expression in clinical specimens. In vitro experiments utilized five human colon cancer cell lines and a normal colon epithelial cell line, with Western blotting and RT-PCR for protein and mRNA quantification, respectively, and lentiviral transfection to modulate FTO expression. Cellular behaviors such as proliferation, migration, invasion, and apoptosis were evaluated using various assays. Immunofluorescence and Seahorse Xfe96 metabolic analysis were employed to study PKM2 expression changes and glycolytic stress. The effects of PKM2 inhibition by shikonin on cell viability and glycolytic activity were assessed using CCK-8 assay and Seahorse analysis. Results: An upregulation of FTO was observed in colon cancer through data mining and analysis of pathological specimens. Besides, we discovered that the impact of FTO on colon cancer glycolysis has significant implications for colon proliferation, invasion, and metastasis. The protein expression of PKM2 and the intensity of fluorescence staining in the nucleus of PKM2 were detected to be increased in colon carcinoma cells with over-expression of FTO. Conclusion: FTO plays a significant role in CRC progression by regulating PKM2 and promoting glycolysis. [ABSTRACT FROM AUTHOR]

BACKGROUND: Currently, there is no drug that can completely cure osteoarthritis and its pathogenesis is still unclear. Circular RNAs (circRNAs) are differentially expressed in patients with osteoarthritis and are closely associated with various pathological processes in osteoarthritis. circRNAs play an important role in various physiological and pathological processes, such as chondrocyte homeostasis, extracellular matrix formation, and inflammatory response. OBJECTIVE: To mainly review the effects of circRNAs on pathological factors related to osteoarthritis, as well as the types and expression levels of circRNAs in osteoarthritis. METHODS: Related articles published from 1976 to August 2023 were retrieved from CNKI, WanFang, VIP, PubMed, Medline, Web of Science and Elsevier databases. The keywords were “osteoarthritis, circular RNA, non-coding RNA, synovial tissue, chondrocytes” in Chinese and English, respectively. All the relevant articles were screened, summarized, analyzed, and finally 69 papers were included in the review. RESULTS AND CONCLUSION: circRNAs are non-coding RNAs widely found in eukaryotic cells, with covalently closed continuous loop structure, but with no 5′ hat structure and 3′poly A tail, which are involved in multi-gene and multi-target regulatory networks and cannot be degraded by nucleic acid exonucleases (RNase R). circRNAs have a high abundance, high conservativeness and stability, and cell and tissue specificity. circRNAs have biological functions such as acting as molecular sponges for miRNAs, regulating linear RNA transcription and RNA shearing, interacting with RNA-bound proteins, and translating proteins. circRNAs regulate chondrocyte apoptosis and proliferation, degradation of cartilage extracellular matrix, and inflammation and other physiopathologic processes. circRNAs are expected to become biomarkers and potential therapeutic targets for clinical diagnosis and prognosis of osteoarthritis, and may become a new strategy for clinical treatment of osteoarthritis in the future. [ABSTRACT FROM AUTHOR]

Necroptosis is a critical process in intervertebral disc degeneration (IDD). This research is aimed at identifying key genes regulating necroptosis in IDD to provide a theoretical basis for early diagnosis and treatment. Transcriptome data from patients with IDD and normal samples were obtained from the GSE34095 and GSE124272 datasets of the Gene Expression Omnibus (GEO) public database. Necroptosis‐related genes (NRGs) were sourced from the GeneCards database and literature. Differentially expressed necroptosis‐related genes (DE‐NRGs) in IDD were identified by intersecting these sources. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) were used for gene annotation analysis. The receiver operating characteristic (ROC) curve and nomogram analyses assessed the diagnostic efficiency of DE‐NRGs. The miRWalk and starBase databases helped construct the competing endogenous RNA (ceRNA) regulatory network of DE‐NRGs. We identified 517 differential genes in tissue and 2974 in blood, with 62 genes in common. DE‐NRGs (AIFM1, CCT8, HNRNPA1, KHDRBS1, SERBP1) were identified by intersecting NRGs with these 62 common genes. The ROC curve showed an area under the curve (AUC) > 0.70 for DE‐NRGs, and the nomogram indicated that a higher DE‐NRG score correlates with a higher risk of IDD. CCT8, KHDRBS1, and AIFM1 emerged as potential therapeutic targets for IDD through target drug prediction. qRT‐PCR (quantitative reverse transcription polymerase chain reaction), Western blot, and immunohistochemistry confirmed the expression of AIFM1, CCT8, HNRNPA1, KHDRBS1, and SERBP1 in patients' nucleus pulposus tissue, suggesting these genes as key targets for IDD risk assessment and drug therapy. [ABSTRACT FROM AUTHOR]

Osteosarcoma is the most common type of bone cancer. Some patients eventually develop recurrent or metastatic diseases and treatment options are extremely limited. Discoidin domain receptor 1 (DDR1) is a unique collagen‐activated tyrosine kinase that participates in various human diseases, including cancer. DDR1 promotes adhesion, proliferation, differentiation, migration, and metastasis of cancer cells. The purpose of this study is to assess the expression, clinical prognostic relationship and functional roles of DDR1 in osteosarcoma. The correlation between DDR1 expression in tumor tissues and clinicopathological features, and prognosis was assessed via immunohistochemical staining of a unique tissue microarray (TMA) constructed from osteosarcoma specimens. DDR1‐specific siRNA and a highly selective DDR1 inhibitor, 7rh, were applied to determine the impact of DDR1 expression on osteosarcoma cell growth and proliferation. Furthermore, the effect of DDR1 inhibition on clonogenicity was evaluated using a clonogenic assay, and a 3D cell culture model was used to mimic DDR1 effects in an in vivo environment. The results demonstrate that higher DDR1 expression significantly correlates with recurrence, metastasis, and shorter overall survival in osteosarcoma patients. The expression of DDR1 is also inversely correlated to the response to neoadjuvant chemotherapy. Therapeutically, DDR1 knockdown with siRNA or selective inhibition with 7rh decreases the proliferation and growth of osteosarcoma cells. In conclusion, our study supports DDR1 expression as an independent predictor of poor prognosis and a promising therapeutic target for osteosarcoma. [ABSTRACT FROM AUTHOR]

There is increasing interest in the potential therapeutic role of 5-HT (serotonin) in the treatment of neurodegenerative diseases, which are characterized by the progressive degeneration and death of nerve cells. 5-HT is a vital neurotransmitter that plays a central role in regulating mood, cognition, and various physiological processes in the body. Disruptions in the 5-HT system have been linked to several neurological and psychiatric disorders, making it an attractive target for therapeutic intervention. Although the exact causes of neurodegenerative diseases such as Alzheimer's disease (AD), Parkinson's disease (PD), and amyotrophic lateral sclerosis (ALS) are not fully understood, researchers believe that regulating the 5-HT system could help alleviate symptoms and potentially slow the progression of these diseases. Here, we delve into the potential of harnessing 5-HT as a therapeutic target for the treatment of neurodegenerative diseases. It is important to note that the current clinical drugs targeting 5-HT are still limited in the treatment of these complex diseases. Therefore, further research and clinical trials are needed to evaluate the feasibility and effectiveness of its clinical application. [ABSTRACT FROM AUTHOR]

Ischemic heart disease (IHD) remains one of the most prominent causes of mortality and morbidity globally, and the risk of ischemia–reperfusion injury is becoming more severe and constant. This underscores the need to develop new methods to protect the heart from damage. DJ‐1 is a multifunctional intracellular protein encoded by the PARK7 gene that plays roles in processes including the control of autophagy, the preservation of mitochondrial integrity, the prevention of apoptosis, and the elimination of oxidative stress. DJ‐1 has recently been the focus of growing interest as a target molecule relevant to treating myocardial ischemia–reperfusion injury due to its protective properties and its role in cellular response mechanisms. Consistently, DJ‐1‐related interventions, such as its exogenous administration or the use of pharmacological agents, have been demonstrated to help protect the myocardium from ischemia–reperfusion injury and associated adverse outcomes. This review provides an overview of DJ‐1 and its therapeutic relevance in the myocardium in the setting of ischemia and reperfusion. [ABSTRACT FROM AUTHOR]

Diabetic kidney disease (DKD), a prevalent complication of diabetes mellitus, is often associated with acute kidney injury (AKI). Thus, the development of preventive and therapeutic strategies is crucial for delaying the progression of AKI and DKD. The GSE183276 dataset, comprising the data of 20 healthy controls and 12 patients with AKI, was downloaded from the Gene Expression Omnibus (GEO) database to analyze the AKI group. For analyzing the DKD group, the GSE131822 dataset, comprising the data of 3 healthy controls and 3 patients with DKD, was downloaded from the GEO database. The common differentially expressed genes (DEGs) in renal tubular epithelial cells (TECs) were subjected to enrichment analyses. Next, a protein-protein interaction (PPI) network was constructed using the Search Tool for the Retrieval of Interacting Genes database to analyze gene-related regulatory networks. Finally, the AKI animal models and the DKD and AKI cell models were established, and the reliability of the identified genes was validated using quantitative real-time polymerase chain reaction analysis. Functional analysis was performed with 40 common DEGs in TECs. Eight hub genes were identified using the PPI and gene-related networks. Finally, validation experiments with the in vivo animal model and the in vitro cellular model revealed the four common DEGs. Four DEGs that share molecular mechanisms in the pathogenesis of DKD and AKI were identified. In particular, the expression of Integrin Subunit Beta 6(ITGB6), a hub and commonly upregulated gene, was upregulated in the in vitro models. ITGB6 may serve as a biomarker for early AKI diagnosis in patients with DKD and as a target for early intervention therapies. [ABSTRACT FROM AUTHOR]

Background: Despite growing knowledge regarding the pathogenesis of autoimmune diseases (ADs) onset, the current treatment remains unsatisfactory. This study aimed to identify innovative therapeutic targets for ADs through various analytical approaches. Research design and methods: Utilizing Mendelian randomization, Bayesian co-localization, phenotype scanning, and protein–protein interaction network, we explored potential therapeutic targets for 14 ADs and externally validated our preliminary findings. Results: This study identified 12 circulating proteins as potential therapeutic targets for six ADs. Specifically, IL12B was judged to be a risk factor for ankylosing spondylitis (p = 1.61E − 07). TYMP (p = 6.28E − 06) was identified as a protective factor for ulcerative colitis. For Crohn's disease, ERAP2 (p = 4.47E − 14), HP (p = 2.08E − 05), and RSPO3 (p = 6.52E − 07), were identified as facilitators, whereas FLRT3 (p = 3.42E − 07) had a protective effect. In rheumatoid arthritis, SWAP70 (p = 3.26E − 10), SIGLEC6 (p = 2.47E − 05), ISG15 (p = 3.69E − 05), and FCRL3 (p = 1.10E − 10) were identified as risk factors. B4GALT1 (p = 6.59E − 05) was associated with a lower risk of Type 1 diabetes (T1D). Interestingly, CTSH was identified as a protective factor for narcolepsy (p = 1.58E − 09) but a risk factor for T1D (p = 7.36E − 11), respectively. External validation supported the associations of eight of these proteins with three ADs. Conclusions: Our integrated study identified 12 potential therapeutic targets for ADs and provided novel insights into future drug development for ADs. [ABSTRACT FROM AUTHOR]

Osteosarcoma (OS) represents the primary form of bone cancer observed in paediatric and adolescent populations. Nearly 10%–15% of patients have metastases at diagnosis, and the 5-year survival rate was less than 20%. Although numerous investigators have offered significant efforts, the survival rates for patients with OS have remained almost unchanged over the past three decades. The most pervasive and abundant modification of internal transcripts in eukaryotic messenger RNAs (mRNAs) is N6-methyladenosine (m6A), and it is regulated by m6A methylation regulators. A number of recent studies have demonstrated that m6A modifications can regulate the biological activities of tumour cells and are intimately linked with cancer development, prognosis, drug resistance, and therapy. N6-methyladenosine modification of Non-coding RNA (ncRNA) has likewise shown a broad potential in gene regulation and tumor biology. Epigenetic changes induced by mRNAs and ncRNAs methylation are important for a better understanding of OS development and targeted drug development. Therefore, this paper summarises the biological functions of m6A-modified regulators in osteosarcoma and the role of mutual regulation between m6A and ncRNAs in osteosarcoma. Furthermore, the potential clinical applications of m6A modifications in OS are presented for consideration. It provides new directions for the future research and clinical treatment strategies of osteosarcoma. • m6A regulators' biological functions in Osteosarcoma. • Effect of m6A regulators on radiotherapy resistance in osteosarcoma. • NcRNA in osteosarcoma. • Interplay between m6A and ncRNAs in osteosarcoma. • m6A and miRNA, circRNA, lncRNA. [ABSTRACT FROM AUTHOR]

Background: Previous research has demonstrated correlations between the complex types and functions of brain cells and the etiology of glioma. However, the causal relationship between gene expression regulation in specific brain cell types and glioma risk, along with its therapeutic implications, remains underexplored. Methods: Utilizing brain cell type‐specific cis‐expression quantitative trait loci (cis‐eQTLs) and glioma genome‐wide association study (GWAS) datasets in conjunction with Mendelian randomization (MR) and colocalization analyses, we conducted a systematic investigation to determine whether an association exists between the gene expression of specific brain cell types and the susceptibility to glioma, including its subtypes. Additionally, the potential pathogenicity was explored utilizing mediation and bioinformatics analyses. This exploration ultimately led to the identification of a series of brain cell‐specific therapeutic targets. Results: A total of 110 statistically significant and robust associations were identified through MR analysis, with most genes exhibiting causal effects exclusively in specific brain cell types or glioma subtypes. Bayesian colocalization analysis validated 36 associations involving 26 genes as potential brain cell‐specific therapeutic targets. Mediation analysis revealed genes indirectly influencing glioma risk via telomere length. Bioinformatics analysis highlighted the involvement of these genes in glioma pathogenesis pathways and supported their enrichment in specific brain cell types. Conclusions: This study, employing an integrated approach, demonstrated the genetic susceptibility between brain cell‐specific gene expression and the risk of glioma and its subtypes. Its findings offer novel insights into glioma etiology and underscore potential therapeutic targets specific to brain cell types. [ABSTRACT FROM AUTHOR]

HIF-1α plays a crucial regulatory role in vascular calcification (VC), primarily influencing the osteogenic differentiation of VSMCs through oxygen-sensing mechanisms. Under hypoxic conditions, the stability of HIF-1α increases, avoiding PHD and VHL protein-mediated degradation, which promotes its accumulation in cells and then activates gene expressions related to calcification. Additionally, HIF-1α modulates the metabolic state of VSMCs by regulating the pathways that govern the switch between glycolysis and oxidative phosphorylation, thereby further advancing the calcification process. The interaction between HIF-1α and other signaling pathways, such as nuclear factor-κB, Notch, and Wnt/β-catenin, creates a complex regulatory network that serves as a critical driving force in VC. Therefore, a deeper understanding of the role and regulatory mechanism of the HIF-1α signaling during the development and progression of VC is of great significance, as it is not only a key molecular marker for understanding the pathological mechanisms of VC but also represents a promising target for future anti-calcification therapies. [ABSTRACT FROM AUTHOR]

Cluster of differentiation 36 (CD36) is a multiligand receptor with important roles in lipid metabolism, angiogenesis and innate immunity, and its diverse effects may depend on the binding of specific ligands in different contexts. CD36 is expressed not only on immune cells in the tumor microenvironment (TME) but also on some hematopoietic cells. CD36 is associated with the growth, metastasis and drug resistance in some hematologic tumors, such as leukemia, lymphoma and myelodysplastic syndrome. Currently, some targeted therapeutic agents against CD36 have been developed, such as anti-CD36 antibodies, CD36 antagonists (small molecules) and CD36 expression inhibitors. This paper not only innovatively addresses the role of CD36 in some hematopoietic cells, such as erythrocytes, hematopoietic stem cells and platelets, but also pays special attention to the role of CD36 in the development of hematologic tumors, and suggests that CD36 may be a potential cancer therapeutic target in hematologic tumors. [ABSTRACT FROM AUTHOR]

It is crucial to identify the metabolic risk factors of cerebral small vessel disease (CSVD) and implement timely and systematic management. Currently, the correlation between residual metabolic risk factors and CSVD is still controversial, and there’s a lack of evidence-based support for the clinical efficacy of targeting risk factors in treating CSVD. This paper comprehensively analyzes the correlation between residual metabolic risk factors such as inflammation, gut microbiota dysbiosis, hyperhomocysteinemia, and hyperuricemia with the occurrence and development of CSVD. It further explores potential therapeutic options targeting metabolic risk factors, emphasizes the important role of metabolomics in the discovery of novel metabolic biomarkers and the establishment of risk prediction models for CSVD, and looks forward to future research directions, to provide a theoretical basis for the early diagnosis, mechanism exploration, risk factor management, and comprehensive multidisciplinary management of CSVD. [ABSTRACT FROM AUTHOR]

MicroRNAs (miRNA) are a class of non-coding RNA molecules that regulate gene expression transcriptionally, playing crucial roles in various cellular processes. Increasing investigation indicate that the Mycobacterium tuberculosis (Mtb) infection alters the expression of numerous miRNAs in host cells, thereby influencing downstream pathways involved in immune responses against tuberculosis (TB) . This review summarizes how changes in miRNA levels post Mtb infection regulate autophagy, apoptosis, and inflammatory responses. It highlights that miRNAs may serve as potential therapeutic targets for TB, providing insights for further research and clinical applications of miRNA in TB. [ABSTRACT FROM AUTHOR]

UBE2C (Ubiquitination-binding enzyme 2C), one of the E2 enzymes encoded in the human genome, is a component of the ubiquitin proteasome system and plays a pivotal role in regulating cell cycle progression. Moreover, UBE2C is highly expressed and may play a pivotal role in both high-incidence and high-mortality malignancies, including lung cancers, breast cancers, and esophageal cancers. UBE2C influences a number of key processes, including cell cycle progression, tumor invasion and metastasis, proliferation, and drug resistance. However, few articles have systematically summarized the role of UBE2C in cancer. The aim of this review is to describe the structure and function of UBE2C, focusing on the current status of UBE2C research in malignant tumors. Furthermore, this review presents the potential of UBE2C as a new therapeutic target and a diagnostic and prognostic biomarker. Finally, future research directions for UBE2C are proposed. It is of great value to explore the mechanism of action of UBE2C in the tumor microenvironment (TME). A comprehensive and coherent comprehension of UBE2C will undoubtedly facilitate its transition from fundamental research to clinical applications. [ABSTRACT FROM AUTHOR]

Asthma is a heterogeneous chronic lung disease that affects nearly 340 million people globally. Airway hyperresponsiveness, remodeling (thickening and fibrosis), and mucus hypersecretion are some hallmarks of asthma. With several current treatments having serious side effects from long-term use and a proportion of patients with uncontrolled asthma, there is an urgent need for new therapies. With an increasing understanding of asthma pathophysiology, there is a recognized need to target therapies to specific cell types of the airway, which necessitates the identification of delivery systems that can overcome increased mucus and thickened airways. Nanoparticles (NPs) that are highly customizable (material, size, charge, and surface modification) are a potential solution for delivery systems of a wide variety of cargoes (nucleic acids, proteins, and/or small molecules), as well as sole therapeutics for asthma. However, there is a need to consider the safety of the NPs in terms of potential for inflammation, toxicity, nonspecific targets, and accumulation in organs. Ongoing clinical trials using NPs, some FDA-approved for therapeutics in other diseases, provide confidence regarding the potential safety and efficacy of NPs in asthma treatment. This review highlights the current state of the use of NPs in asthma, identifying opportunities for further improvements in NP design and utilization for targeting this chronic lung disease. [ABSTRACT FROM AUTHOR]

Background: The vitreous humor serves as a window into the physiological and pathological processes of the eye, particularly the retina. Diabetic retinopathy (DR), a leading cause of blindness, involves hyperglycemia-induced damage to retinal cells, leading to ischemia and elevated nitric oxide levels, culminating in vascular proliferation. Rhegmatogenous retinal detachment (RD) results from a break in the neuroretina, triggering ischemia, photoreceptor death, and cellular proliferation. Proliferative vitreoretinopathy (PVR) further complicates these conditions through fibrous proliferation. Despite their prevalence and potential for blindness, our understanding of the molecular mechanisms underlying these vitreoretinal diseases is incomplete. Methods and results: To elucidate disease mechanisms and identify potential therapeutic targets, we conducted a comparative proteomic analysis of vitreous samples from DR, RD, and macular pucker (P) patients, which were chosen as controls. LC–MS analysis identified 988 quantifiable proteins, with distinct clustering observed among disease groups. Differential expression analysis revealed 202 proteins in RD vs. P and 167 in DR vs. P, highlighting distinct proteomic signatures. Enrichment analysis identified glucose metabolism as an altered process in both diseases, suggesting common pathways despite differing etiologies. Notably, aldo–keto reductase family 1 member B1 (AKR1B1) has emerged as a potential key player in both DR and RD, indicating its role in glucose metabolism and inflammation. In silico drug screening identified diclofenac, an approved ophthalmic non-steroidal anti-inflammatory drug (NSAID), as a potential therapeutic agent targeting AKR1B1. Conclusion: Our study revealed distinct proteomic signatures and common pathways in vitreoretinal diseases, highlighting AKR1B1 as a potential therapeutic target. Using diclofenac during diagnosis and postoperative care for diabetic retinopathy or rhegmatogenous retinal detachment may reduce complications, lower costs, and improve quality of life. Future research will focus on confirming AKR1B1's role in vitreoretinal diseases and understanding diclofenac's mechanism of action. [ABSTRACT FROM AUTHOR]

Background: Cholangiocarcinoma (CCA) is an aggressive malignancy with limited treatment options and poor prognosis. Platelet-Derived Growth Factor CC (PDGF-CC) has been implicated in the progression of various tumors, but its specific role in CCA is not well understood. This study aims to investigate the expression and function of PDGF-CC in CCA and evaluate its potential as a therapeutic target. Methods: We conducted gene expression analysis using the GEPIA database to compare PDGF-CC mRNA levels in CCA tissues and normal tissues. Serum samples from CCA patients were analyzed for PDGF-CC protein levels, and immunohistochemistry was used to assess PDGF-CC expression in tissue samples. The impact of PDGF-CC on CCA cell behavior was examined by knocking out PDGF-CC in HuCCT1 and QBC939 cell lines, followed by assessments of cell proliferation, migration, invasion, and colony formation in vitro. Additionally, the effects of PDGF-CC knockout were evaluated in xenograft models. The therapeutic potential of PDGF-CC inhibition was further explored using pharmacological inhibitors and antibodies. Results: PDGF-CC mRNA and protein levels were significantly elevated in CCA tissues and patient sera compared to normal controls. Immunohistochemical analysis confirmed increased PDGF-CC expression in CCA tissues. High PDGF-CC expression correlated with poor overall survival in CCA patients, as shown by Kaplan-Meier analysis. Functional assays revealed that PDGF-CC knockout significantly reduced proliferation, migration, invasion, and colony formation in HuCCT1 and QBC939 cells, the lines with the highest PDGF-CC levels. In vivo, PDGF-CC knockout markedly decreased tumor growth in xenograft models. Pharmacological inhibition of PDGF-CC mirrored the effects of genetic knockout, suggesting it as a viable therapeutic strategy. Conclusions: This study underscores the critical role of PDGF-CC in CCA progression and supports the potential of PDGF-CC inhibitors as a therapeutic approach. Given the association between high PDGF-CC expression and poor prognosis, targeting PDGF-CC may improve outcomes for CCA patients. Further clinical investigations are warranted to develop PDGF-CC-targeted therapies for CCA. [ABSTRACT FROM AUTHOR]

RNA‐modifying proteins, classified as "writers," "erasers," and "readers," dynamically modulate RNA by adding, removing, or interpreting chemical groups, thereby influencing RNA stability, functionality, and interactions. To date, over 170 distinct RNA chemical modifications and more than 100 RNA‐modifying enzymes have been identified, with ongoing research expanding these numbers. Although significant progress has been made in understanding RNA modification, the regulatory mechanisms that govern RNA‐modifying proteins themselves remain insufficiently explored. Post‐translational modifications (PTMs) such as phosphorylation, ubiquitination, and acetylation are crucial in modulating the function and behavior of these proteins. However, the full extent of PTM influence on RNA‐modifying proteins and their role in disease development remains to be fully elucidated. This review addresses these gaps by offering a comprehensive analysis of the roles PTMs play in regulating RNA‐modifying proteins. Mechanistic insights are provided into how these modifications alter biological processes, contribute to cellular function, and drive disease progression. In addition, the current research landscape is examined, highlighting the therapeutic potential of targeting PTMs on RNA‐modifying proteins for precision medicine. By advancing understanding of these regulatory networks, this review seeks to facilitate the development of more effective therapeutic strategies and inspire future research in the critical area of PTMs in RNA‐modifying proteins. [ABSTRACT FROM AUTHOR]

Targeted vasopeptide therapies have significantly advanced the management of pulmonary arterial hypertension (PAH). However, due to insufficient preclinical evidence regarding the involvement of the endothelin-1 (ET-1) pathway in chronic thromboembolic pulmonary hypertension (CTEPH) pathophysiology, the potential of ET-1 receptor antagonism in treating CTEPH remains uncertain. In this study, we investigated the role of the ET-1 pathway in CTEPH microvasculopathy using a multifaceted approach. Plasma ET-1 levels were measured in a cohort of 59 CTEPH patients and 41 healthy controls. Additionally, we evaluated the expression of key ET-1 pathway members in pulmonary explants from CTEPH, idiopathic PAH, and control patients. We used an in vitro system to test the hypothesis that the turbulent flow, observed near the vascular obstructions pathognomonic of CTEPH, enhances ET-1 expression. Our findings were further validated in vivo using a CTEPH piglet model that contains distinct regions representing pre- and post-thrombus lung territories. We found a twofold increase in circulating ET-1 levels in CTEPH patients compared to healthy subjects. Pulmonary explants from CTEPH patients exhibited pronounced overexpression of ET-1, endothelin receptor A (ETA), and phosphorylated myosin light chain (p-MLC) in muscularized pulmonary microvessels, suggesting heightened vascular contraction. In vitro experiments showed that turbulent flow facilitates ET-1 secretion compared to laminar flow regions. Additionally, in the CTEPH piglet model, elevated plasma ET-1 levels were observed compared to controls. Immunofluorescence and confocal microscopy analyses confirmed increased ETA and p-MLC in remodeled arteries from both pulmonary territories. However, ET-1 protein elevation was exclusively observed in the obstructed territory. These findings collectively indicate impaired vascular tone in microvessels of CTEPH patients and the CTEPH piglet model. Furthermore, our data implicates the ET-1 pathway in microvasculopathy, with turbulent flow playing a pathological role. These insights underscore the potential utility of ET-1 receptor antagonists as a promising therapeutic approach for CTEPH treatment. [ABSTRACT FROM AUTHOR]

Background: Breast cancer is a heterogeneous disease with diverse molecular subtypes, underscoring a better understanding of its molecular features and underlying regulatory mechanisms. Therefore, identifying novel prognostic biomarkers and therapeutic targets is crucial for advancing the current standard of care for breast cancer patients. Methods: Ninety-six formalin-fixed paraffin-embedded (FFPE) breast cancer samples underwent miRNAome profiling using QIAseq microRNA library kit and sequencing on Illumina platform. Mature miRNA quantification was conducted using CLC Genomics Workbench v21.0.5, while Relapse-free survival (RFS) analysis was conducted using RStudio 2023.09.1. Gain-of-function studies were conducted using miRNA mimics, while the effects of miRNA exogenous expression on cancer hallmark were assessed using 2-dimentional (2D) proliferation assay, three-dimensional (3D) organotypic culture, and live-dead staining. TargetScan database and Ingenuity Pathway Analysis (IPA) were used for miRNA target identification. Results: Hierarchical clustering based on miRNA expression revealed distinct patterns in relation to PAM50 classification and identified miRNAs panels associated with luminal, HER2, and basal subtypes. hsa-miR-5683 emerged as a potential prognostic biomarker, showing a favorable correlation with RFS and suppressing tumorigenicity under 2D and 3D conditions in triple-negative breast cancer (TNBC) models. Findings were further extended to the MCF7 hormone receptor positive (HR+) model. Transcriptomic profiling of hsa-miR-5683 overexpressing TNBC cells revealed its potential role in key oncogenic pathways. Integration of downregulated genes and CRISPR-Cas9 perturbational effects identified ACLY, RACGAP1, AK4, MRPL51, CYB5B, MKRN1, TMEM230, NUP54, ANAPC13, PGAM1, and SOD1 as bona fide gene targets for hsa-miR-5683. Conclusions: Our data provides comprehensive miRNA expression atlas in breast cancer subtypes and underscores the prognostic and therapeutic significance of numerous miRNAs, including hsa-miR-5683 in TNBC. The identified gene targets unravel the intricate regulatory network in TNBC progression, suggesting promising avenues for further research and targeted therapeutic interventions. [ABSTRACT FROM AUTHOR]

Balancing the tradeoff between quantity and quality of phenotypic data is critical in omics studies. Measurements below the limit of quantification (BLQ) are often tagged in quality control fields, but these flags are currently underutilized in human genetics studies. Extreme phenotype sampling is advantageous for mapping rare variant effects. We hypothesize that genetic drivers, along with environmental and technical factors, contribute to the presence of BLQ flags. Here, we introduce "hypometric genetics" (hMG) analysis and uncover a genetic basis for BLQ flags, indicating an additional source of genetic signal for genetic discovery, especially from phenotypic extremes. Applying our hMG approach to n = 227,469 UK Biobank individuals with metabolomic profiles, we reveal more than 5% heritability for BLQ flags and report biologically relevant associations, for example, at APOC3 , APOA5 , and PDE3B loci. For common variants, polygenic scores trained only for BLQ flags predict the corresponding quantitative traits with 91% accuracy, validating the genetic basis. For rare coding variant associations, we find an asymmetric 65.4% higher enrichment of metabolite-lowering associations for BLQ flags, highlighting the impact of putative loss-of-function variants with large effects on phenotypic extremes. Joint analysis of binarized BLQ flags and the corresponding quantitative metabolite measurements improves power in Bayesian rare variant aggregation tests, resulting in an average of 181% more prioritized genes. Our approach is broadly applicable to omics profiling. Overall, our results underscore the benefit of integrating quality control flags and quantitative measurements and highlight the advantage of joint analysis of population-based samples and phenotypic extremes in human genetics studies. [Display omitted] Tanigawa and Kellis introduce "hypometric genetics," studying the genetic basis of binarized traits representing the presence of below-the-limit-of-quantification (BLQ) quality control indicators. Their joint analysis of BLQ and quantitative traits leads to improved power in genetic discovery, highlighting the value of considering population-based samples and phenotypic extremes in genetic studies. [ABSTRACT FROM AUTHOR]

The transcription repressor REST in the dorsal root ganglion (DRG) is upregulated by peripheral nerve injury and promotes the development of chronic pain. However, the genes targeted by REST in neuropathic pain development remain unclear. The expression levels of four opioid receptor genes (Oprm1, Oprd1, Oprl1 and Oprk1) and the cannabinoid CB1 receptor (Cnr1) gene in the DRG regulate nociception. In this study, we determined the role of REST in controlling their expression in the DRG induced by spared nerve injury (SNI). SNI induced chronic pain hypersensitivity in wild-type mice and was accompanied by increased levels of Rest transcript and protein. Transcriptomic analyses of wild-type mouse DRGs suggested that SNI upregulates the expression of Rest transcripts and downregulates the transcripts of all four opioid receptor genes and the Cnr1 gene. Quantitative reverse transcription polymerase chain reaction analyses of these tissues validated these results. Analysis of publicly available bioinformatic data suggested that REST binds to the promoter regions of Oprm1 and Cnr1. Chromatin immunoprecipitation analyses indicated the presence of REST at these promoters. Full-length Rest conditional knockout in primary sensory neurons reduced SNI-induced pain hypersensitivity and rescued the SNI-induced reduction in the expression of Oprd1 and Cnr1 in mouse DRG. Our results suggest that nerve injury represses the transcription of at least the Oprd1 and Cnr1 genes via REST in primary sensory neurons and that REST is a potential therapeutic target for neuropathic pain. Thus, inhibiting REST activity could potentially reduce chronic neuropathic pain and augment opioid/cannabinoid analgesic actions by increasing the transcription of Oprd1 and Cnr1 genes in DRG neurons. [ABSTRACT FROM AUTHOR]

Diabetic foot ulcer (DFU) is a chronic and serious complication of diabetes mellitus. It is mainly caused by hyperglycaemia, diabetic peripheral vasculopathy and diabetic peripheral neuropathy. These conditions result in ulceration of foot tissues and chronic wounds. If left untreated, DFU can lead to amputation or even endanger the patient's life. Single‐cell RNA sequencing (scRNA‐seq) is a technique used to identify and characterise transcriptional subpopulations at the single‐cell level. It provides insight into cellular function and the molecular drivers of disease. The objective of this paper is to examine the subpopulations, genes and molecules of cells associated with chronic wounds of diabetic foot by using scRNA‐seq. The paper aims to explore the wound‐healing mechanism of DFU from three aspects: inflammation, angiogenesis and extracellular matrix remodelling. The goal is to gain a better understanding of the mechanism of DFU wound healing and identify possible DFU therapeutic targets, providing new insights for the application of DFU personalised therapy. [ABSTRACT FROM AUTHOR]

Mitochondria are dynamic organelles that continuously undergo fusion/fission to maintain normal cell physiological activities and energy metabolism. When mitochondrial dynamics is unbalanced, mitochondrial homeostasis is broken, thus damaging mitochondrial function. Accumulating evidence demonstrates that impairment in mitochondrial dynamics leads to lung tissue injury and pulmonary disease progression in a variety of disease models, including inflammatory responses, apoptosis, and barrier breakdown, and that the role of mitochondrial dynamics varies among pulmonary diseases. These findings suggest that modulation of mitochondrial dynamics may be considered as a valid therapeutic strategy in pulmonary diseases. In this review, we discuss the current evidence on the role of mitochondrial dynamics in pulmonary diseases, with a particular focus on its underlying mechanisms in the development of acute lung injury (ALI)/acute respiratory distress syndrome (ARDS), chronic obstructive pulmonary disease (COPD), asthma, pulmonary fibrosis (PF), pulmonary arterial hypertension (PAH), lung cancer and bronchopulmonary dysplasia (BPD), and outline effective drugs targeting mitochondrial dynamics‐related proteins, highlighting the great potential of targeting mitochondrial dynamics in the treatment of pulmonary disease. [ABSTRACT FROM AUTHOR]

• SHTN1 had been demonstrated for the first time as a diagnostic and prognostic marker for bladder cancer. • SHTN1 was shown for the first time to be more highly expressed in high-grade bladder cancer. and to be associated with immune cells and the tumor microenvironment. • It had been demonstrated for the first time SHTN1 was associated with immune cells and the tumor microenvironment. Gene therapy in bladder cancer (BLCA) remains an area ripe for exploration. Recent studies have highlighted the crucial role of SHTN1 in the initiation and progression of various cancers and SHTN1 may have interacted with the FGFR gene. However, its specific function in BLCA remains unclear. We investigated the association between SHTN1 expression and prognosis, immune infiltration, and the tumor microenvironment (TME) across multiple malignancies using 433 BLCA samples from The Cancer Genome Atlas (TCGA). Differential gene expression analysis, functional annotation via Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and Gene Set Enrichment Analysis (GSEA) were performed for SHTN1-related genes by using R packages. Immune response and TME scores, along with drug sensitivity profiles of SHTN1, were analyzed using R packages. Immunohistochemistry (IHC) and western blotting were conducted to assess SHTN1 expression in surgical specimens from BLCA patients.CCK8 assay and cells wound healing assay were performed.The bioinformatics was analyzed by R software. Significant differences were evaluated using unpaired t test. SHTN1 expression levels were significantly elevated in BLCA associated with poor prognosis (p < 0.01). Receiver operating characteristic (ROC) curves and nomograms demonstrated the diagnostic and prognostic efficacy of SHTN1 in BLCA. Notably, SHTN1 expression was higher in high-grade BLCA compared to lower-grade (p = 5.6e-10), a finding corroborated by IHC and western blotting. Pathway enrichment analysis revealed significant involvement of the Neuroactive ligand-receptor interaction and Chemical carcinogenesis - DNA adducts signaling pathways among SHTN1 differentially expressed genes. In terms of immune infiltration, T cells CD8, T cells follicular helper, and dendritic cells were predominant in the SHTN1 low-expression group, whereas macrophages M0 and M2, and mast cells were predominant in the high-expression group. Multivariate Cox regression analysis identified SHTN1 as an independent prognostic factor for overall survival (HR = 2.93; 95 % CI = 1.40–6.13; p = 0.004).CCK8 and wound healing experiments showed that SHTN1 knockdown reduced the cell proliferation and migration. Western blot showed that the EMT pathway was clearly associated with SHTN1. Our findings suggest that SHTN1 holds promise as a prognostic and diagnostic biomarker for BLCA. Moreover, it is closely associated with elevated immune infiltration and distinct characteristics of the tumor microenvironment in BLCA. [ABSTRACT FROM AUTHOR]

Objective To analyze the gene expression profiles of gefitinib-sensitive and drug-resistant non-small cell lung cancer (NSCLC) cells in GEO database by bioinformatics, to study the potential key genes leading to acquired drug resistance of NSCLC, and to provide new ideas for the prognosis evaluation of patients with drug-resistant NSCLC. Methods The GEO2R network tool was used to analyze the GSE123066 and GSE83666 data sets to identify differentially expressed genes (DEGs). The key candidate genes were identified by comparing the DEGs between the two groups of data through the Wayne diagram, and then GO analysis. KEGG analysis and protein-protein interaction (PPI) analysis were performed on the candidate genes. The clinical prognosis analysis and expression level analysis of tumor tissues and different stages were performed on the obtained genes. Results A total of 46 core DEGs were significantly associated with drug-resistant NSCLC. Cytoscape identified eight key genes that play an important role in the progression of gefitinib resistance in NSCLC cells, namely SOD2, GADD45A, NCF2, LOX, CYR61, SOX2, JUP and MUC1, respectively. Among them, SOD2 was highly correlated with gefitinib resistance in NSCLC. Conclusion SOD2 may be the key genes leading to acquired drug resistance of NSCLC cells to gefitinib, and their high expression is associated with poor prognosis of NSCLC, indicating that SOD2 may be potential therapeutic targets with clinical application value in the future. [ABSTRACT FROM AUTHOR]

Purpose: Targeted therapy development in soft tissue sarcoma (STS) has been burdened by the heterogeneity of this group of rare tumors. B7 homolog 3 protein (B7-H3) is a molecule in the same family as programmed death-ligand 1 (PD-L1). It has limited expression in noncancerous tissues and is overexpressed in many cancers, making it an attractive target for cancer therapy, and clinical trials targeting B7-H3 are actively underway. While available data demonstrate high expression levels of B7-H3 in individual sarcoma subtypes, its expression patterns across STS subtypes are not well described. The purpose of this study was to characterize the expression patterns of B7-H3 in STS. Patients and methods: This retrospective analysis evaluated STS tumor specimens from patients with a variety of different subtypes. Specimens were evaluated by immunohistochemistry (IHC) for expression and staining pattern of B7-H3 both in tumors and in associated vasculature. Results: Specimens from 153 sarcoma patients included 15 different STS subtypes. B7-H3 was broadly expressed in 97% of samples (95% CI 0.93–0.99) and 69.2% demonstrated high levels of B7-H3 expression (95% CI 0.61–0.76). No significant association between B7-H3 positivity or expression level and prior treatment(s), tumor size, tumor grade, or patient age. B7-H3 positivity in vessels was found in 94.7% (145/153) of samples. In tumors that had been previously assessed for PD-L1 and PD-1, there was no correlation between B7-H3 positivity or expression and the positivity or expression level of PD-L1 or PD-1. Conclusion: These data show high levels of B7-H3 positivity across soft tissue sarcoma subtypes, suggesting its feasibility as a therapeutic target for future sarcoma treatments. Future clinical trials are needed to evaluate whether targeting B7-H3 can provide clinical benefit to help patients with sarcoma. [ABSTRACT FROM AUTHOR]

Background: Hepatocellular carcinoma (HCC) is a malignant tumor characterized by a high mortality rate. The occurrence and progression of HCC are linked to oxidative stress. Glyoxalase-1 (GLO1) plays an important role in regulating oxidative stress, yet the underlying mechanism remains unclear. GLO1 may serve as a prognostic biomarker and therapeutic target for HCC. Methods: Based on TCGA database hepatocellular carcinoma samples, we conducted a bioinformatics analysis to explore the correlation between GLO1 expression and HCC cell proliferation and viability. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis revealed that differentially expressed genes (DEGs) were mainly enriched in the cell cycle pathway. We analyzed the relationships between GLO1 and 24 genes enriched in the cell cycle pathway using a protein-protein interaction (PPI) network. Finally, experimental validation was performed to assess GLO1's impact on the distribution of cells at different cell cycle stages and on the proliferation and migration of HCC cells. Results: Our study demonstrated that GLO1 was overexpressed in HCC tissues and was associated with a poor prognosis. Data analysis indicated that overexpression of GLO1 activated the cell cycle pathway and positively correlated with expression of the majority of key cell cycle genes. Experimental validation showed that GLO1 expression affects the number of HCC cells in G2 and S phases and regulates HCC cell proliferation and migration. Conclusions: GLO1 represents a promising therapeutic target for HCC, providing valuable insights into its role in the viability and proliferation of HCC cells. [ABSTRACT FROM AUTHOR]

Background: Hepatocellular carcinoma (HCC) is a malignant tumor characterized by a high mortality rate. The occurrence and progression of HCC are linked to oxidative stress. Glyoxalase-1 (GLO1) plays an important role in regulating oxidative stress, yet the underlying mechanism remains unclear. GLO1 may serve as a prognostic biomarker and therapeutic target for HCC. Methods: Based on TCGA database hepatocellular carcinoma samples, we conducted a bioinformatics analysis to explore the correlation between GLO1 expression and HCC cell proliferation and viability. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis revealed that differentially expressed genes (DEGs) were mainly enriched in the cell cycle pathway. We analyzed the relationships between GLO1 and 24 genes enriched in the cell cycle pathway using a protein-protein interaction (PPI) network. Finally, experimental validation was performed to assess GLO1’s impact on the distribution of cells at different cell cycle stages and on the proliferation and migration of HCC cells. Results: Our study demonstrated that GLO1 was overexpressed in HCC tissues and was associated with a poor prognosis. Data analysis indicated that overexpression of GLO1 activated the cell cycle pathway and positively correlated with expression of the majority of key cell cycle genes. Experimental validation showed that GLO1 expression affects the number of HCC cells in G2 and S phases and regulates HCC cell proliferation and migration. Conclusions: GLO1 represents a promising therapeutic target for HCC, providing valuable insights into its role in the viability and proliferation of HCC cells. [ABSTRACT FROM AUTHOR]

Background: Systemic lupus erythematosus (SLE) is an autoimmune disease that currently cannot be completely cured with a great health burden. Since the production of autoantibodies plays a key role in the pathogenesis of SLE, discovering the underlying immunoregulation mechanism of B cells will be helpful for developing promising immunotherapy for SLE. In recent studies, dopamine receptors (DRDs), G protein-coupled receptors that include D1-like and D2-like subtypes, are expressed on B cells and participate in various physiological processes, involving immune responses. However, the regulatory effect of DRDs on B cells has not been determined. Methods: This study explored the expression of DRDs on B-cell subsets from SLE patients and healthy individuals. The effects of D1-like receptor on B-cell activation and differentiation were further explored using D1-like receptor agonists or antagonists. RNA-seq and bioinformatics analyses were used to identify specific molecular mechanisms involved. Results: The D1-like DRDs on B cells of SLE patients were highly expressed compared with those of healthy controls (HCs). D1-like receptor agonist treatment exacerbated lupus-like symptoms in pristane-induced lupus-like mice, while D1-like receptor antagonists alleviated the lupus-like phenotypes. Inhibition of D1-like receptor signals impeded B-cell differentiation, while activation of D1-like receptor signals could promote B cell differentiation. Further RNA-seq confirmed that PTGS2, a gene related to B-cell differentiation, was up-regulated once the D1-like receptor signals were activated, while BMP6 and IL-24 were up-regulated once the D1-like receptor signals were inhibited. Conclusion: D1-like receptors probably promote B-cell differentiation through the PTGS2/PRDM1 pathway. [ABSTRACT FROM AUTHOR]

Pancreatic ductal adenocarcinoma (PDAC) is a highly aggressive malignancy, accounting for over 90% of pancreatic cancers, and is characterized by limited treatment options and poor survival rates. Systems biology provides in-depth insights into the molecular mechanisms of PDAC. In this context, novel algorithms and comprehensive strategies are essential for advancing the identification of critical network nodes and therapeutic targets within disease-related protein-protein interaction networks. This study employed a comprehensive computational strategy using the metaheuristic algorithm Trader to enhance the identification of potential therapeutic targets. Analysis of the expression data from the PDAC dataset (GSE132956) involved co-expression analysis and clustering of differentially expressed genes to identify key disease-associated modules. The STRING database was used to construct a network of differentially expressed genes, and the Trader algorithm pinpointed the top 30 DEGs whose removal caused the most significant network disconnections. Enriched gene ontology terms included “Signaling by Rho GTPases,” “Signaling by receptor tyrosine kinases,” and “immune system.” Additionally, nine hub genes—FYN, MAPK3, CDK2, SNRPG, GNAQ, PAK1, LPCAT4, MAP1LC3B, and FBN1—were identified as central to PDAC pathogenesis. This integrated approach, combining co-expression analysis with protein-protein interaction network analysis using a metaheuristic algorithm, provides valuable insights into PDAC mechanisms and highlights several hub genes as potential therapeutic targets. [ABSTRACT FROM AUTHOR]

Background: Primary ovarian insufficiency (POI) is a disorder characterized by the premature decline in ovarian function, leading to significant fertility and health impacts on women under 40. The unclear etiology of POI hinders the development of effective treatments, highlighting the need for novel therapeutic targets. Methods: This study employed genome-wide association analysis (GWAS) integrated with expression quantitative trait loci (eQTL) data from the GTEx and eQTLGen databases. Mendelian randomization (MR) and colocalization analyses were conducted to investigate causal relationships between genetic variants and POI and to identify potential therapeutic targets. Results: We identified 431 genes with available index cis-eQTL signals, of which four (HM13, FANCE, RAB2A, and MLLT10) were significantly associated with POI. Colocalization analysis revealed strong evidence for FANCE and RAB2A, indicating their potential as therapeutic targets. Subsequent druggability assessments identified FANCE and RAB2A as promising candidates for POI treatment, supported by their involvement in DNA repair and autophagy regulation, respectively. Conclusions: Our study establishes a causal link between specific genes and POI, highlighting FANCE and RAB2A as potential drug targets. These findings provide a foundation for future research and therapeutic development, aiming to improve outcomes for women with POI. Validation in further trials is necessary to confirm these potential targets. [ABSTRACT FROM AUTHOR]

Osteosarcoma (OS) is a bone malignant tumor affecting children, adolescents, and young adults. Currently, osteosarcoma is treated with chemotherapy regimens established over 40 years ago. The investigation of novel therapeutic strategies for the treatment of osteosarcoma remains an important clinical need. Cyclin-dependent kinases (CDKs) have been considered promising molecular targets in cancer therapy. Among these, CDK12 has been shown to play a crucial role in the pathogenesis of malignancies, but its clinical significance and biological mechanisms in osteosarcoma remain unclear. In the present study, we aim to determine the expression and function of CDK12 and evaluate its prognostic and therapeutic value in metastatic osteosarcoma. We found that overexpression of CDK12 was associated with high tumor grade, tumor progression and reduced patient survival. The underlying mechanism revealed that knockdown of CDK12 expression with small interfering RNA or functional inhibition with the CDK12-targeting agent THZ531 effectively exhibited time- and dose-dependent cytotoxicity. Downregulation of CDK12 paused transcription by reducing RNAP II phosphorylation, interfered with DNA damage repair with increased γH2AX, and decreased cell proliferation through the PI3K-AKT pathway. This was accompanied by the promotion of apoptosis, as evidenced by enhanced Bax expression and reduced Bcl-xL expression. Furthermore, the CDK12 selective inhibitor THZ531 also hindered ex vivo 3D spheroid formation, growth of in vitro 2D cell colony, and prevented cell mobility. Our findings highlight the clinical importance of CDK12 as a potentially valuable prognostic biomarker and therapeutic target in metastatic osteosarcoma. [ABSTRACT FROM AUTHOR]

Ubiquitination, a multifaceted post-translational modification, regulates protein function, degradation, and gene expression. The pivotal role of ubiquitination in the pathogenesis and progression of cancer, including colorectal, breast, and liver cancer, is well-established. Osteosarcoma, an aggressive bone tumor predominantly affecting adolescents, also exhibits dysregulation of the ubiquitination system, encompassing both ubiquitination and deubiquitination processes. This dysregulation is now recognized as a key driver of osteosarcoma development, progression, and chemoresistance. This review highlights recent progress in elucidating how ubiquitination modulates tumor behavior across signaling pathways. We then focus on the mechanisms by which ubiquitination influences osteosarcoma cell function. Finally, we discuss the potential for targeting the ubiquitin-proteasome system in osteosarcoma therapy. By unraveling the impact of ubiquitination on osteosarcoma cell physiology, we aim to facilitate the development of novel strategies for prognosis, staging, treatment, and overcoming chemoresistance. [ABSTRACT FROM AUTHOR]

It remains challenging to translate the findings from genome-wide association studies (GWAS) of autoimmune diseases (AIDs) into interventional targets, presumably due to the lack of knowledge on how the GWAS risk variants contribute to AIDs. In addition, current immunomodulatory drugs for AIDs are broad in action rather than disease-specific. We performed a comprehensive protein-centric omics integration analysis to identify AIDs-associated plasma proteins through integrating protein quantitative trait loci datasets of plasma protein (1348 proteins and 7213 individuals) and totally ten large-scale GWAS summary statistics of AIDs under a cutting-edge systematic analytic framework. Specifically, we initially screened out the protein-AID associations using proteome-wide association study (PWAS), followed by enrichment analysis to reveal the underlying biological processes and pathways. Then, we performed both Mendelian randomization (MR) and colocalization analyses to further identify protein-AID pairs with putatively causal relationships. We finally prioritized the potential drug targets for AIDs. A total of 174 protein-AID associations were identified by PWAS. AIDs-associated plasma proteins were significantly enriched in immune-related biological process and pathways, such as inflammatory response (P = 3.96 × 10–10). MR analysis further identified 97 protein-AID pairs with potential causal relationships, among which 21 pairs were highly supported by colocalization analysis (PP.H4 > 0.75), 10 of 21 were the newly discovered pairs and not reported in previous GWAS analyses. Further explorations showed that four proteins (TLR3, FCGR2A, IL23R, TCN1) have corresponding drugs, and 17 proteins have druggability. These findings will help us to further understand the biological mechanism of AIDs and highlight the potential of these proteins to develop as therapeutic targets for AIDs. [ABSTRACT FROM AUTHOR]

Coactivator-associated arginine methyltransferase 1 (CARM1), pivotal for catalyzing arginine methylation of histone and non-histone proteins, plays a crucial role in developing various cancers. CARM1 was initially recognized as a transcriptional coregulator by orchestrating chromatin remodeling, transcription regulation, mRNA splicing and stability. This diverse functionality contributes to the recruitment of transcription factors that foster malignancies. Going beyond its established involvement in transcriptional control, CARM1-mediated methylation influences a spectrum of biological processes, including the cell cycle, metabolism, autophagy, redox homeostasis, and inflammation. By manipulating these physiological functions, CARM1 becomes essential in critical processes such as tumorigenesis, metastasis, and therapeutic resistance. Consequently, it emerges as a viable target for therapeutic intervention and a possible biomarker for medication response in specific cancer types. This review provides a comprehensive exploration of the various physiological functions of CARM1 in the context of cancer. Furthermore, we discuss potential CARM1-targeting pharmaceutical interventions for cancer therapy. [ABSTRACT FROM AUTHOR]