Microarray Research Articles

Influence of Mesalazine on Ferroptosis-Related Gene Expression in In Vitro Colorectal Cancer Culture

Background/Objectives: Colorectal cancer (CRC) is one of the most common oncological disorders. Its fundamental treatments include surgery and chemotherapy, predominantly utilizing 5-fluorouracil (5-FU). Despite medical advances, CRC continues to present a high risk of recurrence, metastasis and low survival rates. Consequently, significant emphasis has been directed towards exploring novel types of cell death, particularly ferroptosis. Ferroptosis is characterized by iron imbalance and the accumulation of lipid peroxides and reactive oxygen species (ROS), leading to cellular damage and death. Thus, the discovery of safe inducers of ferroptosis, offering new hope in the struggle against CRC, remains crucial. In this study, we applied the concept of drug repositioning, selecting mesalazine (MES), a non-steroidal anti-inflammatory drug (NSAID), for investigation. Methods: The study was conducted on the colon cancer cell line DLD-1 and normal intestinal epithelial cells from the CCD 841 CoN cell line. Both cell lines were treated with MES solutions at concentrations of 10, 20, 30, 40, and 50 mM. Cytotoxicity was assessed using the MTT assay, while ferroptosis-related gene expression analysis was performed using oligonucleotide microarrays, with RT-qPCR used for validation. Results: MES effectively reduces the viability of DLD-1 cells while minimally affecting normal intestinal cells. Subsequent oligonucleotide microarray analysis revealed that MES significantly alters the expression of 56 genes associated with ferroptosis. Conclusion: Our results suggest that MES may induce ferroptosis in CRC, providing a foundation for further research in this area.

Phenotypes linked to duplication upstream of SOX9: New insights into presentation and diagnosis.

Duplications occurring upstream of the SOX9 gene have been identified in a limited subset of patients with 46,XX testicular/ovotesticular differences/disorders of sex development (DSD). However, comprehensive understanding regarding their clinical presentation and diagnosis is limited. To gain further insight into the diagnosis of a large cohort of 46,XX individuals with duplications upstream of SOX9. We retrospectively analyzed data of 46,XX/SRY-negative individuals with SOX9 upstream duplications. Clinical data were recorded, and genetic etiologies were investigated using karyotyping, fluorescence in situ hybridization (FISH) for SRY analysis, microarray analysis, multiplex ligation-dependent probe amplification (MLPA) and next generation sequencing panels including whole genome sequencing. We analyzed twelve 46,XX individuals with heterozygous duplications upstream of SOX9, ranging from 107-941 kb. Ages at diagnosis ranged from 0.1 to 55 years. Seven (58%) had testicular/ovotesticular DSD, while five (41%) were asymptomatic carriers detected through family screening. There was no significant correlation between duplication size and genital/gonadal phenotype. The duplication was inherited from the father (n=3) or an asymptomatic mother (n=2). In one family, a duplication missed by the 300K microarray was detected by MLPA and confirmed with the 750K microarray. 46,XX individuals with SOX9 upstream duplications may exhibit no symptoms, but thorough family screening is crucial due to the potential inheritance and testicular/ovotesticular DSD risk in subsequent generations. We emphasize the effectiveness of high-resolution microarray analysis (>500K) as the primary diagnostic tool for 46,XX/SRY-negative testicular/ovotesticular DSD individuals, enabling thorough genome-wide assessment of copy number variations and detecting small alterations.

MicroRNA-150-3p enhances the antitumour effects of CGP57380 and is associated with a favourable prognosis in non-small cell lung cancer

MicroRNA (miRNA) dysregulation has been identified in several carcinomas, including non-small cell lung cancer (NSCLC), and is known to play a role in the development and progression of this disease. We initially conducted a miRNA microarray analysis, which revealed that the MNK inhibitor CGP57380 increased the expression of miR-150-3p. A similar analysis was performed using data from The Cancer Genome Atlas (TCGA). Cell proliferation, colony formation and migration assays were validated in A549 and H157 cells treated with miR-150-3p mimics. Quantitative polymerase chain reaction (qPCR) was then used to detect potential target genes. We observed significant downregulation of miR-150-3p in NSCLC samples compared with normal samples (P = 0.035). High miR-150-3p expression was associated with longer overall survival (P = 0.005), as determined via a tissue microarray (TMA). These results were validated in the TCGA and revealed that miR-150-3p was expressed at low levels in NSCLC tissues (P < 0.0001) and that patients with high miR-150-3p expression had a better prognosis (P = 0.042). Moreover, the combination of miR-150-3p and CGP57380 exerted a synergistic inhibitory effect on colony formation, growth, and migration and induced apoptosis in NSCLC cell lines. We investigated the potential targets of miR-150-3p and successfully validated six potential target genes through qPCR analysis. High miR-150-3p expression may enhance the response to immunotherapy, cisplatin and gemcitabine. In summary, this study underscores the promising therapeutic implications of combining miR-150-3p and CGP57380 for NSCLC treatment. Additionally, this study provides valuable insights into the molecular mechanisms underlying the effects of this treatment.

Knockdown of the EEF1A2 gene reduces lung cancer brain metastasis by downregulating the BCL10/NFκB pathway

Aim: Brain metastases (BM) in patients with lung cancer (LC) are linked to unfavorable outcomes. The eukaryotic translation elongation factor 1 alpha 2 (EEF1A2) is notably overexpressed across various cancer types and plays a role in promoting tumor initiation and progression. This research aimed to clarify the function of EEF1A2 in the context of lung cancer brain metastasis (LCBM) and to explore the mechanisms underlying its effects. Methods: To identify genes with differential expression between LC and LCBM samples, transcriptomic microarray analyses were conducted, confirming that EEF1A2 expression is elevated in LCBM. EEF1A2 expression levels were validated in multiple LC cell lines. PC9 and SPCA1 cells were transfected with lentiviral vectors carrying siRNAs targeting EEF1A2 to assess its role both in vitro and in vivo . Tandem mass tag proteomics was employed to identify proteins regulated by EEF1A2. The expression of EEF1A2, BCL10, and phosphorylated NF-κB in tumor tissues from LC and LCBM patients was analyzed. Results: Compared to the LC samples, the LCBM samples exhibited significantly higher levels of EEF1A2 expression. EEF1A2 knockdown in PC9 and SPCA1 cells resulted in substantial reductions in cell proliferation, migration, and invasion. Proteomic profiling revealed that BCL10 protein levels were markedly reduced in EEF1A2-knockdown cells. Additionally, there was a decrease in phosphorylated NF-κB, EGFR, and mesenchymal markers (N-cadherin, Twist, Snail, Slug, and Cdc42), along with an increase in E-cadherin expression. In a mouse model, EEF1A2 knockdown in PC9 cells significantly inhibited brain metastasis. Furthermore, patient samples presented elevated levels of EEF1A2, BCL10, and phosphorylated NF-κB in LCBM tissues than in LC tissues. Conclusion: Our research revealed that EEF1A2 is upregulated in LCBM, and that its knockdown suppresses brain metastasis by decreasing BCL10 expression, inhibiting NF-κB signaling, and reducing epithelial-mesenchymal transition markers. These results suggest that targeting EEF1A2 may be a promising therapeutic approach for preventing and treating brain metastasis in lung cancer patients.

Case Report: Prenatal diagnosis of novel compound heterozygous variants in WDR35 gene causing short-rib thoracic dysplasia 7 with or without polydactyly

BackgroundWhole exome sequencing (WES) technology has been increasingly used for the etiological diagnosis of fetuses with ultrasound anomalies. In this article, we report a novel deletion compound combined with a causative variant in WDR35 gene leading to short-rib thoracic dysplasia 7 (SRTD7) with or without polydactyly using WES.MethodsThis study involved a Chinese fetus with clinical features of skeletal dysplasia on ultrasound imaging, in whom chromosome abnormalities and copy number variants (CNVs) were detected by chromosomal microarray analysis (CMA), and sequence variants were detected by WES. The obtained results were further verified by Sanger sequencing or real time quantitative PCR (qPCR).ResultsNo chromosomal abnormality or CNVs were identified in the fetus by CMA. However, WES result revealed a 14.38-kb large novel deletion compound covering exon 7 to exon 12 combined with a missense variant NM_001006657.2:c.932G&amp;gt;T(p.W311l) in WDR35. Both variants were thought of as pathogenic, which was further confirmed by Sanger sequencing and qPCR. In addition, two compound heterozygous variants NM_015102.5:c.[1196A&amp;gt;G(p.E399G)];[1972C&amp;gt;T(p.R658*)] in NPHP4 gene were also identified in the fetus, which may be partially responsible for fetal kidney hyperechogenicity and oligohydramnios.ConclusionThis is the first study reporting a novel deletion compound combined with a causative missense variant in WDR35 leading to SRTD7. This finding may broaden the spectrum of variants of WDR35 gene and provide a valuable reference for clinical counseling of related abnormalities in pregnancies.

Exploring the comorbidity mechanisms between atherosclerosis and hashimoto’s thyroiditis based on microarray and single-cell sequencing analysis

Abstract Atherosclerosis (AS) is a chronic vascular disease characterized by inflammation of the arterial wall and the formation of cholesterol plaques. Hashimoto’s thyroiditis (HT) is an autoimmune disorder marked by chronic inflammation and destruction of thyroid tissue. Although previous studies have identified common risk factors between AS and HT, the specific etiology and pathogenic mechanisms underlying these associations remain unclear. We obtained relevant datasets for AS and HT from the Gene Expression Omnibus (GEO). By employing the Limma package, we pinpointed common differentially expressed genes (DEGs) and discerned co-expression modules linked to AS and HT via Weighted Gene Co-expression Network Analysis (WGCNA). We elucidated gene functions and regulatory networks across various biological scenarios through enrichment and pathway analysis using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG). Core genes were identified using Cytoscape software and further validated with external datasets. We also conducted immune infiltration analysis on these core genes utilizing the CIBERSORT method. Lastly, Single-cell analysis was instrumental in uncovering common diagnostic markers. Based on differential analysis and WGCNA, we identified 119 candidate genes within the cohorts for AS and HT. KEGG and GO enrichment analyses indicate that these genes are significantly involved in antigen processing and presentation, along with various immune-inflammatory pathways. Two pivotal genes, PTPRC and TYROBP, were identified using five algorithms from the cytoHubba plugin. Validation through external datasets confirmed their substantial diagnostic value for AS and HT. Moreover, the results of Gene Set Enrichment Analysis (GSEA) indicated that these core genes are significantly enriched in various receptor interactions and signaling pathways. Immune infiltration analysis revealed a strong association of lymphocytes and macrophages with the pathogenesis of AS and HT. Single-cell analysis demonstrated predominant expression of the core genes in macrophages, monocytes, T cells and Common Myeloid Progenitor (CMP). This study proposes that an aberrant immune response might represent a shared pathogenic mechanism in AS and HT. The genes PTPRC and TYROBP are identified as critical potential biomarkers and therapeutic targets for these comorbid conditions. Furthermore, the core genes and their interactions with immune cells could serve as promising targets for future diagnostic and therapeutic strategies.

IGF2BP3 Triggers STAT3 Pathway by Stabilizing SRC RNA in an m6A-Dependent Manner to Promote Lymphatic Metastasis in LUAD.

Lymph node metastasis significantly affects the NSCLC patients' staging, treatment strategy, and prognosis. Studies have shown that IGF2BP3, an oncofetal protein and an m6A reader, overexpresses and correlates to lymph node metastasis and worse overall survival in histopathological studies including NSCLC, but its mechanism needs further study. This study explored IGF2BP3's function and mechanism in LUAD lymphatic metastasis using public databases, a human LUAD tissue microarray, human LUAD cells, and a lymphatic metastasis model in male BALB/c nude mice. Firstly, we proved that IGF2BP3 overexpression was positively correlated to patients' lymph node metastasis and worse overall survival in bioinformatics and a human LUAD tissue microarray analysis. IGF2BP3 was knocked out or overexpressed in human LUAD cell lines. Functionally, IGF2BP3 facilitated NCI-H1299, NCI-H358, and A549 cell growth, migration, invasion, and EMT invitro, and promoted tumorigenesis, lymphangiogenesis, and lymphatic metastasis of NCI-H1299 cells in BALB/c nude mice. Mechanically, RIP, RNA pull-down assay, MeRIP, mRNA stability assays, rescue experiments, and immunohistochemical assays were conducted. IGF2BP3 was demonstrated to bind to the m6A site of the 3'UTR region of SRC, stabilizing its mRNA and activating the downstream STAT3 signaling pathway and lymphatic growth factors such as VEGF-C, therefore affecting lymphatic metastasis. The cell migration and EMT function of IGF2BP3 were partially rescued by utilizing SRC siRNA or AZD0530, an SRC inhibitor. This study demonstrated that IGF2BP3 promotes lymphatic metastasis in LUAD via activating the m6A-SRC-STAT3-VEGFC signaling axis, indicating that IGF2BP3 is a potential therapeutic target to overcome metastasis in LUAD patients.

Amantadine modulates novel macrophage phenotypes to enhance neural repair following spinal cord injury

BackgroundSpinal cord injury (SCI) triggers a complex inflammatory response that impedes neural repair and functional recovery. The modulation of macrophage phenotypes is thus considered a promising therapeutic strategy to mitigate inflammation and promote regeneration.MethodsWe employed microarray and single-cell RNA sequencing (scRNA-seq) to investigate gene expression changes and immune cell dynamics in mice following crush injury at 3 and 7 days post-injury (dpi). High-dimensional gene co-expression network analysis (hdWGCNA) and slingshot trajectory analysis were employed to identify key gene modules and macrophage differentiation pathways. Subsequently, immunofluorescence staining, flow cytometry, and western blotting were performed to validate the identified effects of amantadine on macrophage differentiation and inflammation.ResultsTo elucidate the molecular mechanisms underlying the injury response at the transcriptional level, we performed a microarray analysis followed by gene set enrichment analysis (GSEA). The results revealed that pathways related to phagocytosis and macrophage activation are significantly involved post-injury, shedding light on the regulatory role of macrophages in SCI repair. To further investigate macrophage dynamics within the injured spinal cord, we conducted scRNA-Seq, identifying three distinct macrophage subtypes: border-associated macrophages (BAMs), inflammatory macrophages (IMs), and chemotaxis-inducing macrophages (CIMs). Trajectory analysis suggested a differentiation pathway from Il-1b+ IMs to Mrc1+ BAMs, and subsequently to Arg1+ CIMs, indicating a potential maturation process. Given the importance of these pathways in the injury response, we utilized molecular docking to hypothesize that amantadine might modulate this process. Subsequent in vitro and in vivo experiments demonstrated that amantadine reduces Il-1b+ IMs and facilitates the transition to Mrc1+ BAMs and Arg1+ CIMs, likely through modulation of the HIF-1α and NF-κB pathways. This modulation promotes neural regeneration and enhances functional recovery following SCI.ConclusionsAmantadine modulates macrophage phenotypes following SCI, reduces early inflammatory responses, and enhances neural function recovery. These findings highlight the therapeutic potential of amantadine as a treatment for SCI, and provide a foundation for future translational research into its clinical applications.

Histone Demethylase KDM6B Promotes Chondrogenic Differentiation Potential of Stem Cells from the Apical Papilla Via HES1.

Mesenchymal stem cell (MSC)-based therapies have emerged as a promising approach for treating articular cartilage injuries. However, enhancing the chondrogenic differentiation potential of MSCs remains a significant challenge. KDM6B, a histone demethylase that specifically removes H3K27me3 marks, is essential in controlling the maturation of chondrocytes. In this study, we examined how KDM6B influences chondrogenic differentiation in SCAPs and investigated the underlying mechanisms involved. SCAPs were utilized. Alcian Blue staining, pellet culture, and cell transplantation in rabbit knee cartilage defect models assessed MSC chondrogenic differentiation. Western blot, Real-time RT-PCR, and Microarray analysis examined the underlying molecular mechanisms. KDM6B promotes the expression of Aggrecan, COL2A1, COL5, glycosaminoglycans, and collagen fibers, while also increasing the COL2/COL1 ratio in SCAPs. In vivo, SCAPs overexpressing KDM6B significantly enhanced the repair and regeneration of knee cartilage and subchondral bone, with higher levels of glycosaminoglycan and COL5 expression observed within the tissue. KDM6B promotes the chondrogenic differentiation potential of SCAPs by repressing HES1. In addition, knock-down of HES1 enhanced the chondrogenic differentiation of SCAPs. KDM6B enhances the differentiation of SCAPs into chondrocytes and demonstrated its effectiveness in the repair and regeneration of cartilage tissue and subchondral bone in vivo experiments. These findings provide an important foundation for future research on the use of dental tissue-derived stem cells to treat cartilage injuries.

Identification of pennaceous barbule cell factor (PBCF), a novel gene with spatiotemporal expression in barbule cells during feather development.

Bird contour feathers exhibit a complex hierarchical structure composed of a rachis, barbs, and barbules, with barbules playing a crucial role in maintaining feather structure and function. Understanding the molecular mechanisms underlying barbule formation is essential for advancing our knowledge of avian biology and evolution. In this study, we identified a novel gene, pennaceous barbule cell factor (PBCF), using microarray analysis, RT-PCR, and in situ hybridization. PBCF is expressed in barbule cells adjacent to the ramus during pennaceous barbule formation, where these cells fuse with the ramus to establish the feather's branching structure. PBCF expression occurs transiently after melanin pigmentation of the barbule plates but before the expression of barbule-specific keratin 1 (BlSK1). Orthologues of PBCF, predicted to be secreted proteins, are conserved across avian species, with potential homologues detected in reptiles, suggesting an evolutionary lineage-specific adaptation. Additionally, PBCF is expressed in non-vacuolated notochord cells and the extra-embryonic ectoderm of the yolk sac, hinting at its broader developmental significance. The PBCF gene produces two mRNA isoforms via alternative splicing, encoding a secreted protein and a glycophosphatidylinositol (GPI)-anchored membrane-bound protein, indicating functional versatility. These findings suggest that PBCF may be involved as an avian-specific extracellular matrix component in cell adhesion and/or communication, potentially contributing to both feather development and embryogenesis. Further investigation of PBCF's role in feather evolution and its potential functions in other vertebrates could provide new insights into the interplay between development and evolution.

Coptisine inhibits esophageal carcinoma growth by modulating pyroptosis via inhibition of HGF/c-Met signaling.

Esophageal carcinoma is a highly prevalent malignancy worldwide. The present study aimed to investigate the mechanism by which the natural compound coptisine affects pyroptosis in esophageal squamous cell carcinoma (ESCC). The expression of c-Met in ESCC patients was assessed by immunohistochemical analysis of tissue microarrays. Natural drugs that bind to c-Met were identified by screening and molecular docking. The effect of coptisine on the proliferation of ESCC cells was detected by CCK-8 and colony formation assays. Cell cycle progression and cell apoptosis were detected by flow cytometry. The levels of mRNAs related to pyroptosis and miR-21 after coptisine treatment were assessed via real-time quantitative PCR. The effect of pyroptosis was evaluated by reactive oxygen species level detection and transmission electron microscopy (TEM) analysis. The expression of proteins related to pyroptosis and the HGF/c-Met pathway was detected by western blotting. A xenograft tumor model was established, and the inhibitory effect of coptisine was evaluated by observing tumor growth. The results showed that the highly expressed protein c-Met in esophageal cancer could bind with coptisine. Coptisine inhibited c-Met phosphorylation and proliferation in ESCC cells. Furthermore, coptisine inhibited the expression of downstream proteins of the HGF/c-Met signaling pathway and induced ROS generation. Tumor xenograft experiments demonstrated that coptisine effectively inhibited tumor growth by reducing the levels of pyroptosis-associated proteins. In conclusion, these findings indicate that inhibition of the HGF/c-Met signaling pathway suppresses pyroptosis to enhance the antitumor effect of coptisine in ESCC and support the potential use of coptisine for EC treatment.

Clinical significance of trisomy 7 signaled by non-invasive prenatal testing and a literature review

To explore the clinical significance of trisomy 7 signaled by non-invasive prenatal testing (NIPT). Pregnant women with high risk for trisomy 7 by NIPT from January 2017 to December 2023 were selected as the study subjects, and the results of prenatal diagnosis and follow-up were analyzed. Literature related to pregnant women with a high risk for trisomy 7 by NIPT from January 2016 to July 2024 was retrieved from China Biomedical Literature Database, Wanfang Database, China National Knowledge Infrastructure and PubMed database. Relevant information such as the incidence of trisomy 7 by NIPT, positive predictive value (PPV), and pregnancy outcomes were collected. This study has been approved by the Medical Ethics Committee of Lianyungang Maternal and Child Health Care Hospital (Ethics No. JS2022010). A total of 51 women with a high risk for trisomy 7 by NIPT were identified. Thirty-two of them had chosen chromosomal microarray analysis (CMA) of amniotic fluid cells, and 1 case of mosaic trisomy 7 was detected, which had yielded a PPV of 3.13%. Four women had opted termination of pregnancy, 1 had miscarriage, 4 had pre-term and/or low weight birth, whilst the remaining 42 (82.4%) had full-term delivery. In total 19 literature were retrieved, which had involved 278 cases of trisomy 7 signaled by NIPT, among which 5 fetuses with mosaic trisomy 7 (3.14%) were confirmed. Among the 211 women with follow-up outcomes, 2 (0.95%) had intrauterine growth restriction, 3 (1.42%) had abnormal fetal structure detected by ultrasound, 2 (0.95%) had miscarriage, 9 (4.27%) underwent pregnancy termination, 28 (13.27%) had preterm and/or low weight birth, whilst 167 (79.14%) had normal delivery. In 18 cases, chromosomal analysis of placental tissue was carried out, and 17 were confirmed to have mosaicism trisomy 7. The PPV for trisomy 7 signaled by NIPT is extremely low. Although most of such women had a full term delivery, adverse pregnancy outcomes may still occur in a minority of cases. Clinicians should provide adequate genetic counseling for such women and recommend appropriate prenatal diagnosis strategies and optimal perinatal management plans.

Identification of aberrant plasma vesicles containing AAK1 and CCDC18-AS1 in adolescents with major depressive disorder and preliminary exploration of treatment efficacy.

Major depressive disorder (MDD) during adolescence significantly jeopardizes both mental and physical health. However, the etiology underlying MDD in adolescents remains unclear. A total of 74 adolescents with MDD and 40 health controls (HCs) who underwent comprehensive clinical and cognitive assessments were enrolled. Differential expression analysis was conducted on plasma extracellular vesicles (EVs) carrying long non-coding RNAs (lncRNAs) and messenger RNAs (mRNAs) by microarray analysis. Two possible lncRNA-miR-mRNA networks were established and candidate regulatory axes were generated using the StarBase, miRDB, and TargetScan bioinformatics databases. Quantitative real-time polymerase chain reaction (qRT-PCR) was used to validate the candidate molecules and signaling axes in a clinical cohort. A total of 3752 dysregulated lncRNAs and 1789 dysfunctional mRNAs were identified. Two candidate regulatory axes (AC156455.1/miR-126-5p/AAK1 and CCDC18-AS1/miR-6835-5p/CCND2) with potential connections with MDD were selected. The candidate molecules exhibit differential expression patterns among adolescents with MDD and HCs, as well as before and after treatment with sertraline in adolescents with MDD. Furthermore, AAK1, CCDC18-AS1, and miR-6835-5p expressions exhibited significant differences between the response and non-response groups. Baseline expression of CCDC18-AS1, miR-6835-5p, and CCND2 could predict the therapeutic effect of sertraline, which may be associated with reducing suicidal ideation and improving cognitive function. Our study may provide insights into the understanding of the underlying pathological mechanisms in adolescents with MDD.

Metabolic-Immune Suppression Mediated by the SIRT1-CX3CL1 Axis Induces Functional Enhancement of Regulatory T Cells in Colorectal Carcinoma.

Metabolic reprogramming of tumor cells dynamically reshapes the distribution of nutrients and signals in the tumor microenvironment (TME), affecting intercellular interactions and resulting in metabolic immune suppression. Increased glucose uptake and metabolism are characteristic of many tumors. Meanwhile, the progression of colorectal carcinoma (CRC) relies on lipid metabolism. Therefore, investigating the role of glucolipid metabolic reprogramming on tumor immunity contributes to identifying new targets for immune suppression intervention in CRC. Our previous work demonstrated that SIRT1 is the hub gene involved in glucolipid metabolic conversion in CRC. Here, it is found that upregulated SIRT1 in CRC cells increases Treg functionality by promoting the secretion of CX3CL1. The CX3CL1-CX3CR1 signaling activated transcription factors SATB1 and BTG2, promoting the differentiation of TCF7+ Treg cells into functionally enhanced TNFRSF9+ Treg cells. Multiplex immunofluorescence (mIHC) analysis of a CRC tissue microarray confirmed the promoting effect of CX3CL1 on Treg infiltration. Additionally, the therapeutic efficacy of CX3CR1 inhibitor monotherapy and combination therapy is validated with the PD-1 antibody in the humanized subcutaneous CRC mouse model. This study elucidates a potential mechanism that metabolic reprogramming of cancer cells collaborates with subsequent immunosuppression to promote CRC progression.

Orthogonal-Group-Controlled Site-Selective I-Branching of Poly-N-acetyllactosamine Chains Reveals Unique Binding Specificities of Proteins towards I-Antigens.

Poly-N-acetyllactosamine (poly-LacNAc) is ubiquitously expressed on cell surface glycoconjugates, serving as the backbone of complex glycans and an extended scaffold that presents diverse glycan epitopes. The branching of poly-LacNAc, where internal galactose (Gal) residues have β1-6 linked N-acetylglucosamine (GlcNAc) attached, forms the blood group I-antigen, which is closely associated with various physiological and pathological processes including cancer progression. However, the underlying mechanisms remain unclear as many of the I-antigen sequences are undefined and inaccessible. In this study, we developed a highly efficient orthogonal-group-controlled approach to access site-selectively I-branched poly-LacNAc chains. The approach relies on three orthogonal protecting groups, each of them "caps" one internal Gal residue of poly-LacNAc. These groups can be readily "decapped" by specific enzymes or chemical reduction to expose desired sites for GCNT2-catalyzed I-branching. This approach enabled the rapid preparation of a diverse library of 41 linear and branched poly-LacNAc glycans from a single precursor. Glycan microarray analysis using these complex glycans revealed unique recognitions of I-branches by lectins, anti-I mAbs, and galectins. Surprisingly, oxidized forms of linear poly-LacNAc strongly bound to several glycan-binding proteins (GBPs). These findings help to bridge the gap in recognition of I-branching and open new avenues for therapeutic development by targeting galectins.

Molecular and genetic analysis of methicillin-resistant Staphylococcus aureus (MRSA) in a tertiary care hospital in Saudi Arabia.

Methicillin-resistant Staphylococcus aureus (MRSA) continues to pose significant challenges in healthcare settings due to its multi-drug resistance (MDR) and virulence. This retrospective study examines the molecular and resistance profiles of MRSA isolates from a tertiary care hospital in Saudi Arabia, providing valuable insights into regional epidemiology. A total of 190 MRSA strains were analysed to assess antimicrobial susceptibility, genetic diversity, and virulence factors. Antimicrobial susceptibility testing was conducted according to CLSI guidelines, while molecular characterization involved spa typing, SCCmec typing, and DNA microarray analysis to determine clonal complexes (CCs), resistance genes, and virulence determinants. The isolates showed extensive resistance to beta-lactam antibiotics, with 78% classified as MDR. Notably, resistance to fusidic acid and ciprofloxacin was detected in 70% and 55% of isolates, respectively. The most prevalent clonal complexes-CC5, CC6, and CC22-comprised over 60% of the isolates and exhibited diverse spa types. The Panton-Valentine leukocidin (PVL) gene, linked to heightened virulence, was identified in approximately 20% of isolates, particularly within CC5, CC30, and CC80. Enterotoxin genes (sea and seb) and immune evasion genes (sak, chp, and scn) were also commonly detected, reflecting the isolates' capacity to adapt and persist within the hospital environment. These findings underscore the high burden of MDR MRSA with considerable genetic diversity and virulence potential. The study highlights the urgent need for strengthened molecular surveillance and targeted infection control measures to limit MRSA transmission and effectively manage infection risks in healthcare facilities.

MiRNA Expression Profile in Primary Limbal Epithelial Cells of Aniridia Patients.

This study evaluates the microRNA (miRNA) expression profile in primary limbal epithelial cells (pLECs) of patients with aniridia. Primary human LECs were sampled and isolated from 10 patients with aniridia and 10 healthy donors. The miRNA profile was analyzed using miRNA microarrays. The biological roles of miRNA-validated target genes were delineated in silico by the enrichment analyses of the gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway. The expression of the most deregulated miRNAs was analyzed using quantitative real-time PCR (qRT-PCR). Microarray analysis revealed 10 differentially expressed miRNAs in pLECs of patients with aniridia relative to healthy controls (fold change = ≤ -2 or ≥ +2), nevertheless these were only differentially expressed using an unadjusted P value < 0.05. The qRT-PCR validation confirmed the significantly altered expression of miR-138-5p in pLECs of patients with aniridia (P = 0.005). In silico GO analysis of miR-138-5p target genes revealed the potential biological functions of miR-138-5p in regulating various cellular and molecular processes, including the positive regulation of cell motility, G1/S phase cell cycle transition, and cell migration, as well as the negative role in regulating epithelial cell differentiation. Pathway analysis highlighted the main involvement of the PI3K-Akt, Hippo, Wnt, Focal adhesion, cAMP, p53, IL-17, Jak-STAT, and MAPK-signaling pathways. This study revealed miRNA expression profile in pLECs of patients with aniridia using miRNA microarray and identified miRNAs that had not been previously reported for aniridia LECs. Our study also provides functional and pathway information that can be used to predict possible mechanism of miRNA function in LECs, thereby bridging the gap in the pathogenesis of AAK studies.

Differentiating multiple sclerosis with predominant spinal cord and optic nerve involvement from other autoimmune demyelinating diseases using B cell immunophenotyping and gene expression profiling.

Multiple sclerosis (MS) may present with predominant involvement of the spinal cord and optic nerve (MS/w-SCON) and mimic other autoimmune inflammatory demyelinating disorders (AIDD) such as neuromyelitis optica spectrum disorder (NMOSD), and relapsing inflammatory optic neuritis (RION). Thus, biomarkers are required for effective differential diagnosis of AIDD. Patients with MS/w-SCON (n = 20), MS without involvement of SCON (MS/wo-SCON) (n = 22), NMOSD (n = 16), RION (n = 15) and healthy individuals (n = 21) were included. Peripheral blood cell immunophenotypes were analyzed by flow cytometry and gene expression levels of isolated B cells were assessed by microarray analysis and quantitative real-time PCR. Significantly increased Breg, plasmablast, and plasma cell ratios distinguished MS/w-SCON from other groups. Most differentially expressed B cell genes were subjected to protein-protein interaction yielding a network of 13 immune mediators (IL18, IL18R1, P2RY12, CSF3R, TNFSF4, TNFRSF13C, TNFRSF1A, CCL20, CCL5, CCR4, CCL4L2, CXCL5, CXCL10). CCL4L2 and CCR4 expression levels distinguished MS/w-SCON. IL18/IL18R1 and CCL5 were distinguishing factors for NMOSD and RION, respectively. Peripheral blood B cell expression levels of CCL4L2, CCR4, IL18, IL18R1 and CCL5 are candidate biomarkers for differential diagnosis of AIDD of CNS. Our results substantiate the significance of B cells in the pathogenesis of these disorders.

Effects of new lipid ingredients during pregnancy and lactation on rat offspring brain gene expression.

Maternal dietary fat intake during pregnancy and lactation may influence the bioavailability of essential lipophilic nutrients, such as docosahexaenoic acid (DHA), that are important for both the mother and her child's development. This study aimed to evaluate the effects of different maternal fat diets on fat absorption and pup brain development by analyzing gene expression. Rats were fed diets with different lipid matrices during pregnancy and lactation: diet A, mono and diglycerides (MDG) + soy lecithin phospholipids (PL); diet B, MDG + soy lecithin PL + milk-derived PL; and a control diet. All diets contained the same amount of DHA. We determined maternal dietary fat absorption, as well as the offspring fatty acid (FA) profile in both plasma and brain samples at birth and in pups at 14 days post-natal. In addition, microarray analysis was performed to characterize the pup brain gene expression. Maternal dietary fat and DHA apparent absorption was enhanced only with diet B. However, we observed higher plasma DHA and total FA concentrations in lactating pups from the experimental groups A and B compared to the control. Both brain DHA and total FA concentrations were also higher in fetuses and 14-day-old pups from group A with respect to the control, with diet B following the same trend. Offspring brain gene expression was affected by both diets A and B, with changes observed in synaptic and developmental processes in the fetuses, and the detoxification process in 14-day-old pups. Incorporating MDG and PL-rich lipid matrices into maternal diets during pregnancy and lactation may be highly beneficial for ensuring proper neurodevelopment of the fetus and newborn.

M2-like macrophage-derived exosomes inhibit osteoclastogenesis via releasing miR-1227-5p.

Macrophages play a pivotal role in regulating inflammatory response in periodontitis, a condition characterized by excessive osteoclast differentiation. This study aimed to investigate whether exosomes derived from M2 macrophages regulate osteoclast differentiation and to identify the underlying molecular mechanisms. Exosomes were isolated from M2 macrophages and used to treat osteoclasts. Osteoclastogenesis was assessed using tartrate-resistant acid phosphatase staining and reverse transcription-quantitative polymerase chain reaction (RT-qPCR). The molecular mechanism was evaluated using microarray analysis, RT-qPCR, dual-luciferase reporter analysis, and RNA pull-down assay. The results showed that exosomes from M2 macrophages inhibited receptor activator of nuclear factor κ-B ligand (RANKL)-induced osteoclast differentiation. Additionally, miR-1227-5p expression in osteoclasts was increased after treatment with exosomes, and inhibition of miR-1227-5p counteracted the suppressive effects of exosomes on osteoclastogenesis. Moreover, OSCAR is a target of miR-1227-5p. In conclusion, exosomal miR-1227-5p suppresses osteoclast differentiation, potentially via targeting OSCAR. These findings provide new insights into the pathogenesis of periodontitis.