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Does Bilirubin Have a Causal Relationship With Vitiligo? A Mendelian Randomization Study and Bioinformatics Analysis.

BACKGROUND: Vitiligo is a complex acquired pigmentary disorder whose pathogenesis is closely linked to oxidative stress. Although bilirubin, a potent endogenous antioxidant, has been implicated in various dermatological conditions, its specific role in vitiligo remains poorly defined. This study aims to investigate the causal associations between bilirubin and vitiligo using Mendelian randomization (MR) analysis, complemented by bioinformatics validation to unravel the underlying molecular mechanisms. METHODS: Genome-wide association study (GWAS) data pertaining to vitiligo and bilirubin were

Genome-wide association study of bipolar disorder in Canadian and UK populations corroborates disease loci including SYNE1 and CSMD1.

BACKGROUND: Recently, genome-wide association studies (GWAS) for cases versus controls using single nucleotide polymorphism microarray data have shown promising findings for complex neuropsychiatric disorders, including bipolar disorder (BD). METHODS: Here we describe a comprehensive genome-wide study of bipolar disorder (BD), cross-referencing analysis from a family-based study of 229 small families with association analysis from over 950 cases and 950 ethnicity-matched controls from the UK and Canada. Further, loci identified in these analyses were supported by pathways identified through p

Distinct immunological features of oropharyngeal cancer peritumoral tonsillar tissues from inflammatory tonsils and regional lymph nodes: A pilot study.

BACKGROUND: Cancer immune responses are generated in secondary lymphoid organs, such as the lymph nodes and tonsils. In the current study, transcriptional profiles of peritumoral tonsillar tissues (PTTs) from oropharyngeal cancers (OPCs) were assessed and compared with those of inflammatory tonsils and regional lymph nodes (rLNs). METHODS: RNA samples of PTTs and rLNs from 13 OPCs, and 4 inflammatory tonsils were subjected to microarray analysis, and differentially expressed genes (DEGs) identified from 730 nCounter Panel immune-related genes. Gene Set enrichment Analysis (GSEA) was used for …

Identification of Lupus-Associated Genes in the Pathogenesis of Pre-eclampsia Via Bioinformatic Analysis.

Pre-eclampsia (PE) is a severe pregnancy complication that is more common in patients with systemic lupus erythematosus (SLE). Although the exact causes of these conditions are not fully understood, the immune system plays a key role. To investigate the connection between SLE and PE, we analyzed genes associated with SLE that may contribute to the development of PE. We collected 9 microarray data sets from the NCBI GEO database and used Limma to identify the differentially expressed genes (DEGs). In addition, we employed weighted gene co-expression network analysis (WGCNA) to pinpoint the hub

Quantification of the neuropathology of alcohol use disorder using tissue microarrays.

Alcohol use disorder (AUD) is characterized by an inability to stop consuming alcohol. Neuroimaging studies of patients with AUD show mild grey and white matter atrophy, while pathological studies suggest that atrophy is restricted to the white matter. The effects on individual brain cells are largely unknown. Mild neuronal loss has been described in the prefrontal cortex but this has not been consistent. Studies quantifying oligodendrocytes, astrocytes, and microglia are rare. These knowledge gaps impede therapeutic advancements. Here, we piloted the use of tissue microarrays, immunohistochem

Real-time genomic characterization of pediatric acute leukemia using adaptive sampling.

Effective treatment of pediatric acute leukemia is dependent on accurate genomic classification, typically derived from a combination of multiple time-consuming and costly techniques such as flow cytometry, fluorescence in situ hybridization (FISH), karyotype analysis, targeted PCR, and microarrays [1-3]. We investigated the feasibility of a comprehensive single-assay classification approach using long-read sequencing, with real-time genome target enrichment, to classify chromosomal abnormalities and structural variants characteristic of acute leukemia. We performed whole genome sequencing on

Delineation of Novel Autosomal Recessive Mutation in GJA3 and Autosomal Dominant Mutations in GJA8 in Pakistani Congenital Cataract Families.

Congenital cataract is a clinically and genetically heterogeneous disease. The present study was undertaken to find the genetic cause of congenital cataract families. DNA samples of a large consanguineous Pakistani family were genotyped with a high resolution single nucleotide polymorphism Illumina microarray. Homozygosity mapping identified a homozygous region of 4.4 Mb encompassing the gene GJA3. Sanger sequence analysis of the GJA3 gene revealed a novel homozygous variant c.950dup p.(His318ProfsX8) segregating in an autosomal recessive (AR) manner. The previously known mode of inheritance f

A novel homozygous complex deletion in CFTR caused cystic fibrosis in a Chinese patient.

Cystic fibrosis (CF) is the most frequent lethal genetic disorder among Caucasians, but is considered to be a very rare disease in Chinese population. Here, we present an 11-year-old Chinese CF patient with disseminated bronchiectasis and salty sweat, for whom exon sequencing followed by multiplex ligation-dependent probe amplification analysis of the CFTR gene was applied for mutation screening. A homozygous deletion involving exon 20 of CFTR was observed in the patient's genome. Molecular characterization of the breakpoints indicated that both alleles of this locus had an identical novel com

Gene expression-based prediction of myeloma cell sensitivity to histone deacetylase inhibitors.

BACKGROUND: Multiple myeloma (MM) is still a fatal plasma cell cancer. Novel compounds are currently clinically tested as a single agent in relapsing patients, but in best cases with partial response of a fraction of patients, emphasising the need to design tools predicting drug efficacy. Histone deacetylase inhibitors (HDACi) are anticancer agents targeting epigenetic regulation of gene expression and are in clinical development in MM. METHODS: To create a score predicting HDACi efficacy, five MM cell lines were treated with trichostatin A (TSA) and gene expression profiles were determined.

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… Histone deacetylase inhibitor enhances the anti-tumor effect of gemcitabine: a special reference to gene-expression microarray analysis. Oncol Rep. 2011;26 (5:1057–1062. doi: 10.3892/or.2011.1407. Jourdan M, Veyrune JL, Vos JD, Redal N, Couderc G, Klein B. …

Cord blood chemokines differentiate between spontaneous and elective preterm births in singleton pregnancies.

BACKGROUND: Signals originating from both maternal and fetal compartments participate in the preterm labor process. OBJECTIVE: To investigate whether cord blood immunoproteins predict spontaneous preterm labor. METHODS: Cord blood from 125 very preterm (gestational age <32weeks) singleton infants and 33 term infants was collected after birth and analyzed for 107 immunoproteins on microarrays. Immunoproteins from spontaneous preterm births (SPTB) were compared to immunoproteins from preterm births without labor. The placentas were studied for histology and immunohistochemistry. The data was m

Up-regulation of expression of the ubiquitin carboxyl-terminal hydrolase L1 gene in human airway epithelium of cigarette smokers.

Neuroendocrine differentiation is a common feature of lung cancer and increased numbers of neuroendocrine cells and their peptides have been described in chronic smokers. To understand the effects of cigarette smoking on the gene expression profile of neuroendocrine cells, microarray analysis with TaqMan confirmation was used to assess airway epithelial samples obtained by fiberoptic bronchoscopy from 81 individuals [normal nonsmokers, normal smokers, smokers with early chronic obstructive lung disease (COPD), and smokers with established COPD]. Of 11 genes considered to be neuroendocrine cell…

Differential diagnosis between complete and partial mole by TSSC3 antibody completely correlates to DNA diagnosis.

Complete hydatidiform moles (CHMs) are a type of androgenetic fertilization without an ovum. Cases of CHM exhibit a generalized swelling of the villi and are known to be highly associated with persistent disease or carcinoma. In contrast, partial hydatidiform moles (PHMs) also show characteristic hydropic changes among the villi, but the incidence of secondary disease is relatively low. Because PHMs are fertilized by one ovum and two sperm and CHMs are fertilized by one or two sperm alone, we considered whether or not maternally imprinted genes might be useful for achieving a differential diag

Transcriptome-wide co-expression analysis identifies LRRC2 as a novel mediator of mitochondrial and cardiac function.

Mitochondrial dysfunction contributes to myriad monogenic and complex pathologies. To understand the underlying mechanisms, it is essential to define the full complement of proteins that modulate mitochondrial function. To identify such proteins, we performed a meta-analysis of publicly available gene expression data. Gene co-expression analysis of a large and heterogeneous compendium of microarray data nominated a sub-population of transcripts that whilst highly correlated with known mitochondrial protein-encoding transcripts (MPETs), are not themselves recognized as generating proteins eithe

Absence of autoantibodies linked to cancer and autoimmune disorders 26 weeks after BNT162b2 boosting in CoronaVac- primed individuals.

Concerns regarding vaccine-associated autoimmunity and activation of cancer-related pathways persist, yet longitudinal proteome-wide evaluations of heterologous COVID-19 vaccination regimens remain limited. Here, we assessed the stability of the human 'autoantibodyome' in 30 healthy adults receiving a heterologous CoronaVac-BNT162b2 vaccination regimen (inactivated-virus priming followed by an mRNA booster). Paired serum samples collected pre-vaccination and 26 weeks post-booster were analyzed using the i-Ome™ Discovery protein microarray, which measures IgG reactivity against 1,610 native hum

Mitophagy and Immune Infiltration in Primary Sjögren's Disease: Insights from Bioinformatics Analysis.

Primary Sjögren's disease (SjD) is characterized by lymphocyte infiltration into exocrine glands. Mitochondrial dysfunction is a critical pathological mechanism underlying SjD, and mitophagy plays a vital role in clearing damaged mitochondria. This study used bioinformatic analysis to explore the potential roles of mitophagy-related genes in SjD pathogenesis and immune infiltration. Bioinformatic analysis was performed on the SjD microarray datasets to identify differentially expressed genes (DEGs). Mitophagy-related DEGs were selected and analyzed using functional enrichment, protein-protein

Iron Dyshomeostasis and Divergent Antigen Presentation Remodeling in Bronchiectasis: A Dual-Dataset Transcriptomic Analysis.

BACKGROUND: Bronchiectasis features persistent neutrophilic inflammation with recurrent infections, yet why abundant immune infiltrates fail to clear bacteria remains unclear. Ferroptosis-iron-dependent regulated cell death-modulates immunity in oncology but is unexplored in chronic airway diseases. METHODS: We performed dual-dataset transcriptomic analysis integrating bulk lung RNA-sequencing (GSE153131: bronchiectasis, normal, pneumonia) and an in vitro BEAS-2B epithelial microarray dataset (1,004 differentially expressed genes at FDR < 0.05). Ferroptosis gene-set scoring, immune deconvolut

Exploring copy number variations in Lebanese families with rod-cone dystrophy reveals a novel deletion in PRPF31 with haploinsufficiency.

BACKGROUND AND OBJECTIVES: Rod-cone dystrophy (RCD), also known as retinitis pigmentosa, is the most common group of retinal dystrophies, affecting around 1:4,000 individuals worldwide. In the present work, we performed a copy number variation (CNV) analysis on next-generation sequencing (NGS) data from two Lebanese families with RCD, since no disease-causing mutations were identified through the analysis of single nucleotide variants (SNVs) and insertions/deletions (Indels). NGS, real-time PCR (qPCR), and chromosomal microarray were performed to identify, validate, and delineate the causative

FN1 Immunoregulation in Glioblastoma: Insights From Neutrophil-Centric Studies.

Neutrophils, as key components of the tumor microenvironment, play a crucial role in cancer progression and prognosis. This study aimed to i … ulation of FN1 across cancer types, underscoring its broad clinical relevance. Additionally, tissue microarray analysis using multiplex immunofluorescence on 84 GBM samples confirmed co-expression of FN1, SDC1, and TWIST1, with higher levels associated with reduced survival. These findings establish NRGPI as a valuable prognostic biomarker for GBM, offering novel ins …

Identification of ferroptosis-related key genes in tuberculosis by bioinformatics methods.

Tuberculosis, induced by Mycobacterium tuberculosis (Mtb), continues to pose a significant global public health challenge. Ferroptosis has emerged as a pivotal factor in tuberculosis pathogenesis, however, the mechanism has not yet been fully clarified. Therefore, the aim of this study was to hypothesize and validate potential ferroptosis-related genes in Mtb infection through bioinformatics analysis, thereby offering insights for further investigation. The mRNA microarray expression profile datasets were sourced from the Gene Expression Omnibus. The differentially expressed genes (DEGs) were

Advances in genomic and pharmacokinetic profiling for clinical stratification of metastatic breast cancer.

BACKGROUND: Metastatic breast cancer (MBC) is the most significant clinical challenge in patient care; hence, we need new personalized therapeutic targets and innovative inhibitors. Genomic, proteomic, and structural analysis can be a pivotal tool for faster and more cost-efficient lead discovery. METHODS: The study employed gene expression profiling (Microarray, PCR, Bulk RNA-Seq) and computer-aided drug design, including structural modeling, virtual screening, docking, pharmacophore modeling, ADMET analysis, and NMA dynamics. A large compound library was screened to identify stable, high-af