A systematic strategy for identifying causal single nucleotide polymorphisms and their target genes on Juvenile arthritis risk haplotypes.

BACKGROUND: Although genome-wide association studies (GWAS) have identified multiple regions conferring genetic risk for juvenile idiopathic arthritis (JIA), we are still faced with the task of identifying the single nucleotide polymorphisms (SNPs) on the disease haplotypes that exert the biological effects that confer risk. Until we identify the risk-driving variants, identifying the genes influenced by these variants, and therefore translating genetic information to improved clinical care, will remain an insurmountable task. We used a function-based approach for identifying causal variant candidates and the target genes on JIA risk haplotypes. METHODS: We used a massively parallel reporter assay (MPRA) in myeloid K562 cells to query the effects of 5,226 SNPs in non-coding regions on JIA risk haplotypes for their ability to alter gene expression when compared to the common allele. The assay relies on 180 bp oligonucleotide reporters ("oligos") in which the allele of interest is flanked by its cognate genomic sequence. Barcodes were added randomly by PCR to each oligo to achieve > 20 barcodes per oligo to provide a quantitative read-out of gene expression for each allele. Assays were performed in both unstimulated K562 cells and cells stimulated overnight with interferon gamma (IFNg). As proof of concept, we then used CRISPRi to demonstrate the feasibility of identifying the genes regulated by enhancers harboring expression-altering SNPs. RESULTS: We identified 553 expression-altering SNPs in unstimulated K562 cells and an additional 490 in cells stimulated with IFNg. We further filtered the SNPs to identify those plausibly situated within functional chromatin, using open chromatin and H3K27ac ChIPseq peaks in unstimulated cells and open chromatin plus H3K4me1 in stimulated cells. These procedures yielded 42 unique SNPs (total = 84) for each set. Using CRISPRi, we demonstrated that enhancers harboring MPRA-screened variants in the TRAF1 and LNPEP/ERAP2 loci regulated multiple genes, suggesting complex influences of disease-driving variants. CONCLUSION: Using MPRA and CRISPRi, JIA risk haplotypes can be queried to identify plausible candidates for disease-driving variants. Once these candidate variants are identified, target genes can be identified using CRISPRi informed by the 3D chromatin structures that encompass the risk haplotypes.

Pulmonary vascular stenosis scoring in fibrosing mediastinitis.

Aims: This study aims to develop a scoring system for evaluating the degree of pulmonary vascular stenosis in fibrosing mediastinitis (FM). Methods and results: A retrospective single-centre study was conducted on 56 patients with FM in China between April 2014 and August 2021. The involvement of pulmonary vessels in patients with FM was assessed using dual-phase computed tomography pulmonary angiography, and we found that 85.7% of the patients had both pulmonary artery (PA) and vein (PV) involvement. PA involvement was mainly located proximal to both the upper PA and the bilateral basal trunk levels in the lower lungs. The involvement of the superior PV was more common than that of the inferior PV, and the right inferior PV was the least involved. Most of these lesions exhibited moderate or severe stenosis. Additionally, a scoring system for evaluating the degree of pulmonary vascular stenosis was developed. A correlation analysis revealed a negative correlation between the final pulmonary vascular score and the pulmonary arterial pressure, pulmonary vascular resistance, and maximum tricuspid regurgitation velocity. The calculated score of 17.1 was the best cut-off value for the diagnosis of mild and severe pulmonary hypertension (PH). Conclusion: We successfully developed a scoring system for pulmonary vascular stenosis that can be used to evaluate the severity of pulmonary vessel involvement and PH. This scoring system may be relevant in the future development of target-based strategies for percutaneous interventions.

Progress in the Use of Echocardiography in Patients with Tumors.

Advances in cancer treatment have increased patient survival rates, shifting clinical focus towards minimizing treatment-related morbidity, including cardiovascular issues. Since echocardiography allows for a comprehensive non-invasive assessment at all cancer stages, it is well suited to monitor cardiovascular disease secondary to oncology treatment. This has earned it significant attention in the study of cardiac tumors and treatment-induced cardiac alterations. Ultrasound methods-ranging from transthoracic and transesophageal echocardiography to ultrasound diagnostic techniques including myocardial strain imaging, myocardial work indices, three-dimensional cardiac imaging-offer a holistic view of both the tumor and its treatment impact cardiac function. Stress echocardiography, myocardial contrast echocardiography, and myocardial acoustic angiography further augment this capability. Together, these echocardiographic techniques provide clinicians with early detection opportunities for cardiac damage, enabling timely interventions. As such, echocardiography continues to be instrumental in monitoring and managing the cardiovascular health of oncology patients, complementing efforts to optimize their overall treatment and survival outcomes.

Effect of non-enzymatic browning on oysters during hot air drying process: Color and chemical changes and insights into mechanisms.

Hot air drying (HAD) is an extensive method used on oysters and it causes the most intuitive change, a color change. However, the mechanism of color change remains unclear. This study showed that oysters underwent browning during the HAD process. The colorimetric parameter L* decreased while a* and b* increased, all of which were well described by the first-order color kinetic model. Mechanistically, the HDA process induced the oxidative browning of phenols and the generation of Maillard reaction products (5-hydroxymethylfurfural and hydrophilic pyrrole). Meanwhile, the HAD process caused lipid oxidation, leading to the reduction of phosphatidylethanolamine and the generation of reactive carbonyl compounds (aldehydes and α-dicarbonyl compounds). Moreover, the accumulation of hydrophobic pyrroles, a lipid-induced Maillard-like reaction product, was observed. These results suggest that, in addition to phenolic oxidation, sugar- and amino acid-mediated non-enzymatic browning reactions, lipid-mediated Maillard-like reactions play important roles in oyster darkening during the HAD process.

Comparison of the three-dimensional chromatin structures of adolescent and adult peripheral blood B cells: implications for the study of pediatric autoimmune diseases.

Background/Purpose: Knowledge of the 3D genome is essential to elucidate genetic mechanisms driving autoimmune diseases. The 3D genome is distinct for each cell type, and it is uncertain whether cell lines faithfully recapitulate the 3D architecture of primary human cells or whether developmental aspects of the pediatric immune system require use of pediatric samples. We undertook a systematic analysis of B cells and B cell lines to compare 3D genomic features encompassing risk loci for juvenile idiopathic arthritis (JIA), systemic lupus (SLE), and type 1 diabetes (T1D). Methods: We isolated B cells from healthy individuals, ages 9-17. HiChIP was performed using CTCF antibody, and CTCF peaks were identified. CTCF loops within the pediatric were compared to three datasets: 1) self-called CTCF consensus peaks called within the pediatric samples, 2) ENCODE's publicly available GM12878 CTCF ChIP-seq peaks, and 3) ENCODE's primary B cell CTCF ChIPseq peaks from two adult females. Differential looping was assessed within the pediatric samples and each of the three peak datasets. Results: The number of consensus peaks called in the pediatric samples was similar to that identified in ENCODE's GM12878 and primary B cell datasets. We observed <1% of loops that demonstrated significantly differential looping between peaks called within the pediatric samples themselves and when called using ENCODE GM12878 peaks . Significant looping differences were even less when comparing loops of the pediatric called peaks to those of the ENCODE primary B cell peaks. When querying loops found in juvenile idiopathic arthritis, type 1 diabetes, or systemic lupus erythematosus risk haplotypes, we observed significant differences in only 2.2%, 1.0%, and 1.3% loops, respectively, when comparing peaks called within the pediatric samples and ENCODE GM12878 dataset. The differences were even less apparent when comparing loops called with the pediatric vs ENCODE adult primary B cell peak datasets.The 3D chromatin architecture in B cells is similar across pediatric, adult, and EBVtransformed cell lines. This conservation of 3D structure includes regions encompassing autoimmune risk haplotypes. Conclusion: Thus, even for pediatric autoimmune diseases, publicly available adult B cell and cell line datasets may be sufficient for assessing effects exerted in the 3D genomic space.

B lymphocytes in treatment-naive paediatric patients with lupus are epigenetically distinct from healthy children.

BACKGROUND: SLE is likely triggered by gene-environment interactions. We have shown that most SLE-associated haplotypes encompass genomic regions enriched for epigenetic marks associated with enhancer function in lymphocytes, suggesting genetic risk is exerted through altered gene regulation. Data remain scarce on how epigenetic variance contributes to disease risk in paediatric SLE (pSLE). We aim to identify differences in epigenetically regulated chromatin architecture in treatment-naive patients with pSLE compared with healthy children. METHODS: Using the assay for transposase-accessible chromatin with sequencing (ATACseq), we surveyed open chromatin in 10 treatment-naive patients with pSLE, with at least moderate disease severity, and 5 healthy children. We investigated whether regions of open chromatin unique to patients with pSLE demonstrate enrichment for specific transcriptional regulators, using standard computational approaches to identify unique peaks and a false discovery rate of <0.05. Further analyses for histone modification enrichment and variant calling were performed using bioinformatics packages in R and Linux. RESULTS: We identified 30 139 differentially accessible regions (DAR) unique to pSLE B cells; 64.3% are more accessible in pSLE than healthy children. Many DAR are found in distal, intergenic regions and enriched for enhancer histone marks (p=0.027). B cells from adult patients with SLE contain more regions of inaccessible chromatin than those in pSLE. In pSLE B cells, 65.2% of the DAR are located within or near known SLE haplotypes. Further analysis revealed enrichment of transcription factor binding motifs within these DAR that may regulate genes involved in pro-inflammatory responses and cellular adhesion. CONCLUSIONS: We demonstrate an epigenetically distinct profile in pSLE B cells when compared with healthy children and adults with lupus, indicating that pSLE B cells are predisposed for disease onset/development. Increased chromatin accessibility in non-coding genomic regions controlling activation of inflammation suggest that transcriptional dysregulation by regulatory elements controlling B cell activation plays an important role in pSLE pathogenesis.

Progress in the Metabolomics of Acute Coronary Syndrome.

Acute coronary syndrome (ACS) is a severe type of coronary heart disease (CHD) with increasing prevalence and significant challenges for prevention and treatment. Metabolomics is an emerging technology with intrinsic dynamics and flexibility to better delineate the phenotypic and metabolic alterations in organisms at the time of altered pathological states. It provides new insights into the complex pathological mechanisms of cardiovascular disease and contributes to the early detection, monitoring and evaluation of ACS. In this review, we analyze and summarize the literature related to ACS metabolomics which has contributed to the diagnosis and prevention of ACS.

Pulmonary Hypertension Caused by Fibrosing Mediastinitis.

Pulmonary hypertension (PH) is a progressive and severe disorder in pulmonary hemodynamics. PH can be fatal if not well managed. Fibrosing mediastinitis (FM) is a rare and benign fibroproliferative disease in the mediastinum, which may lead to pulmonary vessel compression and PH. PH caused by FM (PH-FM) is a pathologic condition belonging to group 5 in the World Health Organization PH classification. PH-FM has a poor prognosis because of a lack of effective therapeutic modalities and inappropriate diagnosis. With the development of percutaneous pulmonary vascular interventional therapy, the prognosis of PH-FM has been greatly improved in recent years. This article provides a comprehensive review on the epidemiology, pathophysiologic characteristics, clinical manifestations, diagnostic approaches, and treatment modalities of PH-FM based on data from published reports and our medical center with the goal of facilitating the diagnosis and treatment of this fatal disease.

Analysis of chromatin data supports a role for CD14+ monocytes/macrophages in mediating genetic risk for juvenile idiopathic arthritis.

Introduction: Genome wide association studies (GWAS) have identified multiple regions that confer genetic risk for the polyarticular/oligoarticular forms of juvenile idiopathic arthritis (JIA). However, genome-wide scans do not identify the cells impacted by genetic polymorphisms on the risk haplotypes or the genes impacted by those variants. We have shown that genetic variants driving JIA risk are likely to affect both innate and adaptive immune functions. We provide additional evidence that JIA risk variants impact innate immunity. Materials and methods: We queried publicly available H3K4me1/H3K27ac ChIP-seq data in CD14+ monocytes to determine whether the linkage disequilibrium (LD) blocks incorporating the SNPs that tag JIA risk loci showed enrichment for these epigenetic marks. We also queried monocyte/macrophage GROseq data, a functional readout of active enhancers. We defined the topologically associated domains (TADs) encompassing enhancers on the risk haplotypes and identified genes within those TADs expressed in monocytes. We performed ontology analyses of these genes to identify cellular processes that may be impacted by these variants. We also used whole blood RNAseq data from the Genotype-Tissue Expression (GTEx) data base to determine whether SNPs lying within monocyte GROseq peaks influence plausible target genes within the TADs encompassing the JIA risk haplotypes. Results: The LD blocks encompassing the JIA genetic risk regions were enriched for H3K4me1/H3K27ac ChIPseq peaks (p=0.00021 and p=0.022) when compared to genome background. Eleven and sixteen JIA were enriched for resting and activated macrophage GROseq peaks, respectively risk regions (p=0.04385 and p=0.00004). We identified 321 expressed genes within the TADs encompassing the JIA haplotypes in human monocytes. Ontological analysis of these genes showed enrichment for multiple immune functions. Finally, we found that SNPs lying within the GROseq peaks are strongly associated with expression levels of plausible target genes in human whole blood. Conclusions: These findings support the idea that both innate and adaptive immunity are impacted by JIA genetic risk variants.

Origin and Fate of Acrolein in Foods.

Acrolein is a highly toxic agent that may promote the occurrence and development of various diseases. Acrolein is pervasive in all kinds of foods, and dietary intake is one of the main routes of human exposure to acrolein. Considering that acrolein is substantially eliminated after its formation during food processing and re-exposed in the human body after ingestion and metabolism, the origin and fate of acrolein must be traced in food. Focusing on molecular mechanisms, this review introduces the formation of acrolein in food and summarises both in vitro and in vivo fates of acrolein based on its interactions with small molecules and biomacromolecules. Future investigation of acrolein from different perspectives is also discussed.

Formation and Identification of Six Amino Acid - Acrylamide Adducts and Their Cytotoxicity Toward Gastrointestinal Cell Lines.

Acrylamide (AA) is a food contaminant, and amino acids are suggested to mitigate its toxicity by forming adducts. The emergence of acrylamide adducts may cause underestimation of acrylamide exposure level as well as trigger new safety problems. Based on the acrylamide elimination capability of four amino acids, this study chemically synthesized six amino acid-acrylamide adducts. Their structures were analyzed, followed by content determination in 10 commercially baking foods. The Michael adduct formed by one molecule of γ-aminobutyric acid (GABA) and acrylamide was most abundant in foods among six adducts. Furthermore, it markedly decreased the cytotoxicity of acrylamide in Caco-2 cells and GES-1 cells. This finding suggests that amino acids can be used to reduce acrylamide level in processed foods and mitigate its hazardous effects after intake.

Glycine and serine markedly eliminate methylglyoxal in the presence of formaldehyde via the formation of imidazole salts.

l-glycine and l-serine are the building blocks of proteins and exhibit various biological activities. This work found that l-glycine and l-serine show low scavenging capacity for methylglyoxal at moderate conditions (pH 7.0, 37 °C). However, they efficiently eliminate methylglyoxal and formaldehyde when the two aldehydes co-exist, via generation of imidazole salt, a compound formed by one molecule of methylglyoxal and formaldehyde, and two molecules of amino acids. The imidazole salts were identified in biscuits and fried potato crisps. Moreover, the formation of imidazole salts greatly decreased the cytotoxicity of their precursors, methylglyoxal and formaldehydes. This finding suggests that glycine and serine can be used to scavenge these two harmful aldehydes both after intake and during food processing.

Design of a naphthalimide-based probe for acrolein detection in foods and cells.

Acrolein is a highly toxic agent that can be generated exogenously and endogenously. Therefore, a highly specific and sensitive probe for acrolein with potential applications in acrolein detection must be developed. In this research, a novel fluorescent probe named "probe for acrolein detection" (Pr-ACR) was designed and synthesized based on a naphthalimide fluorophore skeleton, and a thiol group (-SH) was introduced into its structure for acrolein recognition. The -SH traps acrolein via Michael addition and the resultant interaction product of the probe inhibits the photoinduced electron transfer process and produce a strong fluorescence at 510 nm. The probe showed high sensitivity and specificity for acrolein. HPLC-MS/MS analysis verified that it can be used to quantify acrolein in foods, such as soda crackers, red wine, and baijiu, with a fluorescence spectrophotometer. After methyl esterification, the methyl esterified probe (mPr-ACR) successfully visualised acrolein in Hela cells under a laser scanning confocal microscope. This finding proved that Pr-ACR and mPr-ACR are potential tools for the detection and visualisation of acrolein from different sources.

CD4+ T cells from children with active juvenile idiopathic arthritis show altered chromatin features associated with transcriptional abnormalities.

Juvenile idiopathic arthritis (JIA) is one of the most common chronic diseases in children. While clinical outcomes for patients with juvenile JIA have improved, the underlying biology of the disease and mechanisms underlying therapeutic response/non-response are poorly understood. We have shown that active JIA is associated with distinct transcriptional abnormalities, and that the attainment of remission is associated with reorganization of transcriptional networks. In this study, we used a multi-omics approach to identify mechanisms driving the transcriptional abnormalities in peripheral blood CD4+ T cells of children with active JIA. We demonstrate that active JIA is associated with alterations in CD4+ T cell chromatin, as assessed by ATACseq studies. However, 3D chromatin architecture, assessed by HiChIP and simultaneous mapping of CTCF anchors of chromatin loops, reveals that normal 3D chromatin architecture is largely preserved. Overlapping CTCF binding, ATACseq, and RNAseq data with known JIA genetic risk loci demonstrated the presence of genetic influences on the observed transcriptional abnormalities and identified candidate target genes. These studies demonstrate the utility of multi-omics approaches for unraveling important questions regarding the pathobiology of autoimmune diseases.

Whole blood transcriptome biomarkers of unruptured intracranial aneurysm.

BACKGROUND: The rupture of an intracranial aneurysm (IA) causes devastating subarachnoid hemorrhages, yet most IAs remain undiscovered until they rupture. Recently, we found an IA RNA expression signature of circulating neutrophils, and used transcriptome data to build predictive models for unruptured IAs. In this study, we evaluate the feasibility of using whole blood transcriptomes to predict the presence of unruptured IAs. METHODS: We subjected RNA from peripheral whole blood of 67 patients (34 with unruptured IA, 33 without IA) to next-generation RNA sequencing. Model genes were identified using the least absolute shrinkage and selection operator (LASSO) in a random training cohort (n = 47). These genes were used to train a Gaussian Support Vector Machine (gSVM) model to distinguish patients with IA. The model was applied to an independent testing cohort (n = 20) to evaluate performance by receiver operating characteristic (ROC) curve. Gene ontology and pathway analyses investigated the underlying biology of the model genes. RESULTS: We identified 18 genes that could distinguish IA patients in a training cohort with 85% accuracy. This SVM model also had 85% accuracy in the testing cohort, with an area under the ROC curve of 0.91. Bioinformatics reflected activation and recruitment of leukocytes, activation of macrophages, and inflammatory response, suggesting that the biomarker captures important processes in IA pathogenesis. CONCLUSIONS: Circulating whole blood transcriptomes can detect the presence of unruptured IAs. Pending additional testing in larger cohorts, this could serve as a foundation to develop a simple blood-based test to facilitate screening and early detection of IAs.

Classification models using circulating neutrophil transcripts can detect unruptured intracranial aneurysm.

BACKGROUND: Intracranial aneurysms (IAs) are dangerous because of their potential to rupture. We previously found significant RNA expression differences in circulating neutrophils between patients with and without unruptured IAs and trained machine learning models to predict presence of IA using 40 neutrophil transcriptomes. Here, we aim to develop a predictive model for unruptured IA using neutrophil transcriptomes from a larger population and more robust machine learning methods. METHODS: Neutrophil RNA extracted from the blood of 134 patients (55 with IA, 79 IA-free controls) was subjected to next-generation RNA sequencing. In a randomly-selected training cohort (n = 94), the Least Absolute Shrinkage and Selection Operator (LASSO) selected transcripts, from which we constructed prediction models via 4 well-established supervised machine-learning algorithms (K-Nearest Neighbors, Random Forest, and Support Vector Machines with Gaussian and cubic kernels). We tested the models in the remaining samples (n = 40) and assessed model performance by receiver-operating-characteristic (ROC) curves. Real-time quantitative polymerase chain reaction (RT-qPCR) of 9 IA-associated genes was used to verify gene expression in a subset of 49 neutrophil RNA samples. We also examined the potential influence of demographics and comorbidities on model prediction. RESULTS: Feature selection using LASSO in the training cohort identified 37 IA-associated transcripts. Models trained using these transcripts had a maximum accuracy of 90% in the testing cohort. The testing performance across all methods had an average area under ROC curve (AUC) = 0.97, an improvement over our previous models. The Random Forest model performed best across both training and testing cohorts. RT-qPCR confirmed expression differences in 7 of 9 genes tested. Gene ontology and IPA network analyses performed on the 37 model genes reflected dysregulated inflammation, cell signaling, and apoptosis processes. In our data, demographics and comorbidities did not affect model performance. CONCLUSIONS: We improved upon our previous IA prediction models based on circulating neutrophil transcriptomes by increasing sample size and by implementing LASSO and more robust machine learning methods. Future studies are needed to validate these models in larger cohorts and further investigate effect of covariates.