bluuebunny/crossref_metadata_2025_split huggingface dataset:
Novel Assay for Detection of Progesterone Receptor-Interacting Endocrine Disruptors
Authors: Stavreva Diana A , Varticovski Lyuba , Raziuddin Razi , Hager Gordon L 
Published: May 2021

Abstract
The presence of progesterone receptor (PR)-interacting compounds in the environment may have serious health consequences for humans and wildlife, but the methods for their detection and monitoring are limited. Here we report the development and testing of a cell line expressing a chimeric construct containing ligand-binding domain of progesterone receptor and green fluorescent protein-tagged domain of the glucocorticoid receptor (GFP-GR-PR) under tetracycline regulation. Unlike the constitutively nuclear PR, this chimera is cytoplasmic in the absence of the ligand and translocates to the nucleus in response to the hormone or its analogues. The GFP-GR-PR chimera maintains specificity for binding to progesterone and does not cross-react with GR-activating hormones. A concentration- and time-dependent translocation in response to progesterone confirmed picomolar sensitivity for detecting PR ligands. Importantly, the assay can detect both agonist and antagonist activities and thus can be used for screening environmental samples for contamination with endocrine disruptors and for drug development. Using this approach, we screened water samples collected at 23 sites along 2 major rivers in Virginia: Mattaponi and Rappahannock Rivers. We detected a low, but reproducible PR-binding activity in 34.8 % of the sites tested. The calculated progesterone equivalent concentration (EQ) in some of these sites reached ~ 0.8 ng/L. The assay provides an effect-based approach for screening PR-interacting endocrine disrupting chemicals regardless of whether they exert agonist or antagonist activities. Either one could be seriously disruptive for the health of humans and wildlife.
Perchlorate and Nitrate Treatments Disrupt the Endoderm and Thyroid Development Through Epigenetic Mechanisms
Authors: Serrano-Nascimento Caroline 
Published: May 2021

Abstract
Nitrate and perchlorate competitively inhibit iodide uptake in thyrocytes and disrupt thyroid function in rodents and humans. Our previous data indicated that the intrauterine exposure to perchlorate or nitrate induced thyroid dysfunction in the offspring rats during adult life. Therefore, this study aimed to investigate the effects of these endocrine disruptors during the embryonic period on the endoderm and thyroid development. Additionally, it was also investigated the role of epigenetic modifications in the programming of gene expression of the evaluated tissues. For this purpose, CD1 pregnant female mice received filtered water (control) or filtered water supplemented with sodium perchlorate (0.3 or 1 ppm) or sodium nitrate (20 or 50 ppm). At gestational day 16.5 (GD16.5), the embryonic thyroid lobes were collected and processed for molecular analysis. Besides the in vivo model, the effect of these thyroid disruptors was also evaluated during the differentiation of mouse embryonic stem cells (mESc) into endoderm and thyroid cells. Endoderm cells differentiation was achieved through the treatment of mESc with several growth factors. During the entire protocol the cells were exposed or not to sodium perchlorate or sodium nitrate (10-5 or 10-7 M). The effects of perchlorate and nitrate were also evaluated during the differentiation of mESC into thyroid cells. For this purpose, mESC-derived endoderm cells were transiently transfected with Pax8/Nkx2.1 expressing vectors. During the endoderm-to-thyrocytes differentiation protocol, the cells were also exposed or not to perchlorate or nitrate (10-5 or 10-7 M). The results demonstrated that both thyroid disruptors reduced the mRNA and protein expression of several endoderm markers (Foxa1, Gata4, Sox17) in the mESc-derived endoderm cells. Moreover, perchlorate or nitrate treatment also reduced the expression of thyroid transcription factors (Pax8, Nkx2.1, Foxe1) and thyroid differentiation markers (Slc5a5, Tpo, Tshr, Tg) both in the embryonic thyroid lobes and in the mESc-derived thyrocytes. Epigenetic mechanisms related to transcription repression seem to be involved in the gene expression downregulation both in vivo and in vitro, since perchlorate and nitrate increased the mRNA expression of Dnmt1, Dnmt3, Hdac and reduced the expression of Hat. Additionally, the methylation of histone H3 was increased, and the acetylation status of this histone was decreased in perchlorate- or nitrate-exposed thyroid lobes and mESc-derived endoderm/thyroid cells. In conclusion, our data strongly suggest that the programming of thyroid dysfunction induced by intrauterine exposure to perchlorate or nitrate involve the disruption of the endoderm and thyroid development during embryonic life through epigenetic mechanisms.
Interactome Profile of Visceral Adipose Tissue in Obesity Links Key Genes to Cancer Pathogenesis
Authors: Roy Dipayan , Modi Anupama , Purohit Purvi 
Published: May 2021

Abstract
Obesity increases the risk of the development of several malignancies. The visceral adipose tissue (VAT) depot is one of the pivotal contributors behind the obesity-related pathogenetic mechanisms. In this study, we analyzed the differential gene expression profile in the VAT of obese children using two Gene Expression Omnibus datasets. GSE29718 and GSE9624 were sorted and 68 common differentially expressed genes (DEG) with fold change 1.5 upregulation or downregulation (cutoff |logFC|≥0.58496) were obtained. Gene ontology and functional enrichment and protein-protein interaction (PPI) network for the DEG were analyzed in Search Tool for the Retrieval of Interacting Genes (STRING), which revealed 37 biological processes, 3 cellular components, and 1 molecular function to be significantly associated. Reactome pathway analysis showed the DEG to be involved in- one carbon pool by folate, glycine degradation, transcriptional regulation by TP53, ERK inactivation, G1/S-specific transcription, Fanconi anemia pathway, beta-catenin phosphorylation cascade, RAF activation, and negative regulation of the MAPK pathway. The PPI network was set with a minimum interaction score of 0.400 and a maximum of 10 interactions, and it was significantly enriched (p-value 0.047) with 66 nodes and 46 edges. Target prediction was performed using miRNet. Several miRNA, including hsa-miR-1-3p, hsa-let-7b-5p, hsa-miR-16-5p, hsa-miR-27a-3p and hsa-miR-34a-5p were part of the mRNA-miRNA interaction network. Using the CytoHubba plugin in Cytoscape, the top 10 hub genes from the PPI network were discovered. Thymidine phosphorylase (TYMP) and dihydrofolate reductase (DHFR), essential components of nucleic acid metabolism, have been shown to be involved in angiogenesis and endothelial cell growth, and correlated to p53 mutations, respectively. Protein phosphatase 2, regulatory subunit A & regulatory subunit B (PPP2R1A and PPP2R1B) mutations are involved in ovarian, endometrial, lung and colorectal cancers. HLA-DQA1 mutation is involved cervical cancer, and it is involved in increased immune sensitivity and liver damage in breast cancer patients. The RAB7Ab and RAB7-interacting lysosomal protein (RILP) are regulators of endo-lysosomal trafficking and suppresses breast cancer cell invasion. To conclude, this study identifies several genes and their regulatory pathways in VAT which may contribute to the increased risk of cancer pathogenesis in obese individuals.
Electronic Health Record-Based Genome-Wide Meta-Analysis Identifies New Susceptibility Loci for Non-Alcoholic Fatty Liver Disease
Authors: Ghodsian Nooshin , Abner Erik , Gobeil Émilie , Taba Nele , Amand Alexis St- , Perrot Nicolas , Couture Christian , Bossé Yohan , Mitchell Patricia , Vohl Marie-Claude , Thériault Sébastien , Tchernof André , Esko Tõnu , Mathieu Patrick , Arsenault Benoit 
Published: May 2021

Abstract
Background: Non-alcoholic fatty liver disease (NAFLD) is the most prevalent form of liver disease. Observational studies documented associations of NAFLD with several chronic and infectious diseases but whether these associations underlie causal effects is unknown. The molecular mechanisms and genetic architecture of NAFLD are poorly understood. Our objectives were to identify genetic loci associated with NAFLD and determine whether the presence of NAFLD was causally associated with human diseases.
Methods: We created a NAFLD genetic instrument through the identification of independent single-nucleotide polymorphisms (SNPs) associated with NAFLD in a meta-analysis of genome-wide association study (GWAS) (6715 cases and 682,748 controls). Using inverse-variance weighted Mendelian Randomization (MR), we investigated the impact of NAFLD on human disease-related phenotypes in the UK Biobank and FinnGen cohorts as well as in the COVID-19 host genetics initiative. Results: We first performed a GWAS meta-analysis of four cohorts and found variants significantly associated with NAFLD (p&lt;5.0E-8) at six genetic loci (MTARC1, GCKR, TRIB1, LMO3, SUGP1 [TM6SF2] and PNPLA3). Using a risk factor informed Bayesian approach (bGWAS), we identify variants at three additional loci (LPL, FTO, and APOE). To determine if the association between NAFLD and human diseases shows evidence of causality, we performed MR across the human disease-related phenome (&gt;800 diseases) using a genetic instrument for NAFLD. Results of these analyses suggest that NAFLD was not causally associated with diseases outside the spectrum of liver diseases. We also found no causal association between genetically predicted NAFLD and COVID-19-related outcomes.
Conclusions: This study identified several new genetic loci associated with NAFLD. NAFLD was not causally associated with diseases outside those of the spectrum of liver diseases. This finding suggests that the resolution of NAFLD might not prevent other diseases previously associated with NAFLD.
In-Silico Analysis of Key Regulatory Pathways and Hub Genes From Peripheral Blood in Type 2 Diabetes Mellitus
Authors: Purohit Purvi , Roy Dipayan , Modi Anupama 
Published: May 2021

Abstract
AbstractBackground: Type II diabetes mellitus (T2DM), characterized by fasting hyperglycemia and impaired insulin secretion and action, is a global health burden. Despite the advances in this field, the mechanism underlying T2DM is far from clear. Objective: The present study sheds light upon a systematic evaluation of the genes, pathways, and interaction networks underlying T2DM with the aid of bioinformatics. Methods: Two Gene Expression Omnibus microarray datasets: GSE148961 and GSE26168 were selected for this study. The common differentially expressed genes (DEG) were sorted by the cutoff |logFC|≥1.0 for the first dataset and |logFC|≥0.263 for the second. Gene Ontology (GO), functional enrichment, and protein-protein interaction (PPI) network were analyzed in Search Tool for the Retrieval of Interacting Genes (STRING). The MCODE and CytoHubba plugins in Cytoscape (v3.7.2) were used to identify gene clusters and top hub genes, respectively. Top 10 nodes were ranked in CytoHubba according to MCC, DMNC, MNC, Degree, and EPC methods, and genes common in at least 3 methods were selected as top nodes. Results: 88 common DEGs were identified by Venn diagram (http://bioinformatics.psb.ugent.be/cgi-bin/liste/Venn/calculate_venn.htpl). GO analysis had 91 significantly enriched biological processes, including regulated exocytosis, secretion, vesicle mediated transport, antibacterial humoral response, and neutrophil degranulation. 4 molecular functions- fibrinogen binding, fibronectin binding, lipopolysaccharide binding, and Extracellular matrix binding; and 38 cellular components, including secretory vesicle, endomembrane system, and adherens junction were significant. The PPI network was highly significant (p-value &lt; 0.001) at medium confidence (0.400) with 88 nodes, 140 edges, and an average node degree of 3.18. The MCODE plugin revealed two clusters, the former with 14 nodes, 73 edges, and a score of 9.733, and the latter with 6 nodes, 14 edges, and a score of 4.000. 9 candidate genes: ELANE, DEFA4, BPI, MPO, LTF, CAMP, OLFM4, LCN2, and VCL were identified, amongst which ELANE, LCN2, and MPO are associated with T2DM pathogenesis, while BPI and LTF have protective effects. OLFM4 deletion has been observed to improve glucose tolerance in mice models. Conclusion: This study provides a comprehensive analysis of genes, pathways, and functions which may be pivotal in T2DM pathogenesis and may represent potential therapeutic targets.
MicroRNA 29 Family Serves a Key Role in Lung Development and the Prevention of Lung Pathology
Authors: Mishra Ritu , Mendelson Carole R 
Published: May 2021

Abstract
Even with remarkable advances in the care of preterm infants, chronic lung disease in the form of bronchopulmonary dysplasia (BPD) continues to be a significant pathologic consequence of prematurity. BPD is caused by the interruption of physiologic lung development and exposure of the immature newborn lung to high O2 tensions. BPD is characterized by a simplified alveolar structure, arrested lung growth, impaired vascular development and lung fibrosis (1). To identify effective treatment strategies for BPD, it is important to understand the molecular mechanisms underlying this disorder. MicroRNAs (miRNA, miR) are known to regulate growth, development and repair of the developing lung; whereas, dysregulation of miRNA expression has been associated with pulmonary disease. Specifically, members of the miR-29 family have been linked to pulmonary cancers, fibrosis, and BPD. Previous studies from our laboratory indicate that developmental induction of miR-29 expression in the fetal lung near term serves a key role in promoting surfactant-producing type II cell differentiation and function through repression of TGF-β2 signaling (2). To understand the role of miR-29 in protection against BPD, in the present study, we created mice in which the entire miR-29 family (miR-29a/b1 and miR-29b2/c) (miR-29 dKO) was disrupted. Upon exposure of miR-29 dKO and WT neonatal mice to hyperoxia (95% O2) for 5 days immediately after birth, expression levels of the proinflammatory cytokines and chemokines, IL-1 β, TGF-β1, CXCL2 and IL-6, were significantly increased in the lungs of miR-29 dKO mice, compared to WT. Furthermore, lungs of miR-29 dKO adult mice manifested increased expression of their direct targets, TGF-β2 and TGF-β3. This was associated with increased collagen deposition, as evidenced by enhanced trichrome staining, suggesting the development of lung fibrosis. HDAC4 (a direct target of miR-29) and proinflammatory TNF-α, which have been implicated in pulmonary fibrosis, also were upregulated in the lungs of miR-29 dKO mice. Overall, our studies suggest a key role of the miR-29 family and its targets in prevention of inflammatory and profibrotic signaling in the neonatal lung leading to lung pathology.
Supported by: NIH R01-HL050022 (C.R.M.)
References: (1)Michael, Zoe, et al. “Bronchopulmonary dysplasia: an update of current pharmacologic therapies and new approaches.” Clinical Medicine Insights: Pediatrics 12 (2018): 1179556518817322.(2)Guo, Wei, Houda Benlhabib, and Carole R. Mendelson. “The microRNA 29 family promotes type II cell differentiation in developing lung.” Molecular and cellular biology 36.16 (2016): 2141-2141.
Novel Mutations in FGFR1 Causing Idiopathic Hypogonadotropic Hypogonadism: A Cohort Study in Eastern Indian Population
Authors: Baidya Arjun , Datta Saptarshi , Mukhopadhyay Satinath , Roy Sib Shankar 
Published: May 2021

Abstract
Introduction: IHH is a clinically and genetically heterogeneous condition with more than 80 different mutations described in literature, some of the important being KAL-1 (anosmin), fibroblast growth factor receptor-1 (FGFR1) and fibroblast growth factor-8 (FGF8). Objective: To characterize the clinical findings and molecular analysis of FGFR1 (KAL2) genes in 10 unrelated patients of idiopathic hypogonadotropic hypogonadism with and without hyposmia/anosmia. Methods: After confirming the diagnosis of IHH from detailed history, clinical and biochemical examination the patients were subjected to MRI of pituitary hypothalamic area and olfactory bulb and tract. For genetic analysis PCR of 18 exons was performed on the genomic DNA. The PCR products were purified, sequenced and analysed using BLAST search from NCBI GenBank. Results: We diagnosed ten unrelated sporadic cases of IHH (9 male and 1 female). Out of 10 cases 6 (60%) had anosmia (KS) 4 had normosmia. A variable degree of pubertal development was observed, including various clinical abnormalities, such as micropenis, dental agenesis, skeletal deformity, seizure disorder and bimanual synkinesis. All the patients who had anosmia (KS) had either hypoplasia or aplasia of olfactory bulb and tract on MRI. Two KS patients had novel sporadic FGFR1 mutation, one had a mutation n.2370 C&gt;A detected at exon 10 of FGFR1 gene and another had a mutation n.1875 GA&gt;CA at exon 8C of FGFR1 gene. Discussion: Loss-of-function sequence variants in FGFR1, encoding the fibroblast growth factor receptor-1, account for one autosomal dominant form of KS. Pathogenic changes in KAL1 or FGFR1 have been detected in approximately 20% of the KS patients, which indicates that other responsible genes are still to be discovered. FGFR1 comprises an extracellular region consisting of three immunoglobulin-like domains (D1-D3), a single transmembrane helix, and an intracellular region containing the tyrosine kinase domain. D2, D3 and the short linker between them house all the determinants of ligand (FGF) binding and specificity. In addition, alternative splicing of exon 8, encoding the D3 C-terminal half, leads to two FGFR1 isoforms, FGFR1b (exon 8A) and FGFR1c (exon 8B), with different specificities towards FGF ligands. All the pathogenic changes in FGFR1 that have been reported in KS so far disrupt both isoforms of FGFR1 i.e. FGF1b and FGF1c, therefore leaving open the question of which isoform(s) is (are) required in the olfactory bulb morphogenetic process. We identified a new mutation in exon 8C (patient no 2). Conclusions: IHH and KS patients present with broad spectrum of clinical manifestations. We identified two novel mutations in FGFR1 gene in two unrelated sporadic cases of KS in the Indian population.
RNA Decay Controls the Kinetics of the Angiotensin II Gene Expression Response
Authors: Wellman Kimberly , Fu Rui , Baldwin Amber , Riemondy Kent , Mukherjee Neelanjan 
Published: May 2021

Abstract
Complex cellular resonses require the temporal coordination of stimulus-induced gene expression programs. Angiotensin II (AngII) is the active 8 amino acid peptide in the renin-angiotensin-aldosterone system that controls blood pressure and fluid balance. AngII binds to type I angiotensin receptor in the adrenal cortex to initiate a cascade of temporally coordinated events leading to the production of aldosterone, a master regulator of blood pressure and volume. We stimulated a steroidogenic human cell line (H295R) with AngII and performed RNA-seq at twelve points. We identified twelve distict temporally distinct groups of gene expression responses each encoding functionally related proteins important for various steps of aldosterone productionl. Interstingly, the shape of the impulse response suggested a key role for RNA decay. Indeed, RNA decay rates in unstimulated H295R cells strongly correlated with the amplitude and peakiness of the gene expression response for each group of genes. We also found evidence for increases in RNA decay during the AngII response. Next, we selected candidate RBPs based on motif finding, adrenal specific expression, and AngII responsiveness. We performed an siRNA knockdown screen on these 22 candidates to identify RBPs that regulate aldosterone levels. Eight of these RBPs exhibited statistically significant changes in aldosterone for at least two independent siRNAs. Interestingly, multiple RBPs that promote RNA decay were found to suppress aldosterone production and induced in response to AngII-stimulation. These RBPs could be responsible for our observed increases in RNA decay. Altogether, these data support a model in which RNA decay is a critical regulator of the timing and strength of AngII-induced gene expression and ultimately aldosterone production.
The rs2442598 Polymorphism in ANGPT-2 Gene Is Associated With Risk for Diabetic Retinopathy in Patients With Type 1 Diabetes Mellitus From a Brazilian Population
Authors: Dieter Cristine , Lemos Natália Emerim , Canani Luis Henrique , Bauer Andrea C , Crispim Daisy 
Published: May 2021

Abstract
Introduction: Angiopoietin-2 (ANGPT-2) is a member of a growth factor family that binds to the endothelial receptor tyrosine kinase 2 and regulates vascular development and function. Under hyperglycemic conditions, ANGPT-2 is upregulated and leads to vascular destabilization, pericyte dropout, and aggravation of inflammation. In this context, studies have reported the involvement of ANGPT-2 in the pathogenesis of diabetic retinopathy (DR). Thus, polymorphisms in ANGPT-2 gene may be of interest in this field. Objective: To investigate the association between the rs2442598 polymorphism in the ANGPT-2 gene and DR. Methods: This case-control study comprised 107 patients with type 1 diabetes mellitus (T1DM) and DR (cases) and 129 patients with T1DM without DR (controls) and with ≥10 years of DM. The ANGPT-2 rs2442598 (G/A) polymorphism was genotyped by real-time PCR using TaqMan MGB probes. Results: Genotype distributions of this polymorphism were consistent with Hardy-Weinberg Equilibrium. Frequency of the rs2442598 A allele was higher in cases compared to controls (P= 0.011). Moreover, the A/A genotype was higher in cases than controls (P= 0.017) and was associated with risk for DR after adjustment for duration of DM, HbA1c, triglycerides, estimated glomerular filtration rate, and presence of hypertension (OR= 5.19, IC95% 1.21 - 22.27). This association was maintained under the recessive (OR= 4.78, IC95% 1.14 - 19.99) and additive (OR= 6.861, IC95% 1.45 - 32.38) inheritance models. Conclusion: Our data demonstrate, for the first time, the association of the ANGPT-2 rs2442598 A allele with risk for DR in T1DM patients from Southern Brazil.