scholarly journals A novel mouse model expressing human forms for complement receptors CR1 and CR2

2019 ◽  
Author(s):  
Harriet M. Jackson ◽  
Kate E. Foley ◽  
Rita O’Rourke ◽  
Timothy M. Stearns ◽  
Dina Fathalla ◽  
...  
Keyword(s):  
Mouse Model ◽  
Lupus Erythematosus ◽  
Transcriptional Profiling ◽  
Enrichment Analysis ◽  
Cell Number ◽  
Gene Set Enrichment Analysis ◽  
Human Populations ◽  
Complement Cascade ◽  
Complement Receptors ◽  
Human Complement

AbstractThe complement cascade is increasingly implicated in development of a variety of diseases with strong immune contributions such as Alzheimer’s disease and Systemic Lupus Erythematosus. Mouse models have been used to determine function of central components of the complement cascade such as C1q and C3. However, species differences in their gene structures mean that mice do not adequately replicate human complement regulators, including CR1 and CR2. Genetic variation in CR1 and CR2 have been implicated in modifying disease states but the mechanisms are not known. To decipher the roles of human CR1 and CR2 in health and disease, we engineered C57BL/6J (B6) mice to replace endogenous murine Cr2 with human complement receptors, CR1 and CR2 (B6.CR2CR1). CR1 has an array of allotypes in human populations and using traditional recombination methods (Flp-frt and Cre-loxP) two of the most common alleles (referred to as CR1long and CR1short) are replicated within this mouse model, along with a CR1 knockout allele (CR1KO). Transcriptional profiling of spleens and brains identifies genes and pathways differentially expressed between mice homozygous for either CR1long, CR1short or CR1KO. Gene set enrichment analysis predicts hematopoietic cell number and cell infiltration are modulated by CR1long, but not CR1short or CR1KO. Therefore, this mouse model provides a novel tool for determining the relationship between human-relevant CR1 alleles and disease.Summary StatementWe present the creation and validation of a novel mouse model that expresses human forms of complement cascade regulators CR1 and CR2.

scholarly journals A novel mouse model expressing human forms for complement receptors CR1 and CR2

BMC Genetics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Harriet M. Jackson ◽  
Kate E. Foley ◽  
Rita O’Rourke ◽  
Timothy M. Stearns ◽  
Dina Fathalla ◽  
...  
Keyword(s):  
Mouse Model ◽  
Lupus Erythematosus ◽  
Transcriptional Profiling ◽  
Enrichment Analysis ◽  
Cell Number ◽  
Gene Set Enrichment Analysis ◽  
Human Populations ◽  
Complement Cascade ◽  
Complement Receptors ◽  
Human Complement

Abstract Background The complement cascade is increasingly implicated in development of a variety of diseases with strong immune contributions such as Alzheimer’s disease and Systemic Lupus Erythematosus. Mouse models have been used to determine function of central components of the complement cascade such as C1q and C3. However, species differences in their gene structures mean that mice do not adequately replicate human complement regulators, including CR1 and CR2. Genetic variation in CR1 and CR2 have been implicated in modifying disease states but the mechanisms are not known. Results To decipher the roles of human CR1 and CR2 in health and disease, we engineered C57BL/6J (B6) mice to replace endogenous murine Cr2 with human complement receptors, CR1 and CR2 (B6.CR2CR1). CR1 has an array of allotypes in human populations and using traditional recombination methods (Flp-frt and Cre-loxP) two of the most common alleles (referred to here as CR1long and CR1short) can be replicated within this mouse model, along with a CR1 knockout allele (CR1KO). Transcriptional profiling of spleens and brains identified genes and pathways differentially expressed between mice homozygous for either CR1long, CR1short or CR1KO. Gene set enrichment analysis predicts hematopoietic cell number and cell infiltration are modulated by CR1long, but not CR1short or CR1KO. Conclusion The B6.CR2CR1 mouse model provides a novel tool for determining the relationship between human-relevant CR1 alleles and disease.

scholarly journals Effects of IRF5 Lupus Risk Haplotype on Pathways Predicted to Influence B Cell Functions

2012 ◽  
Vol 2012 ◽  
pp. 1-12 ◽  
Author(s):  
Joel M. Guthridge ◽  
Daniel N. Clark ◽  
Amanda Templeton ◽  
Nicolas Dominguez ◽  
Rufei Lu ◽  
...  
Keyword(s):  
B Cell ◽  
Lupus Erythematosus ◽  
Enrichment Analysis ◽  
Cell Receptor ◽  
Gene Set Enrichment Analysis ◽  
Interferon Response ◽  
Risk Haplotype ◽  
Interferon Signature ◽  
Cell Functions ◽  
Gene Sets

Both genetic and environmental interactions affect systemic lupus erythematosus (SLE) development and pathogenesis. One known genetic factor associated with lupus is a haplotype of the interferon regulatory factor 5 (IRF5) gene. Analysis of global gene expression microarray data using gene set enrichment analysis identified multiple interferon- and inflammation-related gene sets significantly overrepresented in cells with the risk haplotype. Pathway analysis using expressed genes from the significant gene sets impacted by theIRF5risk haplotype confirmed significant correlation with the interferon pathway, Toll-like receptor pathway, and the B-cell receptor pathway. SLE patients with theIRF5risk haplotype have a heightened interferon signature, even in an unstimulated state (P=0.011), while patients with theIRF5protective haplotype have a B cell interferon signature similar to that of controls. These results identify multiple genes in functionally significant pathways which are affected by IRF5 genotype. They also establish the IRF5 risk haplotype as a key determinant of not only the interferon response, but also other B-cell pathways involved in SLE.

scholarly journals Increased mTOR activation in idiopathic multicentric Castleman disease

Blood ◽  
2020 ◽  
Vol 135 (19) ◽  
pp. 1673-1684 ◽  
Author(s):  
Daniel J. Arenas ◽  
Katherine Floess ◽  
Dale Kobrin ◽  
Ruth-Anne Langan Pai ◽  
Maya B. Srkalovic ◽  
...  
Keyword(s):  
Lymph Nodes ◽  
Lupus Erythematosus ◽  
Enrichment Analysis ◽  
Cell Types ◽  
Castleman Disease ◽  
Gene Set Enrichment Analysis ◽  
Mtor Inhibition ◽  
Multicentric Castleman Disease ◽  
Hematologic Disorder ◽  
Mtorc1 Signaling

Abstract Idiopathic multicentric Castleman disease (iMCD) is a rare and poorly understood hematologic disorder characterized by lymphadenopathy, systemic inflammation, cytopenias, and life-threatening multiorgan dysfunction. Interleukin-6 (IL-6) inhibition effectively treats approximately one-third of patients. Limited options exist for nonresponders, because the etiology, dysregulated cell types, and signaling pathways are unknown. We previously reported 3 anti-IL-6 nonresponders with increased mTOR activation who responded to mTOR inhibition with sirolimus. We investigated mTOR signaling in tissue and serum proteomes from iMCD patients and controls. mTOR activation was increased in the interfollicular space of iMCD lymph nodes (N = 26) compared with control lymph nodes by immunohistochemistry (IHC) for pS6, p4EBP1, and p70S6K, known effectors and readouts of mTORC1 activation. IHC for pS6 also revealed increased mTOR activation in iMCD compared with Hodgkin lymphoma, systemic lupus erythematosus, and reactive lymph nodes, suggesting that the mTOR activation in iMCD is not just a product of lymphoproliferation/inflammatory lymphadenopathy. Further, the degree of mTOR activation in iMCD was comparable to autoimmune lymphoproliferative syndrome, a disease driven by mTOR hyperactivation that responds to sirolimus treatment. Gene set enrichment analysis of serum proteomic data from iMCD patients (n = 88) and controls (n = 42) showed significantly enriched mTORC1 signaling. Finally, functional studies revealed increased baseline mTOR pathway activation in peripheral monocytes and T cells from iMCD remission samples compared with healthy controls. IL-6 stimulation augmented mTOR activation in iMCD patients, which was abrogated with JAK1/2 inhibition. These findings support mTOR activation as a novel therapeutic target for iMCD, which is being investigated through a trial of sirolimus (NCT03933904).

Abstract 29: Isolation of Cardiomyocytes Undergoing Mitosis with Complete Cytokinesis

2017 ◽  
Vol 121 (suppl_1) ◽  
Author(s):  
Hsiaoyun Y Milliron ◽  
Matthew Weiland ◽  
Megan Bowman ◽  
Stefan Jovinge
Keyword(s):  
Cell Cycle ◽  
Molecular Beacon ◽  
Transcriptional Profiling ◽  
Enrichment Analysis ◽  
Cardiac Regeneration ◽  
Gene Set Enrichment Analysis ◽  
Gene Expressions ◽  
M Phase ◽  
Cell Fractions ◽  
Phase Population

Adult cardiomyocytes (CMs) fail to exit the cell cycle and result in polyploidization and multi-nucleation. This extremely limited renewal potential is a key barrier for cardiac regeneration after heart injury. The use of traditional cell cycle assays such as Ki67 or purine analogue administration does not allow for isolation of viable CMs in late-M phase. We hypothesize that a molecular beacon (MB)-based method could be developed to isolate a highly pure population of hiPSC-derived CMs capable of completing mitosis and cytokinesis. We first differentiated human PSCs into cardiomyocytes using the small molecules CHIR and IWR and then applied MBs targeting CDC20 mRNAs, followed by fluorescence-activated cell sorting (FACS). Validation of cell cycle-specific and mitosis-associated gene expressions of cell fractions sorted from G2 and M-phase were performed by RT-qPCR prior to transcriptional profiling by single-cell RNA sequencing. Gene set enrichment analysis (GSEA) confirmed the observation of the gene ontology (GO) analysis. The ‘GO_cytokinesis’ and the ‘GO_cell separation after cytokinesis’ gene sets were highly enriched and predominantly upregulated in the CDC20 (+) (M-phase) population compared with the CDC20 (-) (G2-phase) population. Furthermore, using these data sets we expect to develop robust surface marker based flow cytometry protocols at a number and purity allowing for statistically significant genome-wide integrative transcriptome and epigenome analysis. In conclusion, the isolation of CMs using CDC20 MB and DNA content dye proved to enrich for cells that were confirmed by GSEA to be CMs in cytokinesis.

scholarly journals Comprehensive Analysis to Identify Key Genes Involved in Advanced Atherosclerosis

2021 ◽  
Vol 2021 ◽  
pp. 1-25
Author(s):  
Tian-ming Huo ◽  
Zhi-wei Wang
Keyword(s):  
Gene Expression ◽  
Network Analysis ◽  
Lupus Erythematosus ◽  
Inflammatory Responses ◽  
Therapeutic Targets ◽  
Enrichment Analysis ◽  
Gene Set Enrichment Analysis ◽  
Functional Enrichment ◽  
Hub Genes ◽  
Key Genes

Background. The study was aimed at finding accurate and effective therapeutic targets and deepening our understanding of the mechanisms of advanced atherosclerosis (AA). Methods. We downloaded the gene expression datasets GSE28829, GSE120521, and GSE43292 from Gene Expression Omnibus. Weighted gene coexpression network analysis (WGCNA) was performed for GSE28829, and functional enrichment analysis and protein–protein interaction network analysis were conducted on the key module. Significant genes in the key module were analyzed by molecular complex detection, and genes in the most important subnetwork were defined as hub genes. Multiple dataset analyses for hub genes were conducted. Genes that overlapped between hub genes and differentially expressed genes (DEGs) of GSE28829 and GSE120521 were defined as key genes. Further validation for key genes was performed using GSE28829 and GSE43292. Gene set enrichment analysis (GSEA) was applied to key genes. Results. A total of 77 significant genes in the key module of GSE28829 were screened out that were mainly associated with inflammation and immunity. The subnetwork was obtained from significant genes, and 18 genes in this module were defined as hub genes, which were related to immunity and expressed in multiple diseases, particularly systemic lupus erythematosus. Some hub genes were regulated by SPI1 and associated with the blood, spleen, and lung. After overlapping with DEGs of GSE28829 and GSE120521, a total of 10 genes (HCK, ITGAM, CTSS, TYROBP, LAPTM5, FCER1G, ITGB2, NCF2, AIF1, and CD86) were identified as key genes. All key genes were validated and evaluated successfully and were related to immune response pathways. Conclusion. Our study suggests that the key genes related to immune and inflammatory responses are involved in the development of AA. This may deepen our understanding of the mechanisms of and provide valuable therapeutic targets for AA.

scholarly journals Transcriptional Profiling Reveals Kidney Neutrophil Heterogeneity in Both Healthy People and ccRCC Patients

2021 ◽  
Vol 2021 ◽  
pp. 1-17
Author(s):  
Yiliang Meng ◽  
Kai Cai ◽  
Jingjie Zhao ◽  
Keyu Huang ◽  
Xiumei Ma ◽  
...  
Keyword(s):  
Transcriptional Profiling ◽  
Enrichment Analysis ◽  
Gene Set Enrichment Analysis ◽  
The Other ◽  
Renal Diseases ◽  
Gene Set Enrichment ◽  
Cell Renal Cell Carcinoma ◽  
Tumor Pathology ◽  
Healthy Donors ◽  
Immune Therapies

Neutrophil is known to critically impact the development of renal diseases (e.g., the clear cell renal cell carcinoma (ccRCC)), whereas the heterogeneity of neutrophils in ccRCC remains unclear. In the present study, kidney biopsies from healthy donors and ccRCC tissues were collected for single-cell RNA sequencing (scRNA-seq). In addition, the subpopulations of neutrophils in a healthy kidney and in the tumor microenvironment (TME) of ccRCC were expressed and then analyzed. The genes reported previously were mapped to all subpopulations identified here. On that basis, biological theme comparison and Gene Set Enrichment Analysis (GSEA) were employed to reveal and compare relevant biological functions. In a healthy kidney, neutrophils exhibit two subpopulations: one is more associated with renal autoimmunity, probably acting as therapeutic target; the other is suggested to resist infectious microorganisms. It is noteworthy that six subpopulations were identified in ccRCC biopsy, and two were more relevant to autoimmunity, while the other four are more relevant to the tumor pathology. Besides, ccRCC neutrophil could resist anticancer immune therapies of ipilimumab and pembrolizumab for their low/no expressions of CTLA-4, PD-1, and PD-L1. Thus, this study can help understand the heterogeneity and pathological significance of neutrophils in renal diseases.

scholarly journals CD16+ monocytes give rise to CD103+RALDH2+TCF4+ dendritic cells with unique transcriptional and immunological features

2018 ◽  
Vol 2 (21) ◽  
pp. 2862-2878 ◽  
Author(s):  
Vanessa Sue Wacleche ◽  
Amélie Cattin ◽  
Jean-Philippe Goulet ◽  
Dominique Gauchat ◽  
Annie Gosselin ◽  
...  
Keyword(s):  
Dendritic Cells ◽  
Meta Analysis ◽  
Transcriptional Profiling ◽  
Enrichment Analysis ◽  
Immature Stage ◽  
Gene Set Enrichment Analysis ◽  
Viral Pathogens ◽  
Genome Wide ◽  
Canonical Pathways

Abstract Classical CD16− vs intermediate/nonclassical CD16+ monocytes differ in their homing potential and biological functions, but whether they differentiate into dendritic cells (DCs) with distinct contributions to immunity against bacterial/viral pathogens remains poorly investigated. Here, we employed a systems biology approach to identify clinically relevant differences between CD16+ and CD16− monocyte-derived DCs (MDDCs). Although both CD16+ and CD16− MDDCs acquire classical immature/mature DC markers in vitro, genome-wide transcriptional profiling revealed unique molecular signatures for CD16+ MDDCs, including adhesion molecules (ITGAE/CD103), transcription factors (TCF7L2/TCF4), and enzymes (ALDH1A2/RALDH2), whereas CD16− MDDCs exhibit a CDH1/E-cadherin+ phenotype. Of note, lipopolysaccharides (LPS) upregulated distinct transcripts in CD16+ (eg, CCL8, SIGLEC1, MIR4439, SCIN, interleukin [IL]-7R, PLTP, tumor necrosis factor [TNF]) and CD16− MDDCs (eg, MMP10, MMP1, TGM2, IL-1A, TNFRSF11A, lysosomal-associated membrane protein 1, MMP8). Also, unique sets of HIV-modulated genes were identified in the 2 subsets. Further gene set enrichment analysis identified canonical pathways that pointed to “inflammation” as the major feature of CD16+ MDDCs at immature stage and on LPS/HIV exposure. Finally, functional validations and meta-analysis comparing the transcriptome of monocyte and MDDC subsets revealed that CD16+ vs CD16− monocytes preserved their superior ability to produce TNF-α and CCL22, as well as other sets of transcripts (eg, TCF4), during differentiation into DC. These results provide evidence that monocyte subsets are transcriptionally imprinted/programmed with specific differentiation fates, with intermediate/nonclassical CD16+ monocytes being precursors for pro-inflammatory CD103+RALDH2+TCF4+ DCs that may play key roles in mucosal immunity homeostasis/pathogenesis. Thus, alterations in the CD16+/CD16− monocyte ratios during pathological conditions may dramatically influence the quality of MDDC-mediated immunity.

Identification of key mRNAs, miRNAs, and mRNA-miRNA network involved in papillary thyroid carcinoma

2020 ◽  
Vol 15 ◽  
Author(s):  
Wei Han ◽  
Dongchen Lu ◽  
Chonggao Wang ◽  
Mengdi Cui ◽  
Kai Lu
Keyword(s):  
Papillary Thyroid Carcinoma ◽  
Thyroid Carcinoma ◽  
Differential Expression Analysis ◽  
Interaction Network ◽  
Enrichment Analysis ◽  
Gene Set Enrichment Analysis ◽  
Integrated Analysis ◽  
Papillary Thyroid ◽  
Gene Set Enrichment ◽  
Mirna Expression Data

Background: In the past decades, the incidence of thyroid cancer (TC) has been gradually increasing, owing to the widespread use of ultrasound scanning devices. However, the key mRNAs, miRNAs, and mRNA-miRNA network in papillary thyroid carcinoma (PTC) has not been fully understood. Material and Methods: In this study, multiple bioinformatics methods were employed, including differential expression analysis, gene set enrichment analysis, and miRNA-mRNA interaction network construction. Results: First, we investigated the key miRNAs that regulated significantly more differentially expressed genes based on GSEA method. Second, we searched for the key miRNAs based on the mRNA-miRNA interaction subnetwork involved in PTC. We identified hsa-mir-1275, hsa-mir-1291, hsa-mir-206 and hsa-mir-375 as the key miRNAs involved in PTC pathogenesis. Conclusion: The integrated analysis of the gene and miRNA expression data not only identified key mRNAs, miRNAs, and mRNA-miRNA network involved in papillary thyroid carcinoma, but also improved our understanding of the pathogenesis of PTC.

scholarly journals Placental Transcriptome Adaptations to Maternal Nutrient Restriction in Sheep

2021 ◽  
Vol 22 (14) ◽  
pp. 7654
Author(s):  
Chelsie B. Steinhauser ◽  
Colleen A. Lambo ◽  
Katharine Askelson ◽  
Gregory W. Burns ◽  
Susanta K. Behura ◽  
...  
Keyword(s):  
Mhc Class Ii ◽  
Killer Cell ◽  
National Research Council ◽  
Enrichment Analysis ◽  
Nutrient Utilization ◽  
Gene Set Enrichment Analysis ◽  
Nutrient Restriction ◽  
Placental Development ◽  
Gene Set Enrichment ◽  
Pregnant Sheep

Placental development is modified in response to maternal nutrient restriction (NR), resulting in a spectrum of fetal growth rates. Pregnant sheep carrying singleton fetuses and fed either 100% (n = 8) or 50% (NR; n = 28) of their National Research Council (NRC) recommended intake from days 35–135 of pregnancy were used to elucidate placentome transcriptome alterations at both day 70 and day 135. NR fetuses were further designated into upper (NR NonSGA; n = 7) and lower quartiles (NR SGA; n = 7) based on day 135 fetal weight. At day 70 of pregnancy, there were 22 genes dysregulated between NR SGA and 100% NRC placentomes, 27 genes between NR NonSGA and 100% NRC placentomes, and 22 genes between NR SGA and NR NonSGA placentomes. These genes mediated molecular functions such as MHC class II protein binding, signaling receptor binding, and cytokine activity. Gene set enrichment analysis (GSEA) revealed significant overrepresentation of genes for natural-killer-cell-mediated cytotoxicity in NR SGA compared to 100% NRC placentomes, and alterations in nutrient utilization pathways between NR SGA and NR NonSGA placentomes at day 70. Results identify novel factors associated with impaired function in SGA placentomes and potential for placentomes from NR NonSGA pregnancies to adapt to nutritional hardship.

scholarly journals Identification of candidate genes and pathways in retinopathy of prematurity by whole exome sequencing of preterm infants enriched in phenotypic extremes

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Sang Jin Kim ◽  
◽  
Kemal Sonmez ◽  
Ryan Swan ◽  
J. Peter Campbell ◽  
...  
Keyword(s):  
Exome Sequencing ◽  
Whole Exome Sequencing ◽  
Preterm Infants ◽  
Premature Infants ◽  
Retinopathy Of Prematurity ◽  
Smooth Endoplasmic Reticulum ◽  
Enrichment Analysis ◽  
Retinal Disease ◽  
Gene Set Enrichment Analysis ◽  
Whole Exome

AbstractRetinopathy of prematurity (ROP) is a vasoproliferative retinal disease affecting premature infants. In addition to prematurity itself and oxygen treatment, genetic factors have been suggested to predispose to ROP. We aimed to identify potentially pathogenic genes and biological pathways associated with ROP by analyzing variants from whole exome sequencing (WES) data of premature infants. As part of a multicenter ROP cohort study, 100 non-Hispanic Caucasian preterm infants enriched in phenotypic extremes were subjected to WES. Gene-based testing was done on coding nonsynonymous variants. Genes showing enrichment of qualifying variants in severe ROP compared to mild or no ROP from gene-based tests with adjustment for gestational age and birth weight were selected for gene set enrichment analysis (GSEA). Mean BW of included infants with pre-plus, type-1 or type 2 ROP including aggressive posterior ROP (n = 58) and mild or no ROP (n = 42) were 744 g and 995 g, respectively. No single genes reached genome-wide significance that could account for a severe phenotype. GSEA identified two significantly associated pathways (smooth endoplasmic reticulum and vitamin C metabolism) after correction for multiple tests. WES of premature infants revealed potential pathways that may be important in the pathogenesis of ROP and in further genetic studies.

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