scholarly journals Dynamic mRNA Expression Analysis of the Secondary Palatal Morphogenesis in Miniature Pigs

2019 ◽  
Vol 20 (17) ◽  
pp. 4284
Author(s):  
Jia Liu ◽  
Jing Chen ◽  
Dong Yuan ◽  
Lindong Sun ◽  
Zhipeng Fan ◽  
...  
Keyword(s):  
Gene Expression ◽  
Mrna Expression ◽  
Cleft Lip ◽  
Integration Site ◽  
Expression Profiles ◽  
Mitogen Activated Protein Kinase ◽  
Large Animal Model ◽  
Large Animal ◽  
Palate Development ◽  
Miniature Pigs

Normal mammalian palatogenesis is a complex process that requires the occurrence of a tightly regulated series of specific and sequentially regulated cellular events. Cleft lip/palate (CLP), the most frequent craniofacial malformation birth defects, may occur if any of these events undergo abnormal interference. Such defects not only affect the patients, but also pose a financial risk for the families. In our recent study, the miniature pig was shown to be a valuable alternative large animal model for exploring human palate development by histology. However, few reports exist in the literature to document gene expression and function during swine palatogenesis. To better understand the genetic regulation of palate development, an mRNA expression profiling analysis was performed on miniature pigs, Sus scrofa. Five key developmental stages of miniature pigs from embryonic days (E) 30–50 were selected for transcriptome sequencing. Gene expression profiles in different palate development stages of miniature pigs were identified. Nine hundred twenty significant differentially expressed genes were identified, and the functional characteristics of these genes were determined by gene ontology (GO) function and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis. Some of these genes were associated with HH (hedgehog), WNT (wingless-type mouse mammary tumor virus integration site family), and MAPK (mitogen-activated protein kinase) signaling, etc., which were shown in the literature to affect palate development, while some genes, such as HIP (hedgehog interacting protein), WNT16, MAPK10, and LAMC2 (laminin subunit gamma 2), were additions to the current understanding of palate development. The present study provided a comprehensive analysis for understanding the dynamic gene regulation during palate development and provided potential ideas and resources to further study normal palate development and the etiology of cleft palate.

Characterizing Canine Lymphoma As a Potential Large Animal Model of Human Diffuse Large B-Cell Lymphoma

Blood ◽  
2011 ◽  
Vol 118 (21) ◽  
pp. 5193-5193 ◽  
Author(s):  
Kristy L. Richards ◽  
Alison Motsinger-Reif ◽  
Hsiao-Wei Chen ◽  
Yuri D. Fedoriw ◽  
Cheng Fan ◽  
...  
Keyword(s):  
Gene Expression ◽  
Animal Model ◽  
B Cell ◽  
Cell Lymphoma ◽  
Expression Profiles ◽  
B Cell Lymphoma ◽  
Large Animal Model ◽  
Large Animal ◽  
Large B Cell Lymphoma ◽  
Large B Cell

Abstract Abstract 5193 Diffuse large B-cell lymphoma (DLBCL) affects ∼25,000 people in the U.S. each year, and fewer than half of them are cured with standard therapy. DLBCL can be divided into two subtypes by gene expression profiling, germinal center B-cell (GCB) type and activated B-cell (ABC) type. ABC-type DLBCL patients have significantly poorer outcomes. To improve therapeutic options, better animal models that accurately mimic human DLBCL (hDLBCL) are needed. Canine DLBCL is one of the most common cancers in veterinary oncology. Similar to human DLBCL patients, dogs with lymphoma are treated with both CHOP-like regimens and autologous stem cell transplants. Morphologically, canine lymphomas are similar to hDLBCL, with shared histologic markers, such as CD20 and PAX5. With recent technologies based on knowledge of the canine genome sequence, it is now possible to evaluate dogs as a potential large-animal model for hDLBCL. We evaluated 58 canine B-cell lymphomas by generating comprehensive gene expression profiles and comparing them to previously published hDLBCL expression profiles. Canine B-cell lymphoma expression profiles were similar in some ways to hDLBCLs. For instance, increased expression of NF-kB pathway genes was noted in a subset of lymphomas, mirroring NF-kB pathway activation in human ABC-type DLBCL. Furthermore, immunoglobulin heavy chain (IGH) mutation status, which is correlated with ABC/GCB cell of origin in hDLBCL, separated canine DLBCL into two groups with statistically different progression-free and overall survival times. However, canine DLBCL differed from hDLBCL in other aspects, including rare immunohistochemical positivity for BCL6 and MUM1/IRF4. Collectively, these results define aspects of canine B-cell lymphomas that resemble hDLBCL, identifying molecular similarities that could allow dogs to be used as a representative model of hDLBCL. Further comparative studies, including therapeutic trials, could potentially improve outcomes in both species. Disclosures: No relevant conflicts of interest to declare.

scholarly journals Early Response of CD8+ T Cells in COVID-19 Patients

2021 ◽  
Vol 11 (12) ◽  
pp. 1291
Author(s):  
Deni Ramljak ◽  
Martina Vukoja ◽  
Marina Curlin ◽  
Katarina Vukojevic ◽  
Maja Barbaric ◽  
...  
Keyword(s):  
Gene Expression ◽  
Immune Response ◽  
T Cells ◽  
Mrna Expression ◽  
Cd8 T Cells ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Effector Memory ◽  
Healthy Controls ◽  
Ifn Γ

Healthy and controlled immune response in COVID-19 is crucial for mild forms of the disease. Although CD8+ T cells play important role in this response, there is still a lack of studies showing the gene expression profiles in those cells at the beginning of the disease as potential predictors of more severe forms after the first week. We investigated a proportion of different subpopulations of CD8+ T cells and their gene expression patterns for cytotoxic proteins (perforin-1 (PRF1), granulysin (GNLY), granzyme B (GZMB), granzyme A (GZMA), granzyme K (GZMK)), cytokine interferon-γ (IFN-γ), and apoptotic protein Fas ligand (FASL) in CD8+ T cells from peripheral blood in first weeks of SARS-CoV-2 infection. Sixteen COVID-19 patients and nine healthy controls were included. The absolute counts of total lymphocytes (p = 0.007), CD3+ (p = 0.05), and CD8+ T cells (p = 0.01) in COVID-19 patients were significantly decreased compared to healthy controls. In COVID-19 patients in CD8+ T cell compartment, we observed lower frequency effector memory 1 (EM1) (p = 0.06) and effector memory 4 (EM4) (p < 0.001) CD8+ T cells. Higher mRNA expression of PRF1 (p = 0.05) and lower mRNA expression of FASL (p = 0.05) at the fifth day of the disease were found in COVID-19 patients compared to healthy controls. mRNA expression of PRF1 (p < 0.001) and IFN-γ (p < 0.001) was significantly downregulated in the first week of disease in COVID-19 patients who progressed to moderate and severe forms after the first week, compared to patients with mild symptoms during the entire disease course. GZMK (p < 0.01) and FASL (p < 0.01) mRNA expression was downregulated in all COVID-19 patients compared to healthy controls. Our results can lead to a better understanding of the inappropriate immune response of CD8+ T cells in SARS-CoV2 with the faster progression of the disease.

Secondary Palate Development in the Dog (Canis lupus familiaris)

2020 ◽  
pp. 105566562094377
Author(s):  
Katharina Freiberger ◽  
Shelby Hemker ◽  
Ryan McAnally ◽  
Rachel King ◽  
Vicki N. Meyers-Wallen ◽  
...  
Keyword(s):  
Large Animal Model ◽  
Large Animal ◽  
Canis Lupus Familiaris ◽  
Protein Markers ◽  
Serum Progesterone ◽  
Palate Development ◽  
Secondary Palate ◽  
Intermediate Time ◽  
Palate Repair ◽  
Isolated Cleft Palate

Objective: To investigate the gestational timing of morphologic events in normal canine secondary palate development as a baseline for studies in dog models of isolated cleft palate (CP). Methods: Beagle and beagle/cocker spaniel-hybrid fetal dogs were obtained by cesarean-section on various days of gestation, timed from the initial rise of serum progesterone concentration. Morphology of fetal heads was determined by examining serial coronal sections. Results: On gestational day 35 (d35), the palatal shelves pointed ventrally alongside the tongue. On d36, palatal shelves were elongated and elevated to a horizontal position above the tongue but were not touching. On d37, palatine shelves and vomer were touching, but the medial epithelial seam (MES) between the apposed shelves remained. Immunostaining with epithelial protein markers showed that the MES gradually dissolved and was replaced by mesenchyme during d37-d44, and palate fusion was complete by d44. Examination of remnant MES suggested that fusion of palatal shelves began in mid-palate and moved rostrally and caudally. Conclusion: Palate development occurs in dogs in the steps described in humans and mice, but palate closure occurs at an intermediate time in gestation. These normative data will form the basis of future studies to determine pathophysiologic mechanisms in dog models of CP. Added clinical significance is the enhancement of dogs as a large animal model to test new approaches for palate repair, with the obvious advantage of achieving full maturity within 2 years rather than 2 decades.

scholarly journals Silencing of MBD1 and MeCP2 in prostate-cancer-derived PC3 cells produces differential gene expression profiles and cellular phenotypes

2008 ◽  
Vol 28 (6) ◽  
pp. 319-326 ◽  
Author(s):  
Ahmed Yaqinuddin ◽  
Farhat Abbas ◽  
Syed Z. Naqvi ◽  
Mohammad U. Bashir ◽  
Romena Qazi ◽  
...  
Keyword(s):  
Gene Expression ◽  
Prostate Cancer ◽  
Mrna Expression ◽  
Cellular Proliferation ◽  
Expression Profiles ◽  
Boyden Chamber ◽  
Invasion And Migration ◽  
Pc3 Cells ◽  
And Migration

Alterations in genomic CpG methylation patterns have been found to be associated with cell transformation and neoplasia. Although it is recognized that methylation of CpG residues negatively regulates gene expression, how the various MBPs (methyl-binding proteins) contribute to this process remains elusive. To determine whether the two well characterized proteins MeCP2 (methyl-CpG-binding protein 2) and MBD1 (methyl-CpG-binding domain 1) have distinct or redundant functions, we employed RNAi (RNA interference) to silence their expression in the prostate cancer-derived PC3 cell line, and subsequently compared cell growth, invasion and migration properties of these cell lines in addition to their respective mRNA-expression profiles. Cells devoid of MeCP2 proliferated more poorly compared with MBD1-deficient cells and the parental PC3 cells. Enhanced apoptosis was observed in MeCP2-deficient cells, whereas apoptosis in parental and MBD1-deficient cells appeared to be equivalent. Boyden chamber invasion and wound-healing migration assays showed that MBD1-silenced cells were both more invasive and migratory compared with MeCP2-silenced cells. Finally, gene chip microarray analyses showed striking differences in the mRNA-expression profiles obtained from MeCP2- and MBD1-depleted cells relative to each other as well as when compared with control cells. The results of the present study suggest that MeCP2 and MBD1 silencing appear to affect cellular processes independently in vivo and that discrete sets of genes involved in cellular proliferation, apoptosis, invasion and migration are targeted by each protein.

Genetic control of global gene expression levels in the intestinal mucosa: a human twin study

2009 ◽  
Vol 38 (1) ◽  
pp. 73-79 ◽  
Author(s):  
Robert Häsler ◽  
Alexander Begun ◽  
Sandra Freitag-Wolf ◽  
Martin Kerick ◽  
Nancy Mah ◽  
...  
Keyword(s):  
Gene Expression ◽  
Mrna Expression ◽  
Genetic Control ◽  
Intestinal Mucosa ◽  
Expression Profiles ◽  
Global Gene Expression ◽  
Model Organisms ◽  
Expression Levels ◽  
Molecular Phylogenetic ◽  
Health And Disease

Phenotypic variation between individuals, such as different mRNA expression levels, is influenced by genetic and nongenetic factors. Although several studies have addressed the interplay between genotypes and expression profiles in various model organisms in the recent years, the detailed and relative contributions of genetic and nongenetic factors in regulating plasticity of gene expression in barrier organs (e.g., skin, gut), which are exposed to continuous environmental challenge, are still poorly understood. Here we systematically monitored the level of genetic control over genomewide mRNA expression profiles in the healthy intestinal mucosa of 10 monozygotic and 10 dizygotic human twin pairs with microarray analyses. Our results, which are supported by real-time PCR and analysis of molecular phylogenetic conservation, indicate that genes associated with energy metabolism and cell and tissue regeneration pathways are under strong genetic control. Conversely, genes associated with immune response seem to be mainly controlled by exogenous factors. Further insights into the relative extent of genetic and nongenetic determinants of transcriptomal profiles and their influence on physiological and pathophysiological mechanisms are crucial to understanding the key role played by gene-environment interactions in health and disease.

Abstract P144: Bioinformatic Profiling of the Transcriptional Response of Adult Porcine Bone Marrow Stem Cell during Exposure to Hypoxia

Circulation ◽  
2008 ◽  
Vol 118 (suppl_18) ◽  
Author(s):  
Suna Wang ◽  
Yifu Zhou ◽  
Xiuli Xu ◽  
Timothy Hunt ◽  
Robert F Hoyt ◽  
...  
Keyword(s):  
Gene Expression ◽  
Bone Marrow ◽  
Expression Pattern ◽  
Gene Expression Pattern ◽  
Transcriptional Response ◽  
Culture Conditions ◽  
Large Animal Model ◽  
Homologous Gene ◽  
Large Animal ◽  
Gene Search

Background: Cell-based transplantation therapy in a large animal model has been shown to improve angiogenesis and function of ischemic myocardium. These improvements may be due to the endothelial progenitor cells from bone marrow derived stem cells (BMC) generated under ischemic or hypoxic conditions. However the molecular activities of porcine BMC (PBMC) are largely unknown. Thus, a comprehensive gene expression pattern for PBMC is needed to advance the preclinical work necessary for future human treatment. Methods: Fifteen PBMC were cultured in the medium of EGM 2 for 4 weeks, and then incubated either in a monitored hypoxic chamber (1% O2, 5% CO2) (H) or in normal culture conditions (normoxia, N) for 6, 12, 24 and 48 hrs. Twenty RNAs comprising 5 Ns and 15 Hs (6, 12 and 24hr) were hybridized to Affymetrix Porcine arrays. An additional 40 samples were prepared for data confirmation by qRTPCR and Western blot. Data normalization and pattern recognition in each of these subgroups were achieved using R package 2.4 and GeneSpringGX. Homologous gene search and functional classification based on NCBI Pig Genomic Resources and DAVID Bioinformatics Resources 2007. Results: Significant gene expression levels among the four groups were identified. The patterns of three hypoxia (H) groups were clearly distinct from that of normoxia (N) group. However, the expression pattern of 12hr H was more similar to 24hr H than that of 6hr H. Of 23,928 probes, 394 genes were statistically regulated rapidly in 6hr Hs vs. Ns, including HIF2alpha, VEGFA, PDGFA, ANGPT2, CXCL14 and PGD. Only 182 genes were modulated in 12hr Hs, but 84% (152/182) of the genes appeared either with 6hr or 24hr H groups. 227 genes were significantly over- or down- regulated in 24hr Hs, among the 94 genes were overlapped with 6hr and 12hr Hs. Notably, the 94 genes were the most differentially modulated in all three H groups, some of the genes were known involving in the processes of hypoxic stress, response to inflammatory, wounding, apoptosis and angiogenesis. The 94 genes are considered as hypoxic targets for further study. Conclusions: Our results confirmed the role of several genes involved in hypoxic or ischemic states, and captured a set of genes that associated the PBMC response to hypoxic or ischemic surroundings.

Gene Transfer of Canine FVIIa Results in Partial Correction of Canine Hemophilia: A Model for FVIII/FIX Gene-Based Bypassing Agents.

Blood ◽  
2007 ◽  
Vol 110 (11) ◽  
pp. 195-195 ◽  
Author(s):  
Paris Margaritis ◽  
Elise Roy ◽  
Harre D. Downey ◽  
Shangzen Zhou ◽  
Elizabeth Merricks ◽  
...  
Keyword(s):  
Gene Expression ◽  
Animal Model ◽  
Gene Transfer ◽  
Hemophilia A ◽  
Active Form ◽  
Factor Ix ◽  
Factor Vii ◽  
Large Animal Model ◽  
Large Animal ◽  
Partial Correction

Abstract Despite its extensive use particularly in the management of hemophilic inhibitor patients, recombinant Factor VIIa (rhFVIIa) infusion has important limitations stemming from the nature of FVIIa itself, since its short half-life necessitates repeated injections and also carries high treatment costs. To overcome these, we have designed a gene transfer approach using a modified FVII transgene that is cleaved intracellularly and secreted in the active form, FVIIa. Using the human and murine analogue of this engineered transgene we have shown phenotypic correction of hemophilia B mice, following adeno-associated virus (AAV) - mediated, liver-directed gene delivery (Margaritis et al., 2004). In order to demonstrate efficacy in a large animal model of hemophilia, we cloned the canine Factor VII cDNA and generated the canine homologue of our modified transgene (cFVIIa). Recombinant cFVII zymogen and cFVIIa were purified and characterized in vitro in a clotting-based assay using canine reagents only (activated partial thromboplastin time [aPTT]). We found that cFVIIa had activity indistinguishable from rhFVIIa, while cFVII zymogen had negligible activity (5% rhFVIIa). In order to demonstrate in vivo efficacy, we produced 4 lots of an AAV8-based vector directing liver-specific expression of cFVIIa with similar vector titers (2–5 E13 vector genomes [vg]/ml). In hemophilia A (HA) or B (HB) mice, tail-vein delivery of 0.3 – 1.2 E12 vg/mouse (1.2 – 4.8 E13 vg/kg) resulted in long-term normalization of the hemophilic phenotype, demonstrating that cFVIIa can correct the defect in murine hemophilia. We proceeded to infuse 4 hemophilia dogs, with increasing vector doses: HB male (2.06 E13 vg/kg); HA male (6.25 E13 vg/kg); HA female (1.25 E14 vg/kg); HA male (1.25 E14 vg/kg). None of the dogs showed any adverse effects following vector delivery at any dose (the initial HB dog has been followed for almost 2 years [ongoing]). We followed the level of gene expression by clotting assays (prothrombin time [PT]/aPTT) and whole blood clotting time (WBCT). The initial dose of 2.06 E13 vg/kg resulted in a transient reduction in the PT/aPTT/WBCT. A considerable and sustained reduction in PT (18 sec, normal is ∼25 sec), aPTT (19 sec, normal is ∼30 sec, hemophilic is &gt;40sec) and WBCT (25min, normal is ∼15min, hemophilic is &gt;40min) was observed following administration of 6.25 E13 vg/kg in an HA male dog. Two more HA dogs were infused with 1.25 E14 vg/kg (male and female). The female HA dog exhibited only a modest decrease in aPTT (22sec), despite the vector dose increase, and a reduction in WBCT (30min), an observation that could be due to previously described gender-specific effects on gene expression. From preliminary and ongoing observations, the male HA dog infused also exhibited a decrease in WBCT. As an efficacy endpoint, the dogs exhibited a total of 3 bleeding episodes (none likely to be spontaneous, occurred in the lowest dose HB dog) in a cumulative time period of 38.5 months, compared to the expected 16 episodes (Brunetti-Pierri et al., 2005). In summary, our results demonstrate for the first time that gene transfer using a Factor VIII/Factor IX bypassing agent (canine FVIIa) can result in partial correction of the hemophilic phenotype in a large animal model of hemophilia.

Microarray-Based Gene Expression Analysis Identifies Potential Diagnostic and Prognostic Biomarkers for Waldenström Macroglobulinemia

2018 ◽  
Vol 140 (2) ◽  
pp. 87-96
Author(s):  
Haitao Xu ◽  
Fusheng Yao
Keyword(s):  
Gene Expression ◽  
B Cell ◽  
Signaling Pathway ◽  
Molecular Mechanisms ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Mitogen Activated Protein Kinase ◽  
Ppi Network ◽  
Waldenström Macroglobulinemia ◽  
Waldenstrom Macroglobulinemia

Waldenström macroglobulinemia (WM), also known as lymphoplasmacytic lymphoma, is rare but a clinicopathologically distinct B-cell malignancy. This study assessed differentially expressed genes (DEGs) to identify potential WM biomarkers and uncover the underlying the molecular mechanisms of WM progression using gene expression profiles from the Gene Expression Omnibus database. DEGs were identified using the LIMMA package and their potential functions were then analyzed by using the gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses and the protein-protein interaction (PPI) network analysis by using the Search Tool for the Retrieval of Interacting Genes/Proteins database. Data showed that among 1,756 DEGs, 926 were upregulated and 830 were downregulated by comparing WM BM CD19+ with normal PB CD19+ B cell samples, whereas 241 DEGs (95 upregulated and 146 downregulated) were identified by comparing WM BM CD138+ with normal BM CD138+ plasma cell samples. The DEGs were enriched in different GO terms and pathways, including the apoptotic process, cell cycle arrest, immune response, cell adhesion, mitogen-activated protein kinase signaling pathway, toll-like receptor signaling pathway, and the gonadotropin-releasing hormone signaling pathway. Hub nodes in the PPI network included CDK1, JUN, CREBBP, EP300, CAD, CDK2, and MAPK14. Bioinformatics analysis of the GSE9656 dataset identified 7 hub genes that might play an important role in WM development and progression. Some of the candidate genes and pathways may serve as promising therapeutic targets for WM.

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