scholarly journals RNA isolation from Peyer’s patch lymphocytes and mononuclear phagocytes to determine gene expression profiles using nanostring technology

2018 ◽  
Vol 5 (3) ◽  
pp. 95 ◽  
Author(s):  
Navjot Singh ◽  
Heather C. Gallagher ◽  
Renjie Song ◽  
Jaskiran K. Dhinsa ◽  
Gary R. Ostroff ◽  
...  
Keyword(s):  
Gene Expression ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Rna Isolation ◽  
Mononuclear Phagocytes ◽  
Peyer’S Patch ◽  
Peyer's Patch ◽  
Nanostring Technology

Abstract 149: Regulation of Pathogen-Associated Molecular Pattern Recognition by the Apo A-I Mimetic Peptide 4F

2012 ◽  
Vol 32 (suppl_1) ◽  
Author(s):  
Geeta Datta ◽  
David K Crossman ◽  
Lesley E Smythies ◽  
M N Palgunachari ◽  
Manjula Chaddha ◽  
...  
Keyword(s):  
Gene Expression ◽  
Inflammatory Responses ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Rna Isolation ◽  
Mimetic Peptide ◽  
M1 Macrophage ◽  
Vehicle Treatment ◽  
Anti Inflammatory ◽  
Pre Treatment

The apolipoprotein A-I (apoA-I) mimetic peptide 4F displays prominent anti-inflammatory properties, including the ability to reduce vascular macrophage content. Macrophages are a heterogenous group of cells that are represented by two principal phenotypes, the classically-activated M1 macrophage and an alternatively-activated M2 phenotype. We previously reported that apoA-I and 4F favor the differentiation of human monocytes to an anti-inflammatory phenotype similar to that displayed by M2 macrophages. Further, 4F treatment attenuated LPS-induced inflammatory responses in monocyte-derived macrophages (MDMs). In the current study, we investigated effects of 4F and vehicle on LPS-induced gene expression in human MDMs by microarray analysis. RNA isolation, labeling and hybridization were performed, and the transcriptional profile was examined using the Human Gene ST 1.0 Affymetrix chip. Analysis of MDM gene expression profiles revealed that 4F modulated mRNA expression for 1099 genes (± 2-fold change, p<0.05), of which 149 genes regulated inflammatory responses. LPS treatment of MDMs significantly up-regulated genes encoding Toll-like receptors (TLR1, 2, 4, 6, and 8) compared to vehicle treatment. These responses were attenuated by 4F treatment. MyD88, CD14, IRAK4, TRAF6, TRAF3, MALT1 and IKBKB, genes that modulate NF-κB activation and subsequent cytokine synthesis, were also reduced by 4F. Corroborating this, FACS analyses showed that pre-treatment of MDMs with 4F reduced the LPS-dependent phosphorylation of NF-κB by 70% compared to vehicle treatment. These 4F-induced responses were also associated with a reduction in TNF-α and IL-6 secretion. These data suggest that an important anti-inflammatory mechanism of 4F action may be to down-regulate genes involved in the TLR signaling pathway, thus attenuating the responsiveness of macrophages to LPS and other pathogen-associated molecular patterns (PAMPs).

scholarly journals Differential gene expression profiles are dependent upon method of peripheral blood collection and RNA isolation

BMC Genomics ◽  
2008 ◽  
Vol 9 (1) ◽  
pp. 474 ◽  
Author(s):  
Adam L Asare ◽  
Svetlana A Kolchinsky ◽  
Zhong Gao ◽  
Richard Wang ◽  
Khadir Raddassi ◽  
...  
Keyword(s):  
Gene Expression ◽  
Differential Gene Expression ◽  
Peripheral Blood ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Rna Isolation ◽  
Blood Collection ◽  
Differential Gene

scholarly journals Conjunctival Transcriptome in Scarring Trachoma

2010 ◽  
Vol 79 (1) ◽  
pp. 499-511 ◽  
Author(s):  
Matthew J. Burton ◽  
Saul N. Rajak ◽  
Julien Bauer ◽  
Helen A. Weiss ◽  
Sonda B. Tolbert ◽  
...  
Keyword(s):  
Gene Expression ◽  
Expression Profiles ◽  
Squamous Metaplasia ◽  
Disease Process ◽  
Gene Expression Profiles ◽  
Tissue Remodeling ◽  
Rna Isolation ◽  
Case Control ◽  
Host Responses ◽  
Mrna Targets

ABSTRACTTrachoma is a poorly understood immunofibrogenic disease process, initiated byChlamydia trachomatis. Differences in conjunctival gene expression profiles between Ethiopians with trachomatous trichiasis (with [TTI] or without [TT] inflammation) and controls (C) were investigated to identify relevant host responses. Tarsal conjunctival swab samples were collected for RNA isolation andC. trachomatisPCR. Transcriptome-wide microarray experiments were conducted on 42 samples (TTI,n= 13; TT,n= 15; C,n=14). Specific results were confirmed by using multiplex quantitative reverse transcription-PCR for 16 mRNA targets in an independent collection of case-control samples: 386 case-control pairs (TTI,n= 244; TT,n= 142; C,n= 386). The gene expression profiles of cases were consistent with squamous metaplasia (keratins, SPRR), proinflammatory cytokine production (IL1β,CXCL5, andS100A7), and tissue remodeling (MMP7,MMP9,MMP12, andHAS3). There was no difference in the level ofIFNγ between cases and controls. However, cases had increasedINDO,NOS2A, andIL13RA2and reducedIL13.C. trachomatiswas detected in 1/772. Cases show evidence of ongoing inflammation and tissue remodeling, which were more marked where clinical inflammation was also present. Significantly, these processes appear to be active in the absence of currentC. trachomatisinfection. There was limited evidence of a TH1 response (INDOandNOS2A) and no association between a TH2 response and cases. The epithelium appears to be actively involved in late cicatricial stages of trachoma through the production of proinflammatory factors (IL1β,CXCL5, andS100A7). Longitudinal studies are needed to investigate which etiological factors and pathways are associated with progressive scarring and whether simply controlling chlamydial infection will halt progression in people with established cicatricial disease.

scholarly journals Low-Input RNA-Sequencing in Patients with Cartilage Lesions, Osteoarthritis, and Healthy Cartilage

Cartilage ◽  
2021 ◽  
pp. 194760352110572
Author(s):  
Katherine Wang ◽  
Q.Y. Esbensen ◽  
T.A. Karlsen ◽  
C.N. Eftang ◽  
C. Owesen ◽  
...  
Keyword(s):  
Gene Expression ◽  
Rna Sequencing ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Rna Isolation ◽  
Cartilage Lesion ◽  
Cartilage Injury ◽  
Low Input ◽  
Healthy Cartilage ◽  
High Degree

Objective To analyze and compare cartilage samples from 3 groups of patients utilizing low-input RNA-sequencing. Design Cartilage biopsies were collected from patients in 3 groups ( n = 48): Cartilage lesion (CL) patients had at least ICRS grade 2, osteoarthritis (OA) samples were taken from patients undergoing knee replacement, and healthy cartilage (HC) was taken from ACL-reconstruction patients without CLs. RNA was isolated using an optimized protocol. RNA samples were assessed for quality and sequenced with a low-input SmartSeq2 protocol. Results RNA isolation yielded 48 samples with sufficient quality for sequencing. After quality control, 13 samples in the OA group, 9 in the HC group, and 9 in the CL group were included in the analysis. There was a high degree of co-clustering between the HC and CL groups with only 6 genes significantly up- or downregulated. OA and the combined HC/CL group clustered significantly separate from each other, yielding 659 significantly upregulated and 1,369 downregulated genes. GO-term analysis revealed that genes matched to cartilage and connective tissue development terms. Conclusion The gene expression profiles from the 3 groups suggest that there are no major differences in gene expression between cartilage from knees with a cartilage injury and knees without an apparent cartilage injury. OA cartilage, as expected, showed markedly different gene expression from the other 2 groups. The gene expression profiles resulting from this low-input RNA-sequencing study offer opportunities to discover new pathways not previously recognized that may be explored in future studies.

1327: Gene Expression Profiles in Benign Prostatic Hyperplasia

2004 ◽  
Vol 171 (4S) ◽  
pp. 349-350
Author(s):  
Gaelle Fromont ◽  
Michel Vidaud ◽  
Alain Latil ◽  
Guy Vallancien ◽  
Pierre Validire ◽  
...  
Keyword(s):  
Gene Expression ◽  
Benign Prostatic Hyperplasia ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Prostatic Hyperplasia
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