BMM TB activation IL4

Series:	IN_VITRO DIFFERENTIATION SERIES
Species:	Mouse (Mus musculus)
Genomic View:	Zenbu
Expression table:	FILE
Link to TET:	TET
Sample providers :	Frank Brombacher & Harukazu Suzuki
Germ layer:	mesoderm
Primary cells or cell line:	primary cells
Time span:	120 hours
Number of time points:	11

Overview

The present study was designed uncover the macrophage transcriptom during IFN-g, IL-4 or IL-13 macrophage activation (classical versus alternative), to discriminate differences between IL-4 and IL-13-induced alternative macrophage activation and to uncover the transcriptom dynamics during infection with Mycobacterium tuberculosis HN878 by high throughput transcriptome analysis method, CAGE (cap analysis of gene expression). Helicos CAGE analysis will enable us to construct promoter-based networks of transcriptional regulation in a time course during macrophage activation and during infection in classical and alternative activated macrophages.

Sample description

Experimental Design The experiment was designed across 11 time points: 0, 2, 4, 6, 12, 24, 28, 36, 48, 72, 120 hours after macrophage stimulation and 4, 12, 24, 48, 72 hours after infection. Bone marrow derived macrophages were generated from 8-12 week old BALB/c male mice (n = 5-10 ). After euthanasia, the tibias and femurs aseptically removed and the bone marrow was flushed out with cold DMEM supplemented with 10% FCS and 100U/ml penicillin G, 100μg/ml streptomycin. Bone marrow cells from several animals (n=5-10 ) were pooled and were cultured for 10 days at 37°C under 5% CO2 in PLUTNIK differentiation medium (DMEM supplemented with 10% FCS, 5% Horse serum, 100U/ml penicillin G, 100μg/ml streptomycin 2mML-glutamine, 1mM sodium poyruvate, 50 μM mercaptoethanol and 30% L929 conditioned medium as a source of M-CSF. On day 10, cells (now mature BMDM) were harvested and plated in 6-well TC grade dishes. Each well was seeded with 5x10e6 BMDMs in DMEM supplemented with 10% FCS and 100U/ml penicillin G, 100μg/ml streptomycin in the presence or absence activators (100U/ml IL-4 and/or 100U/ml IL-13 or 100U/ml IFNg). After 24 hours of stimulation, the BMDMs were left alone or infected with live logarithmic phase Mycobacterium tuberculosis (MTB) HN878 at a MOI 5:1 (bacilli:macrophage). Thereafter at specific time points the culture supernatants was removed , aliquoted and stored at -80 degree C until further analysis (.e.g. measure production of cytokines, chemokines and iNOS). The BMDMs were lyzed in situ in the well in 1 ml of Qiazol Lysis Solution (Qiagen) and the lysates stored at -80 degree C until further extraction and analysis at RIKEN. The experiment was done in parallel using 96-well TC plates where 1x105 BMDMs were plated in triplicate and treated as above for the 6-well plates. At the specific time points, the culture supernatants was collected and used for measuring the producton iNOS. The BMDMs were lyzed in 0.1% Triton X100 and cell lysate used for measuring (i) the Arginase 1 activity and (ii) CFU load in the cell lysates. Once all the samples were collected, the Qiazol cell lysates were sent to RIKEN, where the total RNA was isolated using the miRNeasy Mini kit (QIAGEN) and fully analysed. The total RNA was quantified using a NanoDrop spectrophotometer (NanoDrop, USA). The quality and concentration of total RNA was confirmed using the BioAnalyzer (Agilent 2100 BioAnalyzer). The sample quality was checked by performing quatitative RT-PCR for some of the important marker genes of classically activated macrophages (iNOS, IL-1b, TNFa) and alternatively activated macrophages (Arg1, Ym1, IL-10). Three biological replicates were performed. Figure 1. Schematic of experimental design Bone marrow derived macrophages were generated from 8-12 week old BALB/c male mice, harvested and left alone or stimulated with activators to drive polarization to caMphs (100U/ml IFNg) or aaMphs (100U/ml IL-4 and/or 100U/ml IL-13). After 24 hours of stimulation, the BMDMs were left alone or infected with live logarithmic phase Mycobacterium tuberculosis (MTB) Beijing strain HN878 at a MOI 5:1 (bacilli : macrophage). Thereafter at specific time points, culture supernatants were analyzed to quantify the production of cytokines, chemokines and iNOS, and the BMDMs were lyzed in 1 ml of Qiazol Lysis Solution (Qiagen) and the DNA and total RNA (including microRNAs, long non-coding RNAs etc) extracted. The epigenomic footprint of the cells will be studied by analysing the genomic DNA methylation patterns by bisulifte sequencing; and the RNA will be used for RNAseq (microRNA and non-coding long RNA), CAGE analysis (promoter and gene expression) and qRT-PCR (confirmation).

Quality control

These are the well established marker of classical and alternative activation. The role of these genes were evaluated in human and mouse model of macrophage activation. Marker gene Expression from CAGE data ' ' Gene name Referenced in (PMIDs) Classical Activation Nos2 1531844, 21441450, 15036034, 12215441, 10072066, 16920488 Tnf 15070757, 20059482,16920488, 21607943, 21240265, 20717022 CXCL9 20692533,16920488, 14734716, 19819674, 21607943, 20717022 CXCL10 1531844, 11907072,16920488, 14734716, 19105661, 19819674. CXCL11 20692533,19819674, 23029029, 22666284 CCL5 23223452,16920488, 20729857, 9822252, 18350541, 19841166 IL-6 16840796,15036034, 12215441, 10072066, 16920488, 11927645 Irf1 Ref in: 9822252, DOI:10.1016/j.cellimm.2013.01.010 Alternative activation Arginase-1 12098359;15036034, 12511873, 10072066, 12215441, 16920488 CCL22 23275605 ,15036034, 12511873, 10704248, 16920488, 14734716 CCL17 23275605,15036034, 12511873, 16920488, 14734716, 19105661 Ccl24 23275605, 20692533,16920488, 19105661, 20729857, 18350541 Relmα 21093321, 19029990, 12554797, 19105661; 17082649; 15142530 MYC 22067385 Mrc1 18250477,12401408, 15530839, 19029990, 10072066, 19105661 References: [1] Bronte, V. and P. Zanovello (2005). "Regulation of immune responses by L-arginine metabolism." Nat Rev Immunol 5(8): 641-54. [2] Chacon-Salinas, R., J. Serafin-Lopez, et al. (2005). "Differential pattern of cytokine expression by macrophages infected in vitro with different Mycobacterium tuberculosis genotypes." Clin Exp Immunol 140(3): 443-9. [3] Davis, A. S., I. Vergne, et al. (2007). "Mechanism of inducible nitric oxide synthase exclusion from mycobacterial phagosomes." PLoS Pathog 3(12): e186. [4] Ehrt, S., D. Schnappinger, et al. (2001). "Reprogramming of the macrophage transcriptome in response to interferon-gamma and Mycobacterium tuberculosis: signaling roles of nitric oxide synthase-2 and phagocyte oxidase." J Exp Med 194(8): 1123-40. [5] El Kasmi, K. C., J. E. Qualls, et al. (2008). "Toll-like receptor-induced arginase 1 in macrophages thwarts effective immunity against intracellular pathogens." Nat Immunol 9(12): 1399-406. [6] Raju, B., Y. Hoshino, et al. (2008). "Gene expression profiles of bronchoalveolar cells in pulmonary TB." Tuberculosis (Edinb) 88(1): 39-51. [7] Varin, A., S. Mukhopadhyay, et al. "Alternative activation of macrophages by IL-4 impairs phagocytosis of pathogens but potentiates microbial-induced signalling and cytokine secretion." Blood 115(2): 353-62.

Profiled time course samples

Only samples that passed quality controls (Arner et al. 2015) are shown here. The entire set of samples are downloadable from FANTOM5 human / mouse samples

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3560-170A1	macrophage, bone marrow derived	000hr	pool1
3597-170B5	macrophage, TB infection, stimulated BMDM+IL-4(aaMph), without Mtb	002hr	biol_rep1
3598-170C5	macrophage, TB infection, stimulated BMDM+IL-4(aaMph), without Mtb	004hr	biol_rep1
3599-170D5	macrophage, TB infection, stimulated BMDM+IL-4(aaMph), without Mtb	006hr	biol_rep1
3600-170E5	macrophage, TB infection, stimulated BMDM+IL-4(aaMph), without Mtb	012hr	biol_rep1
3601-170F5	macrophage, TB infection, stimulated BMDM+IL-4(aaMph), without Mtb	024hr	biol_rep1
3602-170G5	macrophage, TB infection, stimulated BMDM+IL-4(aaMph), without Mtb	028hr	biol_rep1
3603-170H5	macrophage, TB infection, stimulated BMDM+IL-4(aaMph), without Mtb	036hr	biol_rep1
3604-170I5	macrophage, TB infection, stimulated BMDM+IL-4(aaMph), without Mtb	048hr	biol_rep1
3605-170A6	macrophage, TB infection, stimulated BMDM+IL-4(aaMph), without Mtb	072hr	biol_rep1
3606-170B6	macrophage, TB infection, stimulated BMDM+IL-4(aaMph), without Mtb	120hr	biol_rep1
3627-170E8	macrophage, TB infection, stimulated BMDM+IL-4(aaMph), with Mtb	028hr(004h after stimulation)	biol_rep1
3628-170F8	macrophage, TB infection, stimulated BMDM+IL-4(aaMph), with Mtb	036hr(012h after stimulation)	biol_rep1
3629-170G8	macrophage, TB infection, stimulated BMDM+IL-4(aaMph), with Mtb	048hr(024h after stimulation)	biol_rep1
3630-170H8	macrophage, TB infection, stimulated BMDM+IL-4(aaMph), with Mtb	072hr(048h after stimulation)	biol_rep1
3631-170I8	macrophage, TB infection, stimulated BMDM+IL-4(aaMph), with Mtb	120hr(096h after stimulation)	biol_rep1
3632-171A1	macrophage, bone marrow derived	000hr	pool2
3671-171D5	macrophage, TB infection, stimulated BMDM+IL-4(aaMph), without Mtb	006hr	biol_rep2
3672-171E5	macrophage, TB infection, stimulated BMDM+IL-4(aaMph), without Mtb	012hr	biol_rep2
3673-171F5	macrophage, TB infection, stimulated BMDM+IL-4(aaMph), without Mtb	024hr	biol_rep2
3674-171G5	macrophage, TB infection, stimulated BMDM+IL-4(aaMph), without Mtb	028hr	biol_rep2
3676-171I5	macrophage, TB infection, stimulated BMDM+IL-4(aaMph), without Mtb	048hr	biol_rep2
3677-171A6	macrophage, TB infection, stimulated BMDM+IL-4(aaMph), without Mtb	072hr	biol_rep2
3678-171B6	macrophage, TB infection, stimulated BMDM+IL-4(aaMph), without Mtb	120hr	biol_rep2
3699-171E8	macrophage, TB infection, stimulated BMDM+IL-4(aaMph), with Mtb	028hr(004h after stimulation)	biol_rep2
3700-171F8	macrophage, TB infection, stimulated BMDM+IL-4(aaMph), with Mtb	036hr(012h after stimulation)	biol_rep2
3701-171G8	macrophage, TB infection, stimulated BMDM+IL-4(aaMph), with Mtb	048hr(024h after stimulation)	biol_rep2
3702-171H8	macrophage, TB infection, stimulated BMDM+IL-4(aaMph), with Mtb	072hr(048h after stimulation)	biol_rep2
3703-171I8	macrophage, TB infection, stimulated BMDM+IL-4(aaMph), with Mtb	120hr(096h after stimulation)	biol_rep2
3704-172A1	macrophage, bone marrow derived	000hr	pool3
3744-172E5	macrophage, TB infection, stimulated BMDM+IL-4(aaMph), without Mtb	002hr	biol_rep3
3745-172F5	macrophage, TB infection, stimulated BMDM+IL-4(aaMph), without Mtb	004hr	biol_rep3
3746-172G5	macrophage, TB infection, stimulated BMDM+IL-4(aaMph), without Mtb	006hr	biol_rep3
3747-172H5	macrophage, TB infection, stimulated BMDM+IL-4(aaMph), without Mtb	012hr	biol_rep3
3748-172I5	macrophage, TB infection, stimulated BMDM+IL-4(aaMph), without Mtb	024hr	biol_rep3
3749-172A6	macrophage, TB infection, stimulated BMDM+IL-4(aaMph), without Mtb	028hr	biol_rep3
3750-172B6	macrophage, TB infection, stimulated BMDM+IL-4(aaMph), without Mtb	036hr	biol_rep3
3751-172C6	macrophage, TB infection, stimulated BMDM+IL-4(aaMph), without Mtb	048hr	biol_rep3
3752-172D6	macrophage, TB infection, stimulated BMDM+IL-4(aaMph), without Mtb	072hr	biol_rep3
3753-172E6	macrophage, TB infection, stimulated BMDM+IL-4(aaMph), without Mtb	120hr	biol_rep3
3971-173H4	macrophage, TB infection, stimulated BMDM+IL-4(aaMph), without Mtb	024hr	biol_rep4
3992-173B7	macrophage, TB infection, stimulated BMDM+IL-4(aaMph), with Mtb	028hr(004h after stimulation)	biol_rep4
3993-173C7	macrophage, TB infection, stimulated BMDM+IL-4(aaMph), with Mtb	036hr(012h after stimulation)	biol_rep4
3994-173D7	macrophage, TB infection, stimulated BMDM+IL-4(aaMph), with Mtb	048hr(024h after stimulation)	biol_rep4
3995-173E7	macrophage, TB infection, stimulated BMDM+IL-4(aaMph), with Mtb	072hr(048h after stimulation)	biol_rep4
3996-173F7	macrophage, TB infection, stimulated BMDM+IL-4(aaMph), with Mtb	120hr(096h after stimulation)	biol_rep4