BMM TB infection control: Difference between revisions
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|TCOverview=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. | |TCOverview=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. | ||
|TCQuality_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.<br><br>'''Marker gene Expression from CAGE data'''<br><html><img src=' | |TCQuality_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.<br><br>'''Marker gene Expression from CAGE data'''<br><html><img src='/resource_browser/images/TC_qc/Slide4.jpg' onclick='javascript:window.open("/resource_browser/images/TC_qc/Slide4.jpg", "imgwindow", "width=720,height=960");' style='width:700px;cursor:pointer'/><br><img src='/resource_browser/images/TC_qc/Slide5.jpg' onclick='javascript:window.open("/resource_browser/images/TC_qc/Slide5.jpg", "imgwindow", "width=720,height=960");' style='width:700px;cursor:pointer'/></html><table class="wikitable" border="0"><tr><th>'</th><th>'</th><th>Gene name</th><th>Referenced in (PMIDs)</th></tr><tr><td>Classical Activation</td><td></td><td>Nos2</td><td>1531844, 21441450, 15036034, 12215441, 10072066, 16920488</td></tr><tr><td></td><td></td><td>Tnf</td><td>15070757, 20059482,16920488, 21607943, 21240265, 20717022</td></tr><tr><td></td><td></td><td>CXCL9</td><td>20692533,16920488, 14734716, 19819674, 21607943, 20717022</td></tr><tr><td></td><td></td><td>CXCL10</td><td>1531844, 11907072,16920488, 14734716, 19105661, 19819674.</td></tr><tr><td></td><td></td><td>CXCL11</td><td>20692533,19819674, 23029029, 22666284</td></tr><tr><td></td><td></td><td>CCL5</td><td>23223452,16920488, 20729857, 9822252, 18350541, 19841166</td></tr><tr><td></td><td></td><td>IL-6</td><td>16840796,15036034, 12215441, 10072066, 16920488, 11927645</td></tr><tr><td></td><td></td><td>Irf1</td><td>Ref in: 9822252, DOI:10.1016/j.cellimm.2013.01.010</tr><tr><td>Alternative activation</td><td></td><td>Arginase-1</td><td>12098359;15036034, 12511873, 10072066, 12215441, 16920488</td></tr><tr><td></td><td></td><td>CCL22</td><td>23275605 ,15036034, 12511873, 10704248, 16920488, 14734716</td></tr><tr><td></td><td></td><td>CCL17</td><td>23275605,15036034, 12511873, 16920488, 14734716, 19105661</td></tr><tr><td></td><td></td><td>Ccl24</td><td>23275605, 20692533,16920488, 19105661, 20729857, 18350541</td></tr><tr><td></td><td></td><td>Relmα</td><td>21093321, 19029990, 12554797, 19105661; 17082649; 15142530</td></tr><tr><td></td><td></td><td>MYC</td><td>22067385</td></tr><tr><td></td><td></td><td>Mrc1</td><td>18250477,12401408, 15530839, 19029990, 10072066, 19105661</td></tr></table><br>References:<br>[1] Bronte, V. and P. Zanovello (2005). "Regulation of immune responses by L-arginine metabolism." Nat Rev Immunol 5(8): 641-54.<br>[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.<br>[3] Davis, A. S., I. Vergne, et al. (2007). "Mechanism of inducible nitric oxide synthase exclusion from mycobacterial phagosomes." PLoS Pathog 3(12): e186.<br>[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.<br>[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.<br>[6] Raju, B., Y. Hoshino, et al. (2008). "Gene expression profiles of bronchoalveolar cells in pulmonary TB." Tuberculosis (Edinb) 88(1): 39-51.<br>[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.<br> | ||
|TCSample_description='''Experimental Design'''<br><br>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.<br><br><html><img src=' | |TCSample_description='''Experimental Design'''<br><br>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.<br><br><html><img src='/resource_browser/images/TC_qc/Experimental_design.jpg' onclick='javascript:window.open("/resource_browser/images/TC_qc/Experimental_design.jpg", "imgwindow", "width=960,height=720");' style='width:700px;cursor:pointer'/></html>'''Figure 1. Schematic of experimental design'''<br><br>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).<br> | ||
|Time_Course= | |Time_Course= | ||
|category_treatment=Activation | |category_treatment=Activation | ||
| Line 14: | Line 14: | ||
|series=IN_VITRO DIFFERENTIATION SERIES | |series=IN_VITRO DIFFERENTIATION SERIES | ||
|species=Mouse (Mus musculus) | |species=Mouse (Mus musculus) | ||
|tet_config= | |tet_config=https://fantom.gsc.riken.jp/5/suppl/tet/BMM_TB_infection_nonstimulated.tsv.gz | ||
|tet_file=https://fantom.gsc.riken.jp/5/tet#!/search/?filename=mm9.cage_peak_phase1and2combined_tpm_ann_decoded.osc.txt.gz&file=1&c=1&c=855&c=856&c=857&c=641&c=642&c=635&c=643&c=644&c=636&c=645&c=646&c=637&c=647&c=638&c=649&c=650&c=639&c=651&c=652&c=653&c=654&c=655&c=656&c=640&c=657&c=658&c=659&c=660&c=661&c=662&c=663&c=664&c=665&c=666&c=667&c=668&c=669&c=670&c=671 | |||
|time_points= | |time_points= | ||
|time_span=120 hours | |time_span=120 hours | ||
|timepoint_design=Activation | |timepoint_design=Activation | ||
|tissue_cell_type=Macrophage | |tissue_cell_type=Macrophage | ||
|zenbu_config= | |zenbu_config=https://fantom.gsc.riken.jp/zenbu/gLyphs/#config=5vdr1OI-J1agY1pAWioUD | ||
}} | }} | ||
Latest revision as of 17:27, 14 March 2022
| 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: | 9 |
| 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 |
Figure 1. Schematic of experimental design| Quality control | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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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  
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
| 3561-170B1 | macrophage, TB infection, non-stimulated BMDM, without Mtb | 024hr | biol_rep1 |
| 3562-170C1 | macrophage, TB infection, non-stimulated BMDM, without Mtb | 028hr | biol_rep1 |
| 3563-170D1 | macrophage, TB infection, non-stimulated BMDM, without Mtb | 036hr | biol_rep1 |
| 3564-170E1 | macrophage, TB infection, non-stimulated BMDM, without Mtb | 048hr | biol_rep1 |
| 3565-170F1 | macrophage, TB infection, non-stimulated BMDM, without Mtb | 072hr | biol_rep1 |
| 3566-170G1 | macrophage, TB infection, non-stimulated BMDM, without Mtb | 120hr | biol_rep1 |
| 3607-170C6 | macrophage, TB infection, non-stimulated BMDM, with Mtb | 028hr(004h after stimulation) | biol_rep1 |
| 3608-170D6 | macrophage, TB infection, non-stimulated BMDM, with Mtb | 036hr(012h after stimulation) | biol_rep1 |
| 3609-170E6 | macrophage, TB infection, non-stimulated BMDM, with Mtb | 048hr(024h after stimulation) | biol_rep1 |
| 3610-170F6 | macrophage, TB infection, non-stimulated BMDM, with Mtb | 072hr(048h after stimulation) | biol_rep1 |
| 3611-170G6 | macrophage, TB infection, non-stimulated BMDM, with Mtb | 120hr(096h after stimulation) | biol_rep1 |
| 3633-171B1 | macrophage, TB infection, non-stimulated BMDM, without Mtb | 024hr | biol_rep2 |
| 3634-171C1 | macrophage, TB infection, non-stimulated BMDM, without Mtb | 028hr | biol_rep2 |
| 3635-171D1 | macrophage, TB infection, non-stimulated BMDM, without Mtb | 036hr | biol_rep2 |
| 3636-171E1 | macrophage, TB infection, non-stimulated BMDM, without Mtb | 048hr | biol_rep2 |
| 3637-171F1 | macrophage, TB infection, non-stimulated BMDM, without Mtb | 072hr | biol_rep2 |
| 3638-171G1 | macrophage, TB infection, non-stimulated BMDM, without Mtb | 120hr | biol_rep2 |
| 3679-171C6 | macrophage, TB infection, non-stimulated BMDM, with Mtb | 028hr(004h after stimulation) | biol_rep2 |
| 3680-171D6 | macrophage, TB infection, non-stimulated BMDM, with Mtb | 036hr(012h after stimulation) | biol_rep2 |
| 3681-171E6 | macrophage, TB infection, non-stimulated BMDM, with Mtb | 048hr(024h after stimulation) | biol_rep2 |
| 3683-171G6 | macrophage, TB infection, non-stimulated BMDM, with Mtb | 120hr(096h after stimulation) | biol_rep2 |
| 3705-172B1 | macrophage, TB infection, non-stimulated BMDM, without Mtb | 004hr | biol_rep3 |
| 3706-172C1 | macrophage, TB infection, non-stimulated BMDM, without Mtb | 006hr | biol_rep3 |
| 3707-172D1 | macrophage, TB infection, non-stimulated BMDM, without Mtb | 012hr | biol_rep3 |
| 3708-172E1 | macrophage, TB infection, non-stimulated BMDM, without Mtb | 024hr | biol_rep3 |
| 3709-172F1 | macrophage, TB infection, non-stimulated BMDM, without Mtb | 028hr | biol_rep3 |
| 3710-172G1 | macrophage, TB infection, non-stimulated BMDM, without Mtb | 036hr | biol_rep3 |
| 3711-172H1 | macrophage, TB infection, non-stimulated BMDM, without Mtb | 048hr | biol_rep3 |
| 3712-172I1 | macrophage, TB infection, non-stimulated BMDM, without Mtb | 072hr | biol_rep3 |
| 3713-172A2 | macrophage, TB infection, non-stimulated BMDM, without Mtb | 120hr | biol_rep3 |
| 3967-173D4 | macrophage, TB infection, non-stimulated BMDM, without Mtb | 024hr | biol_rep4 |
| 3972-173I4 | macrophage, TB infection, non-stimulated BMDM, with Mtb | 028hr(004h after stimulation) | biol_rep4 |
| 3973-173A5 | macrophage, TB infection, non-stimulated BMDM, with Mtb | 036hr(012h after stimulation) | biol_rep4 |
| 3974-173B5 | macrophage, TB infection, non-stimulated BMDM, with Mtb | 048hr(024h after stimulation) | biol_rep4 |
| 3975-173C5 | macrophage, TB infection, non-stimulated BMDM, with Mtb | 072hr(048h after stimulation) | biol_rep4 |
| 3976-173D5 | macrophage, TB infection, non-stimulated BMDM, with Mtb | 120hr(096h after stimulation) | biol_rep4 |
