The Human Pathogen Mycobacterium tuberculosis and the Fish Pathogen Mycobacterium marinum Trigger a Core Set of Late Innate Immune Response Genes in Zebrafish Larvae
Abstract
:Simple Summary
Abstract
1. Introduction
2. Materials and Methods
2.1. Bacterial Culture
2.2. Zebrafish Experiments Ethics Statement
2.3. Zebrafish Embryo Injections and Larvae Culturing
2.4. Fluorescence Microscopy
2.5. CFU Counting
2.6. RNA Isolation, MBL Assay and Quantitative RT-PCR
2.7. Statistical Analysis
2.8. Illumina RNAseq Analysis
2.9. Illumina Data Processing
3. Results
3.1. Long-Term Survival of M. tuberculosis in Zebrafish Larvae
3.2. Transcriptional Profiling of Zebrafish Larvae Infected with M. tuberculosis
3.3. Effect of Increased Temperature on Transcriptome Profile of Zebrafish Larvae
3.4. Comparison of Host Transcriptional Response between Zebrafish Larvae Infected with M. tuberculosis and Larvae Infected with M. marinum
3.5. Comparison of Transcriptome Data of Zebrafish Mtb Infection with Human Macrophage Mtb Infection
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Mycobacterium Species | M. tuberculosis | M. marinum |
---|---|---|
natural hosts | humans, cattle | fish, amphibians, zoonosis |
infection route | lung | skin |
optimum temperature | 38 °C | 32 °C |
minimum doubling time | 18 h | 4 h |
biosafety level | 3 | 2 |
genome size | 4.41 Mb | 6.64 Mb |
gene number | 4008 | 5503 |
Gene Code | Gene Name | Gene Description | Mm 3 dpi | Mm 4 dpi | Mm 5 dpi |
---|---|---|---|---|---|
ENSDARG00000101479 | BX908782.3 | three-finger protein 5 (LOC100003647) | √ | √ | √ |
ENSDARG00000093712 | CABZ01021530.1 | Interferon-inducible protein Gig1-like (teleost-specific) | √ | √ | √ |
ENSDARG00000086654 | cbln11 | cerebellin 11 | √ | √ | √ |
ENSDARG00000026417 | ccr12b.2 | chemokine (C-C motif) receptor 12b2 | √ | √ | √ |
ENSDARG00000051912 | hpx | hemopexin | √ | √ | √ |
ENSDARG00000069844 | irg1 | immunoresponsive 1 homolog (aconitate decarboxylase) | √ | √ | √ |
ENSDARG00000003523 | itln3 | intelectin 3 (bacterial arabinogalactan receptor) | √ | √ | √ |
ENSDARG00000090889 | lect2 | leukocyte cell-derived chemotaxin 2 | √ | √ | √ |
ENSDARG00000012395 | mmp13a | matrix metallopeptidase 13a | √ | √ | √ |
ENSDARG00000042816 | mmp9 | matrix metallopeptidase 9 | √ | √ | √ |
ENSDARG00000045999 | saa | serum amyloid A | √ | √ | √ |
ENSDARG00000086337 | si:dkey-102g19.3 | urokinase plasminogen activator surface receptor-like | √ | √ | √ |
ENSDARG00000095798 | si:dkey-119g10.3 | non-protein coding | √ | √ | √ |
ENSDARG00000090352 | si:dkey-97i18.5 | non-protein coding | √ | √ | √ |
ENSDARG00000007769 | sult5a1 | sulfotransferase family 5A, member 1 | √ | √ | √ |
ENSDARG00000045561 | dram1 | DNA-damage regulated autophagy modulator 1 | - | √ | √ |
ENSDARG00000026049 | mxf | myxovirus (influenza virus) resistance F | - | √ | √ |
ENSDARG00000095909 | si:ch211-253b18.3 | non-protein coding | - | √ | √ |
ENSDARG00000086947 | si:ch211-147m6.1 | olfactomedin-4-like | √ | - | - |
ENSDARG00000104399 | CABZ01064972.2 | Uncharacterized protein | - | - | √ |
ENSDARG00000033587 | CABZ01088134.1 | trans-2-enoyl-CoA reductase, mitochondrial-like | - | - | √ |
ENSDARG00000089362 | grn1 | granulin 1 | - | - | √ |
ENSDARG00000069944 | p2ry13 | purinergic receptor P2Y, G-protein coupled, 13 | - | - | - |
Gene Name | Description | |
---|---|---|
Up-Regulated | ||
ENSDARG00000067672 | card9 | caspase recruitment domain family, member 9 |
ENSDARG00000090873 | ccl34a.4 | chemokine (C-C motif) ligand 34a, duplicate 4 |
ENSDARG00000026417 | ccr12b.2 | chemokine (C-C motif) receptor 12b, tandem duplicate 2 |
ENSDARG00000055278 | cfb | complement factor B |
ENSDARG00000051912 | hpx (1 of many) | hemopexin |
ENSDARG00000053131 | irak3 | interleukin-1 receptor-associated kinase 3 |
ENSDARG00000069844 | irg1 | immunoresponsive 1 homolog (mouse) |
ENSDARG00000003523 | itln3 | intelectin 3 |
ENSDARG00000090889 | lect2 (1 of many) | leukocyte cell derived chemotaxin 2 |
ENSDARG00000012395 | mmp13a | matrix metallopeptidase 13a |
ENSDARG00000042816 | mmp9 | matrix metallopeptidase 9 |
ENSDARG00000033735 | ncf1 | neutrophil cytosolic factor 1 |
ENSDARG00000045999 | saa | serum amyloid A |
ENSDARG00000053836 | si:ch211-284o19.8 | si:ch211-284o19.8 |
ENSDARG00000086337 | si:dkey-102g19.3 | si:dkey-102g19.3 |
ENSDARG00000095798 | si:dkey-119g10.3 | si:dkey-119g10.3 |
ENSDARG00000097909 | si:dkey-195m11.11 | si:dkey-195m11.11 |
ENSDARG00000090352 | si:dkey-97i18.5 | si:dkey-97i18.5 |
ENSDARG00000055252 | snap23.2 | synaptosomal-associated protein 23.2 |
ENSDARG00000007769 | sult5a1 | sulfotransferase family 5A, member 1 |
Up-Regulated Genes | |||||
---|---|---|---|---|---|
Zebrafish (Mtb3,4,5,6,8-2379 Genes) | Human Macrophages (MF1 and 2) | Ensembl Gene ID | Gene Name | Description | |
4 hr (11 Genes) | 24 hr (161 Genes) | ||||
x (Mtb3) | x | ENSDARG00000002917 | gls2b | glutaminase 2b (liver, mitochondrial) | |
x (Mtb3) | x | ENSDARG00000093750 | cd180 | CD180 molecule | |
x (Mtb5) | x | ENSDARG00000036106 | rgs18 | regulator of G-protein signaling 18 | |
x (Mtb5) | x | ENSDARG00000101050 | tmc8 | transmembrane channel-like 8 | |
x (Mtb8) | x | ENSDARG00000009978 | icn | ictacalcin | |
x (Mtb8) | x | ENSDARG00000013335 | anxa6 | annexin A6 | |
x (Mtb8) | x | ENSDARG00000087554 | cdk1 | cyclin-dependent kinase 1 | |
x (Mtb8) | x | ENSDARG00000098946 | pald1a | phosphatase domain containing, paladin 1a | |
Down-Regulated Genes | |||||
Zebrafish (Mtb3,4,5,6,8-1520 Genes) | Human Macrophages (MF1 and 2) | Ensembl Gene ID | Gene Name | Description | |
4 hr (149 Genes) | 24 hr (438 Genes) | ||||
x (Mtb6) | x | ENSDARG00000062947 | amn | amnion associated transmembrane protein | |
x (Mtb8) | x | ENSDARG00000030722 | xirp1 | xin actin binding repeat containing 1 | |
x (Mtb8) | x | ENSDARG00000037196 | arid5B | AT-rich interaction domain 5B | |
x (Mtb8) | x | ENSDARG00000056929 | kdm6bb | lysine (K)-specific demethylase 6B, b | |
x (Mtb8) | x | ENSDARG00000070538 | hey1 | hes-related family bHLH transcription factor with YRPW motif 1 | |
x (Mtb8) | x | ENSDARG00000105261 | nfkb1 | nuclear factor of kappa light polypeptide gene enhancer in B-cells 1 | |
x (Mtb5) | x | ENSDARG00000102729 | samd9 | sterile alpha motif domain containing 9 | |
x (Mtb5) | x | ENSDARG00000016733 | psat1 | phosphoserine aminotransferase 1 | |
x (Mtb8) | x | ENSDARG00000005526 | igfn1.1 | immunoglobulin-like and fibronectin type III domain containing 1, tandem duplicate 1 | |
x (Mtb8) | x | ENSDARG00000011257 | enpp2 | ectonucleotide pyrophosphatase/phosphodiesterase 2 | |
x (Mtb8) | x | ENSDARG00000018773 | hivep2 (1 of many) | human immunodeficiency virus type I enhancer binding protein 2 | |
x (Mtb8) | x | ENSDARG00000020581 | otofb | otoferlin b | |
x (Mtb8) | x | ENSDARG00000040523 | smpd2a | sphingomyelin phosphodiesterase 2a, neutral membrane (neutral sphingomyelinase) | |
x (Mtb8) | x | ENSDARG00000042055 * | fam129aa | family with sequence similarity 129, member Aa | |
x (Mtb8) | x | ENSDARG00000045802 | hapln3 | hyaluronan and proteoglycan link protein 3 | |
x (Mtb8) | x | ENSDARG00000057317 | nexn | nexilin (F actin binding protein) | |
x (Mtb8) | x | ENSDARG00000059090 | sstr2 (1 of many) | somatostatin receptor 2 | |
x (Mtb8) | x | ENSDARG00000061070 | chst3a | carbohydrate (chondroitin 6) sulfotransferase 3a | |
x (Mtb8) | x | ENSDARG00000063475 | abcg1 | ATP-binding cassette, sub-family G (WHITE), member 1 | |
x (Mtb8) | x | ENSDARG00000075263 | ankrd1a | ankyrin repeat domain 1a (cardiac muscle) | |
x (Mtb8) | x | ENSDARG00000088137 | adrg2 (1 of many) | adhesion G protein-coupled receptor G2 | |
x (Mtb8) | x | ENSDARG00000088937 | adrg2 (1 of many) | adhesion G protein-coupled receptor G2 | |
x (Mtb8) | x | ENSDARG00000100518 | Uncharacterized | ||
x (Mtb8) | x | x | ENSDARG00000007080 * | rhcgl1 | Rh family, C glycoprotein, like 1 |
x (Mtb8) | x | x | ENSDARG00000013168 | jag1b | jagged 1b |
x (Mtb8) | x | x | ENSDARG00000039232 | dusp8 (1 of many) | dual specificity phosphatase 8 |
x (Mtb8) | x | x | ENSDARG00000089871 | si:ch211-203c7.2 | si:ch211-203c7.2 |
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Dirks, R.P.; Ordas, A.; Jong-Raadsen, S.; Brittijn, S.A.; Haks, M.C.; Henkel, C.V.; Oravcova, K.; Racz, P.I.; Tuinhof-Koelma, N.; Korzeniowska nee Wiweger, M.I.; et al. The Human Pathogen Mycobacterium tuberculosis and the Fish Pathogen Mycobacterium marinum Trigger a Core Set of Late Innate Immune Response Genes in Zebrafish Larvae. Biology 2024, 13, 688. https://doi.org/10.3390/biology13090688
Dirks RP, Ordas A, Jong-Raadsen S, Brittijn SA, Haks MC, Henkel CV, Oravcova K, Racz PI, Tuinhof-Koelma N, Korzeniowska nee Wiweger MI, et al. The Human Pathogen Mycobacterium tuberculosis and the Fish Pathogen Mycobacterium marinum Trigger a Core Set of Late Innate Immune Response Genes in Zebrafish Larvae. Biology. 2024; 13(9):688. https://doi.org/10.3390/biology13090688
Chicago/Turabian StyleDirks, Ron P., Anita Ordas, Susanne Jong-Raadsen, Sebastiaan A. Brittijn, Mariëlle C. Haks, Christiaan V. Henkel, Katarina Oravcova, Peter I. Racz, Nynke Tuinhof-Koelma, Malgorzata I. Korzeniowska nee Wiweger, and et al. 2024. "The Human Pathogen Mycobacterium tuberculosis and the Fish Pathogen Mycobacterium marinum Trigger a Core Set of Late Innate Immune Response Genes in Zebrafish Larvae" Biology 13, no. 9: 688. https://doi.org/10.3390/biology13090688