{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,15]],"date-time":"2026-06-15T23:52:18Z","timestamp":1781567538974,"version":"3.54.5"},"reference-count":78,"publisher":"MDPI AG","issue":"9","license":[{"start":{"date-parts":[[2022,4,20]],"date-time":"2022-04-20T00:00:00Z","timestamp":1650412800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100005739","name":"National Autonomous University of Mexico","doi-asserted-by":"publisher","award":["DGAPA PAPIIT IN214713-3"],"award-info":[{"award-number":["DGAPA PAPIIT IN214713-3"]}],"id":[{"id":"10.13039\/501100005739","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["IJMS"],"abstract":"<jats:p>Currently, the only available vaccine against tuberculosis is Mycobacterium bovis Bacille Calmette-Gu\u00e9rin (BCG). Pulmonary tuberculosis protection provided by the vaccine varies depending on the strain, the patient\u2019s age and the evaluated population. Although the adaptive immune responses induced by different BCG strains have been widely studied, little conclusive data is available regarding innate immune responses, especially in macrophages. Here, we aimed to characterize the innate immune responses of human THP-1-derived macrophages at the transcriptional level following a challenge with either the BCG Mexico (M.BCG) or Phipps (P.BCG) strains. After a brief in vitro characterization of the bacterial strains and the innate immune responses, including nitric oxide production and cytokine profiles, we analyzed the mRNA expression patterns and performed pathway enrichment analysis using RNA microarrays. Our results showed that multiple biological processes were enriched, especially those associated with innate inflammatory and antimicrobial responses, including tumor necrosis factor (TNF)-\u03b1, type I interferon (IFN-I) and IFN-\u03b3. However, four DEGs were identified in macrophages infected with M.BCG compared to P. BCG. These findings indicated the proinflammatory stimulation of macrophages induced by both BCG strains, at the cytokine level and in terms of gene expression, suggesting a differential expression pattern of innate immune transcripts depending on the mycobacterial strain.<\/jats:p>","DOI":"10.3390\/ijms23094525","type":"journal-article","created":{"date-parts":[[2022,4,20]],"date-time":"2022-04-20T02:04:22Z","timestamp":1650420262000},"page":"4525","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":8,"title":["RNA Microarray-Based Comparison of Innate Immune Phenotypes between Human THP-1 Macrophages Stimulated with Two BCG Strains"],"prefix":"10.3390","volume":"23","author":[{"given":"Gabriela","family":"Molina-Olvera","sequence":"first","affiliation":[{"name":"Programa de Inmunolog\u00eda Molecular Microbiana, Departamento de Microbiolog\u00eda y Parasitolog\u00eda, Facultad de Medicina, Universidad Nacional Aut\u00f3noma de M\u00e9xico (UNAM), Ciudad de M\u00e9xico 04510, Mexico"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4932-7659","authenticated-orcid":false,"given":"Claudia I.","family":"Rivas-Ortiz","sequence":"additional","affiliation":[{"name":"Programa de Inmunolog\u00eda Molecular Microbiana, Departamento de Microbiolog\u00eda y Parasitolog\u00eda, Facultad de Medicina, Universidad Nacional Aut\u00f3noma de M\u00e9xico (UNAM), Ciudad de M\u00e9xico 04510, Mexico"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alejandro","family":"Schcolnik-Cabrera","sequence":"additional","affiliation":[{"name":"Programa de Inmunolog\u00eda Molecular Microbiana, Departamento de Microbiolog\u00eda y Parasitolog\u00eda, Facultad de Medicina, Universidad Nacional Aut\u00f3noma de M\u00e9xico (UNAM), Ciudad de M\u00e9xico 04510, Mexico"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Antonia I.","family":"Castillo-Rodal","sequence":"additional","affiliation":[{"name":"Programa de Inmunolog\u00eda Molecular Microbiana, Departamento de Microbiolog\u00eda y Parasitolog\u00eda, Facultad de Medicina, Universidad Nacional Aut\u00f3noma de M\u00e9xico (UNAM), Ciudad de M\u00e9xico 04510, Mexico"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7111-8813","authenticated-orcid":false,"given":"Yolanda","family":"L\u00f3pez-Vidal","sequence":"additional","affiliation":[{"name":"Programa de Inmunolog\u00eda Molecular Microbiana, Departamento de Microbiolog\u00eda y Parasitolog\u00eda, Facultad de Medicina, Universidad Nacional Aut\u00f3noma de M\u00e9xico (UNAM), Ciudad de M\u00e9xico 04510, Mexico"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2022,4,20]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"299","DOI":"10.1016\/S2213-2600(18)30057-2","article-title":"The global tuberculosis epidemic and progress in care, prevention, and research: An overview in year 3 of the End TB era","volume":"6","author":"Floyd","year":"2018","journal-title":"Lancet Respir. Med."},{"key":"ref_2","unstructured":"World Health Organization (2020). Global Tuberculosis Report 2020, World Health Organization."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"1226","DOI":"10.1056\/NEJM199910143411609","article-title":"Exogenous reinfection in tuberculosis","volume":"341","author":"Fine","year":"1999","journal-title":"N. Engl. J. Med."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"400","DOI":"10.1016\/j.ijmyco.2016.09.017","article-title":"Reactivation or reinfection in adult tuberculosis: Is that the question?","volume":"5","author":"Cardona","year":"2016","journal-title":"Int. J. Mycobacteriol."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"1732","DOI":"10.12688\/f1000research.16521.1","article-title":"Research and development of new tuberculosis vaccines: A review","volume":"7","author":"Schrager","year":"2018","journal-title":"F1000Research"},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"1147","DOI":"10.3389\/fimmu.2017.01147","article-title":"The Recombinant Bacille Calmette-Guerin Vaccine VPM1002: Ready for Clinical Efficacy Testing","volume":"8","author":"Nieuwenhuizen","year":"2017","journal-title":"Front. Immunol."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"2284","DOI":"10.3389\/fmicb.2017.02284","article-title":"The Macrophage: A Disputed Fortress in the Battle against Mycobacterium tuberculosis","volume":"23","author":"Queval","year":"2017","journal-title":"Front. Microbiol."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"12420","DOI":"10.1073\/pnas.1635213100","article-title":"The primary mechanism of attenuation of bacillus Calmette\u2013Gu\u00e9rin is a loss of secreted lytic function required for invasion of lung interstitial tissue","volume":"100","author":"Hsu","year":"2003","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"29076","DOI":"10.1038\/srep29076","article-title":"Loss of Lipid Virulence Factors Reduces the Efficacy of the BCG Vaccine","volume":"6","author":"Tran","year":"2016","journal-title":"Sci. Rep."},{"key":"ref_10","doi-asserted-by":"crossref","unstructured":"Abubakar, I., Pimpin, L., Ariti, C., Beynon, R., Mangtani, P., Sterne, J.A., Fine, P.E., Smith, P.G., Lipman, M., and Elliman, D. (2013). Systematic review and meta-analysis of the current evidence on the duration of protection by bacillus Calmette-Guerin vaccination against tuberculosis. Health Technol. Assess., 17.","DOI":"10.3310\/hta17370"},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"5596","DOI":"10.1073\/pnas.0700869104","article-title":"Genome plasticity of BCG and impact on vaccine efficacy","volume":"104","author":"Brosch","year":"2007","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"5035","DOI":"10.1016\/j.vaccine.2015.08.033","article-title":"Prospects in Mycobacterium bovis Bacille Calmette et Guerin (BCG) vaccine diversity and delivery: Why does BCG fail to protect against tuberculosis?","volume":"33","author":"Moliva","year":"2015","journal-title":"Vaccine"},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"200","DOI":"10.1038\/nrg1809","article-title":"Microarray technology: Beyond transcript profiling and genotype analysis","volume":"7","author":"Hoheisel","year":"2006","journal-title":"Nat. Rev. Genet."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"611","DOI":"10.1128\/CMR.00019-09","article-title":"Basic Concepts of Microarrays and Potential Applications in Clinical Microbiology","volume":"22","author":"Miller","year":"2009","journal-title":"Clin. Microbiol. Rev."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"99","DOI":"10.1046\/j.1365-2567.2001.01274.x","article-title":"Changes in gene expression in macrophages infected with Mycobacterium tuberculosis: A combined transcriptomic and proteomic approach","volume":"104","author":"Ragno","year":"2001","journal-title":"Immunology"},{"key":"ref_16","first-page":"420","article-title":"Metabolic reprograming in macrophage polarization","volume":"5","year":"2014","journal-title":"Front. Immunol."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1007\/s10875-014-0103-7","article-title":"Interaction of Pattern Recognition Receptors with Mycobacterium Tuberculosis","volume":"35","author":"Mortaz","year":"2015","journal-title":"J. Clin. Immunol."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"23","DOI":"10.1016\/j.molimm.2017.02.012","article-title":"The molecular mechanisms of signaling by cooperative assembly formation in innate immunity pathways","volume":"86","author":"Vajjhala","year":"2017","journal-title":"Mol. Immunol."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"1718","DOI":"10.1128\/IAI.74.3.1718-1724.2006","article-title":"Mycobacterium bovis BCG substrains confer different levels of protection against Mycobacterium tuberculosis infection in a BALB\/c model of progressive pulmonary tuberculosis","volume":"74","author":"Calva","year":"2006","journal-title":"Infect. Immun."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"37","DOI":"10.1016\/j.intimp.2014.08.002","article-title":"THP-1 cell line: An in vitro cell model for immune modulation approach","volume":"23","author":"Chanput","year":"2014","journal-title":"Int. Immunopharmacol."},{"key":"ref_21","doi-asserted-by":"crossref","unstructured":"Medley, J., Goff, A., Bettencourt, P.J.G., Dare, M., Cole, L., Cantillon, D., and Waddell, S.J. (2022). Dissecting the Mycobacterium bovis BCG Response to Macrophage Infection to Help Prioritize Targets for Anti-Tuberculosis Drug and Vaccine Discovery. Vaccines, 10.","DOI":"10.3390\/vaccines10010113"},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"5712","DOI":"10.1128\/IAI.72.10.5712-5721.2004","article-title":"The down-regulation of cathepsin G in THP-1 monocytes after infection with Mycobacterium tuberculosis is associated with increased intracellular survival of bacilli","volume":"72","author":"Stewart","year":"2004","journal-title":"Infect. Immun."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"116","DOI":"10.1111\/j.1574-695X.2009.00559.x","article-title":"Comparable studies of immunostimulating activities in vitro among Mycobacterium bovis bacillus Calmette-Guerin (BCG) substrains","volume":"56","author":"Hayashi","year":"2009","journal-title":"FEMS Immunol. Med. Microbiol."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"320","DOI":"10.1016\/j.mimet.2009.03.006","article-title":"Separation and molecular characterization of mycolic acid from the cell wall skeleton of Mycobacterium bovis BCG Tokyo 172 (SMP-105) and BCG substrains by normal-phase high performance liquid chromatography and liquid chromatography\/mass spectrometry","volume":"77","author":"Uenishi","year":"2009","journal-title":"J. Microbiol. Methods"},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"130","DOI":"10.5582\/ddt.2011.v5.3.130","article-title":"Arabino-mycolates derived from cell-wall skeleton of Mycobacterium bovis BCG as a prominent structure for recognition by host immunity","volume":"5","author":"Miyauchi","year":"2011","journal-title":"Drug Discov. Ther."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"66","DOI":"10.1016\/j.it.2016.10.009","article-title":"Recognition of Mycobacterial Lipids by Immune Receptors","volume":"38","author":"Ishikawa","year":"2017","journal-title":"Trends Immunol."},{"key":"ref_27","doi-asserted-by":"crossref","unstructured":"Back, Y.W., Choi, S., Choi, H.G., Shin, K.W., Son, Y.J., Paik, T.H., and Kim, H.J. (2019). Cell wall skeleton of Mycobacterium bovis BCG enhances the vaccine potential of antigen 85B against tuberculosis by inducing Th1 and Th17 responses. PLoS ONE, 14.","DOI":"10.1371\/journal.pone.0213536"},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"765","DOI":"10.2174\/0929866524666170818155524","article-title":"BCG Increased Membrane Expression of TRIM59 through the TLR2\/ TLR4\/IRF5 Pathway in RAW264.7 Macrophages","volume":"24","author":"Jin","year":"2017","journal-title":"Protein Pept. Lett."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"2752","DOI":"10.1128\/JCM.36.9.2752-2754.1998","article-title":"Novel method for rapid measurement of growth of mycobacteria in detergent-free media","volume":"36","author":"Meyers","year":"1998","journal-title":"J. Clin. Microbiol."},{"key":"ref_30","doi-asserted-by":"crossref","unstructured":"Pascoe, J., Hendon-Dunn, C.L., Birch, C.P.D., Williams, G.A., Chambers, M.A., and Bacon, J. (2020). Optimisation of Mycobacterium bovis BCG Fermentation and Storage Survival. Pharmaceutics, 12.","DOI":"10.3390\/pharmaceutics12090900"},{"key":"ref_31","doi-asserted-by":"crossref","unstructured":"Orduna, P., Cevallos, M.A., de Leon, S.P., Arvizu, A., Hernandez-Gonzalez, I.L., Mendoza-Hernandez, G., and Lopez-Vidal, Y. (2011). Genomic and proteomic analyses of Mycobacterium bovis BCG Mexico 1931 reveal a diverse immunogenic repertoire against tuberculosis infection. BMC Genom., 12.","DOI":"10.1186\/1471-2164-12-493"},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"4405","DOI":"10.1128\/iai.65.11.4405-4410.1997","article-title":"Interleukin-12 gene expression in human monocyte-derived macrophages stimulated with Mycobacterium bovis BCG: Cytokine regulation and effect of NK cells","volume":"65","author":"Matsumoto","year":"1997","journal-title":"Infect. Immun."},{"key":"ref_33","doi-asserted-by":"crossref","unstructured":"Rienksma, R.A., Suarez-Diez, M., Mollenkopf, H.J., Dolganov, G.M., Dorhoi, A., Schoolnik, G.K., Martins Dos Santos, V.A., Kaufmann, S.H., Schaap, P.J., and Gengenbacher, M. (2015). Comprehensive insights into transcriptional adaptation of intracellular mycobacteria by microbe-enriched dual RNA sequencing. BMC Genom., 16.","DOI":"10.1186\/s12864-014-1197-2"},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"553","DOI":"10.1016\/j.jinf.2013.12.017","article-title":"Analysis of miRNA expression profiling in human macrophages responding to Mycobacterium infection: Induction of the immune regulator miR-146a","volume":"68","author":"Liu","year":"2014","journal-title":"J. Infect."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"437301","DOI":"10.4061\/2011\/437301","article-title":"MiR-146a in Immunity and Disease","volume":"2011","author":"Rusca","year":"2011","journal-title":"Mol. Biol. Int."},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"2874","DOI":"10.3389\/fimmu.2019.02874","article-title":"Transcriptome Profiling of Bovine Macrophages Infected by Mycobacterium avium spp. paratuberculosis Depicts Foam Cell and Innate Immune Tolerance Phenotypes","volume":"10","author":"Ariel","year":"2019","journal-title":"Front. Immunol."},{"key":"ref_37","doi-asserted-by":"crossref","unstructured":"Toka, F.N., Dunaway, K., Smaltz, F., Szulc-Dabrowska, L., Drnevich, J., Mielcarska, M.B., Bossowska-Nowicka, M., and Schweizer, M. (2019). Bacterial and viral pathogen-associated molecular patterns induce divergent early transcriptomic landscapes in a bovine macrophage cell line. BMC Genom., 20.","DOI":"10.1186\/s12864-018-5411-5"},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"1660","DOI":"10.4049\/jimmunol.1700129","article-title":"CXCL1 and CXCL2 Regulate NLRP3 Inflammasome Activation via G-Protein-Coupled Receptor CXCR2","volume":"199","author":"Boro","year":"2017","journal-title":"J. Immunol."},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"196","DOI":"10.3389\/fcimb.2017.00196","article-title":"The Association of OASL and Type I Interferons in the Pathogenesis and Survival of Intracellular Replicating Bacterial Species","volume":"7","author":"Leisching","year":"2017","journal-title":"Front. Cell. Infect. Microbiol."},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"S77","DOI":"10.1016\/j.ijid.2019.02.029","article-title":"OAS1, OAS2 and OAS3 restrict intracellular M. tb replication and enhance cytokine secretion","volume":"80S","author":"Leisching","year":"2019","journal-title":"Int. J. Infect. Dis."},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"24","DOI":"10.1016\/j.intimp.2017.10.026","article-title":"Down-regulation of Notch signaling pathway reverses the Th1\/Th2 imbalance in tuberculosis patients","volume":"54","author":"Li","year":"2018","journal-title":"Int. Immunopharmacol."},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"471","DOI":"10.1016\/j.smim.2014.09.010","article-title":"Macrophage immunoregulatory pathways in tuberculosis","volume":"26","author":"Rajaram","year":"2014","journal-title":"Semin. Immunol."},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"581","DOI":"10.1038\/s41590-019-0372-7","article-title":"SUCNR1 controls an anti-inflammatory program in macrophages to regulate the metabolic response to obesity","volume":"20","author":"Keiran","year":"2019","journal-title":"Nat. Immunol."},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"2643","DOI":"10.3389\/fimmu.2018.02643","article-title":"CD180 Ligation Inhibits TLR7- and TLR9-Mediated Activation of Macrophages and Dendritic Cells through the Lyn-SHP-1\/2 Axis in Murine Lupus","volume":"9","author":"Yang","year":"2018","journal-title":"Front. Immunol."},{"key":"ref_45","doi-asserted-by":"crossref","unstructured":"Welz, B., Bikker, R., Junemann, J., Christmann, M., Neumann, K., Weber, M., Hoffmeister, L., Preuss, K., Pich, A., and Huber, R. (2019). Proteome and Phosphoproteome Analysis in TNF Long Term-Exposed Primary Human Monocytes. Int. J. Mol. Sci., 20.","DOI":"10.3390\/ijms20051241"},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"15874","DOI":"10.1038\/ncomms15874","article-title":"Long noncoding RNA LncHIFCAR\/MIR31HG is a HIF-1alpha co-activator driving oral cancer progression","volume":"8","author":"Shih","year":"2017","journal-title":"Nat. Commun."},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"e45517","DOI":"10.15252\/embr.201745517","article-title":"Serum amyloid A promotes LPS clearance and suppresses LPS-induced inflammation and tissue injury","volume":"19","author":"Cheng","year":"2018","journal-title":"EMBO Rep."},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"250","DOI":"10.1158\/1541-7786.MCR-14-0385","article-title":"Identification of TRIML2, a novel p53 target, that enhances p53 SUMOylation and regulates the transactivation of proapoptotic genes","volume":"13","author":"Kung","year":"2015","journal-title":"Mol. Cancer Res."},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"38963","DOI":"10.1038\/srep38963","article-title":"Microarray analysis of long noncoding RNA and mRNA expression profiles in human macrophages infected with Mycobacterium tuberculosis","volume":"6","author":"Yang","year":"2016","journal-title":"Sci. Rep."},{"key":"ref_50","doi-asserted-by":"crossref","first-page":"288","DOI":"10.1186\/s13046-020-01795-5","article-title":"Long noncoding RNA MIR31HG and its splice variants regulate proliferation and migration: Prognostic implications for muscle invasive bladder cancer","volume":"39","author":"Wu","year":"2020","journal-title":"J. Exp. Clin. Cancer Res."},{"key":"ref_51","doi-asserted-by":"crossref","first-page":"24071","DOI":"10.18632\/aging.203644","article-title":"LncRNA MIR31HG is induced by tocilizumab and ameliorates rheumatoid arthritis fibroblast-like synoviocyte-mediated inflammation via miR-214-PTEN-AKT signaling pathway","volume":"13","author":"Cao","year":"2021","journal-title":"Aging"},{"key":"ref_52","doi-asserted-by":"crossref","first-page":"2459","DOI":"10.1038\/s41467-021-22746-4","article-title":"The long noncoding RNA MIR31HG regulates the senescence associated secretory phenotype","volume":"12","author":"Montes","year":"2021","journal-title":"Nat. Commun."},{"key":"ref_53","doi-asserted-by":"crossref","first-page":"2843","DOI":"10.1002\/ijc.31998","article-title":"Long noncoding RNA MIR31HG is a bona fide prognostic marker with colorectal cancer cell-intrinsic properties","volume":"144","author":"Eide","year":"2019","journal-title":"Int. J. Cancer"},{"key":"ref_54","doi-asserted-by":"crossref","first-page":"768","DOI":"10.4049\/jimmunol.1701048","article-title":"Cyclic GMP-AMP Synthase Is the Cytosolic Sensor of Plasmodium falciparum Genomic DNA and Activates Type I IFN in Malaria","volume":"200","author":"Schrum","year":"2018","journal-title":"J. Immunol."},{"key":"ref_55","doi-asserted-by":"crossref","unstructured":"Carthagena, L., Bergamaschi, A., Luna, J.M., David, A., Uchil, P.D., Margottin-Goguet, F., Mothes, W., Hazan, U., Transy, C., and Pancino, G. (2009). Human TRIM gene expression in response to interferons. PLoS ONE, 4.","DOI":"10.1371\/journal.pone.0004894"},{"key":"ref_56","doi-asserted-by":"crossref","unstructured":"Gu, F., Wang, C., Wei, F., Wang, Y., Zhu, Q., Ding, L., Xu, W., Zhu, C., Cai, C., and Qian, Z. (2018). STAT6 degradation and ubiquitylated TRIML2 are essential for activation of human oncogenic herpesvirus. PLoS Pathog., 14.","DOI":"10.1371\/journal.ppat.1007416"},{"key":"ref_57","first-page":"529","article-title":"Gene expression profiles predicting the response to IFN-beta and a combination of temozolomide and IFN-beta in malignant gliomas","volume":"39","author":"Yoshino","year":"2011","journal-title":"Int. J. Oncol."},{"key":"ref_58","doi-asserted-by":"crossref","first-page":"309","DOI":"10.1038\/s41586-021-03520-4","article-title":"Epigenetic silencing by SETDB1 suppresses tumour intrinsic immunogenicity","volume":"595","author":"Griffin","year":"2021","journal-title":"Nature"},{"key":"ref_59","first-page":"650","article-title":"Human serum amyloid A genes are expressed in monocyte\/macrophage cell lines","volume":"145","author":"Meek","year":"1994","journal-title":"Am. J. Pathol."},{"key":"ref_60","doi-asserted-by":"crossref","unstructured":"Jumeau, C., Awad, F., Assrawi, E., Cobret, L., Duquesnoy, P., Giurgea, I., Valeyre, D., Grateau, G., Amselem, S., and Bernaudin, J.F. (2019). Expression of SAA1, SAA2 and SAA4 genes in human primary monocytes and monocyte-derived macrophages. PLoS ONE, 14.","DOI":"10.1371\/journal.pone.0217005"},{"key":"ref_61","doi-asserted-by":"crossref","first-page":"10","DOI":"10.1016\/j.molcel.2018.08.023","article-title":"Transcript Buffering: A Balancing Act between mRNA Synthesis and mRNA Degradation","volume":"72","author":"Timmers","year":"2018","journal-title":"Mol. Cell"},{"key":"ref_62","first-page":"e15","article-title":"Analysis of translation using polysome profiling","volume":"45","author":"Chasse","year":"2017","journal-title":"Nucleic Acids Res."},{"key":"ref_63","doi-asserted-by":"crossref","first-page":"194","DOI":"10.1111\/pim.12026","article-title":"DEAD-box proteins, like Leishmania eIF4A, modulate interleukin (IL)-12, IL-10 and tumour necrosis factor-alpha production by human monocytes","volume":"35","author":"Barhoumi","year":"2013","journal-title":"Parasite Immunol."},{"key":"ref_64","doi-asserted-by":"crossref","unstructured":"Daigneault, M., Preston, J.A., Marriott, H.M., Whyte, M.K., and Dockrell, D.H. (2010). The identification of markers of macrophage differentiation in PMA-stimulated THP-1 cells and monocyte-derived macrophages. PLoS ONE, 5.","DOI":"10.1371\/journal.pone.0008668"},{"key":"ref_65","doi-asserted-by":"crossref","unstructured":"Genin, M., Clement, F., Fattaccioli, A., Raes, M., and Michiels, C. (2015). M1 and M2 macrophages derived from THP-1 cells differentially modulate the response of cancer cells to etoposide. BMC Cancer, 15.","DOI":"10.1186\/s12885-015-1546-9"},{"key":"ref_66","doi-asserted-by":"crossref","first-page":"65","DOI":"10.1002\/bab.1143","article-title":"Ex vivo cytokine production in peripheral blood mononuclear cells after their stimulation with dsRNA of natural origin","volume":"61","author":"Veinalde","year":"2014","journal-title":"Biotechnol. Appl. Biochem."},{"key":"ref_67","doi-asserted-by":"crossref","first-page":"32456","DOI":"10.18632\/oncotarget.5932","article-title":"Lack of intracellular replication of M. tuberculosis and M. bovis BCG caused by delivering bacilli to lysosomes in murine brain microvascular endothelial cells","volume":"6","author":"Chen","year":"2015","journal-title":"Oncotarget"},{"key":"ref_68","doi-asserted-by":"crossref","first-page":"F993","DOI":"10.1152\/ajprenal.00637.2014","article-title":"Hyperuricemia-induced NLRP3 activation of macrophages contributes to the progression of diabetic nephropathy","volume":"308","author":"Kim","year":"2015","journal-title":"Am. J. Physiol. Renal Physiol."},{"key":"ref_69","doi-asserted-by":"crossref","first-page":"303","DOI":"10.1016\/j.intimp.2014.07.004","article-title":"Interferon gamma induced by resveratrol analog, HS-1793, reverses the properties of tumor associated macrophages","volume":"22","author":"Jeong","year":"2014","journal-title":"Int. Immunopharmacol."},{"key":"ref_70","doi-asserted-by":"crossref","first-page":"328","DOI":"10.1111\/cpr.12030","article-title":"PMA withdrawal in PMA-treated monocytic THP-1 cells and subsequent retinoic acid stimulation, modulate induction of apoptosis and appearance of dendritic cells","volume":"46","author":"Spano","year":"2013","journal-title":"Cell Prolif."},{"key":"ref_71","doi-asserted-by":"crossref","first-page":"185","DOI":"10.1093\/bioinformatics\/19.2.185","article-title":"A comparison of normalization methods for high density oligonucleotide array data based on variance and bias","volume":"19","author":"Bolstad","year":"2003","journal-title":"Bioinformatics"},{"key":"ref_72","doi-asserted-by":"crossref","first-page":"307","DOI":"10.1093\/bioinformatics\/btg405","article-title":"Affy\u2014Analysis of Affymetrix GeneChip data at the probe level","volume":"20","author":"Gautier","year":"2004","journal-title":"Bioinformatics"},{"key":"ref_73","doi-asserted-by":"crossref","unstructured":"Smyth, G.K. (2004). Linear models and empirical bayes methods for assessing differential expression in microarray experiments. Stat. Appl. Genet. Mol. Biol., 3.","DOI":"10.2202\/1544-6115.1027"},{"key":"ref_74","doi-asserted-by":"crossref","first-page":"e47","DOI":"10.1093\/nar\/gkv007","article-title":"Limma powers differential expression analyses for RNA-sequencing and microarray studies","volume":"43","author":"Ritchie","year":"2015","journal-title":"Nucleic Acids Res."},{"key":"ref_75","doi-asserted-by":"crossref","first-page":"44","DOI":"10.1038\/nprot.2008.211","article-title":"Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources","volume":"4","author":"Huang","year":"2009","journal-title":"Nat. Protoc."},{"key":"ref_76","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1093\/nar\/gkn923","article-title":"Bioinformatics enrichment tools: Paths toward the comprehensive functional analysis of large gene lists","volume":"37","author":"Huang","year":"2009","journal-title":"Nucleic Acids Res."},{"key":"ref_77","doi-asserted-by":"crossref","first-page":"267","DOI":"10.1038\/ng1180","article-title":"PGC-1alpha-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes","volume":"34","author":"Mootha","year":"2003","journal-title":"Nat. Genet."},{"key":"ref_78","doi-asserted-by":"crossref","first-page":"15545","DOI":"10.1073\/pnas.0506580102","article-title":"Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles","volume":"102","author":"Subramanian","year":"2005","journal-title":"Proc. Natl. Acad. Sci. USA"}],"container-title":["International Journal of Molecular Sciences"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1422-0067\/23\/9\/4525\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,10]],"date-time":"2025-10-10T22:57:09Z","timestamp":1760137029000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1422-0067\/23\/9\/4525"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,4,20]]},"references-count":78,"journal-issue":{"issue":"9","published-online":{"date-parts":[[2022,5]]}},"alternative-id":["ijms23094525"],"URL":"https:\/\/doi.org\/10.3390\/ijms23094525","relation":{},"ISSN":["1422-0067"],"issn-type":[{"value":"1422-0067","type":"electronic"}],"subject":[],"published":{"date-parts":[[2022,4,20]]}}}