Potentiation of rifampin activity in a mouse model of tuberculosis by activation of host transcription factor EB

Autoři: Ruslana Bryk aff001;  Shashirekha Mundhra aff001;  Xiuju Jiang aff001;  Madeleine Wood aff001;  Daniel Pfau aff001;  Elaina Weber aff001;  Suna Park aff001;  Li Zhang aff001;  Colin Wilson aff003;  Renier Van der Westhuyzen aff003;  Leslie Street aff003;  Kelly Chibale aff003;  Matthew Zimmerman aff005;  Véronique Dartois aff005;  Nunzia Pastore aff006;  Andrea Ballabio aff006;  Natalie Hawryluk aff010;  Stacie Canan aff010;  Vikram Khetani aff011;  Joseph Camardo aff011;  Carl Nathan aff001
Působiště autorů: Department of Microbiology and Immunology, Weill Cornell Medicine, New York, New York, United States of America aff001;  Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, New York, New York, United States of America aff002;  Drug Discovery and Development Centre, H3D, University of Cape Town, Rondebosch, South Africa aff003;  South African Medical Research Council Drug Discovery and Development Research Unit, Department of Chemistry and Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Rondebosch, South Africa aff004;  Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, New Jersey, United States of America aff005;  Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America aff006;  Telethon Institute of Genetics and Medicine (TIGEM), Naples, Italy aff007;  Medical Genetics, Department of Medical and Translational Sciences, Federico II University, Naples, Italy aff008;  Ian and Dan Duncan Neurological Research Institute, Texas Children Hospital, Houston, Texas, United States of America aff009;  Celgene Global Health, San Diego, California, United States of America aff010;  Celgene Global Health, Summit, New Jersey, United States of America aff011
Vyšlo v časopise: Potentiation of rifampin activity in a mouse model of tuberculosis by activation of host transcription factor EB. PLoS Pathog 16(6): e32767. doi:10.1371/journal.ppat.1008567
Kategorie: Research Article
doi: 10.1371/journal.ppat.1008567


Efforts at host-directed therapy of tuberculosis have produced little control of the disease in experimental animals to date. This is not surprising, given that few specific host targets have been validated, and reciprocally, many of the compounds tested potentially impact multiple targets with both beneficial and detrimental consequences. This puts a premium on identifying appropriate molecular targets and subjecting them to more selective modulation. We discovered an aminopyrimidine small molecule, 2062, that had no direct antimycobacterial activity, but synergized with rifampin to reduce bacterial burden in Mtb infected macrophages and mice and also dampened lung immunopathology. We used 2062 and its inactive congeners as tool compounds to identify host targets. By biochemical, pharmacologic, transcriptomic and genetic approaches, we found that 2062’s beneficial effects on Mtb control and clearance in macrophages and in mice are associated with activation of transcription factor EB via an organellar stress response. 2062-dependent TFEB activation led to improved autophagy, lysosomal acidification and lysosomal degradation, promoting bacterial clearance in macrophages. Deletion of TFEB resulted in the loss of IFNγ-dependent control of Mtb replication in macrophages. 2062 also targeted multiple kinases, such as PIKfyve, VPS34, JAKs and Tyk2, whose inhibition likely limited 2062’s efficacy in vivo. These findings support a search for selective activators of TFEB for HDT of TB.

Klíčová slova:

Autophagic cell death – Inflammation – Kinase inhibitors – Lysosomes – Macrophages – Mycobacterium tuberculosis – Tuberculosis – Tuberculosis drug discovery


1. Malherbe ST, Shenai S, Ronacher K, Loxton AG, Dolganov G, Kriel M, et al. Persisting positron emission tomography lesion activity and Mycobacterium tuberculosis mRNA after tuberculosis cure. Nature medicine. 2016 Oct;22(10):1094–100. PMCID: doi: 10.1038/nm.4177 27595324. Epub 2016/09/07.

2. McIlleron H, Wash P, Burger A, Norman J, Folb PI, Smith P. Determinants of rifampin, isoniazid, pyrazinamide, and ethambutol pharmacokinetics in a cohort of tuberculosis patients. Antimicrobial agents and chemotherapy. 2006 Apr;50(4):1170–7. doi: 10.1128/AAC.50.4.1170-1177.2006 16569826. PMCID: PMC1426981. Epub 2006/03/30.

3. van Ingen J, Aarnoutse RE, Donald PR, Diacon AH, Dawson R, Plemper van Balen G, et al. Why Do We Use 600 mg of Rifampicin in Tuberculosis Treatment? Clin Infect Dis. 2011 May;52(9):e194–9. doi: 10.1093/cid/cir184 21467012. Epub 2011/04/07.

4. Hawn TR, Matheson AI, Maley SN, Vandal O. Host-directed therapeutics for tuberculosis: can we harness the host? Microbiology and molecular biology reviews: MMBR. 2013 Dec;77(4):608–27. doi: 10.1128/MMBR.00032-13 24296574. PMCID: 3973381. Epub 2013/12/04.

5. Tobin DM. Host-Directed Therapies for Tuberculosis. Cold Spring Harbor perspectives in medicine. 2015 May 18;5(10). doi: 10.1101/cshperspect.a021196 25986592. PMCID: 4588138. Epub 2015/05/20.

6. Wallis RS, Hafner R. Advancing host-directed therapy for tuberculosis. Nature reviews Immunology. 2015 Apr;15(4):255–63. doi: 10.1038/nri3813 25765201. Epub 2015/03/15.

7. Zumla A, Rao M, Wallis RS, Kaufmann SH, Rustomjee R, Mwaba P, et al. Host-directed therapies for infectious diseases: current status, recent progress, and future prospects. The Lancet Infectious diseases. 2016 Apr;16(4):e47–63. doi: 10.1016/S1473-3099(16)00078-5 27036359. Epub 2016/04/03.

8. Napier RJ, Rafi W, Cheruvu M, Powell KR, Zaunbrecher MA, Bornmann W, et al. Imatinib-sensitive tyrosine kinases regulate mycobacterial pathogenesis and represent therapeutic targets against tuberculosis. Cell host & microbe. 2011 Nov 17;10(5):475–85. doi: 10.1016/j.chom.2011.09.010 22100163. PMCID: 3222875. Epub 2011/11/22.

9. Schiebler M, Brown K, Hegyi K, Newton SM, Renna M, Hepburn L, et al. Functional drug screening reveals anticonvulsants as enhancers of mTOR-independent autophagic killing of Mycobacterium tuberculosis through inositol depletion. EMBO molecular medicine. 2015 Feb;7(2):127–39. doi: 10.15252/emmm.201404137 25535254. PMCID: 4328644. Epub 2014/12/24.

10. Parihar SP, Guler R, Khutlang R, Lang DM, Hurdayal R, Mhlanga MM, et al. Statin therapy reduces the mycobacterium tuberculosis burden in human macrophages and in mice by enhancing autophagy and phagosome maturation. The Journal of infectious diseases. 2014 Mar 1;209(5):754–63. doi: 10.1093/infdis/jit550 24133190. Epub 2013/10/18.

11. Mayer-Barber KD, Andrade BB, Oland SD, Amaral EP, Barber DL, Gonzales J, et al. Host-directed therapy of tuberculosis based on interleukin-1 and type I interferon crosstalk. Nature. 2014 Jul 3;511(7507):99–103. doi: 10.1038/nature13489 24990750. PMCID: 4809146. Epub 2014/07/06.

12. Kumar S, Sharma C, Kaushik SR, Kulshreshtha A, Chaturvedi S, Nanda RK, et al. The phytochemical bergenin as an adjunct immunotherapy for tuberculosis in mice. J Biol Chem. 2019 May 24;294(21):8555–63. doi: 10.1074/jbc.RA119.008005 30975902. Epub 2019/04/13.

13. Subbian S, Koo MS, Tsenova L, Khetani V, Zeldis JB, Fallows D, et al. Pharmacologic Inhibition of Host Phosphodiesterase-4 Improves Isoniazid-Mediated Clearance of Mycobacterium tuberculosis. Frontiers in immunology. 2016;7:238. doi: 10.3389/fimmu.2016.00238 27379099. PMCID: 4911353. Epub 2016/07/06.

14. Stanley SA, Barczak AK, Silvis MR, Luo SS, Sogi K, Vokes M, et al. Identification of host-targeted small molecules that restrict intracellular Mycobacterium tuberculosis growth. PLoS pathogens. 2014 Feb;10(2):e1003946. doi: 10.1371/journal.ppat.1003946 24586159. PMCID: 3930586. Epub 2014/03/04.

15. Ouimet M, Koster S, Sakowski E, Ramkhelawon B, van Solingen C, Oldebeken S, et al. Mycobacterium tuberculosis induces the miR-33 locus to reprogram autophagy and host lipid metabolism. Nature immunology. 2016 Jun;17(6):677–86. doi: 10.1038/ni.3434 27089382. PMCID: 4873392. Epub 2016/04/19.

16. Singhal A, Jie L, Kumar P, Hong GS, Leow MK, Paleja B, et al. Metformin as adjunct antituberculosis therapy. Science translational medicine. 2014 Nov 19;6(263):263ra159. 25411472. Epub 2014/11/21.

17. Dutta NK, Pinn ML, Karakousis PC. Metformin Adjunctive Therapy Does Not Improve the Sterilizing Activity of the First-Line Antitubercular Regimen in Mice. Antimicrobial agents and chemotherapy. 2017 Aug;61(8). doi: 10.1128/AAC.00652-17 28559262. PMCID: 5527622. Epub 2017/06/01.

18. Jayaswal S, Kamal MA, Dua R, Gupta S, Majumdar T, Das G, et al. Identification of host-dependent survival factors for intracellular Mycobacterium tuberculosis through an siRNA screen. PLoS pathogens. 2010 Apr 15;6(4):e1000839. doi: 10.1371/journal.ppat.1000839 20419122. PMCID: PMC2855445. Epub 2010/04/27.

19. Kumar D, Nath L, Kamal MA, Varshney A, Jain A, Singh S, et al. Genome-wide analysis of the host intracellular network that regulates survival of Mycobacterium tuberculosis. Cell. 2010 Mar 5;140(5):731–43. doi: 10.1016/j.cell.2010.02.012 20211141. Epub 2010/03/10.

20. Cheng CY, Gutierrez NM, Marzuki MB, Lu X, Foreman TW, Paleja B, et al. Host sirtuin 1 regulates mycobacterial immunopathogenesis and represents a therapeutic target against tuberculosis. Science immunology. 2017 Mar;2(9). doi: 10.1126/sciimmunol.aaj1789 28707004. PMCID: 5505666. Epub 2017/07/15.

21. Huynh JP, Lin CC, Kimmey JM, Jarjour NN, Schwarzkopf EA, Bradstreet TR, et al. Bhlhe40 is an essential repressor of IL-10 during Mycobacterium tuberculosis infection. The Journal of experimental medicine. 2018 Jul 2;215(7):1823–38. doi: 10.1084/jem.20171704 29773644. PMCID: PMC6028511. Epub 2018/05/19.

22. Sardiello M, Palmieri M, di Ronza A, Medina DL, Valenza M, Gennarino VA, et al. A gene network regulating lysosomal biogenesis and function. Science. 2009 Jul 24;325(5939):473–7. doi: 10.1126/science.1174447 19556463. Epub 2009/06/27.

23. Settembre C, Di Malta C, Polito VA, Garcia Arencibia M, Vetrini F, Erdin S, et al. TFEB links autophagy to lysosomal biogenesis. Science. 2011 Jun 17;332(6036):1429–33. doi: 10.1126/science.1204592 21617040. PMCID: 3638014. Epub 2011/05/28.

24. Lapierre LR, De Magalhaes Filho CD, McQuary PR, Chu CC, Visvikis O, Chang JT, et al. The TFEB orthologue HLH-30 regulates autophagy and modulates longevity in Caenorhabditis elegans. Nature communications. 2013;4:2267. doi: 10.1038/ncomms3267 23925298. PMCID: 3866206. Epub 2013/08/09.

25. Roczniak-Ferguson A, Petit CS, Froehlich F, Qian S, Ky J, Angarola B, et al. The transcription factor TFEB links mTORC1 signaling to transcriptional control of lysosome homeostasis. Science signaling. 2012 Jun 12;5(228):ra42. doi: 10.1126/scisignal.2002790 22692423. PMCID: 3437338. Epub 2012/06/14.

26. Medina DL, Di Paola S, Peluso I, Armani A, De Stefani D, Venditti R, et al. Lysosomal calcium signalling regulates autophagy through calcineurin and TFEB. Nature cell biology. 2015 Mar;17(3):288–99. doi: 10.1038/ncb3114 25720963. PMCID: 4801004. Epub 2015/02/28.

27. Tong Y, Song F. Intracellular calcium signaling regulates autophagy via calcineurin-mediated TFEB dephosphorylation. Autophagy. 2015;11(7):1192–5. doi: 10.1080/15548627.2015.1054594 26043755. PMCID: PMC4590610. Epub 2015/06/06.

28. Clipstone NA, Crabtree GR. Identification of calcineurin as a key signalling enzyme in T-lymphocyte activation. Nature. 1992 Jun 25;357(6380):695–7. doi: 10.1038/357695a0 1377362. Epub 1992/06/25.

29. Pastore N, Brady OA, Diab HI, Martina JA, Sun L, Huynh T, et al. TFEB and TFE3 cooperate in the regulation of the innate immune response in activated macrophages. Autophagy. 2016 Aug 2;12(8):1240–58. doi: 10.1080/15548627.2016.1179405 27171064. PMCID: 4968228. Epub 2016/05/14.

30. Liu Q, Chang JW, Wang J, Kang SA, Thoreen CC, Markhard A, et al. Discovery of 1-(4-(4-propionylpiperazin-1-yl)-3-(trifluoromethyl)phenyl)-9-(quinolin-3-yl)benz o[h][1,6]naphthyridin-2(1H)-one as a highly potent, selective mammalian target of rapamycin (mTOR) inhibitor for the treatment of cancer. Journal of medicinal chemistry. 2010 Oct 14;53(19):7146–55. doi: 10.1021/jm101144f 20860370. PMCID: 3893826. Epub 2010/09/24.

31. Wang C, Niederstrasser H, Douglas PM, Lin R, Jaramillo J, Li Y, et al. Small-molecule TFEB pathway agonists that ameliorate metabolic syndrome in mice and extend C. elegans lifespan. Nature communications. 2017 Dec 22;8(1):2270. doi: 10.1038/s41467-017-02332-3 29273768. PMCID: 5741634. Epub 2017/12/24.

32. Nathan C. Kunkel Lecture: Fundamental immunodeficiency and its correction. The Journal of experimental medicine. 2017 Aug 7;214(8):2175–91. doi: 10.1084/jem.20170637 28701368. PMCID: 5551579. Epub 2017/07/14.

33. Cadena AM, Fortune SM, Flynn JL. Heterogeneity in tuberculosis. Nature reviews Immunology. 2017 Nov;17(11):691–702. doi: 10.1038/nri.2017.69 28736436. Epub 2017/07/25.

34. Kim GH, Dayam RM, Prashar A, Terebiznik M, Botelho RJ. PIKfyve inhibition interferes with phagosome and endosome maturation in macrophages. Traffic. 2014 Oct;15(10):1143–63. doi: 10.1111/tra.12199 25041080. Epub 2014/07/22.

35. Dayam RM, Saric A, Shilliday RE, Botelho RJ. The Phosphoinositide-Gated Lysosomal Ca(2+) Channel, TRPML1, Is Required for Phagosome Maturation. Traffic. 2015 Sep;16(9):1010–26. doi: 10.1111/tra.12303 26010303. Epub 2015/05/27.

36. Ronan B, Flamand O, Vescovi L, Dureuil C, Durand L, Fassy F, et al. A highly potent and selective Vps34 inhibitor alters vesicle trafficking and autophagy. Nature chemical biology. 2014 Dec;10(12):1013–9. doi: 10.1038/nchembio.1681 25326666. Epub 2014/10/20.

37. Casanova JL, Holland SM, Notarangelo LD. Inborn errors of human JAKs and STATs. Immunity. 2012 Apr 20;36(4):515–28. doi: 10.1016/j.immuni.2012.03.016 22520845. PMCID: 3334867. Epub 2012/04/24.

38. Settembre C, Zoncu R, Medina DL, Vetrini F, Erdin S, Erdin S, et al. A lysosome-to-nucleus signalling mechanism senses and regulates the lysosome via mTOR and TFEB. The EMBO journal. 2012 Mar 7;31(5):1095–108. doi: 10.1038/emboj.2012.32 22343943. PMCID: 3298007. Epub 2012/02/22.

39. Decressac M, Mattsson B, Weikop P, Lundblad M, Jakobsson J, Bjorklund A. TFEB-mediated autophagy rescues midbrain dopamine neurons from alpha-synuclein toxicity. Proceedings of the National Academy of Sciences of the United States of America. 2013 May 7;110(19):E1817–26. doi: 10.1073/pnas.1305623110 23610405. PMCID: 3651458. Epub 2013/04/24.

40. Polito VA, Li H, Martini-Stoica H, Wang B, Yang L, Xu Y, et al. Selective clearance of aberrant tau proteins and rescue of neurotoxicity by transcription factor EB. EMBO molecular medicine. 2014 Sep;6(9):1142–60. doi: 10.15252/emmm.201303671 25069841. PMCID: 4197862. Epub 2014/07/30.

41. Sardiello M. Transcription factor EB: from master coordinator of lysosomal pathways to candidate therapeutic target in degenerative storage diseases. Annals of the New York Academy of Sciences. 2016 May;1371(1):3–14. doi: 10.1111/nyas.13131 27299292. PMCID: 5032832. Epub 2016/06/15.

42. Visvikis O, Ihuegbu N, Labed SA, Luhachack LG, Alves AF, Wollenberg AC, et al. Innate host defense requires TFEB-mediated transcription of cytoprotective and antimicrobial genes. Immunity. 2014 Jun 19;40(6):896–909. doi: 10.1016/j.immuni.2014.05.002 24882217. PMCID: 4104614. Epub 2014/06/03.

43. Kim YS, Lee HM, Kim JK, Yang CS, Kim TS, Jung M, et al. PPAR-alpha Activation Mediates Innate Host Defense through Induction of TFEB and Lipid Catabolism. Journal of immunology. 2017 Apr 15;198(8):3283–95. doi: 10.4049/jimmunol.1601920 28275133. Epub 2017/03/10.

44. Chandra V, Bhagyaraj E, Nanduri R, Ahuja N, Gupta P. NR1D1 ameliorates Mycobacterium tuberculosis clearance through regulation of autophagy. Autophagy. 2015 Nov 2;11(11):1987–97. doi: 10.1080/15548627.2015.1091140 26390081. PMCID: 4824569. Epub 2015/09/22.

45. Chen J, Ou Y, Li Y, Hu S, Shao LW, Liu Y. Metformin extends C. elegans lifespan through lysosomal pathway. eLife. 2017 Oct 13;6. doi: 10.7554/eLife.31268 29027899. PMCID: 5685485. Epub 2017/10/14.

46. Bryk R, Gold B, Venugopal A, Singh J, Samy R, Pupek K, et al. Selective killing of nonreplicating mycobacteria. Cell host & microbe. 2008 Mar 13;3(3):137–45. doi: 10.1016/j.chom.2008.02.003 18329613. PMCID: 2423947. Epub 2008/03/11.

47. Oslund RC, Gelb MH. Biochemical characterization of selective inhibitors of human group IIA secreted phospholipase A(2) and hyaluronic acid-linked inhibitor conjugates. Biochemistry. 2012 Oct 30;51(43):8617–26. doi: 10.1021/bi301140b 23020658. PMCID: PMC3549043. Epub 2012/10/02.

Článek vyšel v časopise

PLOS Pathogens

2020 Číslo 6

Nejčtenější v tomto čísle
Zapomenuté heslo

Nemáte účet?  Registrujte se

Zapomenuté heslo

Zadejte e-mailovou adresu, se kterou jste vytvářel(a) účet, budou Vám na ni zaslány informace k nastavení nového hesla.


Nemáte účet?  Registrujte se