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Buglino JA, Ozakman Y, Hatch C, Benjamin A, Tan D, Glickman MS. Chalkophore mediated respiratory oxidase flexibility controls M. tuberculosis virulence. bioRxiv 2024:2024.04.12.589290. [PMID: 38645185 PMCID: PMC11030325 DOI: 10.1101/2024.04.12.589290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
Oxidative phosphorylation has emerged as a critical therapeutic vulnerability of M. tuberculosis, but it is unknown how M. tuberculosis and other pathogens maintain respiration during infection. M. tuberculosis synthesizes diisonitrile lipopeptide chalkophores that chelate copper tightly, but their role in host-pathogen interactions is also unknown. We demonstrate that M. tuberculosis chalkophores maintain the function of the heme-copper bcc:aa3 respiratory oxidase under copper limitation. Chalkophore deficient M. tuberculosis cannot survive, respire to oxygen, or produce ATP under copper deprivation in culture. M. tuberculosis lacking chalkophore biosynthesis is attenuated in mice, a phenotype that is severely exacerbated by loss of the CytBD alternative respiratory oxidase (encoded by cydAB), revealing a multilayered flexibility of the respiratory chain that maintains oxidative phosphorylation during infection. Taken together, these data demonstrate that chalkophores counter host inflicted copper deprivation and highlight that protection of cellular respiration is a critical virulence function in M. tuberculosis.
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Affiliation(s)
- John A. Buglino
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, New York 10065 USA
| | - Yaprak Ozakman
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, New York 10065 USA
| | - Chad Hatch
- Chemical Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, New York 10065 USA
| | - Anna Benjamin
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, New York 10065 USA
| | - Derek Tan
- Chemical Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, New York 10065 USA
- Tri-Institutional Research Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, New York 10065 USA
| | - Michael S. Glickman
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, New York 10065 USA
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Daman AW, Antonelli AC, Redelman-Sidi G, Paddock L, Cheong JG, Jurado LF, Benjamin A, Jiang S, Ahimovic D, Khayat S, Bale MJ, Loutochin O, McPherson VA, Pe'er D, Divangahi M, Pietzak E, Josefowicz SZ, Glickman MS. Microbial cancer immunotherapy reprograms hematopoietic stem cells to enhance anti-tumor immunity. bioRxiv 2024:2024.03.21.586166. [PMID: 38562703 PMCID: PMC10983927 DOI: 10.1101/2024.03.21.586166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Mycobacterium bovis BCG is the vaccine against tuberculosis and an immunotherapy for bladder cancer. When administered intravenously, BCG reprograms bone marrow hematopoietic stem and progenitor cells (HSPCs), leading to heterologous protection against infections. Whether HSPC-reprogramming contributes to the anti-tumor effects of BCG administered into the bladder is unknown. We demonstrate that BCG administered in the bladder in both mice and humans reprograms HSPCs to amplify myelopoiesis and functionally enhance myeloid cell antigen presentation pathways. Reconstitution of naive mice with HSPCs from bladder BCG-treated mice enhances anti-tumor immunity and tumor control, increases intratumoral dendritic cell infiltration, and synergizes with checkpoint blockade. We conclude that bladder BCG acts systemically, reprogramming HSPC-encoded innate immunity, highlighting the broad potential of modulating HSPC phenotypes to improve tumor immunity. One Sentence Summary BCG administered in the bladder reprograms bone marrow HSPCs and contributes to tumor control via enhanced myeloid cells.
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3
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Xiao X, Fay A, Molina PS, Kovach A, Glickman MS, Li H. Structure of the M. tuberculosis DnaK-GrpE complex reveals how key DnaK roles are controlled. Nat Commun 2024; 15:660. [PMID: 38253530 PMCID: PMC10803776 DOI: 10.1038/s41467-024-44933-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 01/08/2024] [Indexed: 01/24/2024] Open
Abstract
The molecular chaperone DnaK is essential for viability of Mycobacterium tuberculosis (Mtb). DnaK hydrolyzes ATP to fold substrates, and the resulting ADP is exchanged for ATP by the nucleotide exchange factor GrpE. It has been unclear how GrpE couples DnaK's nucleotide exchange with substrate release. Here we report a cryo-EM analysis of GrpE bound to an intact Mtb DnaK, revealing an asymmetric 1:2 DnaK-GrpE complex. The GrpE dimer ratchets to modulate both DnaK nucleotide-binding domain and the substrate-binding domain. We further show that the disordered GrpE N-terminus is critical for substrate release, and that the DnaK-GrpE interface is essential for protein folding activity both in vitro and in vivo. Therefore, the Mtb GrpE dimer allosterically regulates DnaK to concomitantly release ADP in the nucleotide-binding domain and substrate peptide in the substrate-binding domain.
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Affiliation(s)
- Xiansha Xiao
- Department of Structural Biology, Van Andel Institute, Grand Rapids, MI, USA
| | - Allison Fay
- Immunology Program, Sloan Kettering Institute, New York, NY, USA
| | | | - Amanda Kovach
- Department of Structural Biology, Van Andel Institute, Grand Rapids, MI, USA
| | | | - Huilin Li
- Department of Structural Biology, Van Andel Institute, Grand Rapids, MI, USA.
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4
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Bhattarai SK, Du M, Zeamer AL, Morzfeld BM, Kellogg TD, Firat K, Benjamin A, Bean JM, Zimmerman M, Mardi G, Vilbrun SC, Walsh KF, Fitzgerald DW, Glickman MS, Bucci V. Commensal antimicrobial resistance mediates microbiome resilience to antibiotic disruption. Sci Transl Med 2024; 16:eadi9711. [PMID: 38232140 PMCID: PMC11017772 DOI: 10.1126/scitranslmed.adi9711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 12/15/2023] [Indexed: 01/19/2024]
Abstract
Despite their therapeutic benefits, antibiotics exert collateral damage on the microbiome and promote antimicrobial resistance. However, the mechanisms governing microbiome recovery from antibiotics are poorly understood. Treatment of Mycobacterium tuberculosis, the world's most common infection, represents the longest antimicrobial exposure in humans. Here, we investigate gut microbiome dynamics over 20 months of multidrug-resistant tuberculosis (TB) and 6 months of drug-sensitive TB treatment in humans. We find that gut microbiome dynamics and TB clearance are shared predictive cofactors of the resolution of TB-driven inflammation. The initial severe taxonomic and functional microbiome disruption, pathobiont domination, and enhancement of antibiotic resistance that initially accompanied long-term antibiotics were countered by later recovery of commensals. This resilience was driven by the competing evolution of antimicrobial resistance mutations in pathobionts and commensals, with commensal strains with resistance mutations reestablishing dominance. Fecal-microbiota transplantation of the antibiotic-resistant commensal microbiome in mice recapitulated resistance to further antibiotic disruption. These findings demonstrate that antimicrobial resistance mutations in commensals can have paradoxically beneficial effects by promoting microbiome resilience to antimicrobials and identify microbiome dynamics as a predictor of disease resolution in antibiotic therapy of a chronic infection.
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Affiliation(s)
- Shakti K Bhattarai
- Department of Microbiology and Physiological Systems, UMass Chan Medical School, Worcester, MA 01605, USA
- Program in Microbiome Dynamics, UMass Chan Medical School, Worcester, MA 01605, USA
| | - Muxue Du
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- Immunology and Microbial Pathogenesis Graduate Program, Weill Cornell Graduate School, New York, NY 10065, USA
| | - Abigail L Zeamer
- Department of Microbiology and Physiological Systems, UMass Chan Medical School, Worcester, MA 01605, USA
- Program in Microbiome Dynamics, UMass Chan Medical School, Worcester, MA 01605, USA
| | - Benedikt M Morzfeld
- Department of Microbiology and Physiological Systems, UMass Chan Medical School, Worcester, MA 01605, USA
- Program in Microbiome Dynamics, UMass Chan Medical School, Worcester, MA 01605, USA
| | - Tasia D Kellogg
- Department of Microbiology and Physiological Systems, UMass Chan Medical School, Worcester, MA 01605, USA
- Program in Microbiome Dynamics, UMass Chan Medical School, Worcester, MA 01605, USA
| | - Kaya Firat
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ 07110, USA
| | - Anna Benjamin
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - James M Bean
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Matthew Zimmerman
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ 07110, USA
| | - Gertrude Mardi
- Haitian Study Group for Kaposi’s Sarcoma and Opportunistic Infections (GHESKIO), Port-au-Prince, Haiti
| | - Stalz Charles Vilbrun
- Haitian Study Group for Kaposi’s Sarcoma and Opportunistic Infections (GHESKIO), Port-au-Prince, Haiti
| | - Kathleen F Walsh
- Center for Global Health, Weill Cornell Medicine, New York, NY 10065, USA
- Division of General Internal Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | | | - Michael S Glickman
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- Immunology and Microbial Pathogenesis Graduate Program, Weill Cornell Graduate School, New York, NY 10065, USA
| | - Vanni Bucci
- Department of Microbiology and Physiological Systems, UMass Chan Medical School, Worcester, MA 01605, USA
- Program in Microbiome Dynamics, UMass Chan Medical School, Worcester, MA 01605, USA
- Immunology and Microbiology Program, UMass Chan Medical School, Worcester, MA 01605, USA
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Nelson SJ, Williams JT, Buglino JA, Nambi S, Lojek LJ, Glickman MS, Ioerger TR, Sassetti CM. The Rip1 intramembrane protease contributes to iron and zinc homeostasis in Mycobacterium tuberculosis. mSphere 2023; 8:e0038922. [PMID: 37318217 PMCID: PMC10449499 DOI: 10.1128/msphere.00389-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 04/28/2023] [Indexed: 06/16/2023] Open
Abstract
Mycobacterium tuberculosis is exposed to a variety of stresses during a chronic infection, as the immune system simultaneously produces bactericidal compounds and starves the pathogen of essential nutrients. The intramembrane protease, Rip1, plays an important role in the adaptation to these stresses, at least partially by the cleavage of membrane-bound transcriptional regulators. Although Rip1 is known to be critical for surviving copper intoxication and nitric oxide exposure, these stresses do not fully account for the regulatory protein's essentiality during infection. In this work, we demonstrate that Rip1 is also necessary for growth in low-iron and low-zinc conditions, similar to those imposed by the immune system. Using a newly generated library of sigma factor mutants, we show that the known regulatory target of Rip1, SigL, shares this defect. Transcriptional profiling under iron-limiting conditions supported the coordinated activity of Rip1 and SigL and demonstrated that the loss of these proteins produces an exaggerated iron starvation response. These observations demonstrate that Rip1 coordinates several aspects of metal homeostasis and suggest that a Rip1- and SigL-dependent pathway is necessary to thrive in the iron-deficient environments encountered during infection. IMPORTANCE Metal homeostasis represents a critical point of interaction between the mammalian immune system and potential pathogens. While the host attempts to intoxicate microbes with high concentrations of copper or starve the invader of iron and zinc, successful pathogens have acquired mechanisms to overcome these defenses. Our work identifies a regulatory pathway consisting of the Rip1 intramembrane protease and the sigma factor, SigL, that is essential for the important human pathogen, Mycobacterium tuberculosis, to grow in low-iron or low-zinc conditions such as those encountered during infection. In conjunction with Rip1's known role in resisting copper toxicity, our work implicates this protein as a critical integration point that coordinates the multiple metal homeostatic systems required for this pathogen to survive in host tissue.
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Affiliation(s)
- Samantha J. Nelson
- Department of Microbiology and Physiological Systems, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - John T. Williams
- Department of Microbiology and Physiological Systems, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - John A. Buglino
- Immunology Program, Sloan Kettering Institute, New York City, New York, USA
| | - Subhalaxmi Nambi
- Department of Microbiology and Physiological Systems, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Lisa J. Lojek
- Department of Microbiology and Physiological Systems, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | | | - Thomas R. Ioerger
- Department of Computer Science and Engineering, Texas A&M University, College Station, Texas, USA
| | - Christopher M. Sassetti
- Department of Microbiology and Physiological Systems, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
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Dupuy P, Ghosh S, Fay A, Adefisayo O, Gupta R, Shuman S, Glickman MS. Roles for mycobacterial DinB2 in frameshift and substitution mutagenesis. eLife 2023; 12:e83094. [PMID: 37141254 PMCID: PMC10159617 DOI: 10.7554/elife.83094] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 04/18/2023] [Indexed: 05/05/2023] Open
Abstract
Translesion synthesis by translesion polymerases is a conserved mechanism of DNA damage tolerance. In bacteria, DinB enzymes are the widely distributed promutagenic translesion polymerases. The role of DinBs in mycobacterial mutagenesis was unclear until recent studies revealed a role for mycobacterial DinB1 in substitution and frameshift mutagenesis, overlapping with that of translesion polymerase DnaE2. Mycobacterium smegmatis encodes two additional DinBs (DinB2 and DinB3) and Mycobacterium tuberculosis encodes DinB2, but the roles of these polymerases in mycobacterial damage tolerance and mutagenesis is unknown. The biochemical properties of DinB2, including facile utilization of ribonucleotides and 8-oxo-guanine, suggest that DinB2 could be a promutagenic polymerase. Here, we examine the effects of DinB2 and DinB3 overexpression in mycobacterial cells. We demonstrate that DinB2 can drive diverse substitution mutations conferring antibiotic resistance. DinB2 induces frameshift mutations in homopolymeric sequences, both in vitro and in vivo. DinB2 switches from less to more mutagenic in the presence of manganese in vitro. This study indicates that DinB2 may contribute to mycobacterial mutagenesis and antibiotic resistance acquisition in combination with DinB1 and DnaE2.
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Affiliation(s)
- Pierre Dupuy
- Immunology Program, Sloan Kettering InstituteNew YorkUnited States
| | - Shreya Ghosh
- Molecular Biology Program, Sloan Kettering InstituteNew YorkUnited States
| | - Allison Fay
- Immunology Program, Sloan Kettering InstituteNew YorkUnited States
| | - Oyindamola Adefisayo
- Immunology Program, Sloan Kettering InstituteNew YorkUnited States
- Immunology and Microbial Pathogenesis Graduate Program, Weill Cornell Graduate SchoolNew YorkUnited States
| | - Richa Gupta
- Immunology Program, Sloan Kettering InstituteNew YorkUnited States
| | - Stewart Shuman
- Molecular Biology Program, Sloan Kettering InstituteNew YorkUnited States
| | - Michael S Glickman
- Immunology Program, Sloan Kettering InstituteNew YorkUnited States
- Immunology and Microbial Pathogenesis Graduate Program, Weill Cornell Graduate SchoolNew YorkUnited States
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7
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Trzeciak AJ, Rojas WS, Liu ZL, Krebs AS, Wang Z, Saavedra PHV, Miranda IC, Lipshutz A, Xie J, Huang CL, Overholtzer M, Glickman MS, Parkhurst CN, Vierbuchen T, Lucas CD, Perry JSA. WNK1 enforces macrophage lineage fidelity. bioRxiv 2023:2023.04.26.538482. [PMID: 37383948 PMCID: PMC10299535 DOI: 10.1101/2023.04.26.538482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/30/2023]
Abstract
The appropriate development of macrophages, the body's professional phagocyte, is essential for organismal development, especially in mammals. This dependence is exemplified by the observation that loss-of-function mutations in colony stimulating factor 1 receptor (CSF1R) results in multiple tissue abnormalities owing to an absence of macrophages. Despite this importance, little is known about the molecular and cell biological regulation of macrophage development. Here, we report the surprising finding that the chloride-sensing kinase With-no-lysine 1 (WNK1) is required for development of tissue-resident macrophages (TRMs). Myeloid-specific deletion of Wnk1 resulted in a dramatic loss of TRMs, disrupted organ development, systemic neutrophilia, and mortality between 3 and 4 weeks of age. Strikingly, we found that myeloid progenitors or precursors lacking WNK1 not only failed to differentiate into macrophages, but instead differentiated into neutrophils. Mechanistically, the cognate CSF1R cytokine macrophage-colony stimulating factor (M-CSF) stimulates macropinocytosis by both mouse and human myeloid progenitors and precursor cells. Macropinocytosis, in turn, induces chloride flux and WNK1 phosphorylation. Importantly, blocking macropinocytosis, perturbing chloride flux during macropinocytosis, and inhibiting WNK1 chloride-sensing activity each skewed myeloid progenitor differentiation from macrophages into neutrophils. Thus, we have elucidated a role for WNK1 during macropinocytosis and discovered a novel function of macropinocytosis in myeloid progenitors and precursor cells to ensure macrophage lineage fidelity. Highlights Myeloid-specific WNK1 loss causes failed macrophage development and premature deathM-CSF-stimulated myeloid progenitors and precursors become neutrophils instead of macrophagesM-CSF induces macropinocytosis by myeloid progenitors, which depends on WNK1Macropinocytosis enforces macrophage lineage commitment.
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8
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Dupuy P, Glickman MS. The C-Terminal Acid Phosphatase Module of the RNase HI Enzyme RnhC Controls Rifampin Sensitivity and Light-Dependent Colony Pigmentation of Mycobacterium smegmatis. J Bacteriol 2023; 205:e0043122. [PMID: 36916909 PMCID: PMC10127661 DOI: 10.1128/jb.00431-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Accepted: 02/16/2023] [Indexed: 03/16/2023] Open
Abstract
RNase H enzymes participate in various processes that require processing of RNA-DNA hybrids, including DNA replication, transcription, and ribonucleotide excision from DNA. Mycobacteria encode multiple RNase H enzymes, and prior data indicate that RNase HI activity is essential for mycobacterial viability. However, the additional roles of mycobacterial RNase Hs are unknown, including whether RNase HII (RnhB and RnhD) excises chromosomal ribonucleotides misincorporated during DNA replication and whether individual RNase HI enzymes (RnhA and RnhC) mediate additional phenotypes. We find that loss of RNase HII activity in Mycobacterium smegmatis (through combined deletion of rnhB/rnhD) or individual RNase HI enzymes does not affect growth, hydroxyurea sensitivity, or mutagenesis, whereas overexpression (OE) of either RNase HII severely compromises bacterial viability. We also show that deletion of rnhC, which encodes a protein with an N-terminal RNase HI domain and a C-terminal acid phosphatase domain, confers sensitivity to rifampin and oxidative stress as well as loss of light-induced carotenoid pigmentation. These phenotypes are due to loss of the activity of the C-terminal acid phosphatase domain rather than the RNase HI activity, suggesting that the acid phosphatase activity may confer rifampin resistance through the antioxidant properties of carotenoid pigment production. IMPORTANCE Mycobacteria encode multiple RNase H enzymes, with RNase HI being essential for viability. Here, we examine additional functions of RNase H enzymes in mycobacteria. We find that RNase HII is not involved in mutagenesis but is highly toxic when overexpressed. The RNase HI enzyme RnhC is required for tolerance to rifampin, but this role is surprisingly independent of its RNase H activity and is instead mediated by an autonomous C-terminal acid phosphatase domain. This study provides new insights into the functions of the multiple RNase H enzymes of mycobacteria.
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Affiliation(s)
- Pierre Dupuy
- Immunology Program, Sloan Kettering Institute, New York, New York, USA
| | - Michael S. Glickman
- Immunology Program, Sloan Kettering Institute, New York, New York, USA
- Immunology and Microbial Pathogenesis Graduate Program, Weill Cornell Graduate School, New York, New York, USA
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Warren GM, Ejaz A, Fay A, Glickman MS, Shuman S. Mycobacterial helicase Lhr abets resistance to DNA crosslinking agents mitomycin C and cisplatin. Nucleic Acids Res 2023; 51:218-235. [PMID: 36610794 PMCID: PMC9841417 DOI: 10.1093/nar/gkac1222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Revised: 12/05/2022] [Accepted: 12/12/2022] [Indexed: 01/09/2023] Open
Abstract
Mycobacterium smegmatis Lhr exemplifies a novel clade of helicases composed of an N-terminal ATPase/helicase domain (Lhr-Core) and a large C-terminal domain (Lhr-CTD) that nucleates a unique homo-tetrameric quaternary structure. Expression of Lhr, and its operonic neighbor Nei2, is induced in mycobacteria exposed to mitomycin C (MMC). Here we report that lhr deletion sensitizes M. smegmatis to killing by DNA crosslinkers MMC and cisplatin but not to killing by monoadduct-forming alkylating agent methyl methanesulfonate or UV irradiation. Testing complementation of MMC and cisplatin sensitivity by expression of Lhr mutants in Δlhr cells established that: (i) Lhr-CTD is essential for DNA repair activity, such that Lhr-Core does not suffice; (ii) ATPase-defective mutant D170A/E171A fails to complement; (iii) ATPase-active, helicase-defective mutant W597A fails to complement and (iv) alanine mutations at the CTD-CTD interface that interdict homo-tetramer formation result in failure to complement. Our results instate Lhr's ATP-driven motor as an agent of inter-strand crosslink repair in vivo, contingent on Lhr's tetrameric quaternary structure. We characterize M. smegmatis Nei2 as a monomeric enzyme with AP β-lyase activity on single-stranded DNA. Counter to previous reports, we find Nei2 is inactive as a lyase at a THF abasic site and has feeble uracil glycosylase activity.
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Affiliation(s)
- Garrett M Warren
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, NY, NY 10065, USA
| | - Anam Ejaz
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, NY, NY 10065, USA
| | - Allison Fay
- Immunology Program, Memorial Sloan Kettering Cancer Center, NY, NY 10065, USA
| | - Michael S Glickman
- Immunology Program, Memorial Sloan Kettering Cancer Center, NY, NY 10065, USA
| | - Stewart Shuman
- To whom correspondence should be addressed. Tel: +1 212 639 7145; E-mail:
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10
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Redelman-Sidi G, Binyamin A, Antonelli AC, Catalano W, Bean J, Al-Ahmadie H, Jungbluth AA, Glickman MS. BCG-Induced Tumor Immunity Requires Tumor-Intrinsic CIITA Independent of MHC-II. Cancer Immunol Res 2022; 10:1241-1253. [PMID: 36040405 PMCID: PMC9532361 DOI: 10.1158/2326-6066.cir-22-0157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 06/09/2022] [Accepted: 07/27/2022] [Indexed: 11/16/2022]
Abstract
For decades, BCG immunotherapy has been the standard of care for non-muscle-invasive bladder cancer. Despite this clinical experience, the mechanism by which BCG stimulates tumor-eliminating immunity is unclear, and there is still a need for more accurate prediction of clinical outcomes in advance of treatment initiation. We have shown that BCG stimulates tumor-specific T-cell immunity that requires tumor cell expression of the IFNγ receptor (IFNGR); however, the downstream components of IFNGR signaling responsible for responsiveness to BCG are unknown. Here, we demonstrate that the IFNγ-driven, tumor cell intrinsic expression of the class II transactivator CIITA is required for activation of a tumor-specific CD4 T-cell response and BCG-induced tumor immunity. Despite the established role for CIITA in controlling MHC-II antigen presentation machinery, the requirement for CIITA is independent of MHC-II and associated genes. Rather, we find that CIITA is required for a broader tumor-intrinsic transcriptional program linked to critical pathways of tumor immunity via mechanisms that remain to be determined. Tumor cell intrinsic expression of CIITA is not required for a response to immunotherapy targeting programmed cell death protein 1 (PD-1), suggesting that different modalities of immunotherapy for bladder cancer could be employed based on tumor-intrinsic characteristics.
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Affiliation(s)
- Gil Redelman-Sidi
- Division of Infectious Diseases, Memorial Sloan Kettering Cancer Center
| | | | - Anthony C. Antonelli
- Immunology Program, Sloan Kettering Institute
- Immunology and Microbial Pathogenesis, Weill Cornell Medicine Graduate School of Medical Sciences
| | | | - James Bean
- Immunology Program, Sloan Kettering Institute
| | | | | | - Michael S. Glickman
- Division of Infectious Diseases, Memorial Sloan Kettering Cancer Center
- Immunology Program, Sloan Kettering Institute
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11
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Dupuy P, Ghosh S, Adefisayo O, Buglino J, Shuman S, Glickman MS. Distinctive roles of translesion polymerases DinB1 and DnaE2 in diversification of the mycobacterial genome through substitution and frameshift mutagenesis. Nat Commun 2022; 13:4493. [PMID: 35918328 PMCID: PMC9346131 DOI: 10.1038/s41467-022-32022-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 07/12/2022] [Indexed: 12/15/2022] Open
Abstract
Antibiotic resistance of Mycobacterium tuberculosis is exclusively a consequence of chromosomal mutations. Translesion synthesis (TLS) is a widely conserved mechanism of DNA damage tolerance and mutagenesis, executed by translesion polymerases such as DinBs. In mycobacteria, DnaE2 is the only known agent of TLS and the role of DinB polymerases is unknown. Here we demonstrate that, when overexpressed, DinB1 promotes missense mutations conferring resistance to rifampicin, with a mutational signature distinct from that of DnaE2, and abets insertion and deletion frameshift mutagenesis in homo-oligonucleotide runs. DinB1 is the primary mediator of spontaneous −1 frameshift mutations in homo-oligonucleotide runs whereas DnaE2 and DinBs are redundant in DNA damage-induced −1 frameshift mutagenesis. These results highlight DinB1 and DnaE2 as drivers of mycobacterial genome diversification with relevance to antimicrobial resistance and host adaptation. This manuscript elucidates new mechanisms of mutagenesis in mycobacteria by implicating two translesion DNA polymerases in genome diversification, including creating the mutations that underlie all antibiotic resistance in these global pathogens.
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Affiliation(s)
- Pierre Dupuy
- Immunology Program, Sloan Kettering Institute, New York, NY, 10065, USA
| | - Shreya Ghosh
- Molecular Biology Program, Sloan-Kettering Institute, New York, NY, 10065, USA
| | - Oyindamola Adefisayo
- Immunology Program, Sloan Kettering Institute, New York, NY, 10065, USA.,Immunology and Microbial Pathogenesis Graduate Program, Weill Cornell Graduate School, 1300 York Avenue, New York, NY, 10065, USA
| | - John Buglino
- Immunology Program, Sloan Kettering Institute, New York, NY, 10065, USA
| | - Stewart Shuman
- Molecular Biology Program, Sloan-Kettering Institute, New York, NY, 10065, USA
| | - Michael S Glickman
- Immunology Program, Sloan Kettering Institute, New York, NY, 10065, USA. .,Immunology and Microbial Pathogenesis Graduate Program, Weill Cornell Graduate School, 1300 York Avenue, New York, NY, 10065, USA.
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12
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Vorkas CK, Krishna C, Li K, Aubé J, Fitzgerald DW, Mazutis L, Leslie CS, Glickman MS. Single-Cell Transcriptional Profiling Reveals Signatures of Helper, Effector, and Regulatory MAIT Cells during Homeostasis and Activation. J Immunol 2022; 208:1042-1056. [PMID: 35149530 PMCID: PMC9012082 DOI: 10.4049/jimmunol.2100522] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 12/09/2021] [Indexed: 02/02/2023]
Abstract
Mucosal-associated invariant T (MAIT) cells are innate-like lymphocytes that recognize microbial vitamin B metabolites and have emerging roles in infectious disease, autoimmunity, and cancer. Although MAIT cells are identified by a semi-invariant TCR, their phenotypic and functional heterogeneity is not well understood. Here we present an integrated single cell transcriptomic analysis of over 76,000 human MAIT cells during early and prolonged Ag-specific activation with the MR1 ligand 5-OP-RU and nonspecific TCR stimulation. We show that MAIT cells span a broad range of homeostatic, effector, helper, tissue-infiltrating, regulatory, and exhausted phenotypes, with distinct gene expression programs associated with CD4+ or CD8+ coexpression. During early activation, MAIT cells rapidly adopt a cytotoxic phenotype characterized by high expression of GZMB, IFNG and TNF In contrast, prolonged stimulation induces heterogeneous states defined by proliferation, cytotoxicity, immune modulation, and exhaustion. We further demonstrate a FOXP3 expressing MAIT cell subset that phenotypically resembles conventional regulatory T cells. Moreover, scRNAseq-defined MAIT cell subpopulations were also detected in individuals recently exposed to Mycobacterium tuberculosis, confirming their presence during human infection. To our knowledge, our study provides the first comprehensive atlas of human MAIT cells in activation conditions and defines substantial functional heterogeneity, suggesting complex roles in health and disease.
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Affiliation(s)
- Charles Kyriakos Vorkas
- Division of Infectious Diseases, Weill Cornell Medicine, Cornell University, New York, NY;,Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Chirag Krishna
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Kelin Li
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Jeffrey Aubé
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Daniel W. Fitzgerald
- Division of Infectious Diseases, Weill Cornell Medicine, Cornell University, New York, NY;,Center for Global Health, Weill Cornell Medicine, Cornell University, New York, NY
| | - Linas Mazutis
- Single Cell Research Initiative, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY; and
| | - Christina S. Leslie
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Michael S. Glickman
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY;,Division of Infectious Diseases, Memorial Sloan Kettering Cancer Center, New York, NY
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13
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Jiang S, Redelman-Sidi G, Pietzak EJ, Bochner BH, Glickman MS. Defining innate immune training potential as a predictor of Bacillus Calmette-Guérin immunotherapy response in nonmuscle-invasive bladder cancer. J Clin Oncol 2022. [DOI: 10.1200/jco.2022.40.6_suppl.522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
522 Background: Intravesical instillation of the live attenuated mycobacterium Bacillus Calmette-Guerin (BCG) remains the most effective therapy for the treatment of non-muscle invasive bladder cancer. The precise mechanism of BCG is thought to involve phagocytosis, induction of inflammation, activation of the innate immune apparatus, and an effective cell-mediated T cell response. An increasing body of evidence suggests that the innate immune system has characteristics that involve a heterologous memory of past insults through a process thought to involve epigenetic reprogramming, termed trained immunity. We seek to investigate the potential for innate immune training as a predictor of the anti-tumor effects of BCG. Methods: A prospective biospecimen collection was performed on venous blood from non-muscle invasive bladder cancer patients prior to receiving intravesical BCG therapy. To investigate the role of trained immunity in primary monocytes, cells were isolated from peripheral blood mononuclear cells (PBMC) by plate adhesion. 2-5 x 105 cells/well were assayed in 96-well format, cultured in RPMI 1640 supplemented with 10% Fetal Bovine Serum and 2mM L-glutamine and stimulated with 10:1 MOI BCG for 24 hours. Cells were then washed in media and allowed to rest 6 days. Media was changed on day 3 of rest. Subsequently, cells were stimulated with 25 ng/ml lipopolysaccharide (a TLR4 agonist) for 24 hours. Cell free supernatant was measured for TNF-alpha production by enzyme-linked immunosorbent assay. Results: In vitro training of primary monocytes induced an increase in proinflammatory cytokine production upon re-stimulation. This phenotype was dose dependent on stimulation with LPS, however, the relative change between trained and untrained cells was diminished at higher concentrations of agonist. In our in vitro training experiments, there was demonstrable interpatient variability seen pre-BCG exposure in a cohort of NMIBC patients. These results will be correlated with future long term BCG response in this prospective cohort. Conclusions: We present data on a trained innate immune phenotype on primary monocytes collected from patient samples. These data serve as proof of principle for the ability to induce a trained phenotype in vitro. These findings will be correlated with prospective clinical data on BCG responsiveness and recurrence free survival to allow us to garner further insight into the role of trained immunity in BCG immunotherapy. Such insight will have potential clinical impact on the development of biomarkers and clinical assays that could predict immune responsiveness to BCG a priori, as well as identify possible immunological adjuvants that could enhance the effect of intravesical BCG.
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Affiliation(s)
- Song Jiang
- Memorial Sloan-Kettering Cancer Center-Fellowship (GME Office), New York, NY
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14
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Adefisayo OO, Dupuy P, Nautiyal A, Bean JM, Glickman MS. Division of labor between SOS and PafBC in mycobacterial DNA repair and mutagenesis. Nucleic Acids Res 2021; 49:12805-12819. [PMID: 34871411 PMCID: PMC8682763 DOI: 10.1093/nar/gkab1169] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 09/30/2021] [Accepted: 11/10/2021] [Indexed: 11/15/2022] Open
Abstract
DNA repair systems allow microbes to survive in diverse environments that compromise chromosomal integrity. Pathogens such as Mycobacterium tuberculosis must contend with the genotoxic host environment, which generates the mutations that underlie antibiotic resistance. Mycobacteria encode the widely distributed SOS pathway, governed by the LexA repressor, but also encode PafBC, a positive regulator of the transcriptional DNA damage response (DDR). Although the transcriptional outputs of these systems have been characterized, their full functional division of labor in survival and mutagenesis is unknown. Here, we specifically ablate the PafBC or SOS pathways, alone and in combination, and test their relative contributions to repair. We find that SOS and PafBC have both distinct and overlapping roles that depend on the type of DNA damage. Most notably, we find that quinolone antibiotics and replication fork perturbation are inducers of the PafBC pathway, and that chromosomal mutagenesis is codependent on PafBC and SOS, through shared regulation of the DnaE2/ImuA/B mutasome. These studies define the complex transcriptional regulatory network of the DDR in mycobacteria and provide new insight into the regulatory mechanisms controlling the genesis of antibiotic resistance in M. tuberculosis.
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Affiliation(s)
- Oyindamola O Adefisayo
- Immunology and Microbial Pathogenesis Graduate Program, Weill Cornell Graduate School, 1300 York Avenue, New York, NY 10065, USA.,Immunology Program, Sloan Kettering Institute, 1275 York Avenue, New York, NY 10025, USA
| | - Pierre Dupuy
- Immunology Program, Sloan Kettering Institute, 1275 York Avenue, New York, NY 10025, USA
| | - Astha Nautiyal
- Immunology Program, Sloan Kettering Institute, 1275 York Avenue, New York, NY 10025, USA
| | - James M Bean
- Immunology Program, Sloan Kettering Institute, 1275 York Avenue, New York, NY 10025, USA
| | - Michael S Glickman
- Immunology and Microbial Pathogenesis Graduate Program, Weill Cornell Graduate School, 1300 York Avenue, New York, NY 10065, USA.,Immunology Program, Sloan Kettering Institute, 1275 York Avenue, New York, NY 10025, USA
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15
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Buglino JA, Sankhe GD, Lazar N, Bean JM, Glickman MS. Integrated sensing of host stresses by inhibition of a cytoplasmic two-component system controls M. tuberculosis acute lung infection. eLife 2021; 10:e65351. [PMID: 34003742 PMCID: PMC8131098 DOI: 10.7554/elife.65351] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 04/25/2021] [Indexed: 12/30/2022] Open
Abstract
Bacterial pathogens that infect phagocytic cells must deploy mechanisms that sense and neutralize host microbicidal effectors. For Mycobacterium tuberculosis, the causative agent of tuberculosis, these mechanisms allow the bacterium to rapidly adapt from aerosol transmission to initial growth in the lung alveolar macrophage. Here, we identify a branched signaling circuit in M. tuberculosis that controls growth in the lung through integrated direct sensing of copper ions and nitric oxide by coupled activity of the Rip1 intramembrane protease and the PdtaS/R two-component system. This circuit uses a two-signal mechanism to inactivate the PdtaS/PdtaR two-component system, which constitutively represses virulence gene expression. Cu and NO inhibit the PdtaS sensor kinase through a dicysteine motif in the N-terminal GAF domain. The NO arm of the pathway is further controlled by sequestration of the PdtaR RNA binding response regulator by an NO-induced small RNA, controlled by the Rip1 intramembrane protease. This coupled Rip1/PdtaS/PdtaR circuit controls NO resistance and acute lung infection in mice by relieving PdtaS/R-mediated repression of isonitrile chalkophore biosynthesis. These studies identify an integrated mechanism by which M. tuberculosis senses and resists macrophage chemical effectors to achieve pathogenesis.
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Affiliation(s)
- John A Buglino
- Immunology Program Sloan Kettering InstituteNew York CityUnited States
| | - Gaurav D Sankhe
- Immunology Program Sloan Kettering InstituteNew York CityUnited States
| | - Nathaniel Lazar
- Immunology and Microbial Pathogenesis Graduate Program, Weill Cornell Graduate SchoolNew York CityUnited States
| | - James M Bean
- Immunology Program Sloan Kettering InstituteNew York CityUnited States
| | - Michael S Glickman
- Immunology Program Sloan Kettering InstituteNew York CityUnited States
- Immunology and Microbial Pathogenesis Graduate Program, Weill Cornell Graduate SchoolNew York CityUnited States
- Division of Infectious Diseases, Memorial Sloan Kettering Cancer CenterNew York CityUnited States
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16
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Yin Y, Feng X, Yu H, Fay A, Kovach A, Glickman MS, Li H. Structural basis for aggregate dissolution and refolding by the Mycobacterium tuberculosis ClpB-DnaK bi-chaperone system. Cell Rep 2021; 35:109166. [PMID: 34038719 PMCID: PMC8209680 DOI: 10.1016/j.celrep.2021.109166] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 12/30/2020] [Accepted: 05/03/2021] [Indexed: 11/30/2022] Open
Abstract
The M. tuberculosis (Mtb) ClpB is a protein disaggregase that helps to rejuvenate the bacterial cell. DnaK is a protein foldase that can function alone, but it can also bind to the ClpB hexamer to physically couple protein disaggregation with protein refolding, although the molecular mechanism is not well understood. Here, we report the cryo-EM analysis of the Mtb ClpB-DnaK bi-chaperone in the presence of ATPγS and a protein substrate. We observe three ClpB conformations in the presence of DnaK, identify a conserved TGIP loop linking the oligonucleotide/oligosaccharide-binding domain and the nucleotide-binding domain that is important for ClpB function, derive the interface between the regulatory middle domain of the ClpB and the DnaK nucleotide-binding domain, and find that DnaK binding stabilizes, but does not bend or tilt, the ClpB middle domain. We propose a model for the synergistic actions of aggregate dissolution and refolding by the Mtb ClpB-DnaK bi-chaperone system. Yin et al. use cryo-EM to analyze the structure of the Mycobacterium tuberculosis ClpB-DnaK bi-chaperone system. They find that the Mtb ClpB middle domain does not bend or tilt when interacting with DnaK. They therefore propose that the Mtb DnaK facilitates protein folding following protein disaggregation by ClpB.
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Affiliation(s)
- Yanting Yin
- Department of Structural Biology, Van Andel Institute, Grand Rapids, MI, USA
| | - Xiang Feng
- Department of Structural Biology, Van Andel Institute, Grand Rapids, MI, USA
| | - Hongjun Yu
- Department of Structural Biology, Van Andel Institute, Grand Rapids, MI, USA
| | - Allison Fay
- Immunology Program, Sloan Kettering Institute, New York, NY, USA
| | - Amanda Kovach
- Department of Structural Biology, Van Andel Institute, Grand Rapids, MI, USA
| | | | - Huilin Li
- Department of Structural Biology, Van Andel Institute, Grand Rapids, MI, USA.
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17
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Wipperman MF, Bhattarai SK, Vorkas CK, Maringati VS, Taur Y, Mathurin L, McAulay K, Vilbrun SC, Francois D, Bean J, Walsh KF, Nathan C, Fitzgerald DW, Glickman MS, Bucci V. Gastrointestinal microbiota composition predicts peripheral inflammatory state during treatment of human tuberculosis. Nat Commun 2021; 12:1141. [PMID: 33602926 PMCID: PMC7892575 DOI: 10.1038/s41467-021-21475-y] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 01/21/2021] [Indexed: 12/15/2022] Open
Abstract
The composition of the gastrointestinal microbiota influences systemic immune responses, but how this affects infectious disease pathogenesis and antibiotic therapy outcome is poorly understood. This question is rarely examined in humans due to the difficulty in dissociating the immunologic effects of antibiotic-induced pathogen clearance and microbiome alteration. Here, we analyze data from two longitudinal studies of tuberculosis (TB) therapy (35 and 20 individuals) and a cross sectional study from 55 healthy controls, in which we collected fecal samples (for microbiome analysis), sputum (for determination of Mycobacterium tuberculosis (Mtb) bacterial load), and peripheral blood (for transcriptomic analysis). We decouple microbiome effects from pathogen sterilization by comparing standard TB therapy with an experimental TB treatment that did not reduce Mtb bacterial load. Random forest regression to the microbiome-transcriptome-sputum data from the two longitudinal datasets reveals that renormalization of the TB inflammatory state is associated with Mtb pathogen clearance, increased abundance of Clusters IV and XIVa Clostridia, and decreased abundance of Bacilli and Proteobacteria. We find similar associations when applying machine learning to peripheral gene expression and microbiota profiling in the independent cohort of healthy individuals. Our findings indicate that antibiotic-induced reduction in pathogen burden and changes in the microbiome are independently associated with treatment-induced changes of the inflammatory response of active TB, and the response to antibiotic therapy may be a combined effect of pathogen killing and microbiome driven immunomodulation. Antibiotic therapy can lead to pathogen clearance, but also to alterations in the gut microbiota and systemic immune responses. Here, the authors analyze data from patients with tuberculosis and healthy subjects to show that pathogen clearance and gut microbiota alterations are independently associated with antibiotic-induced changes of the inflammatory response of active tuberculosis.
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Affiliation(s)
- Matthew F Wipperman
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Clinical and Translational Science Center, Weill Cornell Medicine, New York, NY, USA
| | - Shakti K Bhattarai
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA, USA
| | - Charles Kyriakos Vorkas
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Division of Infectious Diseases, Weill Cornell Medicine, New York, NY, USA
| | - Venkata Suhas Maringati
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA, USA
| | - Ying Taur
- Division of Infectious Diseases, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Laurent Mathurin
- Haitian Study Group for Kaposi's Sarcoma and Opportunistic Infections (GHESKIO), Port-au-Prince, Haiti
| | | | - Stalz Charles Vilbrun
- Haitian Study Group for Kaposi's Sarcoma and Opportunistic Infections (GHESKIO), Port-au-Prince, Haiti
| | - Daphie Francois
- Haitian Study Group for Kaposi's Sarcoma and Opportunistic Infections (GHESKIO), Port-au-Prince, Haiti
| | - James Bean
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kathleen F Walsh
- Center for Global Health, Weill Cornell Medicine, New York, NY, USA
| | - Carl Nathan
- Immunology and Microbial Pathogenesis Graduate Program, Weill Cornell Graduate School, New York, NY, USA
| | | | - Michael S Glickman
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA. .,Division of Infectious Diseases, Weill Cornell Medicine, New York, NY, USA. .,Immunology and Microbial Pathogenesis Graduate Program, Weill Cornell Graduate School, New York, NY, USA.
| | - Vanni Bucci
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA, USA. .,Center for Microbiome Research, University of Massachusetts Medical School, Worcester, MA, USA. .,Program in Systems Biology, University of Massachusetts Medical School, Worcester, MA, USA.
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18
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Robilotti EV, Babady NE, Mead PA, Rolling T, Perez-Johnston R, Bernardes M, Bogler Y, Caldararo M, Figueroa CJ, Glickman MS, Joanow A, Kaltsas A, Lee YJ, Lucca A, Mariano A, Morjaria S, Nawar T, Papanicolaou GA, Predmore J, Redelman-Sidi G, Schmidt E, Seo SK, Sepkowitz K, Shah MK, Wolchok JD, Hohl TM, Taur Y, Kamboj M. Determinants of COVID-19 disease severity in patients with cancer. Nat Med 2020; 26:1218-1223. [PMID: 32581323 DOI: 10.1038/s41591-020-0979-0] [Citation(s) in RCA: 422] [Impact Index Per Article: 105.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 06/11/2020] [Indexed: 12/23/2022]
Abstract
As of 10 April 2020, New York State had 180,458 cases of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and 9,385 reported deaths. Patients with cancer comprised 8.4% of deceased individuals1. Population-based studies from China and Italy suggested a higher coronavirus disease 2019 (COVID-19) death rate in patients with cancer2,3, although there is a knowledge gap as to which aspects of cancer and its treatment confer risk of severe COVID-194. This information is critical to balance the competing safety considerations of reducing SARS-CoV-2 exposure and cancer treatment continuation. From 10 March to 7 April 2020, 423 cases of symptomatic COVID-19 were diagnosed at Memorial Sloan Kettering Cancer Center (from a total of 2,035 patients with cancer tested). Of these, 40% were hospitalized for COVID-19, 20% developed severe respiratory illness (including 9% who required mechanical ventilation) and 12% died within 30 d. Age older than 65 years and treatment with immune checkpoint inhibitors (ICIs) were predictors for hospitalization and severe disease, whereas receipt of chemotherapy and major surgery were not. Overall, COVID-19 in patients with cancer is marked by substantial rates of hospitalization and severe outcomes. The association observed between ICI and COVID-19 outcomes in our study will need further interrogation in tumor-specific cohorts.
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Affiliation(s)
- Elizabeth V Robilotti
- Infectious Diseases, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Infection Control, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Department of Medicine, Joan and Sanford Weill Medical College of Cornell University, New York, NY, USA
| | - N Esther Babady
- Infectious Diseases, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Clinical Microbiology Service, Department of Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Peter A Mead
- Infectious Diseases, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Department of Medicine, Joan and Sanford Weill Medical College of Cornell University, New York, NY, USA
| | - Thierry Rolling
- Infectious Diseases, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Rocio Perez-Johnston
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Marilia Bernardes
- Infectious Diseases, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yael Bogler
- Infectious Diseases, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Mario Caldararo
- Infectious Diseases, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Cesar J Figueroa
- Infectious Diseases, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Department of Medicine, Joan and Sanford Weill Medical College of Cornell University, New York, NY, USA
| | - Michael S Glickman
- Infectious Diseases, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Department of Medicine, Joan and Sanford Weill Medical College of Cornell University, New York, NY, USA
| | - Alexa Joanow
- Infectious Diseases, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Anna Kaltsas
- Infectious Diseases, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Department of Medicine, Joan and Sanford Weill Medical College of Cornell University, New York, NY, USA
| | - Yeon Joo Lee
- Infectious Diseases, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Department of Medicine, Joan and Sanford Weill Medical College of Cornell University, New York, NY, USA
| | - Anabella Lucca
- Infectious Diseases, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Employee Health and Wellness Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Amanda Mariano
- Infectious Diseases, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sejal Morjaria
- Infectious Diseases, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Department of Medicine, Joan and Sanford Weill Medical College of Cornell University, New York, NY, USA
| | - Tamara Nawar
- Infectious Diseases, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Genovefa A Papanicolaou
- Infectious Diseases, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Department of Medicine, Joan and Sanford Weill Medical College of Cornell University, New York, NY, USA
| | - Jacqueline Predmore
- Infectious Diseases, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Gil Redelman-Sidi
- Infectious Diseases, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Department of Medicine, Joan and Sanford Weill Medical College of Cornell University, New York, NY, USA
| | - Elizabeth Schmidt
- Infectious Diseases, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Susan K Seo
- Infectious Diseases, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Department of Medicine, Joan and Sanford Weill Medical College of Cornell University, New York, NY, USA
| | - Kent Sepkowitz
- Infectious Diseases, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Department of Medicine, Joan and Sanford Weill Medical College of Cornell University, New York, NY, USA
| | - Monika K Shah
- Infectious Diseases, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Department of Medicine, Joan and Sanford Weill Medical College of Cornell University, New York, NY, USA
| | - Jedd D Wolchok
- Department of Medicine, Joan and Sanford Weill Medical College of Cornell University, New York, NY, USA.,Human Oncology and Pathogenesis Program, Department of Medicine, Ludwig Center and Parker Institute for Cancer Immunotherapy at Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Tobias M Hohl
- Infectious Diseases, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Department of Medicine, Joan and Sanford Weill Medical College of Cornell University, New York, NY, USA
| | - Ying Taur
- Infectious Diseases, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Department of Medicine, Joan and Sanford Weill Medical College of Cornell University, New York, NY, USA
| | - Mini Kamboj
- Infectious Diseases, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA. .,Infection Control, Memorial Sloan Kettering Cancer Center, New York, NY, USA. .,Department of Medicine, Joan and Sanford Weill Medical College of Cornell University, New York, NY, USA.
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19
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Stallings CL, Glickman MS. Editorial overview: Attrition warfare: host cell weapons against intracellular pathogens, and how the pathogens fight back. Curr Opin Immunol 2019; 60:vi-ix. [PMID: 31471114 PMCID: PMC7383339 DOI: 10.1016/j.coi.2019.07.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Christina L Stallings
- Department of Molecular Microbiology, Washington University School of Medicine, United States.
| | - Michael S Glickman
- Immunology Program, Sloan Kettering Institute, United States; Division of Infectious Diseases, Memorial Sloan Kettering Cancer Center, United States; Immunology and Microbial Pathogenesis Graduate Program, Weill Cornell Graduate School, United States.
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20
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Abstract
Physicians who seek to become laboratory-based physician-scientists, especially those without a PhD degree, face substantial challenges during the critical transition period between clinical and laboratory training. These challenges range from the complex process of adopting new logic structures and standards of proof to the more mundane but important challenges that accompany extending training in a new discipline when other career options are available. Discussion of these challenges can inform individual and institutional strategies to enhance entry and retention of physicians in the physician-scientist career path.
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Affiliation(s)
- Michael S Glickman
- Immunology Program, Memorial Sloan Kettering Cancer Center New York, New York.,Division of Infectious Diseases, Memorial Sloan Kettering Cancer Center New York, New York
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21
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Scott AC, Dündar F, Zumbo P, Chandran SS, Klebanoff CA, Shakiba M, Trivedi P, Menocal L, Appleby H, Camara S, Zamarin D, Walther T, Snyder A, Femia MR, Comen EA, Wen HY, Hellmann MD, Anandasabapathy N, Liu Y, Altorki NK, Lauer P, Levy O, Glickman MS, Kaye J, Betel D, Philip M, Schietinger A. TOX is a critical regulator of tumour-specific T cell differentiation. Nature 2019; 571:270-274. [PMID: 31207604 PMCID: PMC7698992 DOI: 10.1038/s41586-019-1324-y] [Citation(s) in RCA: 619] [Impact Index Per Article: 123.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Accepted: 06/04/2019] [Indexed: 01/18/2023]
Abstract
Tumour-specific CD8 T cell dysfunction is a differentiation state that is distinct from the functional effector or memory T cell states1–6. Here we identify the nuclear factor TOX as a crucial regulator of the differentiation of tumour-specific T (TST) cells. We show that TOX is highly expressed in dysfunctional TST cells from tumours and in exhausted T cells during chronic viral infection. Expression of TOX is driven by chronic T cell receptor stimulation and NFAT activation. Ectopic expression of TOX in effector T cells in vitro induced a transcriptional program associated with T cell exhaustion. Conversely, deletion of Tox in TST cells in tumours abrogated the exhaustion program: Tox-deleted TST cells did not upregulate genes for inhibitory receptors (such as Pdcd1, Entpd1, Havcr2, Cd244 and Tigit), the chromatin of which remained largely inaccessible, and retained high expression of transcription factors such as TCF-1. Despite their normal, ‘non-exhausted’ immunophenotype, Tox-deleted TST cells remained dysfunctional, which suggests that the regulation of expression of inhibitory receptors is uncoupled from the loss of effector function. Notably, although Tox-deleted CD8 T cells differentiated normally to effector and memory states in response to acute infection, Tox-deleted TST cells failed to persist in tumours. We hypothesize that the TOX-induced exhaustion program serves to prevent the overstimulation of T cells and activation-induced cell death in settings of chronic antigen stimulation such as cancer.
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Affiliation(s)
- Andrew C Scott
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, New York, NY, USA
| | - Friederike Dündar
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA.,Applied Bioinformatics Core, Weill Cornell Medicine, New York, NY, USA
| | - Paul Zumbo
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA.,Applied Bioinformatics Core, Weill Cornell Medicine, New York, NY, USA
| | - Smita S Chandran
- Parker Institute for Cancer Immunotherapy, New York, NY, USA.,Center for Cell Engineering, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Christopher A Klebanoff
- Parker Institute for Cancer Immunotherapy, New York, NY, USA.,Center for Cell Engineering, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Weill Cornell Medical College, New York, NY, USA
| | - Mojdeh Shakiba
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Prerak Trivedi
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Laura Menocal
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, New York, NY, USA
| | - Heather Appleby
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Steven Camara
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Dmitriy Zamarin
- Parker Institute for Cancer Immunotherapy, New York, NY, USA.,Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Tyler Walther
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Alexandra Snyder
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Matthew R Femia
- Parker Institute for Cancer Immunotherapy, New York, NY, USA.,Center for Cell Engineering, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Elizabeth A Comen
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Weill Cornell Medical College, New York, NY, USA
| | - Hannah Y Wen
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Matthew D Hellmann
- Parker Institute for Cancer Immunotherapy, New York, NY, USA.,Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Weill Cornell Medical College, New York, NY, USA
| | - Niroshana Anandasabapathy
- Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, New York, NY, USA.,Department of Dermatology, Weill Cornell Medical College, New York, NY, USA
| | - Yong Liu
- Department of Dermatology, Weill Cornell Medical College, New York, NY, USA
| | - Nasser K Altorki
- Department of Cardiothoracic Surgery, Weill Cornell Medicine, New York Presbyterian Hospital, New York, NY, USA
| | | | - Olivier Levy
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Michael S Glickman
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, New York, NY, USA
| | - Jonathan Kaye
- Research Division of Immunology, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Doron Betel
- Applied Bioinformatics Core, Weill Cornell Medicine, New York, NY, USA.,Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA.,Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | - Mary Philip
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA. .,Department of Medicine, Division of Hematology and Oncology, Vanderbilt University Medical Center, Nashville, TN, USA.
| | - Andrea Schietinger
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA. .,Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, New York, NY, USA. .,Parker Institute for Cancer Immunotherapy, New York, NY, USA.
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22
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Peek J, Lilic M, Montiel D, Milshteyn A, Woodworth I, Biggins JB, Ternei MA, Calle PY, Danziger M, Warrier T, Saito K, Braffman N, Fay A, Glickman MS, Darst SA, Campbell EA, Brady SF. Rifamycin congeners kanglemycins are active against rifampicin-resistant bacteria via a distinct mechanism. Nat Commun 2018; 9:4147. [PMID: 30297823 PMCID: PMC6175910 DOI: 10.1038/s41467-018-06587-2] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 08/29/2018] [Indexed: 11/25/2022] Open
Abstract
Rifamycin antibiotics (Rifs) target bacterial RNA polymerases (RNAPs) and are widely used to treat infections including tuberculosis. The utility of these compounds is threatened by the increasing incidence of resistance (RifR). As resistance mechanisms found in clinical settings may also occur in natural environments, here we postulated that bacteria could have evolved to produce rifamycin congeners active against clinically relevant resistance phenotypes. We survey soil metagenomes and identify a tailoring enzyme-rich family of gene clusters encoding biosynthesis of rifamycin congeners (kanglemycins, Kangs) with potent in vivo and in vitro activity against the most common clinically relevant RifR mutations. Our structural and mechanistic analyses reveal the basis for Kang inhibition of RifR RNAP. Unlike Rifs, Kangs function through a mechanism that includes interfering with 5'-initiating substrate binding. Our results suggest that examining soil microbiomes for new analogues of clinically used antibiotics may uncover metabolites capable of circumventing clinically important resistance mechanisms.
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Affiliation(s)
- James Peek
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA
| | - Mirjana Lilic
- Laboratory of Molecular Biophysics, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA
| | - Daniel Montiel
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA
| | - Aleksandr Milshteyn
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA
| | - Ian Woodworth
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA
| | - John B Biggins
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA
| | - Melinda A Ternei
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA
| | - Paula Y Calle
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA
| | - Michael Danziger
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA
| | - Thulasi Warrier
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Kohta Saito
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY, 10065, USA
- Department of Medicine, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Nathaniel Braffman
- Laboratory of Molecular Biophysics, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA
| | - Allison Fay
- Immunology Program, Sloan-Kettering Institute, New York, NY, 10065, USA
| | | | - Seth A Darst
- Laboratory of Molecular Biophysics, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA
| | - Elizabeth A Campbell
- Laboratory of Molecular Biophysics, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA.
| | - Sean F Brady
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA.
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23
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Vorkas CK, Wipperman MF, Li K, Bean J, Bhattarai SK, Adamow M, Wong P, Aubé J, Juste MAJ, Bucci V, Fitzgerald DW, Glickman MS. Mucosal-associated invariant and γδ T cell subsets respond to initial Mycobacterium tuberculosis infection. JCI Insight 2018; 3:121899. [PMID: 30282828 PMCID: PMC6237486 DOI: 10.1172/jci.insight.121899] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 08/29/2018] [Indexed: 01/01/2023] Open
Abstract
Innate immune responses that control early Mtb infection are poorly understood, but understanding these responses may inform vaccination and immunotherapy strategies. Innate T cells that respond to conserved bacterial ligands such as mucosal-associated invariant T (MAIT) and γδ T cells are prime candidates to mediate these early innate responses but have not been examined in subjects who have been recently exposed to Mtb. We recruited a cohort living in the same household with an active tuberculosis (TB) case and examined the abundance and functional phenotypes of 3 innate T cell populations reactive to M. tuberculosis: γδ T, invariant NK T (iNKT), and MAIT cells. Both MAIT and γδ T cells from subjects with Mtb exposure display ex vivo phenotypes consistent with recent activation. However, both MAIT and γδ T cell subsets have distinct response profiles, with CD4+ MAIT and γδ T cells accumulating after infection. Examination of exposed but uninfected contacts demonstrates that resistance to initial infection is accompanied by robust MAIT cell CD25 expression and granzyme B production coupled with a depressed CD69 and IFNγ response. Finally, we demonstrate that MAIT cell abundance and function correlate with the abundance of specific gut microbes, suggesting that responses to initial infection may be modulated by the intestinal microbiome.
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Affiliation(s)
- Charles Kyriakos Vorkas
- Division of Infectious Diseases, Weill Cornell Medicine (WCM), New York, New York, USA
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center (MSKCC), New York, New York, USA
| | - Matthew F. Wipperman
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center (MSKCC), New York, New York, USA
- Clinical and Translational Science Center, WCM, New York, New York, USA
| | - Kelin Li
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - James Bean
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center (MSKCC), New York, New York, USA
| | - Shakti K. Bhattarai
- Department of Bioengineering, University of Massachusetts, Dartmouth, North Dartmouth, Massachusetts, USA
| | - Matthew Adamow
- Immune Monitoring Core Facility, Ludwig Center for Cancer Immunotherapy, Sloan Kettering Institute, MSKCC, New York, New York, USA
| | - Phillip Wong
- Immune Monitoring Core Facility, Ludwig Center for Cancer Immunotherapy, Sloan Kettering Institute, MSKCC, New York, New York, USA
| | - Jeffrey Aubé
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | | | - Vanni Bucci
- Department of Bioengineering, University of Massachusetts, Dartmouth, North Dartmouth, Massachusetts, USA
| | - Daniel W. Fitzgerald
- Division of Infectious Diseases, Weill Cornell Medicine (WCM), New York, New York, USA
- GHESKIO Centers, Port-au-Prince, Haiti
- Center for Global Health, WCM, New York, New York, USA
| | - Michael S. Glickman
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center (MSKCC), New York, New York, USA
- Division of Infectious Diseases, MSKCC, New York, New York, USA
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24
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Wipperman MF, Heaton BE, Nautiyal A, Adefisayo O, Evans H, Gupta R, van Ditmarsch D, Soni R, Hendrickson R, Johnson J, Krogan N, Glickman MS. Mycobacterial Mutagenesis and Drug Resistance Are Controlled by Phosphorylation- and Cardiolipin-Mediated Inhibition of the RecA Coprotease. Mol Cell 2018; 72:152-161.e7. [PMID: 30174294 DOI: 10.1016/j.molcel.2018.07.037] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Revised: 05/30/2018] [Accepted: 07/25/2018] [Indexed: 11/19/2022]
Abstract
Infection with Mycobacterium tuberculosis continues to cause substantial human mortality, in part because of the emergence of antimicrobial resistance. Antimicrobial resistance in tuberculosis is solely the result of chromosomal mutations that modify drug activators or targets, yet the mechanisms controlling the mycobacterial DNA-damage response (DDR) remain incompletely defined. Here, we identify RecA serine 207 as a multifunctional signaling hub that controls the DDR in mycobacteria. RecA S207 is phosphorylated after DNA damage, which suppresses the emergence of antibiotic resistance by selectively inhibiting the LexA coprotease function of RecA without affecting its ATPase or strand exchange functions. Additionally, RecA associates with the cytoplasmic membrane during the mycobacterial DDR, where cardiolipin can specifically inhibit the LexA coprotease function of unmodified, but not S207 phosphorylated, RecA. These findings reveal that RecA S207 controls mutagenesis and antibiotic resistance in mycobacteria through phosphorylation and cardiolipin-mediated inhibition of RecA coprotease function.
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Affiliation(s)
- Matthew F Wipperman
- Immunology Program, Sloan Kettering Institute, New York, NY, USA; Clinical & Translational Science Center, Weill Cornell Medicine, New York, NY, USA
| | - Brook E Heaton
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC, USA
| | - Astha Nautiyal
- Immunology Program, Sloan Kettering Institute, New York, NY, USA
| | - Oyindamola Adefisayo
- Immunology and Microbial Pathogenesis Graduate Program, Weill Cornell Graduate School, New York, NY, USA
| | - Henry Evans
- Immunology Program, Sloan Kettering Institute, New York, NY, USA
| | - Richa Gupta
- Immunology Program, Sloan Kettering Institute, New York, NY, USA
| | | | - Rajesh Soni
- Microchemistry and Proteomics Core, MSKCC, New York, NY, USA
| | - Ron Hendrickson
- Microchemistry and Proteomics Core, MSKCC, New York, NY, USA
| | - Jeff Johnson
- Department of Cellular and Molecular Pharmacology, UCSF, San Francisco, CA, USA
| | - Nevan Krogan
- Department of Cellular and Molecular Pharmacology, UCSF, San Francisco, CA, USA
| | - Michael S Glickman
- Immunology Program, Sloan Kettering Institute, New York, NY, USA; Division of Infectious Diseases, Memorial Sloan Kettering Cancer Center (MSKCC), New York, NY, USA; Immunology and Microbial Pathogenesis Graduate Program, Weill Cornell Graduate School, New York, NY, USA.
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25
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Redelman-Sidi G, Binyamin A, Gaeta I, Palm W, Thompson CB, Romesser PB, Lowe SW, Bagul M, Doench JG, Root DE, Glickman MS. The Canonical Wnt Pathway Drives Macropinocytosis in Cancer. Cancer Res 2018; 78:4658-4670. [PMID: 29871936 DOI: 10.1158/0008-5472.can-17-3199] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Revised: 03/05/2018] [Accepted: 06/01/2018] [Indexed: 12/26/2022]
Abstract
Macropinocytosis has emerged as an important pathway of protein acquisition in cancer cells, particularly in tumors with activated Ras such as pancreatic and colon cancer. Macropinocytosis is also the route of entry of Bacillus Calmette-Guerin (BCG) and other microbial therapies of cancer. Despite this important role in tumor biology and therapy, the full mechanisms by which cancer cells can activate macropinocytosis remain incompletely defined. Using BCG uptake to assay macropinocytosis, we executed a genome-wide shRNA screen for macropinocytosis activators and identified Wnt pathway activation as a strong driver of macropinocytosis. Wnt-driven macropinocytosis was downstream of the β-catenin-dependent canonical Wnt pathway, was PAK1 dependent, and supported albumin-dependent growth in Ras-WT cells. In cells with activated Ras-dependent macropinocytosis, pharmacologic or genetic inhibition of Wnt signaling suppressed macropinocytosis. In a mouse model of Wnt-driven colonic hyperplasia via APC silencing, Wnt-activated macropinocytosis stimulated uptake of luminal microbiota, a process reversed by topical pharmacologic inhibition of macropinocytosis. Our findings indicate that Wnt pathway activation drives macropinocytosis in cancer, and its inhibition could provide a therapeutic vulnerability in Wnt-driven intestinal polyposis and cancers with Wnt activation.Significance: The Wnt pathway drives macropinocytosis in cancer cells, thereby contributing to cancer growth in nutrient-deficient conditions and, in the context of colon cancer, to the early phases of oncogenesis. Cancer Res; 78(16); 4658-70. ©2018 AACR.
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Affiliation(s)
- Gil Redelman-Sidi
- Division of Infectious Diseases, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Anna Binyamin
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Isabella Gaeta
- Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Wilhelm Palm
- Cancer Biology and Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Craig B Thompson
- Cancer Biology and Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Paul B Romesser
- Cancer Biology and Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Scott W Lowe
- Cancer Biology and Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Mukta Bagul
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts
| | - John G Doench
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts
| | - David E Root
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts
| | - Michael S Glickman
- Division of Infectious Diseases, Memorial Sloan Kettering Cancer Center, New York, New York. .,Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York
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26
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Li K, Vorkas CK, Chaudhry A, Bell DL, Willis RA, Rudensky A, Altman JD, Glickman MS, Aubé J. Synthesis, stabilization, and characterization of the MR1 ligand precursor 5-amino-6-D-ribitylaminouracil (5-A-RU). PLoS One 2018; 13:e0191837. [PMID: 29401462 PMCID: PMC5798775 DOI: 10.1371/journal.pone.0191837] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Accepted: 01/11/2018] [Indexed: 01/08/2023] Open
Abstract
Mucosal-associated invariant T (MAIT) cells are an abundant class of innate T cells restricted by the MHC I-related molecule MR1. MAIT cells can recognize bacterially-derived metabolic intermediates from the riboflavin pathway presented by MR1 and are postulated to play a role in innate antibacterial immunity through production of cytokines and direct bacterial killing. MR1 tetramers, typically stabilized by the adduct of 5-amino-6-D-ribitylaminouracil (5-A-RU) and methylglyoxal (MeG), are important tools for the study of MAIT cells. A long-standing problem with 5-A-RU is that it is unstable upon storage. Herein we report an efficient synthetic approach to the HCl salt of this ligand, which has improved stability during storage. We also show that synthetic 5-A-RU•HCl produced by this method may be used in protocols for the stimulation of human MAIT cells and production of both human and mouse MR1 tetramers for MAIT cell identification.
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Affiliation(s)
- Kelin Li
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Charles K. Vorkas
- Division of Infectious Diseases, Weill Cornell Medicine, New York, New York, United States of America
- Immunology Program, Sloan Kettering Institute, New York, New York, United States of America
| | - Ashutosh Chaudhry
- Immunology Program, Sloan Kettering Institute, New York, New York, United States of America
| | - Donielle L. Bell
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Richard A. Willis
- Division of Infectious Diseases, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
| | - Alexander Rudensky
- Immunology Program, Sloan Kettering Institute, New York, New York, United States of America
| | - John D. Altman
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Michael S. Glickman
- Division of Infectious Diseases, Weill Cornell Medicine, New York, New York, United States of America
- Immunology Program, Sloan Kettering Institute, New York, New York, United States of America
- Division of Infectious Diseases, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
| | - Jeffrey Aubé
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina, United States of America
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27
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Lazar N, Fay A, Nandakumar M, Boyle KE, Xavier J, Rhee K, Glickman MS. Control of biotin biosynthesis in mycobacteria by a pyruvate carboxylase dependent metabolic signal. Mol Microbiol 2017; 106:1018-1031. [PMID: 29052269 PMCID: PMC5916780 DOI: 10.1111/mmi.13865] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/12/2017] [Indexed: 01/15/2023]
Abstract
Biotin is an essential cofactor utilized by all domains of life, but only synthesized by bacteria, fungi and plants, making biotin biosynthesis a target for antimicrobial development. To understand biotin biosynthesis in mycobacteria, we executed a genetic screen in Mycobacterium smegmatis for biotin auxotrophs and identified pyruvate carboxylase (Pyc) as required for biotin biosynthesis. The biotin auxotrophy of the pyc::tn strain is due to failure to transcriptionally induce late stage biotin biosynthetic genes in low biotin conditions. Loss of bioQ, the repressor of biotin biosynthesis, in the pyc::tn strain reverted biotin auxotrophy, as did reconstituting the last step of the pathway through heterologous expression of BioB and provision of its substrate DTB. The role of Pyc in biotin regulation required its catalytic activities and could be supported by M. tuberculosis Pyc. Quantitation of the kinetics of depletion of biotinylated proteins after biotin withdrawal revealed that Pyc is the most rapidly depleted biotinylated protein and metabolomics revealed a broad metabolic shift in wild type cells upon biotin withdrawal which was blunted in cell lacking Pyc. Our data indicate that mycobacterial cells monitor biotin sufficiency through a metabolic signal generated by dysfunction of a biotinylated protein of central metabolism.
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Affiliation(s)
- Nathaniel Lazar
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
- Program in Immunology and Microbial Pathogenesis, Weill-Cornell Graduate School of Medical Sciences, New York, New York, USA
| | - Allison Fay
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | | | - Kerry E. Boyle
- Program in Immunology and Microbial Pathogenesis, Weill-Cornell Graduate School of Medical Sciences, New York, New York, USA
- Program in Computational Biology, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA
| | - Joao Xavier
- Program in Computational Biology, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA
| | - Kyu Rhee
- Program in Immunology and Microbial Pathogenesis, Weill-Cornell Graduate School of Medical Sciences, New York, New York, USA
- Weill-Cornell Medical College, New York, New York, USA
| | - Michael S. Glickman
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
- Program in Immunology and Microbial Pathogenesis, Weill-Cornell Graduate School of Medical Sciences, New York, New York, USA
- Infectious Diseases Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
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28
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Wipperman MF, Fitzgerald DW, Juste MAJ, Taur Y, Namasivayam S, Sher A, Bean JM, Bucci V, Glickman MS. Antibiotic treatment for Tuberculosis induces a profound dysbiosis of the microbiome that persists long after therapy is completed. Sci Rep 2017; 7:10767. [PMID: 28883399 PMCID: PMC5589918 DOI: 10.1038/s41598-017-10346-6] [Citation(s) in RCA: 113] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 08/08/2017] [Indexed: 02/08/2023] Open
Abstract
Mycobacterium tuberculosis, the cause of Tuberculosis (TB), infects one third of the world’s population and causes substantial mortality worldwide. In its shortest format, treatment of TB requires six months of multidrug therapy with a mixture of broad spectrum and mycobacterial specific antibiotics, and treatment of multidrug resistant TB is longer. The widespread use of this regimen makes this one of the largest exposures of humans to antimicrobials, yet the effects of TB treatment on intestinal microbiome composition and long-term stability are unknown. We compared the microbiome composition, assessed by both 16S rDNA and metagenomic DNA sequencing, of TB cases during antimycobacterial treatment and following cure by 6 months of antibiotics. TB treatment does not perturb overall diversity, but nonetheless dramatically depletes multiple immunologically significant commensal bacteria. The microbiomic perturbation of TB therapy can persist for at least 1.2 years, indicating that the effects of TB treatment are long lasting. These results demonstrate that TB treatment has dramatic effects on the intestinal microbiome and highlight unexpected durable consequences of treatment for the world’s most common infection on human ecology.
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Affiliation(s)
- Matthew F Wipperman
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA.,Clinical and Translational Science Center, Weill Cornell Medical College, New York, New York, USA
| | - Daniel W Fitzgerald
- Weill Cornell Medical College, New York, New York, USA.,GHESKIO Centers, Port-au-Prince, Haiti
| | | | - Ying Taur
- Infectious Diseases Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Sivaranjani Namasivayam
- Immunobiology Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Alan Sher
- Immunobiology Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - James M Bean
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA.,Weill Cornell Medical College, New York, New York, USA
| | - Vanni Bucci
- Department of Biology, Program in Biotechnology and Biomedical Engineering, University of Massachusetts Dartmouth, Dartmouth, Massachusetts, USA.
| | - Michael S Glickman
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA. .,Infectious Diseases Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA. .,Weill Cornell Medical College, New York, New York, USA.
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29
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Romero FA, Powell EA, Babady NE, Kaltsas A, Figueroa CJ, Pulitzer M, Mehrara BJ, Glickman MS, Morjaria S. Nontuberculous Mycobacterial Infections After Silicone Breast Implant Reconstruction Emphasize a Diversity of Infecting Mycobacteria. Open Forum Infect Dis 2017; 4:ofx189. [PMID: 29308399 PMCID: PMC5751029 DOI: 10.1093/ofid/ofx189] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Accepted: 08/14/2017] [Indexed: 11/14/2022] Open
Abstract
Postsurgical skin and soft tissue infections (SSTIs) caused by nontuberculous mycobacteria (NTM) are uncommon, indolent, difficult to treat, and often mimic pyogenic bacterial infections. Here we present 3 cases of NTM infections following placement of silicone implants for reconstructive breast surgery. These cases emphasize the importance of a high index of suspicion for NTM in patients with SSI after a prosthetic reconstruction refractory to conventional antibiotic therapy and the importance of early investigation with mycobacterial-specific diagnostics.
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Affiliation(s)
- Fabian A Romero
- Infectious Disease Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Eleanor A Powell
- Clinical Microbiology Service, Department of Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - N Esther Babady
- Clinical Microbiology Service, Department of Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Anna Kaltsas
- Infectious Disease Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.,Division of Plastic and Reconstructive Surgery, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Cesar J Figueroa
- Infectious Disease Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.,Division of Plastic and Reconstructive Surgery, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Melissa Pulitzer
- Department of Pathology, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Babak J Mehrara
- Division of Plastic and Reconstructive Surgery, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Michael S Glickman
- Infectious Disease Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Sejal Morjaria
- Infectious Disease Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
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30
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Namasivayam S, Maiga M, Yuan W, Thovarai V, Costa DL, Mittereder LR, Wipperman MF, Glickman MS, Dzutsev A, Trinchieri G, Sher A. Longitudinal profiling reveals a persistent intestinal dysbiosis triggered by conventional anti-tuberculosis therapy. Microbiome 2017; 5:71. [PMID: 28683818 PMCID: PMC5501520 DOI: 10.1186/s40168-017-0286-2] [Citation(s) in RCA: 90] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Accepted: 06/06/2017] [Indexed: 05/21/2023]
Abstract
BACKGROUND Effective treatment of Mycobacterium tuberculosis (Mtb) infection requires at least 6 months of daily therapy with multiple orally administered antibiotics. Although this drug regimen is administered annually to millions worldwide, the impact of such intensive antimicrobial treatment on the host microbiome has never been formally investigated. Here, we characterized the longitudinal outcome of conventional isoniazid-rifampin-pyrazinamide (HRZ) TB drug administration on the diversity and composition of the intestinal microbiota in Mtb-infected mice by means of 16S rRNA sequencing. We also investigated the effects of each of the individual antibiotics alone and in different combinations. RESULTS While inducing only a transient decrease in microbial diversity, HRZ treatment triggered a marked, immediate and reproducible alteration in community structure that persisted for the entire course of therapy and for at least 3 months following its cessation. Members of order Clostridiales were among the taxa that decreased in relative frequencies during treatment and family Porphyromonadaceae significantly increased post treatment. Experiments comparing monotherapy and different combination therapies identified rifampin as the major driver of the observed alterations induced by the HRZ cocktail but also revealed unexpected effects of isoniazid and pyrazinamide in certain drug pairings. CONCLUSIONS This report provides the first detailed analysis of the longitudinal changes in the intestinal microbiota due to anti-tuberculosis therapy. Importantly, many of the affected taxa have been previously shown in other systems to be associated with modifications in immunologic function. Together, our findings reveal that the antibiotics used in conventional TB treatment induce a distinct and long lasting dysbiosis. In addition, they establish a murine model for studying the potential impact of this dysbiosis on host resistance and physiology.
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Affiliation(s)
- Sivaranjani Namasivayam
- Immunobiology Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Building 33, Room 1W10A, 33 North Drive, MSC 3202, Bethesda, MD, 20892-3202, USA
| | - Mamoudou Maiga
- Immunobiology Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Building 33, Room 1W10A, 33 North Drive, MSC 3202, Bethesda, MD, 20892-3202, USA
- Present Address: Center for Innovation in Global Health Technologies, Northwestern University, Evanston, IL, USA
| | - Wuxing Yuan
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Vishal Thovarai
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Diego L Costa
- Immunobiology Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Building 33, Room 1W10A, 33 North Drive, MSC 3202, Bethesda, MD, 20892-3202, USA
| | - Lara R Mittereder
- Immunobiology Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Building 33, Room 1W10A, 33 North Drive, MSC 3202, Bethesda, MD, 20892-3202, USA
| | - Matthew F Wipperman
- Immunology Program, New York, NY, USA
- Clinical and Translational Science Center, Weill Cornell Medical College, New York, NY, USA
| | - Michael S Glickman
- Immunology Program, New York, NY, USA
- Infectious Diseases Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medical College, New York, NY, USA
| | - Amiran Dzutsev
- Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Giorgio Trinchieri
- Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Alan Sher
- Immunobiology Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Building 33, Room 1W10A, 33 North Drive, MSC 3202, Bethesda, MD, 20892-3202, USA.
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31
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Hubin EA, Fay A, Xu C, Bean JM, Saecker RM, Glickman MS, Darst SA, Campbell EA. Structure and function of the mycobacterial transcription initiation complex with the essential regulator RbpA. eLife 2017; 6. [PMID: 28067618 PMCID: PMC5302886 DOI: 10.7554/elife.22520] [Citation(s) in RCA: 89] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Accepted: 01/07/2017] [Indexed: 02/07/2023] Open
Abstract
RbpA and CarD are essential transcription regulators in mycobacteria. Mechanistic analyses of promoter open complex (RPo) formation establish that RbpA and CarD cooperatively stimulate formation of an intermediate (RP2) leading to RPo; formation of RP2 is likely a bottleneck step at the majority of mycobacterial promoters. Once RPo forms, CarD also disfavors its isomerization back to RP2. We determined a 2.76 Å-resolution crystal structure of a mycobacterial transcription initiation complex (TIC) with RbpA as well as a CarD/RbpA/TIC model. Both CarD and RbpA bind near the upstream edge of the −10 element where they likely facilitate DNA bending and impede transcription bubble collapse. In vivo studies demonstrate the essential role of RbpA, show the effects of RbpA truncations on transcription and cell physiology, and indicate additional functions for RbpA not evident in vitro. This work provides a framework to understand the control of mycobacterial transcription by RbpA and CarD. DOI:http://dx.doi.org/10.7554/eLife.22520.001
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Affiliation(s)
| | - Allison Fay
- Immunology Program, Sloan-Kettering Institute, New York, United States
| | - Catherine Xu
- The Rockefeller University, New York, United States
| | - James M Bean
- Immunology Program, Sloan-Kettering Institute, New York, United States
| | | | - Michael S Glickman
- Immunology Program, Sloan-Kettering Institute, New York, United States.,Division of Infectious Diseases, Memorial Sloan-Kettering Cancer Center, New York, United States
| | - Seth A Darst
- The Rockefeller University, New York, United States
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32
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Botella H, Vaubourgeix J, Lee MH, Song N, Xu W, Makinoshima H, Glickman MS, Ehrt S. Mycobacterium tuberculosis protease MarP activates a peptidoglycan hydrolase during acid stress. EMBO J 2017; 36:536-548. [PMID: 28057704 DOI: 10.15252/embj.201695028] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Revised: 11/28/2016] [Accepted: 12/02/2016] [Indexed: 11/09/2022] Open
Abstract
Mycobacterium tuberculosis (Mtb) can persist in the human host in a latent state for decades, in part because it has the ability to withstand numerous stresses imposed by host immunity. Prior studies have established the essentiality of the periplasmic protease MarP for Mtb to survive in acidified phagosomes and establish and maintain infection in mice. However, the proteolytic substrates of MarP that mediate these phenotypes were unknown. Here, we used biochemical methods coupled with supravital chemical probes that facilitate imaging of nascent peptidoglycan to demonstrate that during acid stress MarP cleaves the peptidoglycan hydrolase RipA, a process required for RipA's activation. Failure of RipA processing in MarP-deficient cells leads to cell elongation and chain formation, a hallmark of progeny cell separation arrest. Our results suggest that sustaining peptidoglycan hydrolysis, a process required for cell elongation, separation of progeny cells, and cell wall homeostasis in growing cells, may also be essential for Mtb's survival in acidic conditions.
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Affiliation(s)
- Helene Botella
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY, USA
| | - Julien Vaubourgeix
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY, USA
| | - Myung Hee Lee
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Naomi Song
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY, USA
| | - Weizhen Xu
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY, USA
| | - Hideki Makinoshima
- Division of Infectious Diseases, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Michael S Glickman
- Division of Infectious Diseases, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sabine Ehrt
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY, USA
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33
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Gupta R, Unciuleac MC, Shuman S, Glickman MS. Homologous recombination mediated by the mycobacterial AdnAB helicase without end resection by the AdnAB nucleases. Nucleic Acids Res 2016; 45:762-774. [PMID: 27899634 PMCID: PMC5314763 DOI: 10.1093/nar/gkw1130] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Revised: 10/26/2016] [Accepted: 10/29/2016] [Indexed: 01/31/2023] Open
Abstract
Current models of bacterial homologous recombination (HR) posit that extensive resection of a DNA double-strand break (DSB) by a multisubunit helicase–nuclease machine (e.g. RecBCD, AddAB or AdnAB) generates the requisite 3′ single-strand DNA substrate for RecA-mediated strand invasion. AdnAB, the helicase–nuclease implicated in mycobacterial HR, consists of two subunits, AdnA and AdnB, each composed of an N-terminal ATPase domain and a C-terminal nuclease domain. DSB unwinding by AdnAB in vitro is stringently dependent on the ATPase activity of the ‘lead’ AdnB motor translocating on the 3′ ssDNA strand, but not on the putative ‘lagging’ AdnA ATPase. Here, we queried genetically which activities of AdnAB are pertinent to its role in HR and DNA damage repair in vivo by inactivating each of the four catalytic domains. Complete nuclease-dead AdnAB enzyme can sustain recombination in vivo, as long as its AdnB motor is intact and RecO and RecR are available. We conclude that AdnAB's processive DSB unwinding activity suffices for AdnAB function in HR. Albeit not excluding the agency of a backup nuclease, our findings suggest that mycobacterial HR can proceed via DSB unwinding and protein capture of the displaced 3′-OH single strand, without a need for extensive end-resection.
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Affiliation(s)
- Richa Gupta
- Immunology Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA
| | - Mihaela-Carmen Unciuleac
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA
| | - Stewart Shuman
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA
| | - Michael S Glickman
- Immunology Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA .,Division of Infectious Diseases, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA
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34
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Gupta R, Chatterjee D, Glickman MS, Shuman S. Division of labor among Mycobacterium smegmatis RNase H enzymes: RNase H1 activity of RnhA or RnhC is essential for growth whereas RnhB and RnhA guard against killing by hydrogen peroxide in stationary phase. Nucleic Acids Res 2016; 45:1-14. [PMID: 27899559 PMCID: PMC5224475 DOI: 10.1093/nar/gkw1046] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Revised: 10/16/2016] [Accepted: 10/20/2016] [Indexed: 02/05/2023] Open
Abstract
RNase H enzymes sense the presence of ribonucleotides in the genome and initiate their removal by incising the ribonucleotide-containing strand of an RNA:DNA hybrid. Mycobacterium smegmatis encodes four RNase H enzymes: RnhA, RnhB, RnhC and RnhD. Here, we interrogate the biochemical activity and nucleic acid substrate specificity of RnhA. We report that RnhA (like RnhC characterized previously) is an RNase H1-type magnesium-dependent endonuclease with stringent specificity for RNA:DNA hybrid duplexes. Whereas RnhA does not incise an embedded mono-ribonucleotide, it can efficiently cleave within tracts of four or more ribonucleotides in duplex DNA. We gained genetic insights to the division of labor among mycobacterial RNases H by deleting the rnhA, rnhB, rnhC and rnhD genes, individually and in various combinations. The salient conclusions are that: (i) RNase H1 activity is essential for mycobacterial growth and can be provided by either RnhC or RnhA; (ii) the RNase H2 enzymes RnhB and RnhD are dispensable for growth and (iii) RnhB and RnhA collaborate to protect M. smegmatis against oxidative damage in stationary phase. Our findings highlight RnhC, the sole RNase H1 in pathogenic mycobacteria, as a candidate drug discovery target for tuberculosis and leprosy.
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Affiliation(s)
- Richa Gupta
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Debashree Chatterjee
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Michael S Glickman
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA .,Division of Infectious Diseases, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Stewart Shuman
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
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35
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Abstract
Inhaled environmental pollutants, most prominently from cigarettes, confer an increased risk of tuberculosis. A recent study published in Cell by Berg et al., (2016) using the zebrafish model of Mycobacterium marinum infection provides new insights into the role of macrophage lysosomal engorgement in compromising host defense against mycobacteria.
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Affiliation(s)
- Michael S Glickman
- Immunology Program, Sloan Kettering Institute, and Division of Infectious Diseases, Memorial Sloan Kettering Cancer Center, Box 477, 1275 York Avenue, New York, NY 10065, USA.
| | - Neil Schluger
- Division of Pulmonary, Allergy, and Critical Care Medicine, Columbia University Medical Center, 622 West 168 Street, New York, NY 10032, USA
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36
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Figueroa CJ, Riedel E, Glickman MS. Clinical and radiographic differentiation of lung nodules caused by mycobacteria and lung cancer: a case-control study. BMC Infect Dis 2015; 15:482. [PMID: 26515268 PMCID: PMC4625432 DOI: 10.1186/s12879-015-1185-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Accepted: 10/06/2015] [Indexed: 12/18/2022] Open
Abstract
Background Lung nodules caused by mycobacteria can resemble lung cancer on chest imaging. The advent of lung cancer screening with low-dose Computed Tomography is accompanied by high false-positive rates, making it necessary to establish criteria to differentiate malignant from benign nodules. Methods We conducted a retrospective case–control study of 52 patients with mycobacterial lung nodules and 139 patients with lung cancer, diagnosed between 2010 and 2012. We compared clinical and radiographic characteristics to identify predictors of disease by univariate and multivariate analysis. The discriminatory power of maximum Standardized Uptake Values from Positron-Emission-Tomography was also evaluated. Results Several variables were correlated with a diagnosis of mycobacterial infection or lung cancer on univariate analysis. Such variable include smoking status and history, lesion size and imaging evidence of tree-in-bud opacities, lymphadenopathy or emphysema on computed tomography. Upon author consensus, the most clinically-relevant variables were selected to undergo multivariate analysis. A history of current or former smoking [OR 4.4 (95 % CI 1.2–15.6) and 2.7 (95 % CI 1.1–6.8), respectively P = 0.04] was correlated with diagnoses of lung cancer. Contrarily, the presence of tree-in-bud opacities was less likely to be correlated with a diagnosis of malignancy [OR 0.04 (95 % CI 0.0–1.0), P = 0.05]. Additionally, higher maximum standardized uptake values from positron emission tomography were associated with malignancy on multivariate analysis [OR 1.1 (95 % CI 1.0–1.2), P = 0.04]; but the accuracy of the values in differentiating between diseases was only 0.67 as measured by the area under the curve. Lesion size was not independently associated with diagnosis [OR 0.5 (95 % CI 0.2–1.2), (P = 0.12)]. Conclusions Establishing the likelihood of malignancy for lung nodules based on isolated clinical or radiographic criteria is difficult. Using the variables found in this study may allow clinicians to stratify patients into groups of high and low risk for malignancy, and therefore establish efficient diagnostic strategies. Electronic supplementary material The online version of this article (doi:10.1186/s12879-015-1185-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Cesar J Figueroa
- Department of Medicine, Infectious Diseases, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA.
| | - Elyn Riedel
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA.
| | - Michael S Glickman
- Department of Medicine, Infectious Diseases, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA. .,Immunology Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA.
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37
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Landick R, Krek A, Glickman MS, Socci ND, Stallings CL. Genome-Wide Mapping of the Distribution of CarD, RNAP σ A, and RNAP β on the Mycobacterium smegmatis Chromosome using Chromatin Immunoprecipitation Sequencing. Genom Data 2014; 2:110-113. [PMID: 25089258 PMCID: PMC4115788 DOI: 10.1016/j.gdata.2014.05.012] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
CarD is an essential mycobacterial protein that binds the RNA polymerase (RNAP) and affects the transcriptional profile of Mycobacterium smegmatis and Mycobacterium tuberculosis [6]. We predicted that CarD was directly regulating RNAP function but our prior experiments had not determined at what stage of transcription CarD was functioning and at which genes CarD interacted with the RNAP. To begin to address these open questions, we performed chromatin immunoprecipitation sequencing (ChIP-seq) to survey the distribution of CarD throughout the M. smegmatis chromosome. The distribution of RNAP subunits β and σA were also profiled. We expected that RNAP β would be present throughout transcribed regions and RNAP σA would be predominantly enriched at promoters based on work in Escherichia coli [3], however this had yet to be determined in mycobacteria. The ChIP-seq analyses revealed that CarD was never present on the genome in the absence of RNAP, was primarily associated with promoter regions, and was highly correlated with the distribution of RNAP σA. The colocalization of σA and CarD led us to propose that in vivo, CarD associates with RNAP initiation complexes at most promoters and is therefore a global regulator of transcription initiation. Here we describe in detail the data from the ChIP-seq experiments associated with the study published by Srivastava and colleagues in the Proceedings of the National Academy of Science in 2013 [5] as well as discuss the findings from this dataset in relation to both CarD and mycobacterial transcription as a whole. The ChIP-seq data have been deposited in the Gene Expression Omnibus (GEO) database, www.ncbi.nlm.nih.gov/geo (accession no. GSE48164).
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Affiliation(s)
- Robert Landick
- Departments of Biochemistry and Bacteriology, University of Wisconsin, Madison, WI, 53706, USA
| | - Azra Krek
- Bioinformatics Core, Memorial Sloan-Kettering Cancer Center, New York, NY, 10065, USA
| | - Michael S Glickman
- Immunology Program, Sloan-Kettering Institute, and Division of Infectious Diseases, Memorial Sloan-Kettering Cancer Center, New York, NY, 10065, USA
| | - Nicholas D Socci
- Bioinformatics Core, Memorial Sloan-Kettering Cancer Center, New York, NY, 10065, USA
| | - Christina L Stallings
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA
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38
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Harris KK, Fay A, Yan HG, Kunwar P, Socci ND, Pottabathini N, Juventhala RR, Djaballah H, Glickman MS. Novel imidazoline antimicrobial scaffold that inhibits DNA replication with activity against mycobacteria and drug resistant Gram-positive cocci. ACS Chem Biol 2014; 9:2572-83. [PMID: 25222597 PMCID: PMC4245167 DOI: 10.1021/cb500573z] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
![]()
Bacterial
antimicrobial resistance is an escalating public health
threat, yet the current antimicrobial pipeline remains alarmingly
depleted, making the development of new antimicrobials an urgent need.
Here, we identify a novel, potent, imidazoline antimicrobial compound,
SKI-356313, with bactericidal activity against Mycobacterium
tuberculosis and Gram-positive cocci, including vancomycin-resistant Enterococcus faecium (VRE) and methicillin-resistant Staphylococcus aureus (MRSA). SKI-356313 is active in murine
models of Streptococcus pneumoniae and MRSA infection
and is potently bactericidal for both replicating and nonreplicating M. tuberculosis. Using a combination of genetics, whole
genome sequencing, and a novel target ID approach using real time
imaging of core macromolecular biosynthesis, we show that SKI-356313
inhibits DNA replication and displaces the replisome from the bacterial
nucleoid. These results identify a new antimicrobial scaffold with
a novel mechanism of action and potential therapeutic utility against
nonreplicating M. tuberculosis and antibiotic resistant
Gram-positive cocci.
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Affiliation(s)
- Kendra K. Harris
- Program
in Immunology and Microbial Pathogenesis, Weill Cornell Graduate School of Medical Sciences, New York, New York 10021, United States
- Weill Cornell,
Rockefeller, Sloan Kettering Tri-Institutional MD-PhD Program, New York, New York 10065, United States
| | | | | | - Pratima Kunwar
- Viral
Vaccine Program, Seattle Biomedical Research Institute, Seattle, Washington 98109, United States
- Department
of Global Health, University of Washington School of Medicine, Seattle, Washington 98109, United States
| | | | - Narender Pottabathini
- Discovery
Services Division, GVK Biosciences Pvt. Ltd, Plot 28A, IDA Nacharam, Hyderabad 500076, India
| | - Ramakrishna R. Juventhala
- Discovery
Services Division, GVK Biosciences Pvt. Ltd, Plot 28A, IDA Nacharam, Hyderabad 500076, India
| | | | - Michael S. Glickman
- Program
in Immunology and Microbial Pathogenesis, Weill Cornell Graduate School of Medical Sciences, New York, New York 10021, United States
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Abstract
Bacillus Calmette-Guérin (BCG) has been used to treat non-muscle-invasive bladder cancer for more than 30 years. It is one of the most successful biotherapies for cancer in use. Despite long clinical experience with BCG, the mechanism of its therapeutic effect is still under investigation. Available evidence suggests that urothelial cells (including bladder cancer cells themselves) and cells of the immune system both have crucial roles in the therapeutic antitumour effect of BCG. The possible involvement of bladder cancer cells includes attachment and internalization of BCG, secretion of cytokines and chemokines, and presentation of BCG and/or cancer cell antigens to cells of the immune system. Immune system cell subsets that have potential roles in BCG therapy include CD4(+) and CD8(+) lymphocytes, natural killer cells, granulocytes, macrophages, and dendritic cells. Bladder cancer cells are killed through direct cytotoxicity by these cells, by secretion of soluble factors such as TRAIL (tumour necrosis factor-related apoptosis-inducing ligand), and, to some degree, by the direct action of BCG. Several gaps still exist in our knowledge that should be addressed in future efforts to understand this biotherapy of cancer.
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Affiliation(s)
- Gil Redelman-Sidi
- Sloan-Kettering Cancer Center, 1275 York Avenue, Box 9, New York, NY 10065, USA
| | - Michael S Glickman
- Sloan-Kettering Cancer Center, 1275 York Avenue, Box 9, New York, NY 10065, USA
| | - Bernard H Bochner
- Sloan-Kettering Cancer Center, 1275 York Avenue, Box 9, New York, NY 10065, USA
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40
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Schneider JS, Glickman MS. Function of site-2 proteases in bacteria and bacterial pathogens. Biochim Biophys Acta 2013; 1828:2808-14. [PMID: 24099002 DOI: 10.1016/j.bbamem.2013.04.019] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2013] [Revised: 04/11/2013] [Accepted: 04/15/2013] [Indexed: 01/02/2023]
Abstract
Site-2 proteases (S2Ps) are a class of intramembrane metalloproteases named after the founding member of this protein family, human S2P, which control cholesterol and fatty acid biosynthesis by cleaving Sterol Regulatory Element Binding Proteins which control cholesterol and fatty acid biosynthesis. S2Ps are widely distributed in bacteria and participate in diverse pathways that control such diverse functions as membrane integrity, sporulation, lipid biosynthesis, pheromone production, virulence, and others. The most common signaling mechanism mediated by S2Ps is the coupled degradation of transmembrane anti-Sigma factors to activate ECF Sigma factor regulons. However, additional signaling mechanisms continue to emerge as more prokaryotic S2Ps are characterized, including direct proteolysis of membrane embedded transcription factors and proteolysis of non-transcriptional membrane proteins or membrane protein remnants. In this review we seek to comprehensively review the functions of S2Ps in bacteria and bacterial pathogens and attempt to organize these proteases into conceptual groups that will spur further study. This article is part of a Special Issue entitled: Intramembrane Proteases.
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Affiliation(s)
- Jessica S Schneider
- Immunology Program, Memorial Sloan Kettering Cancer Center, 1275 York Ave., New York, NY 10065, USA; Program in Immunology and Microbial Pathogenesis, Weill Cornell Graduate School of Biomedical Sciences, USA
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41
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Samstein M, Schreiber HA, Leiner IM, Susac B, Glickman MS, Pamer EG. Essential yet limited role for CCR2⁺ inflammatory monocytes during Mycobacterium tuberculosis-specific T cell priming. eLife 2013; 2:e01086. [PMID: 24220507 PMCID: PMC3820971 DOI: 10.7554/elife.01086] [Citation(s) in RCA: 103] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Defense against infection by Mycobacterium tuberculosis (Mtb) is mediated by CD4 T cells. CCR2+ inflammatory monocytes (IMs) have been implicated in Mtb-specific CD4 T cell responses but their in vivo contribution remains unresolved. Herein, we show that transient ablation of IMs during infection prevents Mtb delivery to pulmonary lymph nodes, reducing CD4 T cell responses. Transfer of MHC class II-expressing IMs to MHC class II-deficient, monocyte-depleted recipients, while restoring Mtb transport to mLNs, does not enable Mtb-specific CD4 T cell priming. On the other hand, transfer of MHC class II-deficient IMs corrects CD4 T cell priming in monocyte-depleted, MHC class II-expressing mice. Specific depletion of classical DCs does not reduce Mtb delivery to pulmonary lymph nodes but markedly reduces CD4 T cell priming. Thus, although IMs acquire characteristics of DCs while delivering Mtb to lymph nodes, cDCs but not moDCs induce proliferation of Mtb-specific CD4 T cells. DOI:http://dx.doi.org/10.7554/eLife.01086.001 Tuberculosis is a disease that kills more than one million people every year. It is caused by mycobacteria, notably Mycobacterium tuberculosis, and the World Health Organization estimates that about one third of the world’s population has latent tuberculosis, although only one person in 10 goes on to develop an active infection. Understanding why some individuals develop active infections, whereas most do not, could help with the development of a vaccine to prevent tuberculosis and/or new treatments for the disease. Disappointing results from vaccine trials and the emergence of drug-resistant strains of tuberculosis have increased the need for more research into the interactions between mycobacteria and the human immune system. Tuberculosis is spread when an infected person coughs or sneezes and someone else inhales the mycobacteria spread by the first person. When M. tuberculosis first enters the human respiratory tract, the innate immune system tries to identify and destroy cells that have been infected. However, if this initial response is not effective, the M. tuberculosis can persist in the lungs and trigger the adaptive immune response. This involves CD4 T cells working to eliminate the infection, but our understanding of the adaptive immune response is not complete. Samstein et al. probed the role that immune cells known as inflammatory monocytes play in the adaptive immune response. Previous research has suggested that inflammatory monocytes may develop into dendritic cells that directly prime the CD4 T cells to respond when the lung has been infected. However, Samstein et al. demonstrate that the inflammatory monocytes carry M. tuberculosis from the lungs of infected mice to the draining lymph nodes during the second week of infection. These monocytes develop many of the characteristics of dendritic cells, but they do not activate the CD4 T cells. Samstein et al. show that dendritic cells, contrary to previous evidence, are not necessary for the transport of the M. tuberculosis from the lungs to the draining lymph nodes. Without the dendritic cells, however, fewer CD4 T cell are primed in the lymph nodes. Samstein et al. suggest that the inflammatory monocytes play a crucial role by transporting the live bacteria to the lymph nodes. And once in the lymph nodes, the monocytes transfer invading antigens to dendritic cells to initiate the production of the CD4 T cells to lead the fight against the infection. DOI:http://dx.doi.org/10.7554/eLife.01086.002
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Affiliation(s)
- Miriam Samstein
- Program in Immunology and Microbial Pathogenesis, Weill Cornell Graduate School of Medical Sciences, New York, United States
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42
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Hedhli D, Denis O, Barkan D, Daffé M, Glickman MS, Huygen K. M.tuberculosis mutants lacking oxygenated mycolates show increased immunogenicity and protective efficacy as compared to M. bovis BCG vaccine in an experimental mouse model. PLoS One 2013; 8:e76442. [PMID: 24146869 PMCID: PMC3798287 DOI: 10.1371/journal.pone.0076442] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2013] [Accepted: 08/26/2013] [Indexed: 11/21/2022] Open
Abstract
The existing vaccine against tuberculosis (M. bovis BCG) exerts some protection against the extrapulmonary forms of the disease, particularly in young children, but is not very effective against the pulmonary form of TB, which often results from the reactivation of a latent M. tuberculosis (M.tb)infection. Among the new approaches in TB vaccine development, live attenuated M.tb mutants are a promising new avenue. Here we report on the vaccine potential of two highly attenuated M.tb mutants, MGM1991 and M.tbhma::hyg (HMA), lacking all oxygenated mycolates in their cell wall. In C57BL/6 mice, stronger Th1 (IFN-γ, IL-2 and TNF-α) and IL-17 responses could be induced following subcutaneous vaccination with either of the two mutants, than following vaccination with M. bovis BCG. Significantly more mycobacteria specific IFN-γ producing CD4+ and particularly CD8+ T cells could be detected by intracellular cytokine staining in mice vaccinated with the M.tb mutants. Finally, vaccination with either of the two mutants conferred stronger protection against intratracheal M.tb challenge than vaccination with BCG, as indicated by reduced bacterial replication in lungs at 4 to 12 weeks after challenge. Protection against M. tb dissemination, as indicated by reduced bacterial numbers in spleen, was comparable for both mutants to protection conferred by BCG.
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Affiliation(s)
- Dorsaf Hedhli
- Service Immunology, Scientific Institute of Public Health (WIV-ISP, Site Ukkel), Brussels, Belgium
| | - Olivier Denis
- Service Immunology, Scientific Institute of Public Health (WIV-ISP, Site Ukkel), Brussels, Belgium
| | - Daniel Barkan
- Immunology Program and Division of Infectious Diseases, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
| | - Mamadou Daffé
- Département de Mécanismes Moléculaires des Infections Mycobactériennes, Institut de Pharmacologie et Biologie Structurale du CNRS et de l'Université Paul Sabatier (UMR 5089), Toulouse, France
| | - Michael S. Glickman
- Immunology Program and Division of Infectious Diseases, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
| | - Kris Huygen
- Service Immunology, Scientific Institute of Public Health (WIV-ISP, Site Ukkel), Brussels, Belgium
- *E-mail:
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Redelman-Sidi G, Iyer G, Solit DB, Glickman MS. Oncogenic activation of Pak1-dependent pathway of macropinocytosis determines BCG entry into bladder cancer cells. Cancer Res 2013; 73:1156-67. [PMID: 23378476 DOI: 10.1158/0008-5472.can-12-1882] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Bacille Calmette-Guerin (BCG) is an attenuated strain of Mycobacterium bovis that is used widely as a vaccine for tuberculosis and is used as an effective treatment for superficial bladder carcinoma. Despite being the most successful cancer biotherapy, its mechanism of action and response determinants remain obscure. Here, we establish a model system to analyze BCG interaction with bladder cancer cells, using it to show that these cells vary dramatically in their susceptibility to BCG infection. Unexpectedly, the uptake of BCG by bladder cancer cells occurs by macropinocytosis rather than phagocytosis. BCG entry into bladder cancer cells relied upon Rac1, Cdc42, and their effector kinase Pak1. The difference in susceptibility between BCG-permissive and -resistant bladder cancer cells was due to oncogenic activation of signaling pathways that activate macropinocytosis, with phosphoinositide 3-kinase inhibitor activation stimulating BCG uptake independently of Akt. Similarly, activated Ras strongly activated Pak1-dependent uptake of BCG. These results reveal that oncogenic activation of macropinocytosis determines BCG uptake by bladder cancer cells, implying that tumor responsiveness to BCG may be governed by the specific mutations present in the treated cancer cell.
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Affiliation(s)
- Gil Redelman-Sidi
- Infectious Diseases Service, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
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Gupta R, Ryzhikov M, Koroleva O, Unciuleac M, Shuman S, Korolev S, Glickman MS. A dual role for mycobacterial RecO in RecA-dependent homologous recombination and RecA-independent single-strand annealing. Nucleic Acids Res 2013; 41:2284-95. [PMID: 23295671 PMCID: PMC3575820 DOI: 10.1093/nar/gks1298] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Mycobacteria have two genetically distinct pathways for the homology-directed repair of DNA double-strand breaks: homologous recombination (HR) and single-strand annealing (SSA). HR is abolished by deletion of RecA and reduced in the absence of the AdnAB helicase/nuclease. By contrast, SSA is RecA-independent and requires RecBCD. Here we examine the function of RecO in mycobacterial DNA recombination and repair. Loss of RecO elicits hypersensitivity to DNA damaging agents similar to that caused by deletion of RecA. We show that RecO participates in RecA-dependent HR in a pathway parallel to the AdnAB pathway. We also find that RecO plays a role in the RecA-independent SSA pathway. The mycobacterial RecO protein displays a zinc-dependent DNA binding activity in vitro and accelerates the annealing of SSB-coated single-stranded DNA. These findings establish a role for RecO in two pathways of mycobacterial DNA double-strand break repair and suggest an in vivo function for the DNA annealing activity of RecO proteins, thereby underscoring their similarity to eukaryal Rad52.
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Affiliation(s)
- Richa Gupta
- Division of Infectious Diseases, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA
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Zhu H, Bhattarai H, Yan HG, Shuman S, Glickman MS. Characterization of Mycobacterium smegmatis PolD2 and PolD1 as RNA/DNA polymerases homologous to the POL domain of bacterial DNA ligase D. Biochemistry 2012. [PMID: 23198659 DOI: 10.1021/bi301202e] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Mycobacteria exploit nonhomologous end-joining (NHEJ) to repair DNA double-strand breaks. The core NHEJ machinery comprises the homodimeric DNA end-binding protein Ku and DNA ligase D (LigD), a modular enzyme composed of a C-terminal ATP-dependent ligase domain (LIG), a central 3'-phosphoesterase domain (PE), and an N-terminal polymerase domain (POL). LigD POL is proficient at adding templated and nontemplated deoxynucleotides and ribonucleotides to DNA ends in vitro and is the catalyst in vivo of unfaithful NHEJ events involving nontemplated single-nucleotide additions to blunt DSB ends. Here, we identify two mycobacterial proteins, PolD1 and PolD2, as stand-alone homologues of the LigD POL domain. Biochemical characterization of PolD1 and PolD2 shows that they resemble LigD POL in their monomeric quaternary structures, their ability to add templated and nontemplated nucleotides to primer-templates and blunt ends, and their preference for rNTPs versus dNTPs. Deletion of polD1, polD2, or both from a Mycobacterium smegmatis strain carrying an inactivating mutation in LigD POL failed to reveal a role for PolD1 or PolD2 in templated nucleotide additions during NHEJ of 5'-overhang DSBs or in clastogen resistance. Whereas our results document the existence and characteristics of new stand-alone members of the LigD POL family of RNA/DNA polymerases, they imply that other polymerases can perform fill-in synthesis during mycobacterial NHEJ.
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Affiliation(s)
- Hui Zhu
- Molecular Biology Program, Sloan-Kettering Institute, New York, NY 10065, USA
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46
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Stallings CL, Glickman MS. CarD: a new RNA polymerase modulator in mycobacteria. Transcription 2012; 2:15-8. [PMID: 21326904 DOI: 10.4161/trns.2.1.13628] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2010] [Revised: 09/13/2010] [Accepted: 09/14/2010] [Indexed: 01/13/2023] Open
Abstract
Mycobacteria CarD is an essential RNAP binding protein that regulates many transcripts including rRNA. This article will review our present state of knowledge regarding CarD and compare the known functions of CarD with other RNAP binding proteins in E. coli, emphasizing how this information can guide future investigations.
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Abstract
The tumor suppressor PTEN is a lipid phosphatase that is frequently mutated in various human cancers. PTEN suppresses tumor cell proliferation, survival, and growth mainly by inhibiting the PI3K-Akt signaling pathway through dephosphorylation of phosphatidylinositol 3,4,5-triphosphate. In addition to it role in tumor suppression, the PTEN-PI3K pathway controls many cellular functions, some of which may be important for cellular resistance to infection. Currently, the intersection between tumorigenic signaling pathways and cellular susceptibility to infection is not well defined. In this study we report that PTEN signaling regulates infection of both noncancerous and cancerous cells by multiple intracellular mycobacterial pathogens and that pharmacological modulation of PTEN signaling can affect mycobacterial infection. We found that PTEN deficiency renders multiple types of cells hyper-susceptible to infection by Mycoplasma and Mycobacterium bovis Bacillus Calmette-Guérin (BCG). The lipid phosphatase activity of PTEN is required for attenuating infection. Furthermore, we found mycobacterial infection activates host cell Akt phosphorylation, and pharmacological inhibition of Akt or PI3K activity reduced levels of intracellular infection. Intriguingly, inhibition of mTOR, one of the downstream components of the Akt signaling and a promising cancer therapeutic target, also lowered intracellular Bacillus Calmette-Guérin levels in mammary epithelial cancer MCF-7 cells. These findings demonstrate a critical role of PTEN-regulated pathways in pathogen infection. The relationship of PTEN-PI3K-Akt mTOR status and susceptibility to mycobacterial infection suggests that the interaction of mycobacterial pathogens with cancer cells may be influenced by genetic alterations in the tumor cells.
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Affiliation(s)
- Guochang Huang
- Cell Biology Program, Memorial Sloan-Kettering Cancer Center, New York, New York 10065, USA
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Abstract
During the past decade, cancer drug development has shifted from a focus on cytotoxic chemotherapies to drugs that target specific molecular alterations in tumors. Although these drugs dramatically shrink tumors, the responses are temporary. Research is now focused on overcoming drug resistance, a frequent cause of treatment failure. Here we reflect on analogous challenges faced by researchers in infectious diseases. We compare and contrast the resistance mechanisms arising in cancer and infectious diseases and discuss how approaches for overcoming viral and bacterial infections, such as HIV and tuberculosis, are instructive for developing a more rational approach for cancer therapy. In particular, maximizing the effect of the initial treatment response, which often requires synergistic combination therapy, is foremost among these approaches. A remaining challenge in both fields is identifying drugs that eliminate drug-tolerant "persister" cells (infectious disease) or tumor-initiating/stem cells (cancer) to prevent late relapse and shorten treatment duration.
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Affiliation(s)
- Michael S Glickman
- Infectious Diseases Service and Immunology Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA.
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Stallings CL, Chu L, Li LX, Glickman MS. Catalytic and non-catalytic roles for the mono-ADP-ribosyltransferase Arr in the mycobacterial DNA damage response. PLoS One 2011; 6:e21807. [PMID: 21789183 PMCID: PMC3138739 DOI: 10.1371/journal.pone.0021807] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2011] [Accepted: 06/07/2011] [Indexed: 01/28/2023] Open
Abstract
Recent evidence indicates that the mycobacterial response to DNA double strand breaks (DSBs) differs substantially from previously characterized bacteria. These differences include the use of three DSB repair pathways (HR, NHEJ, SSA), and the CarD pathway, which integrates DNA damage with transcription. Here we identify a role for the mono-ADP-ribosyltransferase Arr in the mycobacterial DNA damage response. Arr is transcriptionally induced following DNA damage and cellular stress. Although Arr is not required for induction of a core set of DNA repair genes, Arr is necessary for suppression of a set of ribosomal protein genes and rRNA during DNA damage, placing Arr in a similar pathway as CarD. Surprisingly, the catalytic activity of Arr is not required for this function, as catalytically inactive Arr was still able to suppress ribosomal protein and rRNA expression during DNA damage. In contrast, Arr substrate binding and catalytic activities were required for regulation of a small subset of other DNA damage responsive genes, indicating that Arr has both catalytic and noncatalytic roles in the DNA damage response. Our findings establish an endogenous cellular function for a mono-ADP-ribosyltransferase apart from its role in mediating Rifampin resistance.
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Affiliation(s)
- Christina L. Stallings
- Department of Molecular Microbiology Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Linda Chu
- Immunology program, Sloan Kettering Institute, New York, New York, United States of America
| | - Lucy X. Li
- Gerstner Sloan Kettering Graduate School of Biomedical Sciences, Summer Undergraduate Research Program, New York, New York, United States of America
| | - Michael S. Glickman
- Division of Infectious Diseases, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
- Immunology program, Sloan Kettering Institute, New York, New York, United States of America
- * E-mail:
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50
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Gallegos AM, van Heijst JWJ, Samstein M, Su X, Pamer EG, Glickman MS. A gamma interferon independent mechanism of CD4 T cell mediated control of M. tuberculosis infection in vivo. PLoS Pathog 2011; 7:e1002052. [PMID: 21625591 PMCID: PMC3098235 DOI: 10.1371/journal.ppat.1002052] [Citation(s) in RCA: 165] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2010] [Accepted: 03/19/2011] [Indexed: 12/12/2022] Open
Abstract
CD4 T cell deficiency or defective IFNγ signaling render humans and mice highly susceptible to Mycobacterium tuberculosis (Mtb) infection. The prevailing model is that Th1 CD4 T cells produce IFNγ to activate bactericidal effector mechanisms of infected macrophages. Here we test this model by directly interrogating the effector functions of Th1 CD4 T cells required to control Mtb in vivo. While Th1 CD4 T cells specific for the Mtb antigen ESAT-6 restrict in vivo Mtb growth, this inhibition is independent of IFNγ or TNF and does not require the perforin or FAS effector pathways. Adoptive transfer of Th17 CD4 T cells specific for ESAT-6 partially inhibited Mtb growth while Th2 CD4 T cells were largely ineffective. These results imply a previously unrecognized IFNγ/TNF independent pathway that efficiently controls Mtb and suggest that optimization of this alternative effector function may provide new therapeutic avenues to combat Mtb through vaccination.
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Affiliation(s)
- Alena M. Gallegos
- NIH/NIAID Laboratory of Parasitic Diseases,
Bethesda, Maryland, United States of America
- Immunology Program, Infectious Disease
Service, Memorial Sloan-Kettering Cancer Center, New York, New York, United
States of America
| | - Jeroen W. J. van Heijst
- Immunology Program, Infectious Disease
Service, Memorial Sloan-Kettering Cancer Center, New York, New York, United
States of America
| | - Miriam Samstein
- Program in Immunology and Microbial
Pathogenesis, Weill Graduate School of Medical Sciences, New York, New York,
United States of America
| | - Xiaodi Su
- Program in Immunology and Microbial
Pathogenesis, Weill Graduate School of Medical Sciences, New York, New York,
United States of America
| | - Eric G. Pamer
- Immunology Program, Infectious Disease
Service, Memorial Sloan-Kettering Cancer Center, New York, New York, United
States of America
- * E-mail: (EGP); (MSG)
| | - Michael S. Glickman
- Immunology Program, Infectious Disease
Service, Memorial Sloan-Kettering Cancer Center, New York, New York, United
States of America
- * E-mail: (EGP); (MSG)
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