Publications

Publications

  1. Rock JR*, Lang UF*, Chase MR, Ford CB, Gerrick ER, Gawande R, Coscolla M, Gagneux S, Fortune SM*, Lamers MH* (*co-first, co-corresponding authors). Replication fidelity in tuberculosis is mediated by an ancestral prokaryotic proofreader. Nature Genetics, accepted for publication.
  1. Gideon HP, Phuah JY, Myers AJ, Bryson BD, Rodgers MA, Coleman MT, Maiello P, Rutledge T, Marino S, Fortune S, Kirschner DE, Lin PL, Flynn JL. Variability in tuberculosis granuloma T cell responses exists, but a balance of pro- and anti-inflammatory cytokines is associated with sterilization. PLoS Pathog. 2015 Jan 22;11(1):e1004603. doi: 10.1371/journal.ppat.1004603. eCollection 2015 Jan. PMID: 25611466.
  1. Ramsdell TL*, Huppert LA*, Sysoeva TA, Fortune SM*, Burton BM* (*co-first, co-corresponding authors). Linked Domain, Architectures Allow for Specialization of Function in the FtsK/SpoIIIE ATPases of ESX Secretion Systems. J Mol Biol. 2014 Jun 27. pii: S0022-2836(14)00306-4. doi: 10.1016/j.jmb.2014.06.013. [Epub ahead of print] PubMed PMID: 24979678.
  1. Huppert LA, Ramsdell TL, Chase MR, Sarracino DA, Fortune SM, Burton BM. The ESX system in Bacillus subtilis mediates protein secretion. PLoS One. 2014 May 5;9(5):e96267. doi: 10.1371/journal.pone.0096267. eCollection 2014. PubMed PMID: 24798022; PubMed Central PMCID: PMC4010439.
  1. Layre E, Lee HJ, Young DC, Martinot AJ, Buter J, Minnaard AJ, Annand JW, Fortune SM, Snider BB, Matsunaga I, Rubin EJ, Alber T, Moody DB. Molecular profiling of Mycobacterium tuberculosis identifies tuberculosinyl nucleoside products of the virulence-associated enzyme Rv3378c. Proc Natl Acad Sci U S A. 2014 Feb 25;111(8):2978-83. doi: 10.1073/pnas.1315883111. Epub 2014 Feb 10. PubMed PMID: 24516143; PubMed Central PMCID: PMC3939896.
  1. Lin PL*, Ford CB*, Coleman MT, Myers AJ, Gawande R, Ioerger T, Sacchettini J, Fortune SM*, Flynn JL.* (*co-first, co-corresponding authors). Sterilization of granulomas is common in active and latent tuberculosis despite within-host variability in bacterial killing. Nat Med. 2014 Jan;20(1):75-9. doi: 10.1038/nm.3412. Epub 2013 Dec 15. PubMed PMID: 24336248; PubMed Central PMCID: PMC3947310.
  1. Shell SS, Prestwich EG, Baek SH, Shah RR, Sassetti CM, Dedon PC, Fortune SM. DNA methylation impacts gene expression and ensures hypoxic survival of Mycobacterium tuberculosis. PLoS Pathog. 2013;9(7):e1003419. doi: 10.1371/journal.ppat.1003419. Epub 2013 Jul 4. PubMed PMID: 23853579; PubMed Central PMCID: PMC3701705.
  1. Ford CB, Shah RR, Maeda MK, Gagneux S, Murray MB, Cohen T, Johnston JC, Gardy J, Lipsitch M, Fortune SM. Mycobacterium tuberculosis mutation rate estimates from different lineages predict substantial differences in the emergence of drug-resistant tuberculosis. Nat Genet. 2013 Jul;45(7):784-90. doi: 10.1038/ng.2656. Epub 2013 Jun 9. PubMed PMID: 23749189; PubMed Central PMCID: PMC3777616.
  1. Liong M, Hoang AN, Chung J, Gural N, Ford CB, Min C, Shah RR, Ahmad R, Fernandez-Suarez M, Fortune SM, Toner M, Lee H, Weissleder R. Magnetic barcode assay for genetic detection of pathogens. Nat Commun. 2013;4:1752. doi: 10.1038/ncomms2745. PubMed PMID: 23612293; PubMed Central PMCID: PMC3635151.
  1. Ragheb MN, Ford CB, Chase MR, Lin PL, Flynn JL, Fortune SM. The mutation rate of mycobacterial repetitive unit loci in strains of M. tuberculosis from cynomolgus macaque infection. BMC Genomics. 2013 Mar 5;14:145. doi: 10.1186/1471-2164-14-145. PubMed PMID: 23496945; PubMed Central PMCID: PMC3635867.
  1. Chao MC, Kieser KJ, Minami S, Mavrici D, Aldridge BB, Fortune SM, Alber T, Rubin EJ. Protein complexes and proteolytic activation of the cell wall hydrolase RipA regulate septal resolution in mycobacteria. PLoS Pathog. 2013 Feb;9(2):e1003197. doi: 10.1371/journal.ppat.1003197. Epub 2013 Feb 28. PubMed PMID: 23468634; PubMed Central PMCID: PMC3585148.
  1. Fong EJ, Sharma Y, Fallica B, Tierney DB, Fortune SM, Zaman MH. Decoupling directed and passive motion in dynamic systems: particle tracking microrheology of sputum. Ann Biomed Eng. 2013 Apr;41(4):837-46. doi: 10.1007/s10439-012-0721-2. Epub 2012 Dec 28. PubMed PMID: 23271563; PubMed Central PMCID: PMC3763957.
  1. Martin CJ, Booty MG, Rosebrock TR, Nunes-Alves C, Desjardins DM, Keren I, Fortune SM, Remold HG, Behar SM. Efferocytosis is an innate antibacterial mechanism. Cell Host Microbe. 2012 Sep 13;12(3):289-300. doi: 10.1016/j.chom.2012.06.010. PubMed PMID: 22980326; PubMed Central PMCID: PMC3517204.
  1. Lee HJ, Lang PT, Fortune SM, Sassetti CM, Alber T. Cyclic AMP regulation of protein lysine acetylation in Mycobacterium tuberculosis. Nat Struct Mol Biol. 2012 Aug;19(8):811-8. doi: 10.1038/nsmb.2318. Epub 2012 Jul 8. PubMed PMID: 22773105; PubMed Central PMCID: PMC3414669.
  1. Wirth SE, Krywy JA, Aldridge BB, Fortune SM, Fernandez-Suarez M, Gray TA, Derbyshire KM. Polar assembly and scaffolding proteins of the virulence-associated ESX-1 secretory apparatus in mycobacteria. Mol Microbiol. 2012 Feb;83(3):654-64. doi: 10.1111/j.1365-2958.2011.07958.x. Epub 2012 Jan 11. PubMed PMID: 22233444; PubMed Central PMCID: PMC3277861.
  1. Aldridge BB, Fernandez-Suarez M, Heller D, Ambravaneswaran V, Irimia D, Toner M, Fortune SM. Asymmetry and aging of mycobacterial cells lead to variable growth and antibiotic susceptibility. Science. 2012 Jan 6;335(6064):100-4. doi: 10.1126/science.1216166. Epub 2011 Dec 15. PubMed PMID: 22174129; PubMed Central PMCID: PMC3397429.
  1. Liong M, Fernandez-Suarez M, Issadore D, Min C, Tassa C, Reiner T, Fortune SM, Toner M, Lee H, Weissleder R. Specific pathogen detection using bioorthogonal chemistry and diagnostic magnetic resonance. Bioconjug Chem. 2011 Dec 21;22(12):2390-4. doi: 10.1021/bc200490r. Epub 2011 Nov 7. PubMed PMID: 22043803; PubMed Central PMCID: PMC3263317.
  1. Sille FC, Martin C, Jayaraman P, Rothchild A, Fortune S, Besra GS, Behar SM, Boes M. Requirement for Invariant chain in macrophages for Mycobacterium tuberculosis replication and CD1d antigen presentation. Infect Immun. 2011. 2011 Aug;79(8):3053-63. Epub 2011 May 16. PMCID: PMC3147586.
  1. Ford CB, Lin PL, Chase MR, Shah RR, Iartchouk O, Galagan J, Mohaideen N, Ioerger TR, Sacchettini JC, Lipsitch M, Flynn JL, Fortune SM. Use of whole genome sequencing to estimate the mutation rate of Mycobacterium tuberculosis during latent infection. Nat Genet. 2011 May;43(5):482-6. doi: 10.1038/ng.811. Epub 2011 Apr 24. PubMed PMID: 21516081; PubMed Central PMCID: PMC3101871.
  1. Millington KA, Fortune SM, Low J, Garces A, Hingley-Wilson SM, Wickremasinghe M, Kon OM, Lalvani A. Rv3615c is a highly immunodominant RD1 (Region of Difference 1)-dependent secreted antigen specific for Mycobacterium tuberculosis infection. Proc Natl Acad Sci U S A. 2011 Apr 5;108(14):5730-5. doi: 10.1073/pnas.1015153108. Epub 2011 Mar 22. PubMed PMID: 21427227; PubMed Central PMCID: PMC3078386.
  1. Woodworth JS, Shin D, Volman M, Nunes-Alves C, Fortune SM, Behar SM. Mycobacterium tuberculosis directs immunofocusing of CD8+ T cell responses despite vaccination. J Immunol. 2011 Feb 1;186(3):1627-37. doi: 10.4049/jimmunol.1002911. Epub 2010 Dec 22. PubMed PMID: 21178003; PubMed Central PMCID: PMC3133636.
  1. Garces A, Atmakuri K, Chase MR, Woodworth JS, Krastins B, Rothchild AC, Ramsdell TL, Lopez MF, Behar SM, Sarracino DA, Fortune SM. EspA acts as a critical mediator of ESX1-dependent virulence in Mycobacterium tuberculosis by affecting bacterial cell wall integrity. PLoS Pathog. 2010 Jun 24;6(6):e1000957. doi: 10.1371/journal.ppat.1000957. PubMed PMID: 20585630; PubMed Central PMCID: PMC2891827.
  1. Siegrist MS, Unnikrishnan M, McConnell MJ, Borowsky M, Cheng TY, Siddiqi N, Fortune SM, Moody DB, Rubin EJ. Mycobacterial Esx-3 is required for mycobactin-mediated iron acquisition. Proc Natl Acad Sci U S A. 2009 Nov 3;106(44):18792-7. doi: 10.1073/pnas.0900589106. Epub 2009 Oct 21. PubMed PMID: 19846780; PubMed Central PMCID: PMC2774023.
  1. Divangahi M, Chen M, Gan H, Desjardins D, Hickman TT, Lee DM, Fortune S, Behar SM, Remold HG. Mycobacterium tuberculosis evades macrophage defenses by inhibiting plasma membrane repair. Nature Immunology. 2009 Aug 10; (8):899-906. PMCID: PMC2730354.
  1. Pandey AK, Yang Y, Jiang Z, Fortune SM, Coulombe F, Behr MA, Fitzgerald KA, Sassetti CM, Kelliher MA. NOD2, RIP2 and IRF5 play a critical role in the type I interferon response to Mycobacterium tuberculosis. PLoS Pathog. 2009 Jul;5(7):e1000500. doi: 10.1371/journal.ppat.1000500. Epub 2009 Jul 3. PubMed PMID: 19578435; PubMed Central PMCID: PMC2698121.
  1. Woodworth JS, Fortune SM, Behar SM. Bacterial protein secretion is required for priming of CD8+ T cells specific for the Mycobacterium tuberculosis antigen CFP10. Infect Immun. 2008 Sep;76(9):4199-205. doi: 10.1128/IAI.00307-08. Epub 2008 Jun 30. PubMed PMID: 18591224; PubMed Central PMCID: PMC2519428.
  1. Hett EC, Chao MC, Steyn AJ, Fortune SM, Deng LL, Rubin EJ. A partner for the resuscitation-promoting factors of Mycobacterium tuberculosis. Mol Microbiol. 2007 Nov;66(3):658-68. Epub 2007 Oct 4. PubMed PMID: 17919286.
  1. Joshi SM, Pandey AK, Capite N, Fortune SM, Rubin EJ, Sassetti CM. Characterization of mycobacterial virulence genes through genetic interaction mapping. Proc Natl Acad Sci U S A. 2006 Aug 1;103(31):11760-5. Epub 2006 Jul 25. PubMed PMID: 16868085; PubMed Central PMCID: PMC1544243.
  1. Fortune SM, Jaeger A, Sarracino DA, Chase MR, Sassetti CM, Sherman DR, Bloom BR, Rubin EJ. Mutually dependent secretion of proteins required for mycobacterial virulence. Proc Natl Acad Sci U S A. 2005 Jul 26;102(30):10676-81. Epub 2005 Jul 19. PubMed PMID: 16030141; PubMed Central PMCID: PMC1176248.
  1. Fortune SM, Solache A, Jaeger A, Hill PJ, Belisle JT, Bloom BR, Rubin EJ, Ernst JD. Mycobacterium tuberculosis inhibits macrophage responses to IFN-gamma through myeloid differentiation factor 88-dependent and -independent mechanisms. J Immunol. 2004 May 15;172(10):6272-80. PubMed PMID: 15128816.
  1. Wain J, Diem Nga LT, Kidgell C, James K, Fortune S, Song Diep T, Ali T, O Gaora P, Parry C, Parkhill J, Farrar J, White NJ, and Dougan G.   Molecular analysis of incHI1 antimicrobial resistance plasmids from Salmonella serovar Typhi strains associated with typhoid fever. Antimicrob Agents Chemother. 2003 Sep;47(9):2732-9. PMCID: PMC182646.
  1. Fortune SM, Kaelin CM, Gulizia JM, Daily JP. Cat scratch disease presenting as a breast mass. Obstet Gynecol. 2000 Jun;95(6 Pt 2):1027. PubMed PMID: 10808015.
  1. Cleary AM, Fortune SM, Yellin MJ, Chess L, Lederman S. Opposing roles of CD95(Fas/APO-1) and CD40 in the death and rescue of human low density tonsillar B cells. J Immunol. 1995 Oct 1;155(7):3329-37. PubMed PMID: 7561026.
  1. Yellin MJ, Winikoff S, Fortune SM, Baum D, Crow MK, Lederman S, Chess L. Ligation of CD40 on fibroblasts induces CD54 (ICAM-1) and CD106 (VCAM-1) up-regulation and IL-6 production and proliferation. J Leukoc Biol. 1995 Aug;58(2):209-16. PubMed PMID: 7543921.
  1. Kester JC, Fortune SM. Persisters and beyond: mechanisms of phenotypic drug resistance and drug tolerance in bacteria. Crit Rev Biochem Mol Biol. 2014 Mar-Apr;49(2):91-101. doi: 10.3109/10409238.2013.869543. Epub 2013 Dec 13. PubMed PMID: 24328927.
  1. Fortune SM. The surprising diversity of Mycobacterium tuberculosis: change you can believe in. J Infect Dis. 2012 Dec 1;206(11):1642-4. doi: 10.1093/infdis/jis603. Epub 2012 Sep 14. PubMed PMID: 22984117.
  1. Fortune SM, Rubin EJ. Host transcription in active and latent tuberculosis. Genome Biol. 2010;11(9):135. doi: 10.1186/gb-2010-11-9-135. Epub 2010 Sep 28. PubMed PMID: 20920149; PubMed Central PMCID: PMC2965379.
  1. Bitter W, Houben EN, Bottai D, Brodin P, Brown EJ, Cox JS, Derbyshire K, Fortune SM, Gao LY, Liu J, Gey van Pittius NC, Pym AS, Rubin EJ, Sherman DR, Cole ST, Brosch R. Systematic genetic nomenclature for type VII secretion systems PLoS Pathog. 2009 Oct;5(10):e1000507. doi: 10.1371/journal.ppat.1000507. Epub 2009 Oct 30. PubMed PMID: 19876390; PubMed Central PMCID: PMC2763215.
  1. Atmakuri K, Fortune SM. Regulation of protein secretion by … protein secretion? Cell Host Microbe. 2008 Sep 11;4(3):190-1. doi 10.1016/j.chom.2008.08.009. PubMed PMID: 18779042.
  1. Fortune SM, Rubin EJ. The complex relationship between mycobacteria and macrophages: it’s not all bliss. Cell Host Microbe. 2007 Jul 12;2(1):5-6. PubMed PMID: 18005712.
  1. Fortune SM, Chase MR, Rubin EJ. Dividing oceans into pools: strategies for the global analysis of bacterial genes. Microbes Infect. 2006 May;8(6):1631-6. Epub 2006 Jan 25. Review. PubMed PMID: 16697239.
  1. Lederman S, Yellin MJ, Cleary AM, Fortune SM, Chess L. The understanding of contact-dependent T-cell helper function in molecular, cellular and physiological detail. Res Immunol. 1994 Mar-Apr;145(3):215-21; discussion 244-9. Review. PubMed PMID: 7527578
  1. Shell SS, Wang J, Mir M, Chase MR, DeJesus MA, Ioerger TR, Ahmad R, Derbyshire K, Fortune SM, Wade JT, Gray TA. Noncanonical translation inititation is widespread and conserved in mycobacteria. Plos Genetics, in revision.
  1. Shell SS, Chase MR, Gray TA, Wade JT, Navjot S, DeJesus M, Sacchettini JC, Ioerger TR, Fortune SM. mRNA processing shapes mycobacterial transcriptomes and stabilizes the esxB-esxA virulence factor transcript. Genome Biology, in revision.