2017 Nature TB mini-collection

An editor-suggested 'further reading' list of diverse TB articles published in the last year across the Nature journals.

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Mar 24, 2017
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The theme of this year’s World TB Day is ‘Unite to End TB’. Part of advocating for greater attention to TB is celebrating the scientific advances we have made in understanding Mycobacterium tuberculosis infection biology and the new avenues we have opened up for eradicating the disease. Supporting this message, we have assembled a ‘Further Reading’ list highlighting such pioneering research from across the Nature journals within the last year or so:

A. The Background:

For those unfamiliar with TB (or even TB researchers who are focused on a specific line of investigation), reviews are a great way to approach and interpret the complexity of the bacterium and its interaction with the host.

  • Since ESX-1 was identified as a major virulence locus (its deletion largely accounts for the attenuation of the BCG vaccine), the five Type VII ESX secretion systems have been a major area of interest for those hoping to understand how M. tuberculosis communicates with and subverts the host. Last year, Brosch and colleagues published a review in Nature Reviews Microbiology on the function of these secretion systems and their roles in infection.


B. TB pathogenesis and host response:

M. tuberculosis has evolved alongside the immune system. Understanding the molecular bases of the interactions between the bacterium and host is a prerequisite for unraveling the complicated crosstalk involved in causing persistent infection.

1. Avoiding autophagy: work from Stallings and colleagues in 2015 in Nature found that xenophagy (degradation of pathogens through autophagy pathways) surprisingly did not appear to mediate TB control (in contrast to other intracellular pathogens). That, then logically left us with the major question of how TB avoids this innate immune defense.

  • In Nature Microbiology, Porcelli and colleagues investigated the bacterial side of the equation and identified a gene, rv2741 (encoding PE_PGRS47), that was required to inhibit autophagy in macrophages and reduce MHC-II antigen presentation. This gene was also required for full virulence in mice at late stages of infection.
  • On the host side, Phillips, Moore and colleagues in Nature Immunology showed that TB induced the miR-33 pathway to inhibit autophagy and support bacterial replication. Silencing the pathway enhanced xenophagy and TB clearance in mice, representing a potential avenue for host-directed therapy.

2. Inhibiting immune responses: natural TB infection generally does not elicit effective long-term immunity. Understanding the reason for this reduced immunogenicity will aid in the design of a long sought-after efficacious vaccine.

    • In their Nature Microbiology paper, Jacobs, Philips and colleagues demonstrated that the ESX-3 secretion substrate EsxH inhibits ESCRT trafficking, leading to decreased TB antigen presentation in phagocytes and enhanced bacterial replication in mice.
    • Sintim, Bishai and colleagues in Nature Chemical Biology define a cyclic dinucleotide-based axis of immune activation. While infection releases both bacterial c-di-AMP and induces host production of cGAMP, TB encodes a phosphodiesterase CdnP to hydrolyse these signals and block inflammatory cytokine induction. Disruption of cdnP leads to bacterial attenuation and enhanced mouse survival during infection.


    C. Human TB infection:

    Animal models of TB vary in their ability to reproduce the spectrum of pathology and disease progression seen in human infections. Thus, it remains critical to understand the host response in natural human infections and define clinical parameters that can affect patient cure and relapse rates.

    • In their Nature Medicine study, Cohen, Kishony and colleagues investigate TB disease progression in HIV-positive individuals, a group particularly susceptible to symptomatic disease and death. From autopsy samples, they observed that multiple lineages evolved in parallel and persisted for years in patients, with evidence of equal dissemination rates between lung regions and to extrapulmonary sites.

    • While the above work captured TB diversity within individuals, the M. tuberculosis species comprises of distinct lineages with varying geographical ranges. Gagneux and colleagues in Nature Genetics carried out phylogenetic reconstruction of diverse TB strains, which suggested that the global Lineage 4 originated in Europe and disseminated via human migration. Analysis of immune epitopes in these global strains showed more diversity compared to more geographically restricted lineages, suggesting these changes may be driven by adaptation to different immune pressures across diverse human populations.

    • Esmail, Wilkinson and colleagues in Nature Medicine, describe how FDG positron emission coupled with computed tomography (PET-CT) can identify individuals with pulmonary changes reminiscent of active disease despite being clinically consistent with latent infection. These individuals had greater likelihood of disease progression, challenging the binary view of active vs. latent disease as a discriminatory clinical diagnosis.
    • Malherbe and colleagues in Nature Medicine also used PET-CT to assess lung inflammation during and after curative antibiotic treatment. They found that only a minority of individuals had inert lesions despite clinical cure. Some of these individuals also had detectable M. tuberculosis mRNA in sputum or bronchial alveolar lavage samples, suggesting clinical cure may not necessarily mean microbial sterilization and that ongoing immunological control even after treatment is likely a key factor in preventing relapse.
    • But how do these host-pathogen forces molecularly play out in human infections? In Nature Medicine, Dartois, Rubin and colleagues utilized proteomics to create a spatial map of immune responses in human TB granulomas. This map showed a physical segregation of pro- and anti-inflammatory signals—while central necrotic regions were rich with antimicrobial peptides, reactive oxygen species and pro-inflammatory cytokines, an anti-inflammatory signature was seen in the peripheral regions. This immunological split was reproduced in the rabbit infection model, suggesting that spatial effects are a common lens through which net TB immune responses can be interpreted in the future.


    D. Resistance:

    With around half a million multidrug resistant TB infections in 2015, antibiotic resistance is a threat to the clinical efficacy of our first line antibiotics. Greater surveillance and characterization of resistance mutations have provided a broader view of global drug resistance emergence and has enabled better prediction of clinical resistance from genome sequences.

    • In a Nature Genetics article, Earl and colleagues analyzed 5,310 TB genome sequences and showed that regardless of geography, similar drug resistance mutations were globally observed. In particular, a katG S315T mutation arose before rifampicin resistance mutations in diverse regions, suggesting this represents a common route for multidrug resistance emergence and offers new markers for better assessing likelihoods of MDR-TB evolution.
    • Javid and colleagues in Nature Microbiology found that clinically relevant mutations in the glutamine amidotransferase subunit GatA leads to increased mistranslation rates and enhanced phenotypic rifampicin tolerance.
    • Iqbal and colleagues in Nature Communications analysed whole genome sequences to create de Bruijn representations of known resistance alleles. This approach allowed them to produce resistance reports for clinicians with good sensitivity and specificity when compared with gold standard clinical resistance testing.


    E. Drug development:

    After decades of quiescence, several new anti-TB compounds have been licensed, including Bedaquiline in 2012 and Delamanid in 2014 (which is specifically geared towards treating multidrug resistant TB). Work still remains on improving our understanding of how promising pre-clinical candidates can kill TB, developing new compounds with improved potency and identifying synergistic combinations of existing drugs to shorten treatment times.

    • Futterer, Ballell, Besra and colleagues in Nature Microbiology showed that the anti-tubercular compound tetrahydropyrazo[1,5-a]pyrimidine-3-carboxamide (THPP) inhibits EchA6 to block mycolic acid synthesis. This is in contrast to previously observed resistance mutations in MmpL3, suggesting MmpL3 may act as a drug importer for this compound instead.

    • Baliga and colleagues in Nature Microbiology found that bedaquiline treatment induced a transcriptional response associated with drug tolerance and required two transcription factors, Rv0324 and Rv0880. Systems analysis of expression data showed that pretonamid induced similar changes to the deletion of Rv0880, and thus was able to synergize with bedaquiline.

    • In Nature Chemical Biology, Lamichhane and colleagues found that carbapenem antibiotics can target the 3->3 L,D peptidoglycan transpeptidases in addition to the canonical 4->3 D,D transpeptidases. Using structural modeling, they developed new carbapenems that had improved L,D transpeptidase inhibition, which increased their potency against TB (as well as against other major human pathogens).

    • In their Nature Communications work, Horwitz and colleagues used a computational approach to screen billions of potential drug interactions to identify combinations with better killing kinetics. They found several regimens that offered up to 75% faster TB clearance in mice compared to current gold-standard treatment.


    F. Tools:

    In trying to unravel the complexity of TB infection, researchers have had to develop new tools with better resolution and greater functionality. Further methodological innovation will certainly be required to dig even deeper and answer ever more difficult questions.

    • From bacteria to eukaryotes and back again, CRISPR-Cas tools are now being used for genome engineering in TB. Fortune and colleagues in Nature Microbiology identified a Streptococcus thermophilus Cas9 variant that offered a programmable CRISPRi system for M. tuberculosis with improved transcriptional knockdown over other methods.

    • Love, Shalek and colleagues in Nature Methods advanced single cell RNA-seq by developing a low-cost platform that integrates mRNA capture and barcoding and reduces cross contamination, while being portable enough for isolation of TB infected cells in a BSL3 facility. RNA-seq analysis of TB infected cells showed 3 distinct macrophages expression profiles suggesting TB infection is heterogeneous.

    • While not specific to TB, in Nature Reviews Genetics, Power, Parkhill and de Oliveira review methods for conducting microbial genome-wide association studies to define genetic markers associated with disease and resistance. Also, see work in Nature Microbiology from Wilson and colleagues on how to control for lineage affects that can bias microbial GWAS studies. And also a News and Views on this work from Falush.


    References:

    1. Madhukar Pai, Marcel A. Behr, David Dowdy, Keertan Dheda, Maziar Divangahi, Catharina C. Boehme, Ann Ginsberg, Soumya Swaminathan, Melvin Spigelman, Haileyesus Getahun, Dick Menzies & Mario Raviglione. Tuberculosis. Nature Reviews Disease Primers 2:16076 (2016).

    2. Barbara E. Laughon & Carol A. Nacy. Tuberculosis — drugs in the 2016 development pipeline. Nature Reviews Disease Primers 3, 17015 (2017).

    3. Matthias I. Gröschel, Fadel Sayes, Roxane Simeone, Laleh Majlessi & Roland Brosch. ESX secretion systems: mycobacterial evolution to counter host immunity. Nature Reviews Microbiology14:677-691. (2016).

    4. Jacqueline M. Kimmey, Jeremy P. Huynh, Leslie A. Weiss, Sunmin Park, Amal Kambal, Jayanta Debnath, Herbert W. Virgin & Christina L. Stallings. Unique role for ATG5 in neutrophil-mediated immunopathology during M. tuberculosis infection, Nature 528, 565–569 (2015).

    5. Neeraj K. Saini, Andres Baena, Tony W. Ng, Manjunatha M. Venkataswamy, Steven C. Kennedy, Shajo Kunnath-Velayudhan, Leandro J. Carreño, Jiayong Xu, John Chan, Michelle H. Larsen, William R. Jacobs Jr & Steven A. Porcelli, Suppression of autophagy and antigen presentation by Mycobacterium tuberculosis PE_PGRS47. Nature Microbiology 1: 16133 (2016).

    6. Mireille Ouimet, Stefan Koster, Erik Sakowski, Bhama Ramkhelawon, Coen van Solingen, Scott Oldebeken, Denuja Karunakaran, Cynthia Portal-Celhay, Frederick J Sheedy, Tathagat Dutta Ray, Katharine Cecchini, Philip D Zamore, Katey J Rayner, Yves L Marcel, Jennifer A Philips & Kathryn J Moore. Mycobacterium tuberculosis induces the miR-33 locus to reprogram autophagy and host lipid metabolism. Nature Immunology 17:677-86 (2016).

    7. Cynthia Portal-Celhay, JoAnn M. Tufariello, Smita Srivastava, Aleena Zahra, Thais Klevorn, Patricia S. Grace, Alka Mehra, Heidi S. Park, Joel D. Ernst, William R. Jacobs Jr & Jennifer A. Philips. Mycobacterium tuberculosis EsxH inhibits ESCRT-dependent CD4+ T-cell activation, Nature Microbiology 2: 16232 (2016).

    8. Ruchi Jain Dey, Bappaditya Dey, Yue Zheng, Laurene S Cheung, Jie Zhou, David Sayre, Pankaj Kumar, Haidan Guo, Gyanu Lamichhane, Herman O Sintim & William R Bishai. Inhibition of innate immune cytosolic surveillance by an M. tuberculosis phosphodiesterase. Nature Chemical Biology 13, 210–217 (2017).

    9. Tami D Lieberman, Douglas Wilson, Reshma Misra, Lealia L Xiong, Prashini Moodley, Ted Cohen & Roy Kishony. Genomic diversity in autopsy samples reveals within-host dissemination of HIV-associated Mycobacterium tuberculosis. Nature Medicine 22:1470-1474 (2016).

    10. Stucki D1,2, Brites D1,2, Jeljeli L3,4, Coscolla M1,2, Liu Q5, Trauner A1,2, Fenner L1,2,6, Rutaihwa L1,2, Borrell S1,2, Luo T7, Gao Q5, Kato-Maeda M8, Ballif M1,2,6, Egger M6, Macedo R9, Mardassi H4, Moreno M10, Vilanova GT11, Fyfe J12, Globan M12, Thomas J13, Jamieson F14, Guthrie JL14, Asante-Poku A15, Yeboah-Manu D15, Wampande E16, Ssengooba W16,17, Joloba M16, Boom WH18, Basu I19, Bower J19, Saraiva M20,21, Vasconcellos SE22, Suffys P22, Koch A23, Wilkinson R23,24,25, Gail-Bekker L23, Malla B1,2, Ley SD1,2,26, Beck HP1,2, de Jong BC27, Toit K28, Sanchez-Padilla E29, Bonnet M29, Gil-Brusola A30, Frank M31, Penlap Beng VN32, Eisenach K33, Alani I34, Ndung'u PW35, Revathi G36, Gehre F27,37, Akter S27, Ntoumi F31,38, Stewart-Isherwood L39, Ntinginya NE40, Rachow A41, Hoelscher M41, Cirillo DM42, Skenders G43, Hoffner S44, Bakonyte D45, Stakenas P45, Diel R46, Crudu V47, Moldovan O48, Al-Hajoj S49, Otero L50, Barletta F50, Carter EJ51,52, Diero L52, Supply P53, Comas I54,55, Niemann S3,56, Gagneux S1,2. Mycobacterium tuberculosis lineage 4 comprises globally distributed and geographically restricted sublineages. Nature Genetics 48:1535-1543 (2016).

    11. Hanif Esmail, Rachel P Lai, Maia Lesosky, Katalin A Wilkinson, Christine M Graham, Anna K Coussens, Tolu Oni, James M Warwick, Qonita Said-Hartley, Coenraad F Koegelenberg, Gerhard Walzl, JoAnne L Flynn, Douglas B Young, Clifton E Barry III, Anne O'Garra & Robert J Wilkinson. Characterization of progressive HIV-associated tuberculosis using 2-deoxy-2-[18F]fluoro-D-glucose positron emission and computed tomography. Nature Medicine 22:1090-1093 (2016).

    12. Stephanus T Malherbe, Shubhada Shenai, Katharina Ronacher, Andre G Loxton, Gregory Dolganov, Magdalena Kriel, Tran Van, Ray Y Chen, James Warwick, Laura E Via, Taeksun Song, Myungsun Lee, Gary Schoolnik, Gerard Tromp, David Alland, Clifton E Barry III, Jill Winter, Gerhard Walzl, the Catalysis TB–Biomarker Consortium, Lance Lucas, Gian van der Spuy, Kim Stanley, Lani Theart, Bronwyn Smith, Nelita Du Plessis, Caroline G G Beltran, Elizna Maasdorp, Annare Ellmann, Hongjo Choi, Joonsung Joh, Lori E Dodd, Brian Allwood, Coenie Kogelenberg, Morné Vorster & Stephanie Griffith-Richards. Persisting positron emission tomography lesion activity and Mycobacterium tuberculosis mRNA after tuberculosis cure. Nature Medicine 22:1094-1100 (2016).

    13. Mohlopheni J Marakalala, Ravikiran M Raju, Kirti Sharma, Yanjia J Zhang, Eliseo A Eugenin, Brendan Prideaux, Isaac B Daudelin, Pei-Yu Chen, Matthew G Booty, Jin Hee Kim, Seok Yong Eum, Laura E Via, Samuel M Behar, Clifton E Barry III, Matthias Mann, Véronique Dartois & Eric J Rubin. Inflammatory signaling in human tuberculosis granulomas is spatially organized. Nature Medicine 22:531-8 (2016).

    14. Abigail L Manson, Keira A Cohen, Thomas Abeel, Christopher A Desjardins, Derek T Armstrong, Clifton E Barry III, Jeannette Brand, TBResist Global Genome Consortium, Sinéad B Chapman, Sang-Nae Cho, Andrei Gabrielian, James Gomez, Andreea M Jodals, Moses Joloba, Pontus Jureen, Jong Seok Lee, Lesibana Malinga, Mamoudou Maiga, Dale Nordenberg, Ecaterina Noroc, Elena Romancenco, Alex Salazar, Willy Ssengooba, A A Velayati, Kathryn Winglee, Aksana Zalutskaya, Laura E Via, Gail H Cassell, Susan E Dorman, Jerrold Ellner, Parissa Farnia, James E Galagan, Alex Rosenthal, Valeriu Crudu, Daniela Homorodean, Po-Ren Hsueh, Sujatha Narayanan, Alexander S Pym, Alena Skrahina, Soumya Swaminathan, Martie Van der Walt, David Alland, William R Bishai, Ted Cohen, Sven Hoffner, Bruce W Birren & Ashlee M Earl. Genomic analysis of globally diverse Mycobacterium tuberculosis strains provides insights into the emergence and spread of multidrug resistance.Nature Genetics 49:395-402 (2017).

    15. Hong-Wei Su, Jun-Hao Zhu, Hao Li, Rong-Jun Cai, Christopher Ealand, Xun Wang, Yu-Xiang Chen, Masood ur Rehman Kayani, Ting F. Zhu, Danesh Moradigaravand, Hairong Huang, Bavesh D. Kana & Babak Javid. The essential mycobacterial amidotransferase GatCAB is a modulator of specific translational fidelity. Nature Microbiology 1: 16147 (2016).

    16. Phelim Bradley, N. Claire Gordon, Timothy M. Walker, Laura Dunn, Simon Heys, Bill Huang, Sarah Earle, Louise J. Pankhurst, Luke Anson, Mariateresa de Cesare, Paolo Piazza, Antonina A. Votintseva, Tanya Golubchik, Daniel J. Wilson, David H. Wyllie, Roland Diel, Stefan Niemann, Silke Feuerriegel, Thomas A. Kohl, Nazir Ismail, Shaheed V. Omar, E. Grace Smith, David Buck, Gil McVean, A. Sarah Walker, Tim E. A. Peto, Derrick W. Crook & Zamin Iqbal. Rapid antibiotic-resistance predictions from genome sequence data for Staphylococcus aureus and Mycobacterium tuberculosis. Nature Communications 6:10063 (2015).

    17. Jonathan A. G. Cox, Katherine A. Abrahams, Carlos Alemparte, Sonja Ghidelli-Disse, Joaquín Rullas, Iñigo Angulo-Barturen, Albel Singh, Sudagar S. Gurcha, Vijayashankar Nataraj, Stephen Bethell, Modesto J. Remuiñán, Lourdes Encinas, Peter J. Jervis, Nicholas C. Cammack, Apoorva Bhatt, Ulrich Kruse, Marcus Bantscheff, Klaus Fütterer, David Barros, Lluis Ballell, Gerard Drewes & Gurdyal S. Besra. THPP target assignment reveals EchA6 as an essential fatty acid shuttle in mycobacteria. Nature Microbiology 1: 15006 (2016).

    18. Eliza J. R. Peterson, Shuyi Ma, David R. Sherman & Nitin S. Baliga. Network analysis identifies Rv0324 and Rv0880 as regulators of bedaquiline tolerance in Mycobacterium tuberculosis. Nature Microbiology 1: 16078 (2016)

    19. Kumar P1, Kaushik A1, Lloyd EP2, Li SG3, Mattoo R1, Ammerman NC1, Bell DT1, Perryman AL3, Zandi TA4, Ekins S5, Ginell SL6, Townsend CA2, Freundlich JS3, Lamichhane G1. Non-classical transpeptidases yield insight into new antibacterials. Nature Chemical Biology 13:54-61 (2017).

    20. Bai-Yu Lee, Daniel L. Clemens, Aleidy Silva, Barbara Jane Dillon, Saša Masleša-Galić, Susana Nava, Xianting Ding, Chih-Ming Ho & Marcus A. Horwitz. Drug regimens identified and optimized by output-driven platform markedly reduce tuberculosis treatment time. Nature Communications 8:14183 (2017).

    21. Jeremy M. Rock, Forrest F. Hopkins, Alejandro Chavez, Marieme Diallo, Michael R. Chase, Elias R. Gerrick, Justin R. Pritchard, George M. Church, Eric J. Rubin, Christopher M. Sassetti, Dirk Schnappinger & Sarah M. Fortune. Programmable transcriptional repression in mycobacteria using an orthogonal CRISPR interference platform. Nature Microbiology 2: 16274 (2017).

    22. Todd M Gierahn, Marc H Wadsworth II, Travis K Hughes, Bryan D Bryson, Andrew Butler, Rahul Satija, Sarah Fortune, J Christopher Love & Alex K Shalek. Seq-Well: portable, low-cost RNA sequencing of single cells at high throughput. Nature Methods. doi: 10.1038/nmeth.4179 (2017). [Epub ahead of print]

    23. Robert A. Power, Julian Parkhill & Tulio de Oliveira. Microbial genome-wide association studies: lessons from human GWAS. Nature Reviews Genetics 18: 41–50 (2017).

    24. Sarah G. Earle, Chieh-Hsi Wu, Jane Charlesworth, Nicole Stoesser, N. Claire Gordon, Timothy M. Walker, Chris C. A. Spencer, Zamin Iqbal, David A. Clifton, Katie L. Hopkins, Neil Woodford, E. Grace Smith, Nazir Ismail, Martin J. Llewelyn, Tim E. Peto, Derrick W. Crook, Gil McVean, A. Sarah Walker & Daniel J. Wilson. Identifying lineage effects when controlling for population structure improves power in bacterial association studies. Nature Microbiology 1, Article number: 16041 (2016).

    25. Daniel Falush. Bacterial genomics: Microbial GWAS coming of age. Nature Microbiology 1: 16059 (2016).

    Go to the profile of Michael Chao

    Michael Chao

    Associate Editor, Nature Microbiology

    I first developed an interest in bacterial pathogenesis while at Cornell University. I then earned my PhD in Biomedical and Biological Sciences from Harvard University in Eric Rubin’s laboratory, studying cell wall remodelling in Mycobacterium tuberculosis. From 2012-2015, I continued my training as a postdoctoral fellow in Matthew Waldor’s lab at Harvard Medical School, investigating the role of DNA methylation on regulating fundamental cellular processes in Vibrio cholerae.

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