About Dr. Kyle Rohde
Studies (i) Pathogenesis and gene regulation in Mycobacterium tuberculosis and M. abscessus (ii) Antibiotic drug discovery targeting Mycobacteria (iii)Mechanisms of drug resistance in pathogenic Mycobacteria (iv) Diagnostic tools for detection of drug resistant TB
Tuberculosis (TB), caused by the bacterium Mycobacterium tuberculosis (Mtb), infects ~9 million new people and claims ~1.5 million lives each year. This ongoing global health crisis stems from the lack of an effective vaccine, inadequate diagnostics and drug regimens, emergence of multi-drug resistant strains, and synergism with HIV infection. Thus, there is an urgent need to better understand how Mtb causes disease in order to develop reliable diagnostics, protective vaccines, and fast-acting drugs effective against Mtb.
An important key to the success of Mtb as an intracellular pathogen is the ability to survive inside macrophages which are capable of killing most bacteria. Mtb is able to prevent trafficking to acidic, degradative lysosomes and adapt its metabolism and physiology to survive inside a specialized compartment. Long-term growth in this niche requires that Mtb regulate gene expression in response to cues and stresses encountered within macrophages. Another defining feature of TB disease is the development of latent infections in which asymptomatic patients harbor dormant Mtb bacteria for years which can reactivate upon suppression of the immune system.
My lab is exploiting several approaches to address to root causes of the TB health crisis.
1) Mtb genetics and Host Interactions: How does TB survive inside hostile macrophages? What genes are required for Mtb to grow and cause disease? How does Mtb regulate its genes in response to host-derived stresses? Do different strains of Mtb use different strategies to be successful? Answers to these questions will help to identify vulnerable targets for new drugs.
- A) Transcriptional adaptation of Mtb required for survival in macrophages. We developed a novel RNA amplification and microarray methodology to monitor mycobacterial global gene expression within macrophages. This allowed high-resolution temporal profiling of Mtb genes actively modulated during macrophage invasion in response to host-derived cues/stressors. For example, we found that acidification of the Mtb vacuole is a major trigger of the early transcriptional responses. Future studies will characterize specific regulatory pathways involved in Mtb intracellular survival and stress responses relevant during human infections. Gene products and pathways that are essential for adaptation within the host represent potential new drug targets.
- B) Functional Evolution of Mtb Transcriptional Regulatory Networks. This project is exploring the impact of genomic diversity among clinical isolates on Mtb pathogenesis, specifically intracellular survival and gene expression. Thus far, studies of Mtb have mainly focused on a few lab strains, despite evidence of important genetic and phenotypic differences among clinical isolates. By extending our microarray studies to a panel of 17 phylogenetically diverse clinical isolates, we found that the genetic diversity of clinical isolates has a significant impact on global gene expression, affecting basal transcript levels in vitro and responses to intracellular cues encountered during macrophage invasion. Coupled with the distinct abilities of strains to survive inside macrophages, these observations suggest that dysregulation of gene expression is a powerful potential mechanism by which genomic diversity could influence Mtb-host interactions. Future work will focus initially on selected virulence regulators with strain-dependent expression patterns to begin to identify the underlying mechanisms and significance of lineage-specific gene regulation. We are collaborating with Dr. Stefan Niemann of the National Reference Center for Mycobacteria in Borstel, Germany.
2) Point-of-care diagnostics: We are developing DNA-based molecular diagnostics, called binary deoxyribozyme sensors, designed to allow fast, cheap, and accurate detection of Mtb in sputum samples in point-of-care settings. These tools will also permit detection of drug-resistant strains of Mtb to guide the rational design of drug therapy regimens. This project is in collaboration with Dr. Dmitry Kolpashchikov (UCF, Department of Chemistry).
3) TB Drug Discovery: Our aim is to discover novel chemical compounds capable of killing Mtb under conditions that mimic the in vivo environment during infection. Our current screening of a library of thousands of marine natural products against “glow in the dark” Mtb we engineered to be fluorescent has already revealed several promising “hit” compounds. Additional studies will hopefully uncover many more so-called lead compounds that may help effectively treat TB. This NIH-funded project is a collaboration with Dr. Amy Wright of Harbor Branch Oceanographic Institute and Dr. Pappachan Kolattukudy of the Burnett School of Biomedical Sciences, UCF.
By taking a multifaceted approach to improve our understanding of this disease and add to our arsenal of tools aimed at this pathogen, we hope to make a significant contribution to the fight against TB.
- Ma Z, Abendroth J, Buchko GW, Rohde KH, Davidson VL. Crystal structure of a hemerythrin-like protein from Mycobacterium kansasii and homology model of the orthologous Rv2633c protein of M. tuberculosis. Biochem J. 2020 Jan 31;477(2):567-581. doi: 10.1042/BCJ20190827.
- Rodrigues Felix C, Roberts JC, Winder PL, Gupta R, Diaz MC, Pomponi SA, Wright AE, Rohde KH.Plakinamine P, A Steroidal Alkaloid with Bactericidal Activity against Mycobacterium tuberculosis. Mar Drugs. 2019 Dec 16;17(12). pii: E707. doi: 10.3390/md17120707.
- Schneider A, Wood HN, Geden S, Greene CJ, Yates RM, Masternak MM, Rohde KH. Growth hormone-mediated reprogramming of macrophage transcriptome and effector functions. Sci Rep. 2019 Dec 18;9(1):19348. doi: 10.1038/s41598-019-56017-6.
- Osterman AL, Rodionova I, Li X, Sergienko E, Ma CT, Catanzaro A, Pettigrove ME, Reed RW, Gupta R, Rohde KH, Korotkov KV, Sorci L. Novel Antimycobacterial Compounds Suppress NAD Biogenesis by Targeting a Unique Pocket of NaMN Adenylyltransferase. ACS Chem Biol. 2019 May 17;14(5):949-958. doi: 10.1021/acschembio.9b00124. Epub 2019 Apr 17.
- Wood HN, Venken T, Willems H, Jacobs A, Reis AJ, Almeida da Silva PE, Homolka S, Niemann S, Rohde KH, Hooyberghs J. Molecular drug susceptibility testing and strain typing of tuberculosis by DNA hybridization. PLoS One. 2019 Feb 7;14(2):e0212064. doi: 10.1371/journal.pone.0212064. eCollection 2019.
- Wood HN, Sidders AE, Brumsey LE, Morozkin ES, Gerasimova YV, Rohde KH. Species Typing of Nontuberculous Mycobacteria by Use of Deoxyribozyme Sensors. Clin Chem. 2019 Feb;65(2):333-341. doi: 10.1373/clinchem.2018.295212. Epub 2018 Dec 6.
- Demers DH, Knestrick MA, Fleeman R, Tawfik R, Azhari A, Souza A, Vesely B, Netherton M, Gupta R, Colon BL, Rice CA, Rodríguez-Pérez MA, Rohde KH, Kyle DE, Shaw LN, Baker BJ. Exploitation of Mangrove Endophytic Fungi for Infectious Disease Drug Discovery. Mar Drugs. 2018 Oct 10;16(10). pii: E376. doi: 10.3390/md16100376.
- Gupta R*, Rodrigues Felix C*, Akerman MP, Akerman KJ, Slabber CA, Wang W, Adams J, Shaw LN, Tse-Dinh YC, Munro OQ, Rohde KH. Evidence for Inhibition of Topoisomerase 1A by Gold(III) Macrocycles and Chelates Targeting Mycobacterium tuberculosis and Mycobacterium abscessus. Antimicrob Agents Chemother. 2018 Apr 26;62(5). pii: e01696-17. doi: 10.1128/AAC.01696-17. *equal contribution
- Ma Z, Strickland KT, Cherne MD, Sehanobish E, Rohde KH, Self WT, Davidson VL. The Rv2633c protein of Mycobacterium tuberculosis is a non-heme di-iron catalase with a possible role in defenses against oxidative stress. J Biol Chem. 2017 Dec 14 (Epub ahead of print).
- Gupta R, Netherton M, Byrd TF, Rohde KH*. Reporter-based assays for high-throughput drug screening against Mycobacterium abscessus. Frontiers in Microbiology. 2017 Nov 10:8:2204.
- Rodrigues Felix C, Gupta R, Geden S, Roberts J, Winder P, Pomponi S, Diaz M, Reed J, Wright A, and Rohde KH*. Selective Killing Of Dormant Mycobacterium tuberculosis By Marine Natural Products. Antimicrob Agents Chemotherapy. August 2017 vol. 61 no. 8 e00743-17.
- Cumming B, Rahman A, Lamprecht D, Rohde KH, Saini V, Adamson J, Russell DG, Steyn AJC. Mycobacterium tuberculosis arrests host cycle at the G1/S transition to establish long term infection. PLoS Pathogens. 2017. 13(5): e1006389. https://doi.org/10.1371/ppat.1006389.
- Bengtson HN, Homolka S, Niemann S, Reis AJ, da Silva PEA, Gerasimova YV, Kolpashchikov DM, Rohde KH*. Multiplex detection of extensively drug resistant tuberculosis using binary deoxyribozyme sensors. Biosensors and Bioelectronics. 2017 Aug 15;94:176-183. doi: 10.1016/j.bios.2017.02.051.
- Wright AE, Killday KB, Chakrabarti D, Guzmán E, Harmody D, McCarthy PJ, Pitts T, Pomponi S, Reed JK, Roberts BF, Rodrigues Felix C, Rohde KH. Dragmacidin G, a Bioactive Bis-Indole Alkaloid from a Deep-Water Sponge of the Genus Spongosorites. Marine Drugs. In press
- Rohde KH, Michaels HA, Nefzi A, 2016. Synthesis and Antitubercular Activity of 1,2,4-Trisubstituted Piperazines. Bioorganic and Medicinal Chemistry Letters. 26(9):2206-9.
- Sandhaus S, Annamalai T, Welmaker G, Houghten RA, Paz C, Garcia PK, Andres A, Narula G, Rodrigues Felix C, Geden S, Netherton M, Gupta R, Rohde KH, Giulianotti MA, Tse-Dinh YC. 2016. Small molecule inhibitors targeting topoisomerase 1 as novel antituberculosis agents. Antimicrob Agents Chemother.. Apr 25. pii: AAC.00288-16. [Epub ahead of print].
- Liu Y, Tan S, Huang L, Abramovitch R, Rohde KH, Zimmerman M, Chen C, Dartois V, VanderVen B, and Russell DG. 2016. Immune activation of the host cell induces drug tolerance in Mycobacterium tuberculosis both in vitro and in vivo. J Exp Med. 213(5):809-25.
- Cox AJ, Bengtson HN, Gerasimova YV, Rohde KH, Kolpashchikov DM. 2016. DNA Antenna Tile-Associated Deoxyribozyme Sensor with Improved Sensitivity. Chembiochem. 17 (21); 2038-2041.
- Cox AJ, Bengtson HN, Rohde KH, Kolpashchikov DM. 2016. DNA nanotechnology for nucleic acid analysis: Multifunctional molecular DNA machine for RNA detection. ChemComm. 52 (99): 14318-14321.
- Stout MB, Swindell WR, Zhi X, Rohde KH, List EO, Berryman DE, Kopchick JJ, Gesing A, Fang Y, and Masternak MM. 2015. Transcriptome profiling reveals divergent expression shifts in brown and white adipose tissue from long-lived GHRKO mice. Oncotarget. 6(29): 26702-15.
- Gerasimova YV, Cornett EM, Edwards E, Su X, Rohde KH, Kolpashchikov D.M. 2013. Deoxyribozyme Cascade for Visual Detection of Bacterial RNA. Chembiochem. Nov 4;14(16):2087-90.
- Sakamoto K, Kim MJ, Rhoades ER, Allavena RE, Ehrt S, Wainwright HC, Russell DG, Rohde KH. 2013. Mycobacterial trehalose dimycolate reprograms macrophage global gene expression and activates matrix metalloproteinases. Infect Immun. 81(3): 764-76.
- Rohde KH*, Veiga DFT, Caldwell S, Balázsi G, Russell DG. 2012. Linking the Transcriptional Profiles and the Physiological States of Mycobacterium tuberculosis during an Extended Intracellular Infection. PLoS Pathog 8(6): e1002769. doi:10.1371/journal.ppat.1002769. *corresponding author
- Abramovitch RB, Rohde KH, Hsu FF and Russell DG. 2011. aprABC: A Mycobacterium tuberculosis complex- specific locus that modulates pH-driven adaptation to the macrophage phagosome. Mol Microbiol. May;80(3):678-94.
- Homolka S, Niemann S, Russell DG, Rohde KH. 2010. Functional Genetic Diversity among Mycobacterium tuberculosis Complex Clinical Isolates: Delineation of Conserved Core and Lineage-Specific Transcriptomes during Intracellular Survival. PLoS Pathog. 6(7): e1000988. doi:10.1371/journal.ppat.1000988.
- Hagedorn M, Rohde KH, Russell DG, Soldati T. 2009. Infection by tubercular mycobacteria is spread by nonlytic ejection from their amoeba hosts. Science. 323(5922): 1729-1733.
- Schwab U, Rohde KH, Wang Z, Chess PR, Notter RH, Russell DG. 2009. Transcriptional responses of Mycobacterium tuberculosis to lung surfactant. Microb Pathog. 46(4): 185-193.
- Rohde KH, Abramovitch RB, Russell DG. 2007. Mycobacterium tuberculosis invasion of macrophages: Linking bacterial gene expression to environmental cues. Cell Host and Microbe. 2: 352-364.
- Russell DG, Purdy GE, Owens RM, Rohde KH, and Yates RM. 2005. Mycobacterium tuberculosis and the Four-Minute Phagosome. ASM News. 71 (10); 459-463.