Ying Kong, PhD

Our laboratory is interested in:  1) tuberculosis pathogenesis; and 2) discovery of novel anti-tuberculosis therapeutics. With high morbidity and mortality, tuberculosis remains one of the biggest challenges to public health. The major causative pathogen of tuberculosis, Mycobacterium tuberculosis (Mtb), has an unusually slow growth rate. Quantifying Mtb with conventional colony forming unit (CFU) counting requires four weeks to have visible colonies present on the agar plates after plating. We have developed a variety of non-invasive optical in vivo imaging tools to study TB in animal models. By using non-invasive real-time imaging technologies to monitor TB in small animals, infections can be visualized within individual animals while images are collected. Combining these in vivo imaging tools with other cutting-edge in vitro technologies, we are studying and identifying bacterial and host factors affecting bacterial infection, survival, persistence, and reactivation. The results from these studies will contribute to development of improved diagnostic tools, anti-tuberculosis drugs, and vaccines.

1. TB pathogenesis:
   
   Our laboratory has been working on identification of Mtb genes important for cell entry and intracellular survival, using a fluorescent imaging probe to label each mutant strain of Mtb from a mutant library. We now have a list of candidate genes that are involved in Mtb lipid metabolism and are critical for intracellular survival. We are investigating these genes’ functions and roles in TB pathogenesis.
2. Development of anti-TB therapies from aurone analogues:
   
   Our laboratory has screened hundreds of synthetic aurone analogues and identified two aurones that have anti-TB effects in vitro and in vivo. We have analyzed the mechanism of these two aurones against Mtb, and have found that these two aurones inhibit Mtb chorismate synthase, which leads to reduction of aromatic amino acids. We are working on more aurone derivatives to identify compounds having higher efficacies against TB.

Vancomycin-Cy5.5 conjugate labeling dormant Mtb.A. Vancomycin-Cy5.5 conjugate labeling dormant Mtb smeared on slides. The Mtb strain was integrated with a tdTomato gene and was cultured in Wayne model to reach dormant status. It was then labeled with Vancomycin-Cy5.5. Red:Cy5.5; Green:tdTomato. B. Vancomycin-Cy5.5 conjugate labeling dormant Mtb in cells. After labeling the dormant Mtb strain with Vancomycin-Cy5.5 conjugate, it was loaded into the wells seeded with THP-1 cells and phagocytosed by the cells.

CNIR5 labeling non-replicating Mtb in vitro. A. CNIR5 label the non-replicating tdTomato-expressing Mtb CDC1551 strain smeared on slides. The non-replicating tdTomato-expressing Mtb strain was cultured in the Wayne model and then labeled with CNIR5 (carrying the Cy5.5 dye). B. The non-replicating Mtb in THP-1 macrophages labeled with CNIR5. The non-replicating tdTomato-expressing Mtb strain cultured in the Wayne model was used to infect PMA activated THP-1 cells, and then incubated with CNIR5. The tdTomato fluorescence is pseudo-colored green; CNIR5 fluorescence dye Cy5.5 is pseudo-colored red; and nuclei were stained with DAPI (blue).

 

1. Yang D, Li S, Stabenow J, Zalduondo L, Kong Y*. Mycobacterium tuberculosis LipE has a lipase activity and is important for intracellular growth and in vivo infection. Infection and Immunity. Accepted doi: 1128/IAI.00750-19. (*Corresponding author)
2. Sule P, Tilvawala R, Mustapha T, Hassounah H, Noormohamed A, Kundu S, Graviss EA, Walkup GK, Kong Y, Cirillo JD. Rapid Tuberculosis Diagnosis Using Reporter Enzyme Fluorescence (REF). J Clin Microbiol. 2019 Sep 11;. doi: 10.1128/JCM.01462-19. [Epub ahead of print] PubMed PMID: 31511338.
3. Yang D, He X, Li S, Liu J, Stabenow J, Zalduondo L, White S, Kong Y*. Rv1075c of Mycobacterium tuberculosis is a GDSL-Like Esterase and is Important for Intracellular Survival. J Infect Dis. 2019 Apr 18;. doi: 10.1093/infdis/jiz169. [Epub ahead of print] PubMed PMID: 31001637. (*Corresponding author)
4. Lemieux MR, Siricilla S, Mitachi K, Eslamimehr S, Wang Y, Yang D, Pressly JD, Kong Y, Park F, Franzblau SG, Kurosu M. An antimycobacterial pleuromutilin analogue effective against dormant bacilli. Bioorg Med Chem. 2018 Sep 15;26(17):4787-4796. doi: 10.1016/j.bmc.2018.07.034. Epub 2018 Aug 18. PubMed PMID: 30145051; PubMed Central PMCID: PMC6154393.
5. Kong Y*, Cirillo JD. Fluorescence Imaging of Mycobacterial Infection in Live Mice Using Fluorescent Protein-Expressing Strains. Methods Mol Biol. 2018;1790:75-85. doi: 10.1007/978-1-4939-7860-1_6. PubMed PMID: 29858784. (*Corresponding author)
6. Yang HJ^#, Kong Y^#, Cheng Y, Janagama H, Hassounah H, Xie H, Rao J, Cirillo JD. Real-time Imaging of Mycobacterium tuberculosis, Using a Novel Near-Infrared Fluorescent Substrate. J Infect Dis. 2017 Feb 1;215(3):405-414. doi: 10.1093/infdis/jiw298. PubMed PMID: 27421748; PubMed Central PMCID: PMC6061879. (^#Have contributed equally)
7. Yang D, Ding F, Mitachi K, Kurosu M, Lee RE, Kong Y*. A Fluorescent Probe for Detecting Mycobacterium tuberculosisand Identifying Genes Critical for Cell Entry. Front Microbiol. 2016;7:2021. doi: 10.3389/fmicb.2016.02021. eCollection 2016. PubMed PMID: 28066347; PubMed Central PMCID: PMC5168438. (*Corresponding author)
8. Mitachi K, Siricilla S, Yang D, Kong Y, Skorupinska-Tudek K, Swiezewska E, Franzblau SG, Kurosu M. Fluorescence-based assay for polyprenyl phosphate-GlcNAc-1-phosphate transferase (WecA) and identification of novel antimycobacterial WecA inhibitors. Anal Biochem. 2016 Nov 1;512:78-90. doi: 10.1016/j.ab.2016.08.008. Epub 2016 Aug 13. PubMed PMID: 27530653; PubMed Central PMCID: PMC5012913.
9. Kong Y*, Yang D, Cirillo SL, Li S, Akin A, Francis KP, Maloney T, Cirillo JD*. Application of Fluorescent Protein Expressing Strains to Evaluation of Anti-Tuberculosis Therapeutic Efficacy In Vitro and In Vivo. PLoS One. 2016;11(3):e0149972. doi: 10.1371/journal.pone.0149972. eCollection 2016. PubMed PMID: 26934495; PubMed Central PMCID: PMC4774912. (*Corresponding author)
10. Nooshabadi F, Yang HJ, Bixler JN, Kong Y, Cirillo JD, Maitland KC. Intravital Fluorescence Excitation in Whole-Animal Optical Imaging. PLoS One. 2016;11(2):e0149932. doi: 10.1371/journal.pone.0149932. eCollection 2016. PubMed PMID: 26901051; PubMed Central PMCID: PMC4762773.
11. Yang D, Kong Y*. The bacterial and host factors associated with extrapulmonary dissemination of Mycobacterium tuberculosis. Front Biol (Beijing). 2015 Jun;10(3):252-261. doi: 10.1007/s11515-015-1358-y. Epub 2015 Apr 27. PubMed PMID: 26557138; PubMed Central PMCID: PMC4636013. (*Corresponding author)
12. Ding F, Kong Y*.  Host immune factors related to susceptibility to tuberculosis in animal models. Journal of Immune Research. 2015 January; 2(1). (*Corresponding author)
13. Cheng Y, Xie H, Sule P, Hassounah H, Graviss EA, Kong Y, Cirillo JD, Rao J. Fluorogenic probes with substitutions at the 2 and 7 positions of cephalosporin are highly BlaC-specific for rapid Mycobacterium tuberculosis detection. Angew Chem Int Ed Engl. 2014 Aug 25;53(35):9360-4. doi: 10.1002/anie.201405243. Epub 2014 Jul 2. PubMed PMID: 24989449; PubMed Central PMCID: PMC4499257.
14. Xie H^#, Mire J^#, Kong Y^#, Chang M, Hassounah HA, Thornton CN, Sacchettini JC, Cirillo JD, Rao J. Rapid point-of-care detection of the tuberculosis pathogen using a BlaC-specific fluorogenic probe. Nat Chem. 2012 Oct;4(10):802-9. doi: 10.1038/nchem.1435. Epub 2012 Sep 2. PubMed PMID: 23000993; PubMed Central PMCID: PMC4136554. (^#Have contributed equally)
15. Zhou Y, Torres A, Chen L, Kong Y, Cirillo J, Liang H. Fluid-shear method to evaluate bacterial adhesion to glass surfaces. Journal of applied physics. 2012 July; 112. doi: http://dx.doi.org/10.1063/1.4733685.
16. Zhou Y, Kong Y, Kundu S, Cirillo JD, Liang H. Antibacterial activities of gold and silver nanoparticles against Escherichia coli and bacillus Calmette-Guérin. J Nanobiotechnology. 2012 May 6;10:19. doi: 10.1186/1477-3155-10-19. PubMed PMID: 22559747; PubMed Central PMCID: PMC3405418.
17. Kong Y, Shi Y, Chang M, Akin AR, Francis KP, Zhang N, Troy TL, Yao H, Rao J, Cirillo SL, Cirillo JD. Whole-body imaging of infection using bioluminescence. Curr Protoc Microbiol. 2011 May;Chapter 2:Unit 2C.4. doi: 10.1002/9780471729259.mc02c04s21. PubMed PMID: 21538305; PubMed Central PMCID: PMC4540481.
18. Kong Y, Akin AR, Francis KP, Zhang N, Troy TL, Xie H, Rao J, Cirillo SL, Cirillo JD. Whole-body imaging of infection using fluorescence. Curr Protoc Microbiol. 2011 May;Chapter 2:Unit 2C.3. doi: 10.1002/9780471729259.mc02c03s21. PubMed PMID: 21538304; NIHMSID:NIHMS995208.
19. Mufti N, Kong Y, Cirillo JD, Maitland KC. Fiber optic microendoscopy for preclinical study of bacterial infection dynamics. Biomed Opt Express. 2011 Apr 7;2(5):1121-34. doi: 10.1364/BOE.2.001121. PubMed PMID: 21559125; PubMed Central PMCID: PMC3087570.
20. Feng Y^#, Kong Y^#, Barnes PF, Huang FF, Klucar P, Wang X, Samten B, Sengupta M, Machona B, Donis R, Tvinnereim AR, Shams H. Exposure to cigarette smoke inhibits the pulmonary T-cell response to influenza virus and Mycobacterium tuberculosis. Infect Immun. 2011 Jan;79(1):229-37. doi: 10.1128/IAI.00709-10. Epub 2010 Oct 25. PubMed PMID: 20974820; PubMed Central PMCID: PMC3019896. (^#Have contributed equally)
21. Kong Y, Cirillo JD. Reporter enzyme fluorescence (REF) imaging and quantification of tuberculosis in live animals. 2010 Nov-Dec;1(6):558-62. doi: 10.4161/viru.1.6.13901. Epub 2010 Nov 1. PubMed PMID: 21178505; PubMed Central PMCID: PMC3073363.
22. Kong Y, Yao H, Ren H, Subbian S, Cirillo SL, Sacchettini JC, Rao J, Cirillo JD. Imaging tuberculosis with endogenous beta-lactamase reporter enzyme fluorescence in live mice. Proc Natl Acad Sci U S A. 2010 Jul 6;107(27):12239-44. doi: 10.1073/pnas.1000643107. Epub 2010 Jun 21. PubMed PMID: 20566877; PubMed Central PMCID: PMC2901431.
23. Kong Y, Subbian S, Cirillo SL, Cirillo JD. Application of optical imaging to study of extrapulmonary spread by tuberculosis. Tuberculosis (Edinb). 2009 Dec;89 Suppl 1:S15-7. doi: 10.1016/S1472-9792(09)70006-X. PubMed PMID: 20006298; PubMed Central PMCID: PMC4137470.
24. Klucar P, Barnes PF, Kong Y, Howard ST, Pang X, Huang FF, Tvinnereim AR, Samten B, Shams H. Vaccination strategies to enhance local immunity and protection against Mycobacteriun tuberculosis. 2009 Mar 13;27(12):1816-24. doi: 10.1016/j.vaccine.2009.01.119. PubMed PMID: 19402204; PubMed Central PMCID: PMC2768422.
25. Klucar P, Barnes PF, Kong Y, Samten B, Tvinnereim A, Spallek R, Nepom GT, Singh M, Shams H. Characterization of effector functions of human peptide-specific CD4+ T-cell clones for an intracellular pathogen. Hum Immunol. 2008 Aug;69(8):475-83. doi: 10.1016/j.humimm.2008.05.008. Epub 2008 Jun 25. PubMed PMID: 18588932.
26. Kong Y, Cave MD, Zhang L, Foxman B, Marrs CF, Bates JH, Yang ZH. Association between Mycobacterium tuberculosis Beijing/W lineage strain infection and extrathoracic tuberculosis: Insights from epidemiologic and clinical characterization of the three principal genetic groups of M. tuberculosis clinical isolates. J Clin Microbiol. 2007 Feb;45(2):409-14. doi: 10.1128/JCM.01459-06. Epub 2006 Dec 13. PubMed PMID: 17166963; PubMed Central PMCID: PMC1829078.
27. Kong Y, Cave MD, Zhang L, Foxman B, Marrs CF, Bates JH, Yang ZH. Population-based study of deletions in five different genomic regions of Mycobacterium tuberculosis and possible clinical relevance of the deletions. J Clin Microbiol. 2006 Nov;44(11):3940-6. doi: 10.1128/JCM.01146-06. Epub 2006 Sep 6. PubMed PMID: 16957037; PubMed Central PMCID: PMC1698370.
28. Kong Y, Cave MD, Yang D, Zhang L, Marrs CF, Foxman B, Bates JH, Wilson F, Mukasa LN, Yang ZH. Distribution of insertion- and deletion-associated genetic polymorphisms among four Mycobacterium tuberculosis phospholipase C genes and associations with extrathoracic tuberculosis: a population-based study. J Clin Microbiol. 2005 Dec;43(12):6048-53. doi: 10.1128/JCM.43.12.6048-6053.2005. PubMed PMID: 16333097; PubMed Central PMCID: PMC1317199.
29. Yang Z, Yang D, Kong Y, Zhang L, Marrs CF, Foxman B, Bates JH, Wilson F, Cave MD. Clinical relevance of Mycobacterium tuberculosis plcD gene mutations. Am J Respir Crit Care Med. 2005 Jun 15;171(12):1436-42. doi: 10.1164/rccm.200408-1147OC. Epub 2005 Apr 1. PubMed PMID: 15805187; PubMed Central PMCID: PMC2718484.
30. Yang Z, Kong Y, Wilson F, Foxman B, Fowler AH, Marrs CF, Cave MD, Bates JH. Identification of risk factors for extrapulmonary tuberculosis. Clin Infect Dis. 2004 Jan 15;38(2):199-205. doi: 10.1086/380644. Epub 2003 Dec 19. PubMed PMID: 14699451.

Patents:

• Inventors: Kong Y, Yang D, Taylor Z, Handy S, Altman E. Aurones and methods of using aurones to treat tuberculosis. United States patent application 62/840,788. 2019 April.
• Inventors: Maitland KC, Cirillo JD, Kong Y, Bixler J. Localized fluorescence excitation in whole body optical imaging. United States patent application 20140221829. 2014 August.

Books:

Tuberculosis Host-Pathogen Interactions. Cirillo JD, Kong Y, editors. Springer Nature Switzerland AG: Springer; 2019.

Book Chapters:

Sharan R, Galbadage T, Saenkham P, Moule M, Sule P, Kong Y, Cirillo JD. Optical in vivo imaging in tuberculosis research. In: Tuberculosis Host-Pathogen Interactions. Cirillo JD, Kong Y, editors. Springer Nature Switzerland AG: Springer; 2019. Chapter 8; p.155-200.