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Modulating Oral Delivery and Gastrointestinal Kinetics of Recombinant Proteins via Engineered Fungi

  • Research Article
  • Theme: Rising Stars in Drug Delivery and Novel Carriers
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Abstract

A new modality in microbe-mediated drug delivery has recently emerged wherein genetically engineered microbes are used to locally deliver recombinant therapeutic proteins to the gastrointestinal tract. These engineered microbes are often referred to as live biotherapeutic products (LBPs). Despite advanced genetic engineering and recombinant protein expression approaches, little is known on how to control the spatiotemporal dynamics of LBPs and their secreted therapeutics within the gastrointestinal tract. To date, the fundamental pharmacokinetic analyses for microbe-mediated drug delivery systems have not been described. Here, we explore the pharmacokinetics of an engineered, model protein-secreting Saccharomyces cerevisiae, which serves as an ideal organism for the oral delivery of complex, post-translationally modified proteins. We establish three methods to modulate the pharmacokinetics of an engineered, recombinant protein-secreting fungi system: (i) altering oral dose of engineered fungi, (ii) co-administering antibiotics, and (iii) altering recombinant protein secretion titer. Our findings establish the fundamental pharmacokinetics which will be essential in controlling downstream therapeutic response for this new delivery modality.

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References

  1. Human Microbiome Project C. Structure, function and diversity of the healthy human microbiome. Nature. 2012;486(7402):207–14.

    Article  CAS  Google Scholar 

  2. Belkaid Y, Hand TW. Role of the microbiota in immunity and inflammation. Cell. 2014;157(1):121–41.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  3. Cho I, Blaser MJ. The human microbiome: at the interface of health and disease. Nat Rev Genet. 2012;13(4):260–70.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. Yatsunenko T, Rey FE, Manary MJ, Trehan I, Dominguez-Bello MG, Contreras M, et al. Human gut microbiome viewed across age and geography. Nature. 2012;486(7402):222–7.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Nkamga VD, Henrissat B, Drancourt M. Archaea: essential inhabitants of the human digestive microbiota. Hum Microb J. 2017;3:1–8.

    Article  Google Scholar 

  6. Underhill DM, Iliev ID. The mycobiota: interactions between commensal fungi and the host immune system. Nat Rev Immunol. 2014;14(6):405–16.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Subramanian S, Blanton LV, Frese SA, Charbonneau M, Mills DA, Gordon JI. Cultivating healthy growth and nutrition through the gut microbiota. Cell. 2015;161(1):36–48.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Lukes J, Stensvold CR, Jirku-Pomajbikova K, Wegener PL. Are human intestinal eukaryotes beneficial or commensals? PLoS Pathog. 2015;11(8):e1005039.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  9. Fischbach MA, Sonnenburg JL. Eating for two: how metabolism establishes interspecies interactions in the gut. Cell Host Microbe. 2011;10(4):336–47.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Cerf-Bensussan N, Gaboriau-Routhiau V. The immune system and the gut microbiota: friends or foes? Nat Rev Immunol. 2010;10(10):735–44.

    Article  CAS  PubMed  Google Scholar 

  11. Zuo T, Ng SC. The gut microbiota in the pathogenesis and therapeutics of inflammatory bowel disease. Front Microbiol. 2018;9:2247.

    Article  PubMed  PubMed Central  Google Scholar 

  12. Louis P, Hold GL, Flint HJ. The gut microbiota, bacterial metabolites and colorectal cancer. Nat Rev Microbiol. 2014;12(10):661–72.

    Article  CAS  PubMed  Google Scholar 

  13. Sampson TR, Debelius JW, Thron T, Janssen S, Shastri GG, Ilhan ZE, et al. Gut microbiota regulate motor deficits and neuroinflammation in a model of parkinson’s disease. Cell. 2016;167(6):1469–80 e12.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Riglar DT, Silver PA. Engineering bacteria for diagnostic and therapeutic applications. Nat Rev Microbiol. 2018;16(4):214–25.

    Article  CAS  PubMed  Google Scholar 

  15. Charbonneau MR, Isabella VM, Li N, Kurtz CB. Developing a new class of engineered live bacterial therapeutics to treat human diseases. Nat Commun. 2020;11(1):1738.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Claesen J, Fischbach MA. Synthetic microbes as drug delivery systems. ACS Synth Biol. 2015;4(4):358–64.

    Article  CAS  PubMed  Google Scholar 

  17. Isabella VM, Ha BN, Castillo MJ, Lubkowicz DJ, Rowe SE, Millet YA, et al. Development of a synthetic live bacterial therapeutic for the human metabolic disease phenylketonuria. Nat Biotechnol. 2018;36(9):857–64.

    Article  CAS  PubMed  Google Scholar 

  18. Daeffler KN, Galley JD, Sheth RU, Ortiz-Velez LC, Bibb CO, Shroyer NF, et al. Engineering bacterial thiosulfate and tetrathionate sensors for detecting gut inflammation. Mol Syst Biol. 2017;13(4):923.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  19. Leventhal DS, Sokolovska A, Li N, Plescia C, Kolodziej SA, Gallant CW, et al. Immunotherapy with engineered bacteria by targeting the STING pathway for anti-tumor immunity. Nat Commun. 2020;11(1):2739.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Steidler L, Hans W, Schotte L, Neirynck S, Obermeier F, Falk W, et al. Treatment of murine colitis by Lactococcus lactis secreting interleukin-10. Science. 2000;289(5483):1352–5.

    Article  CAS  PubMed  Google Scholar 

  21. Durmusoglu D, Al’Abri IS, Collins SP, Cheng J, Eroglu A, Beisel CL, et al. In situ biomanufacturing of small molecules in the mammalian gut by probiotic saccharomyces boulardii. ACS Synth Biol. 2021.

  22. Brown TD, Whitehead KA, Mitragotri S. Materials for oral delivery of proteins and peptides. Nat Rev Mater. 2019;5(2):127–48.

    Article  Google Scholar 

  23. Anselmo AC, Gokarn Y, Mitragotri S. Non-invasive delivery strategies for biologics. Nat Rev Drug Discov. 2019;18(1):19–40.

    Article  CAS  PubMed  Google Scholar 

  24. Vargason AM, Anselmo AC. Clinical translation of microbe-based therapies: current clinical landscape and preclinical outlook. Bioeng Transl Med. 2018;3(2):124–37.

    Article  PubMed  PubMed Central  Google Scholar 

  25. Wang LLW, Janes ME, Kumbhojkar N, Kapate N, Clegg JR, Prakash S, et al. Cell therapies in the clinic. Bioeng Transl Med. 2021;n/a(n/a):e10214.

  26. Rowland M, Peck C, Tucker G. Physiologically-based pharmacokinetics in drug development and regulatory science. Annu Rev Pharmacol Toxicol. 2011;51:45–73.

    Article  CAS  PubMed  Google Scholar 

  27. Shah DK, Betts AM. Towards a platform PBPK model to characterize the plasma and tissue disposition of monoclonal antibodies in preclinical species and human. J Pharmacokinet Pharmacodyn. 2012;39(1):67–86.

    Article  CAS  PubMed  Google Scholar 

  28. Gobeau N, Stringer R, De Buck S, Tuntland T, Faller B. Evaluation of the GastroPlus Advanced Compartmental and Transit (ACAT) Model in Early Discovery. Pharm Res. 2016;33(9):2126–39.

    Article  CAS  PubMed  Google Scholar 

  29. Jimenez M, Langer R, Traverso G. Microbial therapeutics: new opportunities for drug delivery. J Exp Med. 2019;216(5):1005–9.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  30. Eisenstein M. The hunt for a healthy microbiome. Nature. 2020;577(7792):S6–8.

    Article  CAS  PubMed  Google Scholar 

  31. Lichtman JS, Sonnenburg JL, Elias JE. Monitoring host responses to the gut microbiota. ISME J. 2015;9(9):1908–15.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  32. Zhang S, Ermann J, Succi MD, Zhou A, Hamilton MJ, Cao B, et al. An inflammation-targeting hydrogel for local drug delivery in inflammatory bowel disease. Sci Transl Med. 2015;7(300):300ra128.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  33. Xie YH, Chen YX, Fang JY. Comprehensive review of targeted therapy for colorectal cancer. Sign Transduct Target Ther. 2020;5(1):22.

    Article  CAS  Google Scholar 

  34. Huang M, Bao J, Hallstrom BM, Petranovic D, Nielsen J. Efficient protein production by yeast requires global tuning of metabolism. Nat Commun. 2017;8(1):1131.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  35. Costenoble R, Adler L, Niklasson C, Liden G. Engineering of the metabolism of Saccharomyces cerevisiae for anaerobic production of mannitol. FEMS Yeast Res. 2003;3(1):17–25.

    CAS  PubMed  Google Scholar 

  36. Espey MG. Role of oxygen gradients in shaping redox relationships between the human intestine and its microbiota. Free Radic Biol Med. 2013;55:130–40.

    Article  CAS  PubMed  Google Scholar 

  37. Jeong H, Arif B, Caetano-Anolles G, Kim KM, Nasir A. Horizontal gene transfer in human-associated microorganisms inferred by phylogenetic reconstruction and reconciliation. Sci Rep. 2019;9(1):5953.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  38. Lerner A, Matthias T, Aminov R. Potential effects of horizontal gene exchange in the human gut. Front Immunol. 2017;8:1630.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  39. Fitzgerald I, Glick BS. Secretion of a foreign protein from budding yeasts is enhanced by cotranslational translocation and by suppression of vacuolar targeting. Microb Cell Factories. 2014;13(1):125.

    Article  CAS  Google Scholar 

  40. Dolinski K, Muir S, Cardenas M, Heitman J. All cyclophilins and FK506 binding proteins are, individually and collectively, dispensable for viability in Saccharomyces cerevisiae. Proc Natl Acad Sci U S A. 1997;94(24):13093–8.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  41. Chao G, Lau WL, Hackel BJ, Sazinsky SL, Lippow SM, Wittrup KD. Isolating and engineering human antibodies using yeast surface display. Nat Protoc. 2006;1(2):755–68.

    Article  CAS  PubMed  Google Scholar 

  42. Gietz RD, Schiestl RH. High-efficiency yeast transformation using the LiAc/SS carrier DNA/PEG method. Nat Protoc. 2007;2(1):31–4.

    Article  CAS  PubMed  Google Scholar 

  43. Jiang TT, Shao TY, Ang WXG, Kinder JM, Turner LH, Pham G, et al. Commensal fungi recapitulate the protective benefits of intestinal bacteria. Cell Host Microbe. 2017;22(6):809–16 e4.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  44. Jiang TT, Chaturvedi V, Ertelt JM, Xin L, Clark DR, Kinder JM, et al. Commensal enteric bacteria lipopolysaccharide impairs host defense against disseminated Candida albicans fungal infection. Mucosal Immunol. 2015;8(4):886–95.

    Article  CAS  PubMed  Google Scholar 

  45. Bzducha-Wrobel A, Blazejak S, Kawarska A, Stasiak-Rozanska L, Gientka I, Majewska E. Evaluation of the efficiency of different disruption methods on yeast cell wall preparation for beta-glucan isolation. Molecules. 2014;19(12):20941–61.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  46. Plessis A, Dujon B. Multiple tandem integrations of transforming DNA sequences in yeast chromosomes suggest a mechanism for integrative transformation by homologous recombination. Gene. 1993;134(1):41–50.

    Article  CAS  PubMed  Google Scholar 

  47. Casler JC, Glick BS. Visualizing secretory cargo transport in budding yeast. Curr Protoc Cell Biol. 2019;83(1):e80.

    Article  PubMed  CAS  Google Scholar 

  48. Verstrepen KJ, Jansen A, Lewitter F, Fink GR. Intragenic tandem repeats generate functional variability. Nat Genet. 2005;37(9):986–90.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  49. Evanko D. Training GFP to fold. Nat Methods. 2006;3(2):76.

    Article  CAS  PubMed  Google Scholar 

  50. Zheng L, Kelly CJ, Colgan SP. Physiologic hypoxia and oxygen homeostasis in the healthy intestine. A review in the theme: cellular responses to hypoxia. Am J Phys Cell Physiol. 2015;309(6):C350–60.

    Article  CAS  Google Scholar 

  51. Munna MS, Humayun S, Noor R. Influence of heat shock and osmotic stresses on the growth and viability of Saccharomyces cerevisiae SUBSC01. BMC Res Notes. 2015;8(1):369.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  52. Pizarro FJ, Jewett MC, Nielsen J, Agosin E. Growth temperature exerts differential physiological and transcriptional responses in laboratory and wine strains of Saccharomyces cerevisiae. Appl Environ Microbiol. 2008;74(20):6358–68.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  53. Prasher DC, Eckenrode VK, Ward WW, Prendergast FG, Cormier MJ. Primary structure of the Aequorea victoria green-fluorescent protein. Gene. 1992;111(2):229–33.

    Article  CAS  PubMed  Google Scholar 

  54. Garber K. First microbiome-based drug clears phase III, in clinical trial turnaround. Nat Rev Drug Discov. 2020;19(10):655–6.

    Article  CAS  PubMed  Google Scholar 

  55. Cordaillat-Simmons M, Rouanet A, Pot B. Live biotherapeutic products: the importance of a defined regulatory framework. Exp Mol Med. 2020;52(9):1397–406.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  56. Auchtung TA, Fofanova TY, Stewart CJ, Nash AK, Wong MC, Gesell JR, et al. Investigating colonization of the healthy adult gastrointestinal tract by fungi. mSphere. 2018;3(2):e00092–18.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  57. Arike L, Seiman A, van der Post S, Rodriguez Pineiro AM, Ermund A, Schutte A, et al. Protein turnover in epithelial cells and mucus along the gastrointestinal tract is coordinated by the spatial location and microbiota. Cell Rep. 2020;30(4):1077–87 e3.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  58. Sorbara MT, Pamer EG. Interbacterial mechanisms of colonization resistance and the strategies pathogens use to overcome them. Mucosal Immunol. 2019;12(1):1–9.

    Article  CAS  PubMed  Google Scholar 

  59. Ducarmon QR, Zwittink RD, Hornung BVH, van Schaik W, Young VB, Kuijper EJ. Gut microbiota and colonization resistance against bacterial enteric infection. Microbiol Mol Biol Rev. 2019;83(3):e00007–19.

    Article  PubMed  PubMed Central  Google Scholar 

  60. Oliphant K, Cochrane K, Schroeter K, Daigneault MC, Yen S, Verdu EF, et al. Effects of antibiotic pretreatment of an ulcerative colitis-derived fecal microbial community on the integration of therapeutic bacteria in vitro. mSystems. 2020;5(1):e00404–19.

    Article  PubMed  PubMed Central  Google Scholar 

  61. Gopalakrishnan V, Weiner B, Ford CB, Sellman BR, Hammond SA, Freeman DJ, et al. Intervention strategies for microbial therapeutics in cancer immunotherapy. Immuno-Oncol Technol. 2020;6:9–17.

    Article  Google Scholar 

  62. Schwartz DJ, Langdon AE, Dantas G. Understanding the impact of antibiotic perturbation on the human microbiome. Genome Med. 2020;12(1):82.

    Article  PubMed  PubMed Central  Google Scholar 

  63. Wolfe RR, Park S, Kim IY, Starck C, Marquis BJ, Ferrando AA, et al. Quantifying the contribution of dietary protein to whole body protein kinetics: examination of the intrinsically labeled proteins method. Am J Physiol Endocrinol Metab. 2019;317(1):E74–84.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  64. Di L. Strategic approaches to optimizing peptide ADME properties. AAPS J. 2015;17(1):134–43.

    Article  CAS  PubMed  Google Scholar 

  65. Scheving LA. Biological clocks and the digestive system. Gastroenterology. 2000;119(2):536–49.

    Article  CAS  PubMed  Google Scholar 

  66. Martchenko A, Martchenko SE, Biancolin AD, Brubaker PL. Circadian rhythms and the gastrointestinal tract: relationship to metabolism and gut hormones. Endocrinology. 2020;161(12).

  67. Vargason AM, Santhosh S, Anselmo AC. Surface modifications for improved delivery and function of therapeutic bacteria. Small. 2020;16(25):e2001705.

    Article  PubMed  CAS  Google Scholar 

  68. Goodman AL, Kallstrom G, Faith JJ, Reyes A, Moore A, Dantas G, et al. Extensive personal human gut microbiota culture collections characterized and manipulated in gnotobiotic mice. Proc Natl Acad Sci U S A. 2011;108(15):6252–7.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  69. Maclaren OJ, Parker A, Pin C, Carding SR, Watson AJM, Fletcher AG, et al. A hierarchical Bayesian model for understanding the spatiotemporal dynamics of the intestinal epithelium. PLoS Comput Biol. 2017;13(7):e1005688.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  70. Diether NE, Willing BP. Microbial fermentation of dietary protein: an important factor in diet(-)Microbe(-)host interaction. Microorganisms. 2019;7(1).

  71. Yang Y, Gunasekara M, Muhammednazaar S, Li Z, Hong H. Proteolysis mediated by the membrane-integrated ATP-dependent protease FtsH has a unique nonlinear dependence on ATP hydrolysis rates. Protein Sci. 2019;28(7):1262–75.

    CAS  PubMed  PubMed Central  Google Scholar 

  72. Ando H, Hisaka A, Suzuki H. A new physiologically based pharmacokinetic model for the prediction of gastrointestinal drug absorption: translocation model. Drug Metab Dispos. 2015;43(4):590–602.

    Article  CAS  PubMed  Google Scholar 

  73. Vaidya H, Makinde OD, Choudhari R, Prasad KV, Khan SU, Vajravelu K. Peristaltic flow of non-Newtonian fluid through an inclined complaint nonlinear tube: application to chyme transport in the gastrointestinal tract. Eur Phys J Plus. 2020;135(11):934.

    Article  CAS  Google Scholar 

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Acknowledgements

We thank Dr. J. Heitman for kindly gifting the wild type fungal strain. We thank UNC Nanomedicines Characterization Core Facility for training and equipment utilization for western blot imaging. Illustrations created with BioRender.com.

Funding

Research reported in this publication was supported by the National Institute of General Medical Sciences of the National Institutes of Health under Award Number R35GM137898.

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M.H. and A.A. conceived the ideas presented, designed the studies, organized experimental work, and wrote and revised the manuscript. M.H. performed all experiments and data analyses. A.A. supervised the project and data analyses. M.H. and A.A agree to be accountable for all aspects of the work in ensuring that questions related to the accuracy or integrity of any part of the work are appropriately investigated and resolved.

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Correspondence to Aaron C. Anselmo.

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Heavey, M.K., Anselmo, A.C. Modulating Oral Delivery and Gastrointestinal Kinetics of Recombinant Proteins via Engineered Fungi. AAPS J 23, 76 (2021). https://doi.org/10.1208/s12248-021-00606-9

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