(2j) Leveraging Linked Organ-on-a-Chip Platforms to Study Gut Microbiome Effects on Human Health and Disease

My long term research interests lie in the development of organ-on-a-chip models for the study of gut microbiome dynamics and its effect on human health. Specifically, I will use chip systems to enable study of the effects of gut microbiome compositions and their metabolite products on both local and distal tissues. Work in my future lab will leverage these chip systems to develop dietary interventions, such as targeted fiber supplements, to improve health outcomes across populations with varying dietary backgrounds and nutrition access. We will also use gut microbiome and other tissue chips to study risk factors mediated by particular microbes and how these metabolic pathways might be in inhibited or promoted in at risk individuals. For example, we will use gut microbiome and tumor chips developed during my postdoc to investigate the effect of the bacterial enzyme beta-glucuronidase on breast cancer progression.

Organ-on-a-chip systems have the potential to improve upon classic in vivo and in vitro model systems to better replicate patient biology for understanding disease mechanisms and therapeutic design. These improvements will have the added benefit of reducing our overall use of animals for drug discovery and testing. In the realm of gut microbiome studies, these systems enable support of difficult to culture bacteria and precise monitoring of their response to distinct perturbations.

During my undergraduate research I developed experience with both cell culture and mouse models while studying nutrition at The University of Texas. These works gave me great appreciation for the vast impacts dietary interventions can have upon disease progression. However, I struggled with the abundance of animals used each year across the health fields to conduct these studies and was driven to pursue more targeted approaches and improved model systems. For this, I joined a multi-university research initiative grant on the development of artificial cell systems for my thesis work. This project not only gave me experience in chemistry, microscopy, and microfluidics fabrication, but also an appreciation for how cross-discipline collaboration can solve complex problems.

Experiences during my undergraduate and graduate studies exposed me to the world of organs-on-chips and ignited the passion within me to leverage these systems for improving disease modelling and to better understand how gut microbiomes exert powerful effects upon organs through the body via innate signaling and metabolic responses to dietary changes. My postdoc at the Cancer Early Detection Advanced Research (CEDAR) center at the Knight Cancer Institute has enabled my further training in organs-on-chips and supported me to initiate my own organ-on-a-chip project. CEDAR is built upon the principle of bringing together scientists from a vast range of backgrounds to drive innovative solutions to the complex issue of early cancer study and detection. Here, I have built a team of scientists and mentors to support my independent project aimed at developing a linked organ-on-a-chip system to study the relationship between gut bacteria and breast cancer progression.

Vast numbers of sequencing studies using patient fecal samples have unearthed correlations between gut microbiome composition and various diseases, including the progression of distal solid tumors such as those in the breast. However, the mechanisms by which this relationship develops is poorly understood and current model systems often translate poorly to the clinic. Here, organ-on-a-chip systems enable better replication of human physiology with the added benefit of isolating impacts of one organ on the other for identification of causative agents for future therapeutic or diagnostic purposes. One prominent hypothesis regarding bacteria and hormone driven disease centers upon the expression of the bacterial enzyme beta-glucuronidase which frees estrogen molecules excreted by the liver, returning them to the circulation. To study the impact of estrogen metabolism by gut bacteria on breast cancer progression, I have constructed two organ-on-a-chip platforms. One platform houses the gut epithelium-bacteria interface and enables culture of oxygen sensitive bacteria from the cancer-associated microbiome for two days. Gut microbiome chips also replicate the epithelial barrier through tight junction protein expression and exhibit differentiation of caco2 cells into traditional villus populations, such as goblet-like cells which produce mucin. The other chip cultures tumor tissue models within a support matrix under constant flow while enabling high resolution imaging of the model tissue. Ongoing work will connect these two platforms and assess impacts of beta glucuronidase activity and other metabolites upon markers of progression in ER+ tumor models.

Teaching Interests:

Throughout my career I have had a great passion for teaching and mentorship. During my undergraduate studies, I participated in a program to mentor effective study group leaders in notoriously difficult courses. In graduate school, I was a teaching assistant for the course Creative Technology which exposed students in a vast range of programs to engineering concepts. For this course, I developed teaching and assessment materials for small, weekly review lessons and lead a couple of these sessions myself. Later in my graduate studies, I was a teaching assistant for a course covering pharmaceutical development and gave two lectures. Outside of the classroom, I mentored several undergraduate students in the lab, exposing them to opportunities in research and training them in a range of techniques. I also volunteered at and coordinated events designed to expose young students to STEM such as Expanding Your Horizons and working with the I Have a Dream Foundation. While mentorship opportunities have been more limited during my postdoctoral tenure at a research hospital, I strive to provide mentorship and share my passion for STEM research wherever I can. Throughout my time here, I have mentored junior graduate students, gave a lecture to my center on the field of microfluidics, participate in summer intern programs to mentor undergraduates in the lab, spoke at an online forum highlighting local research by female scientists hosted by AACR, and contribute to online and shadowing experiences for high school students with interest in STEM. I am deeply devoted to teaching and inspiring the next generation of scientists. I look forward to teaching undergraduate courses, particularly introductory courses, and continuing my outreach work to expose as many young minds to STEM research as possible. In the lab, I will utilize the gut microbiome and solid tissue chips I have developed to provide independent training opportunities for both undergraduate and graduate students. My platforms can be easily deployed with different bacteria of interest alongside spheroids from a wide range of tissue origins to support students to develop and interrogate their own scientific questions.

Selected References:

Konetski, D.; Gong, T.; Bowman, C.N. Photo-Induced Vesicle Formation via the Copper-Catalyzed Azide-Alkyne Cycloaddition Reaction. Langmuir 2016, 32(32), 8195-8201.

Zhang, D.; Liu, Z.; Konetski, D.; Wang, C.; Worrell, B.; Bowman, C. Liposomes Formed from Photo-Cleavable Phospholipids-In-Situ Formation and Photo-Induced Enhancement in Permeability. RSC Adv. 2018, 8, 14669-14675.

Konetski, D.; Zhang, D.; Schwartz, D.K.; Bowman, C.N. Photo-induced Pinocytosis for Artificial and Proto-Cell Systems. Chem. Mater. 2018, 30, 8757-8763.

Konetski, D.; Baranek, A.; Mavila, S.; Zhang, X.; Bowman, C.N. Formation of Lipid Vesicles in Situ Utilizing the Thiol-Michael Reaction. Soft Matter 2018, 14, 7645-7652.

Konetski, D.; Worrell, B.; Wang, C.; Mavila, S.; Bowman, C.N. Production of Dynamic Lipid Bilayers Using the Reversible Thiol-Thioester Exchange Reaction. Chem. Commun. 2018, 54, 8108-8111.

Figure Caption:

A) gut microbiome chip B) Caco-2 cells expressing mucin granules in co-culture with commensal bacteria C) solid tissue chip D) confocal imaging on-chip of a breast cancer spheroid.