(2mc) Engineering and stabilizing cell aggregates for synthetic multicellularity

Multicellularity provides advantages over unicellularity that are useful for bioproduction and living materials, such as higher metabolite concentrations and increased productivity through division of labor. While well-characterized parts exist to engineer complex logic in individual cells, a deeper understanding of the key design principles of multicellularity is necessary to produce well-controlled, functional cellular assemblies. In my graduate and postdoctoral work, I combined cell engineering, quantitative analysis, and lab automation to study minimal versions of key multicellular systems for a ”build to understand” approach, studying both cell-cell signaling and cell-cell adhesion. To extend this work, my research program will focus on three areas of inquiry, first using Saccharomyces cerevisiae as a model system: (1) quantifying the effects of adhesion on cell fitness, (2) designing synthetic adhesion genes, and (3) engineering cooperative behaviors within aggregates. The design principles gleaned from this work can guide the construction of living materials and novel approaches to biomanufacturing, as well as providing insight into the roles of adhesion in biofilms, tumors, and the evolution of multicellularity.

Research Experience:

Design principles of cell-cell adhesion, Department of Biomedical Engineering, Boston University (Advisors: Ahmad (Mo) Khalil and Mary J. Dunlop)

Engineering cell-cell adhesion can enable novel biotechnologies that benefit from the increased robustness and complexity of multicellularity. However, adhesion can also alter cell fitness, by limiting nutrient flux or altering the distribution of physical forces. In fact, expression of adhesion genes often occurs as a stress response, such as antibiotic-induced biofilms or yeast flocculation at high ethanol concentrations. Moreover, naturally occurring adhesion genes include a diversity of domains and architectures whose roles in tuning cell-cell interactions are not completely understood. In my postdoc, I combine yeast synthetic biology tools with hardware for continuous culture to understand the robustness of engineered multicellularity. First, by controlling expression of native and synthetic adhesion genes, I have explored how these genes tune overall aggregate size. Second, by leveraging the Khalil lab’s eVOLVER platform, I have cultured aggregates for over one hundred generations in various conditions, exploring how media richness and aggregate size affect long-term evolutionary outcomes. Going forward, I will generate a set of programmable adhesion parts, with known effects on aggregate size as well as overall cell fitness, which can be deployed in many exciting applications for yeast, including bioremediation, where groups of cells can more efficiently bind or convert toxins, and biomanufacturing, where the metabolic burden of engineered synthesis pathways is split between cell types.

Context-dependent, combinatorial logic of BMP signaling, Biology and Bioengineering Division, Caltech (Advisor: Michael B. Elowitz)

Multicellular development relies on key signaling pathways to pattern tissues and instruct cell fates. Many pathways, such as the Bone Morphogenetic Protein (BMP) pathway, take on diverse roles across tissues and developmental timepoints, despite comprising relatively few signaling proteins. To better understand how signaling proteins of the BMP pathway behave in combinations and across contexts, I programmed a liquid handling robot to prepare hundreds of BMP combinations and concentrations. Using flow cytometry to quantify a fluorescent reporter of pathway activity, I showed that some BMPs are fully equivalent, producing the same effects as individual proteins and when paired with any other BMP, while others are not, having unique inhibitory effects on all other BMPs. However, repeating this experiment in different cell lines revealed that these groupings are flexible, and a change in the expression of a single receptor was sufficient to break or fuse previously identified equivalence groups. These data were consistent with a mathematical model of promiscuous receptor-ligand interactions and recapitulated some previously observed tissue-specific differences in BMP function. This work not only highlights the flexibility of BMP signaling in general, but also provides specific insights into the properties of these highly similar proteins, as well as establishing a framework for understanding combinatorial signaling.

Selected Publications:

Klumpe HE, Garcia-Ojalvo J, Elowitz MB, Antebi YE. The computational capabilities of many-to-many protein interaction networks. Cell Systems, 2023.

Klumpe HE*, Lugagne JB*+, Khalil AS, Dunlop MJ. Deep neural networks for predicting single cell responses and probability landscapes. ACS Synthetic Biology, 2023 (*co-first, +co-corresponding)

Klumpe HE, Langley MA, Linton JM, Su CJ, Antebi YE, Elowitz MB. The context-dependent, combinatorial logic of BMP signaling. Cell Systems, 2022.

Antebi YE, Linton JM, Klumpe HE, Bintu B, Gong M, Su CJ, McCardell R, Elowitz MB. Combinatorial signal perception in the BMP pathway. Cell, 2017.

Selected Awards:

MIT ChE Rising Star (2023)

Damon Runyon Postdoctoral Fellowship (2022 – present)

Boston University Kilachand Postdoctoral Fellowship (2021 – 2022)

Caltech Graduate Student Council Mentoring Award (2019)

National Science Foundation Graduate Research Fellowship (2016 - 2020)

Barry M. Goldwater Scholarship (2011 – 2013)

Teaching Interests:

Based on my undergraduate and graduate coursework in chemical engineering, I am qualified to teach core classes in thermodynamics, transport phenomena, chemical kinetics, separations, process systems analysis and control, fluid mechanics, and mathematical modeling. I have additional experience working as a graduate teaching assistant in thermodynamics (graduate level) and chemical reactor and kinetics engineering (undergraduate level), as well as Bayesian statistics and Python programming (graduate and undergraduate level). As a faculty member, I am also interested in designing elective courses related to biochemical engineering, bioreactor design, biological transport phenomena, cell engineering, and synthetic biology. Additionally, because of my undergraduate degree in English and involvement in science communication, I am interested in professional development courses in written and oral communication skills.

Teaching Experience:

Biomedical signals and controls (Boston University), Guest lecturer (2022)

Introduction to programming bootcamp (Caltech), Co-instructor (2021)

Storytelling for Scientists (Caltech), Co-instructor (2020)

Chemical Reaction Engineering (Caltech), Teaching assistant (2018)

Data Analysis in the Biological Sciences (Caltech), Teaching assistant (2016, 2017)

Chemical Thermodynamics (Caltech), Teaching assistant (2015)