Genomics, stem cells, microfluidics

Engineering the 3D microenvironment of stem cells

Advisor: Todd C. McDevitt, PhD
Georgia Institute of Technology (relocated to the Gladstone Institutes)

Embryonic stem cells (ESCs) have the unique ability to differentiate into cell types of all germ lineages. However, there are several challenges in using ESCs for regenerative medicine and stem cell bio-manufacturing applications, namely dynamic regulation of cell fate and scalable cell production. A recent paradigm shift has emerged suggesting that the beneficial effects of stem cells may not be restricted to cell restoration alone, but also due to their transient paracrine actions. Approaches, such as microencapsulation and hypoxic conditioning, can be utilized to engineer paracrine delivery for enhanced therapeutic efficacy. First, microencapsulation of ESCs in alginate can be exploited to modulate cell phenotype and secretory profile via the ratio of guluronic and mannuronic acid content, as well as allow for high density culture in bioreactors. Second, conditioning of ESCs under low oxygen tension (3% O2) has promoted expression of several growth factors (in particular, VEGF and BMP-4) and mimics in vivo embryogenesis conditions. Therefore, the objective of this study was to assess cell viability and secretion of native growth factors of hypoxic-conditioned murine ESCs within alginate microcapsules of varying compositions.

DNA methylation of monoallelically expressed genes

Advisor: Alexander Gimelbrant, PhD
Dana-Farber Cancer Institute, Harvard Medical School

The generation of functionally diverse cells from common progenitors is one of the most fundamental processes in metazoan biology. Autosomal monoallelic expression (MAE) is the least understood epigenetic mechanism involved in the generation of mitotically stable cell sub-populations through the separate regulation of each allele. Several lines of evidence imply that MAE establishment and maintenance are controlled by a variety of genetic elements. Here, we show evidence of allele-specific DNA methylation among MAE genes using padlock probe technology in clonal lymphoblast cell lines. Allele-specific DNA methylation is significantly enriched, particularly upstream of MAE genes’ transcriptional start site. This finding is the first evidence of epigenetic associations with MAE genes along autosomes.

Temperature dependent developmental variation within wild strains of D. melanogaster

Advisor: Michael Eisen, PhD
University of California, Berkeley

Cellular processes and embryonic ontogenesis must be properly coordinated for successful development in multicellular organisms. Since the relative timing of embryonic events in the fruit fly Drosophila remains constant between several species as temperature varies, Drosophila may possess a single, shared biological mechanism that dictates the cadence of embryogenesis. However, the nature and biological range of this mechanism remains largely unknown. We sought to characterize this mechanism with systematic and high-throughput screenings of Drosophila embryos at various temperatures (19°C, 21°C and 30°C). A portable, acrylic enclosure using a top-down mounted light source was designed for inverted time-lapse imaging of embryos of several, wild-caught D. melanogaster strains (R303, R324, R437 and Ln6-3). The time-lapse embryo-imaging assay can be multiplexed to screen approximately 900 embryos in three days. Semi-autonomous, biophysics-based image processing scripts were written in MATLAB to quantify the relative hatching time of individual embryos from acquired time-lapse movies. Preliminary data indicates that embryogenesis of intact embryos is faster than chemically dechorionated embryos across all strains and temperatures. The duration of embryogenesis was consistent with logarithmically-correlation to temperature, such that warmer temperatures result in faster development. The distribution and variability of developmental time is approximately equivalent for all temperatures of a given strain, indicating that the hypothesized biological mechanism dictating embryogenesis may not be biased by temperatures ranging from 19-30°C. Developmental time is also consistent between all strains at a given temperature. This project ultimately enables high-throughput, concurrent time-lapse imaging of several populations of Drosophila embryos to elucidate and characterize the distribution of temperature-dependent timing of embryogenesis.