Reconstructing the regulatory circuit of cell fate determination in yeast mating response

Microfluidic-Enabled Multi-Cell-Densities-Patterning and Culture Device for Characterization of Yeast Strains’ Growth Rates under Mating Pheromone

Yeast studies usually focus on exploring diversity in terms of a specific trait (such as growth rate, antibiotic resistance, or fertility) among extensive strains. Microfluidic chips improve these biological studies in a manner of high throughput and high efficiency. For a population study of yeast, it is of great significance to set a proper initial cell density for every strain under specific circumstances. Herein, we introduced a novel design of chip, which enables users to load cells in a gradient order (six alternatives) of initial cell density within one channel. We discussed several guidelines to choose the appropriate chamber to ensure successful data recording. With this chip, we successfully studied the growth rate of yeast strains under a mating response, which is crucial for yeasts to control growth behaviors for prosperous mating. We investigated the growth rate of eight different yeast strains under three different mating pheromone levels (0.3 μM, 1 μM, and 10 μM). Strains with, even, a six-fold in growth rate can be recorded, with the available data produced simultaneously. This work has provided an efficient and time-saving microfluidic platform, which enables loading cells in a pattern of multi-cell densities for a yeast population experiment, especially for a high-throughput study. Besides, a quantitatively analyzed growth rate of different yeast strains shall reveal inspiring perspectives for studies concerning yeast population behavior with a stimulated mating pheromone.

A novel two-layer-integrated microfluidic device for high-throughput yeast proteomic dynamics analysis at the single-cell level

Current microfluidic methods for studying multicell strains (e.g., m-types) with multienvironments (e.g., n-types) require large numbers of inlets/outlets (m*n), a complicated procedure or expensive machinery. Here, we developed a novel two-layer-integrated method to combine different PDMS microchannel layers with different functions into one chip by a PDMS through-hole array, which improved the design of a PDMS-based microfluidic system. Using this method, we succeeded in converting 2 × m × n inlets/outlets into m + n inlets/outlets and reduced the time cost of loading processing (from m × n to m) of the device for studying multicell strains (e.g., m-types) in varied multitemporal environments (i.e., n-types). Using this device, the dynamic behavior of the cell-stress-response proteins was studied when the glucose concentration decreased from 2% to a series of lower concentrations. Our device could also be widely used in high-throughput studies of various stress responses, and the new concept of a multilayer-integrated fabrication method could greatly improve the design of PDMS-based microfluidic systems.

High-throughput cell migration assay under combinatorial chemical environments by a novel 24-well-plate based device

The quantitative studies of cell proliferation and migration under different chemical environments are important for both scientists and clinicians searching for new therapeutics. In this study, we developed a new device to pattern several types of cells in 24-well-plate and demonstrated its' application in cancer cell proliferation and migration assay. The new device combined 3D-printed-silica-part for multi cell types loading with PDMS-through-hole-layer-part for cell micro-patterning which was matched with commercial 24-well-plate. This 24-well-plate based device is flexible and feasible in many applications and can be used in one piece or multi pieces. Besides the application for two types of cells proliferation and migration assay in one chemical condition, as a demonstration, the migration behaviors of four types of cells under 24 types of EGF + bFGF combinatorial conditions were studied. We believed this device could be widely used in clinical searching for new anti-cancer therapeutics and other related studies.

Robotic Cell Printing for Constructing Living Yeast Cell Microarrays in Microfluidic Chips

Living cell microarrays in microfluidic chips allow the non-invasive multiplexed molecular analysis of single cells. Here, we developed a simple and affordable perfusion microfluidic chip containing a living yeast cell array composed of a population of cell variants (green fluorescent protein (GFP)-tagged Saccharomyces cerevisiae clones). We combined mechanical patterning in 102 microwells and robotic piezoelectric cell dispensing in the microwells to construct the cell arrays. Robotic yeast cell dispensing of a yeast collection from a multiwell plate to the microfluidic chip microwells was optimized. The developed microfluidic chip and procedure were validated by observing the growth of GFP-tagged yeast clones that are linked to the cell cycle by time-lapse fluorescence microscopy over a few generations. The developed microfluidic technology has the potential to be easily upscaled to a high-density cell array allowing us to perform dynamic proteomics and localizomics experiments.

Mitogen-activated protein kinase (MAPK) dynamics determine cell fate in the yeast mating response

In the yeast Saccharomyces cerevisiae, the exposure to mating pheromone activates a prototypic mitogen-activated protein kinase (MAPK) cascade and triggers a dose-dependent differentiation response. Whereas a high pheromone dose induces growth arrest and formation of a shmoo-like morphology in yeast cells, lower pheromone doses elicit elongated cell growth. Previous population-level analysis has revealed that the MAPK Fus3 plays an important role in mediating this differentiation switch. To further investigate how Fus3 controls the fate decision process at the single-cell level, we developed a specific translocation-based reporter for monitoring Fus3 activity in individual live cells. Using this reporter, we observed strikingly different dynamic patterns of Fus3 activation in single cells differentiated into distinct fates. Cells committed to growth arrest and shmoo formation exhibited sustained Fus3 activation. In contrast, most cells undergoing elongated growth showed either a delayed gradual increase or pulsatile dynamics of Fus3 activity. Furthermore, we found that chemically perturbing Fus3 dynamics with a specific inhibitor could effectively redirect the mating differentiation, confirming the causative role of Fus3 dynamics in driving cell fate decisions. MAPKs mediate proliferation and differentiation signals in mammals and are therapeutic targets in many cancers. Our results highlight the importance of MAPK dynamics in regulating single-cell responses and open up the possibility that MAPK signaling dynamics could be a pharmacological target in therapeutic interventions.