Keynote Speaker: Evaluation of FluidFM technology for single-cell genome editing - Session - Genome Engineering
9/5/23, 2:20 PM - 9/5/23, 2:55 PM (Europe/Zurich) (35 minutes)

Keynote Speaker: Evaluation of FluidFM technology for single-cell genome editing - Session - Genome Engineering
Dr. Simona Patange

Keynote Speaker Highlight

Meet Simona Patange, PhD, biologist from the NIST Genome Editing Program. Let's find out how Simona has successfully employed FluidFM for delivery of genome editing reagents into single cells, for picking and placing single cells, and extracting cytoplasmic biopsies from single cells.

FluidFM Adhesion Measurement of Preosteoblasts - Research Summary By Cytosurge

Dr. Simona Patange of the NIST Genome Editing Program in process of calibrating a probe on the FluidFM OMNIUM.

How did you begin working with FluidFM technology?

The vision for bringing the FluidFM OMNIUM to NIST came from Dr. Samantha Maragh, my group leader and head of the NIST Genome Editing Consortium. Dr. Maragh was looking for technologies to fill a challenging need for her stakeholders: the ability to manipulate single human cells in a non-destructive automated manner for genome editing assays. Specifically, Dr. Maragh was looking for a technology that could precisely control the dose of reagent each cell received, so it could be directly linked to the genome editing outcome for that cell. A few years ago Dr. Maragh met Cytosurge at a conference, and out of those discussions it appeared FluidFM could meet this need for controlled single-cell manipulation.

I joined the NIST Genome Editing Program within the same year the FluidFM OMNIUM arrived to NIST. I have a background in biophysics and microscopy, so the timing was perfect because it was easy for me to step in and understand the principles of force control and microfluidics underlying FluidFM, and quickly take the lead on instrument operations for our Genome Editing Program and the Biosystems and Biomaterials Division at NIST

How has FluidFM influenced the way you approach your work?

The FluidFM OMNIUM has been a refreshing change in perspective because now I think about manipulating cells in terms of the ‘Bars’ of pressure, ‘Volts’ of deflection, and ‘Newtons’ of force! 🙂 Even had I not had a physics background, it was an easy perspective to adopt thanks to the instruction I received from several members of the Cytosurge team: Dario Ossola (OMNIUM Product Manager) who installed the instrument at NIST; Maria Milla Astals (Head of Customer Success) and Tamás Gerecsei (OMNIUM Sales Manager), who provided me with intensive training on the instrument; and Cytosurge’s application specialists who I’ve had many detailed discussions with since the time I've been operating the OMNIUM independently.

Can you share with us an example of a successful experiment or application you have accomplished using FluidFM technology?

My program is interested in several FluidFM capabilities useful to the genome editing process: single-cell injections; single-cell isolation; and more recently the ability to obtain single-cell biopsies, thanks to Orane Guillame-Gentil’s development of the Live-Seq method and Cytosurge’s adaptation of the technique for the OMNIUM. 

I’ve had success physically achieving all three of these capabilities on my OMNIUM instrument at NIST. I’ve injected genome editing reagents and other biomolecules, and confirmed their delivery into cells; I’ve picked and placed cells from one location to another in plates; and most recently I’ve had the privilege of being one of the first OMNIUM users to successfully extract cytoplasmic biopsies from cells. 

I am now working to apply NIST metrology methods to build confidence in the measurements that are made with the OMNIUM, such as the volumes or number of molecules that are injected into or extracted from a cell. This gets towards our aim of understanding and controlling dose at the single-cell level. I appreciate the many discussions I’ve had with Tobias Beyer and his CellEDIT team on using FluidFM for genome editing applications.

How do you envision the future evolution of FluidFM technology?

At NIST we seek to leverage FluidFM and other single-cell manipulation and measurement technologies for genome editing. Current tools traditionally operate at a bulk level: perturbations are applied to a population of cells, and measurements such as DNA sequencing or RNA and protein identification/quantitation are usually also performed upon a bulk sample obtained from a population of cells. 

The genome editing field has been able to make advances in biological understanding and therapeutic product development thanks to bulk manipulation and measurement methods, but it is becoming increasingly clear that these methods leave gaps in understanding that are becoming ever more important to fill. For instance, we know that spatial and temporal heterogeneity exists in a cell population. This means a population-averaged measurement may not accurately describe and could lead to misinterpretation about the characteristics of individual cells. Applying a genome editing perturbation to cells adds a further layer of heterogeneity, because different outcomes can occur in different cells.

For these reasons we seek the potential of FluidFM and other technologies that would allow us to have control over dose delivery and cellular sampling at the single cell level, and allow us to achieve high-resolution data on the single-cell distribution of genotypic and phenotypic information. My program recently published two Perspectives articles related to these concepts of considering a population vs. single cell viewpoint, where we take a critical look at the components of genome editing formulations (Patange & Maragh, 2022), and the variability in the source materials that are inputs in a genome editing process (Patange, Miller, & Maragh, 2023). 

What impact do you see this having for your research and the field?

From my own research with the FluidFM OMNIUM, I see that this instrument has pushed the boundaries of what we consider typical inputs and output quantities used in genome editing experiments. FluidFM allows us to work at a microscopic scale with quantities of cells and reagents not traditionally used in molecular biology assays.

This forces us to think differently about the measurements and quality control steps that need to be in place when processing samples for downstream assays and analyses. The NIST Genome Editing Program looks forward to continuing to include FluidFM in our research studies, building confidence in measurements obtained with single-cell manipulation technologies, and publishing our findings so they can be broadly informative to the biomedical research community. 

NIST DisclaimerCertain commercial equipment, instruments, materials, and suppliers, are identified in this interview to foster understanding. Such identification does not imply recommendation or endorsement by the National Institute of Standards and Technology, nor does it imply that the materials or equipment identified are necessarily the best available for the purpose.

Abstract: Genome editing is a rapidly evolving biotechnology with the potential to transform many sectors of industry. In order to introduce genome editing biomolecules into cells, one must use a reagent delivery method that could either manipulate cells in bulk or at the single-cell level. In this talk, I present our results using the “FluidFM OMNIUM,” a single-cell manipulation technology with potential applications for genome editing. I present our data on the OMNIUM measurement capabilities such as spatial recall, fluorescence detection, and microfluidic flow analysis— as well as its capability for targeted single-cell injections of genome editing reagents into human cells. Our research with FluidFM technology builds upon guidance provided in our recent publication [1], in which we summarize technologies related to research applications where it is advantageous to have controlled dose delivery of reagents and/or high-resolution data on the distribution of genomic and phenotypic outcomes of individual cells within a population.

[1] Patange, Simona, and Samantha Maragh. "Fire Burn and Cauldron Bubble: What Is in Your Genome Editing Brew?." Biochemistry (2022).