NEW YORK — A molecular cell biologist and a computational biologist have combined forces to offer a new approach for tracking cell lines in the lab, with the hope of improving research reproducibility.
With a new software tool, Sophie Zaaijer and Tyler Joseph, cofounders of Find Genomics, aim to enable researchers to improve their lab workflows and track their cell lines more easily, including genetic changes that have occurred in them.
Concerns about the reproducibility of research findings, particularly in the preclinical space, have been around for years. These worries have not only touched off efforts to reproduce findings from key papers but also brought attention to slight differences in protocols and organismal strains that might also influence research results.
Cell lines have been a particular source of concern, as between 18 percent and 36 percent of common cell lines are suspected of being mislabeled or contaminated. Additionally, new cell lineages may form due to selection in the lab — either conscious or unconscious — as well as through genetic modifications, such as with CRISPR.
Part of these issues may be avoided by keeping better track of cell lines and limiting slight deviations from protocols, according to Zaaijer, the CEO of the New York-based startup.
"One of the things we wanted to solve is that there's not a good way to really record, to monitor, and to de-risk experiments," she said. "This is where we saw an opportunity to really help biomedicine move faster, and that's also why our mission became to accelerate biomedicine by reproducible cell-based science."
In a recent article in Nature Biotechnology, Zaaijer, New York University's Simon Groen, and Neville Sanjana from NYU and the New York Genome Center noted that lineage formations among cell lines in the lab are inevitable and unavoidable. Many can be traced to common laboratory practices such as the establishment of cell lines themselves, as cells must adapt to a two-dimensional environment, as well as passaging protocols and freeze-thaw frequencies.
"You cannot stop evolution. But you can track it and understand when an error or when a change happens," Zaaijer added.
The Find Cell tool, which launched last month, aims to do just that. It is a secure, cloud-based software program where researchers can use graphical representations to track their cell lines. At first, a single cell line is represented by a circle — a petri dish — but when researchers note they have passaged their lines, two circles appear, and these circles eventually form what is akin to a cell line family tree. Next-generation sequencing data on the cell lines can also be incorporated to confirm cell line identity and stability.
Researchers can further share this cell line information with collaborators, both in their own lab and elsewhere, according to Zaaijer.
Sandy Vogt, a Ph.D. student at NYU who served as a beta tester of Find Cell, uses the program to keep track of the pancreatic cancer and fibroblast cell lines she is working with and their associated protocols. She said that the tool could help with research reproducibility by making it easier for researchers to note when they thawed new cell lines or when they passaged them.
"Especially with cancer cell lines, if you keep them in culture for too long, they're going to maybe acquire new mutations or shift genetically in an undesirable way that could influence how your experiments are turning out," Vogt said.
By keeping close track of cell lines, when freezes occurred, and when tests for Mycoplasma contamination were run, researchers may be able to salvage more of their work if something does go awry. "Maybe the error happened last week, then you can basically only go back a week ago and not have to go back five years because you don't have any provenance information," Zaaijer said.
This, she added, saves not only time, but also money in the form of salary and reagent costs.
Currently, academic labs can use Find Cell to manage their cell lines for free. Zaaijer noted that the firm is offering the tool to academic researchers as they helped the company build and beta-test it and as one of their aims is to bolster academic biomedical research. Pharmaceutical companies, though, need a subscription, which varies in price based on the size of the company.
Find Genomics, which is housed at Cornell Tech on Roosevelt Island in New York City, currently has funding from angel investors and consists of Zaaijer, Joseph, and part-time contractors who have aided with development and operations.
Zaaijer added that the firm is continuing to optimize its tool based on feedback from users, and, though it is focusing on Find Cell, has plans to develop additional tools, as it aims to be a source for everything related to cells line.