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Japanese Researchers Use Fluidigm's BioMark Platform for Stem Cell Expression Studies

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By Justin Petrone

This story has been updated to include more comments from Toshio Suda.

Fluidigm last week said that two leading Japanese stem cell experts have adopted its integrated fluidic circuit-based BioMark System for genetic analysis.

Toshio Suda of Keio University’s Graduate School of Medicine will use the BioMark to survey expression of mouse hematopoietic single stem cells, Fluidigm said. Shinya Yamanaka of Kyoto University's Institute for Integrated Cell-Material Sciences will use the system to analyze selected genes in induced pluripotent stem cells and quantify copies of specific genes transferred into a cell to generate iPS cells.

Suda and Yamanaka are "two of the most important stem-cell researchers and [are] at the very top of the list for Japan," according a Fluidigm spokesperson. She said the deals contributed to a recent "surge in Japanese sales."

Though Fluidigm has maintained a subsidiary in Tokyo since 2004 and has a "small sales team" to "work directly with customers," its actual sales in the country are coordinated through distributors, the spokesperson told BioArray News this week.

Founded in 1999, Fluidigm has commercialized three research platforms based on its IFC technology, which is a silicon-enclosed microfluidic chip designed to assay hundreds of reactions.

The three are: its TOPAZ system, which enables researchers to study protein crystallization; its EP1 system, which supports SNP genotyping and qPCR; and its BioMark system, which allows users to run qPCR, genotyping, and expression experiments on its 96.96 Dynamic Arrays. According to the firm, the arrays can produce up to 9,216 data points within single cells. Users can also perform digital PCR on the BioMark using Fluidigm's Digital Array chips.

Single-cell expression is a feature application for the platform and stem cell customers like Yamanaka and Suda choose the BioMark system because of this ability, the spokesperson said.

"Single-cell gene expression, stem cell, T cells in immunology, and more [research areas] are focused on understanding the variability of each individual cell," she said.

Keio and Kyoto

Suda and Yamanaka are both "important" in the Japanese stem cell research community, but have different research interests, Fluidigm's spokesperson said.

According to Fluidigm, Suda, who is part of Keio's 21st Century Center of Excellence Program, will use the BioMark to analyze selected genes in mouse hematopoietic stem cells. The interaction of HSCs within their particular microenvironment, known as the stem cell niche, is critical for adult hematopoiesis in bone marrow. He will explore how these niches maintain a balance between self-renewal and differentiation, information he hopes will ultimately lead to techniques for niche-based therapy, Fluidigm said.

Suda, who plans to use Fluidigm's Digital and Dynamic Arrays in his study, told BioArray News in an e-mail this week that prior to adopting BioMark, he had used quantitative PCR and microarrays to perform gene-expression profiling of HSCs and iPS cells. He said that he decided to adopt BioMark because the cost of running arrays is "expensive" so his lab "cannot repeat the experiments." In the past, Suda used Affymetrix's mouse genome 430 2.0 array.

Suda added that "stem cell genes are already known," and there is a need to "clarify which genes are most interesting" in a setting where monitoring the expression of a small number of cells is possible.

In addition to studying HSC expression, Suda said that he plans to conduct epigenetic analyses on iPS cells using the Fluidigm system. The benefit to healthcare will be the ex vivo expansion of HSCs, increased efficiency of the selection of iPS cells, and clarification of the mechanisms of reprograming of somatic cells," he added.

Meantime, Yamanaka and his group have developed a method to turn adult skin cells into the equivalent of human embryonic stem cells without using an actual embryo He hopes eventually to channel his efforts into treatments by growing replacement tissues for patients, Fluidigm said.

Yamanaka, who is the director of Kyoto's Center for iPS Cell Research and Application, plans to use the BioMark to analyze selected genes in iPS cells and quantify copies of specific genes transferred into a cell to generate iPS cells. Yamanaka declined an interview.

Suda and Yamanaka are not the first researchers to use the BioMark system for stem cell profiling. Other customers who have used the platform for surveying stem cells include Stanford University researchers Stephen Quake, Irving Weissman, and Mylene Yao, as well as Mikael Kubista, an investigator at the TATAA Biocenter in Göteborg, Sweden, according to the firm's spokesperson.

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