Cell by Cell Mapping of the Cancer Transcriptome

Genetic Engineering News – by Richard Stein – A biological system may resist interrogation, slowing our efforts to identify system components and understand how they work, individually and in combination. And so we work to enhance our interrogation techniques, for while extracting information from a biological system is challenging, it is also indispensable to a range of missions: revealing how cells organize into tissues, dissecting disease pathogenesis, and advancing diagnostic and treatment efforts.

To find ways of improving cell-level intelligence gathering, a global initiative was organized in late 2016. This initiative, called the Human Cell Atlas, proposes to create comprehensive reference maps of all human cells as a basis for both understanding human health and diagnosing, monitoring, and treating disease. The Human Cell Atlas relies, to a great extent, on the use of transcriptome sequencing to profile the gene expression of individual cells.

Not-So-Hidden GemCodes

“We developed a fast way of profiling tens of thousands of cells, where for each cell, we capture gene expression in an unbiased way,” says Benjamin J. Hindson, Ph.D., CSO, president, and cofounder of 10x Genomics. The resulting profile, he noted, is “essentially like a fingerprint of each different cell in a particular sample.”

In a recent study, Dr. Hindson and colleagues described 10x Genomics’ GemCode technology, a droplet-based platform that combines microfluidics with molecular barcoding and custom bioinformatics software to enable 3′ mRNA counting from thousands of single cells. With GemCode, cells are captured in droplets, and the reverse transcription that occurs within each droplet is used to generate barcoded cDNA.

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