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NIH Director’s Early Independence Award

A GPS-like System for Single-Cell Analysis

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Courtesy of the Chen and Macosko labs

A few years ago, I highlighted a really cool technology called Drop-seq for simultaneously analyzing the gene expression activity inside thousands of individual cells. Today, one of its creators, Evan Macosko, reports significant progress in developing even better tools for single-cell analysis—with support from an NIH Director’s New Innovator Award.

In a paper in the journal Science, Macosko, Fei Chen, and colleagues at the Broad Institute of Harvard and Massachusetts Institute of Technology (MIT), Cambridge, recently unveiled another exciting creation called Slide-seq [1]. This technology acts as a GPS-like system for mapping the exact location of each of the thousands of individual cells undergoing genomic analysis in a tissue sample.

This 3D video shows the exquisite precision of this new cellular form of GPS, which was used to generate a high-resolution map of the different cell types found in a tiny cube of mouse brain tissue. Specifically, it provides locations of the cell types and gene expression in the hippocampal regions called CA1 (green), CA2/3 (blue), and dentate gyrus (red).

Because using Slide-seq in the lab requires no specialized imaging equipment or skills, it should prove valuable to researchers across many different biomedical disciplines who want to look at cellular relationships or study gene activity in tissues, organs, or even whole organisms.

How does Slide-seq work? Macosko says one of the main innovations is an inexpensive rubber-coated glass slide nicknamed a puck. About 3 millimeters in diameter, pucks are studded with tens of thousands of 10 micron-sized beads, each one decorated with a random snippet of genetic material—an RNA barcode—that serves as its unique identifier of the bead.

The barcodes are sequenced en masse, and the exact location of each barcoded bead is indexed using innovative software developed by a team led by Chen, who is an NIH Director’s Early Independence awardee.
Then, the researchers place a sample of fresh-frozen tissue (typically, 10 micrometers, or 0.00039 inches, thick) on the puck and dissolve the tissue, lysing the cells and releasing their messenger RNA (mRNA). That leaves only the barcoded beads binding the mRNA transcripts expressed by the cells in the tissue—a biological record of the genes that were turned on at the time the sample was frozen.

The barcoded mRNA is then sequenced. The spatial position of each mRNA molecule can be inferred, using the reference index on the puck. This gives researchers a great deal of biological information about the cells in the tissue, often including their cell type and their gene expression pattern. All the data can then be mapped out in ways similar to those seen in this video, which was created using data from 66 pucks.

Slide-seq has been tested on a range of tissues from both mouse and human, replicating results from similar maps created using existing approaches, but also uncovering new biology. For example, in the mouse cerebellum, Slide-seq allowed the researchers to detect bands of variable gene activity across the tissues. This intriguing finding suggests that there may be subpopulations of cells in this part of the brain that have gene activity influenced by their physical locations.

Such results demonstrate the value of combining cell location with genomic information. In fact, Macosko now hopes to use Slide-seq to study the response of brain cells that are located near the buildup of damaged amyloid protein associated with the early-stage Alzheimer’s disease. Meanwhile, Chen is interested in pursuing cell lineage studies in a variety of tissues to see how and where changes in the molecular dynamics of tissues can lead to disease.

These are just a few examples of how Slide-seq will add to the investigative power of single-cell analysis in the years ahead. In meantime, the Macosko and Chen labs are working hard to develop even more innovative approaches to this rapidly emerging areas of biomedical research, so who knows what “seq” we will be talking about next?


[1] Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution. Rodriques SG, Stickels RR, Goeva A, Martin CA, Murray E, Vanderburg CR, Welch J, Chen LM, Chen F, Macosko EZ. Science. 2019 Mar 29;363(6434):1463-1467.


Single Cell Analysis (NIH)

Macosko Lab (Broad Institute of Harvard and MIT, Cambridge)

Chen Lab (Broad Institute)

NIH Support: National Institute on Aging; Common Fund

Creative Minds: Do Celebrity Endorsements Influence Teens’ Health?

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Marie Bragg

Marie Bragg

Marie Bragg is a first-generation American, raised by a mother who immigrated to Florida from Trinidad. She watched her uncle in Florida cope effectively with type 2 diabetes, taking prescription drugs and following doctor-recommended dietary changes. But several of her Trinidadian relatives also had type 2 diabetes, and often sought to manage their diabetes by alternative means—through home remedies and spiritual practices.

This situation prompted Bragg to develop, at an early age, a strong interest in how approaches to health care may differ between cultures. But that wasn’t Bragg’s only interest—her other love was sports, having played on a high school soccer team that earned two state championships in Florida. That made her keenly aware of the sway that celebrity athletes, such as Michael Jordan and Serena Williams, could have on the public, particularly on young people. Today, Bragg combines both of her childhood interests—the influence of celebrities and the power of cultural narratives—in research that she is conducting as an Assistant Professor of Population Health at New York University Langone Medical Center and as a 2015 recipient of an NIH Director’s Early Independence Award.

Creative Minds: Applying CRISPR Technology to Cancer Drug Resistance

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Patrick Hsu

Patrick Hsu

As a child, Patrick Hsu once settled a disagreement with his mother over antibacterial wipes by testing them in controlled experiments in the kitchen. When the family moved to Palo Alto, CA, instead of trying out for the football team or asking to borrow the family car like other high school kids might have done, Hsu went knocking on doors of scientists at Stanford University. He found his way into a neuroscience lab, where he gained experience with the fundamental tools of biology and a fascination for understanding how the brain works. But Hsu would soon become impatient with the tools that were available to ask some of the big questions he wanted to study.

As a Salk Helmsley Fellow and principal investigator at the Salk Institute for Biological Studies, La Jolla, CA, Hsu now works at the intersection of bioengineering, genomics, and neuroscience with a DNA editing tool called CRISPR/Cas9 that is revolutionizing the way scientists can ask and answer those big questions. (This blog has previously featured several examples of how this technology is revolutionizing biomedical research.) Hsu has received a 2015 NIH Director’s Early Independence award to adapt CRISPR/Cas9 technology so its use can be extended to that other critically important information-containing nucleic acid—RNA.Specifically, Hsu aims to develop ways to use this new tool to examine the role of a certain type of RNA in cancer drug resistance.

Creative Minds: Fighting Cancer with Supercomputers

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Amanda Randles

Amanda Randles

After graduating college with degrees in physics and computer science, Amanda Randles landed her dream first job. She joined IBM in 2005 to work on its Blue Gene Project, which had just unveiled the world’s fastest supercomputer. So fast, in fact, it’s said that a scientist with a calculator would have to work nonstop for 177,000 years to perform the operations that Blue Gene could complete in one second. As a member of the applications team, Randles was charged with writing new code to make the next model run even faster.

Randles left IBM in 2009 for graduate school, with the goal to apply her supercomputing expertise to biomedical research. She spent the next several years developing the necessary algorithms to produce a high-resolution 3D model of the human cardiovascular system, complete with realistic blood flow. Now, an assistant professor at Duke University, Durham, NC, and a 2014 NIH Director’s Early Independence awardee, Randles will build on her earlier work to attempt something even more challenging: simulating the movement of cancer cells through the circulation to predict where a tumor is most likely to spread. Randles hopes all of her late nights writing code will one day lead to software that helps doctors stage cancer more precisely and gives patients accurate personalized computer simulations that put an earlier, potentially life-saving bullseye on secondary tumors.

Creative Minds: Harnessing Technologies to Study Air Pollution’s Health Risks

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Perry Hystad

Perry Hystad
Credit: Hannah O’Leary, Oregon State University

After college, Perry Hystad took a trip to India and, while touring several large cities, noticed the vast clouds of exhaust from vehicles, smoke from factories, and soot from biomass-burning cook stoves. As he watched the rapid urban expansion all around him, Hystad remembers thinking: What effect does breathing such pollution day in and day out have upon these people’s health?

This question stuck with Hystad, and he soon developed a profound interest in environmental health. In 2013, Hystad completed his Ph.D. in his native Canada, studying the environmental risk factors for lung cancer [1, 2, 3]. Now, with the support of an NIH Director’s Early Independence Award, Hystad has launched his own lab at Oregon State University, Corvallis, to investigate further the health impacts of air pollution, which one recent analysis indicates may contribute to as many as several million deaths worldwide each year [4].

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