Forum for Science, Industry and Business

Sponsored by:     3M 
Search our Site:

 

New device for low-cost single-cell analysis identifies fibroblast subtypes in RA patients

26.02.2018

Portable, low-cost microfluidic device brings single-cell technology to the bedside; identifies cells that may prove to be important drug targets

Single-cell analysis holds enormous potential to study how individual cells influence disease and respond to treatment, but the lack of cost-effective and user-friendly instrumentation remains challenging. As described in a study published today in Nature Communications, researchers at the New York Genome Center (NYGC) and New York University (NYU) have taken steps to facilitate broad access to single-cell sequencing by developing a 3D-printed, portable and low-cost microfluidic controller.


Researchers at the New York Genome Center (NYGC) and New York University (NYU) have taken steps to facilitate broad access to single-cell sequencing by developing a 3-D-printed, portable and low-cost microfluidic controller. To demonstrate the utility of the instrument in clinical environments, the researchers deployed the device to study synovial tissue from patients with rheumatoid arthritis (RA) at the Hospital for Special Surgery (HSS).

Credit: New York Genome Center

To demonstrate the utility of the instrument in clinical environments, the researchers deployed the device to study synovial tissue from patients with rheumatoid arthritis (RA) at the Hospital for Special Surgery (HSS).

In the study, the researchers describe the 3D-printed custom device, which, along with its electronic and pneumatic components, can be easily obtained and assembled for a total cost of about $600, a fraction of the cost of comparable commercial systems. The device occupies a small footprint as well, not much larger than a tissue box.

"Most commercial microfluidic instruments are very costly; as a result, not every lab has access to exciting technology for single-cell analysis," said William Stephenson PhD, Senior Research Engineer in the NYGC's Technology Innovation Lab, who led the development of the instrument and is a lead author on the study. "We designed the instrument to perform droplet microfluidics and in particular Drop-seq, a massively parallel technology for single cell RNA-sequencing."

In collaboration with researchers and clinicians at HSS, a world leader in rheumatology research and disease treatment, the group used the instrument to profile joint synovial tissue from RA patients. RA is an autoimmune disease that affects 1% of the population and is associated with painful swelling in the joints. The precise cause of RA is undetermined and muddled by the diversity of cells found in the swollen joints of patients.

The portability of the controller permitted patient samples to be processed on-site and immediately after surgery, minimizing handling and transport to optimize sample quality. The researchers collected samples from five RA patients totaling 20,387 cells and looked at the individual gene expression patterns for each cell.

"This dataset gave us the opportunity to identify individual subpopulations of cells that could drive the progression of RA, even if they have not been previously characterized," said Rahul Satija PhD, a Core Faculty Member at NYGC, Assistant Professor of Biology at NYU, and senior author on the study.

By analyzing the complete dataset and searching for clusters of similar cells, the researchers identified 13 groups, representing both infiltrating immune and inflamed stromal populations. Of particular interest were distinct groups of fibroblasts with strikingly different gene expression patterns.

"Roughly an hour after surgical excision, individual cells from patient tissues were labeled for single-cell sequencing. From this work, we have classified unrecognized fibroblast subtypes that may prove to be important drug targets for our RA patients," said Laura Donlin, Co-Director of the HSS Precision Medicine Lab and Assistant Professor at Weill Cornell Medicine, and a lead author on the study. The researchers were able to validate the presence of these multiple groups using flow cytometry, and discovered that they exhibited distinct localization patterns with the joint tissue as well.

The dataset is a step towards creating a comprehensive "cell atlas" for synovial tissue from RA patients. Moving forward, the researchers are compiling data from additional RA patients, and aim to obtain patient samples from other arthritic conditions such as psoriatic arthritis and osteoarthritis. In addition, they plan to use CITE-seq, a technique also developed in the Technology Innovation Lab at the NYGC, to more precisely classify cell types by measuring the presence of surface proteins in addition to the transcriptome.

They also envision that technology will be useful for profiling samples that are difficult to study in a standard lab, such as highly infectious samples in biocontainment facilities or samples being collected in field research settings. To facilitate its widespread use in the scientific and medical community, the instrument has been fully "open-sourced."

Instructions and assembly manuals for the instrument can be found online at the popular microfluidics repository Metafluidics. "We hope that this instrument lowers the hurdles associated with performing single-cell transcriptome profiling experiments in basic research and clinical settings," Dr. Stephenson said.

###

About the New York Genome Center

The New York Genome Center (NYGC) is an independent, nonprofit academic research institution at the forefront of transforming biomedical research and clinical care. Founded as a collaborative venture by the region's premier academic, medical and industry leaders, the New York Genome Center's goal is to translate genomic research into new diagnostics, therapeutics and treatments for human disease. NYGC member organizations and partners are united in this unprecedented collaboration of technology, science and medicine, designed to harness the power of innovation and discoveries to advance genomic services. Their shared objective is the acceleration of medical genomics and precision medicine to benefit patients around the world.

Member institutions include: Albert Einstein College of Medicine, American Museum of Natural History, Cold Spring Harbor Laboratory, Columbia University, Hospital for Special Surgery, The Jackson Laboratory, Memorial Sloan Kettering Cancer Center, Icahn School of Medicine at Mount Sinai, New York-Presbyterian Hospital, The New York Stem Cell Foundation, New York University, Northwell Health, Princeton University, The Rockefeller University, Roswell Park Cancer Institute, Stony Brook University, Weill Cornell Medicine and IBM. For more information on the NYGC, please visit http://www.nygenome.org.

Media Contact:

Karen Zipern, Director, Communications, NYGC
kzipern@nygenome.org
o: 646-977-7065
c: 917-415-8134

Karen Zipern | EurekAlert!

More articles from Life Sciences:

nachricht Researchers target protein that protects bacteria's DNA 'recipes'
21.08.2018 | University of Rochester

nachricht Protein interaction helps Yersinia cause disease
21.08.2018 | Schwedischer Forschungsrat - The Swedish Research Council

All articles from Life Sciences >>>

The most recent press releases about innovation >>>

Die letzten 5 Focus-News des innovations-reports im Überblick:

Im Focus: It’s All in the Mix: Jülich Researchers are Developing Fast-Charging Solid-State Batteries

There are currently great hopes for solid-state batteries. They contain no liquid parts that could leak or catch fire. For this reason, they do not require cooling and are considered to be much safer, more reliable, and longer lasting than traditional lithium-ion batteries. Jülich scientists have now introduced a new concept that allows currents up to ten times greater during charging and discharging than previously described in the literature. The improvement was achieved by a “clever” choice of materials with a focus on consistently good compatibility. All components were made from phosphate compounds, which are well matched both chemically and mechanically.

The low current is considered one of the biggest hurdles in the development of solid-state batteries. It is the reason why the batteries take a relatively long...

Im Focus: Color effects from transparent 3D-printed nanostructures

New design tool automatically creates nanostructure 3D-print templates for user-given colors
Scientists present work at prestigious SIGGRAPH conference

Most of the objects we see are colored by pigments, but using pigments has disadvantages: such colors can fade, industrial pigments are often toxic, and...

Im Focus: Unraveling the nature of 'whistlers' from space in the lab

A new study sheds light on how ultralow frequency radio waves and plasmas interact

Scientists at the University of California, Los Angeles present new research on a curious cosmic phenomenon known as "whistlers" -- very low frequency packets...

Im Focus: New interactive machine learning tool makes car designs more aerodynamic

Scientists develop first tool to use machine learning methods to compute flow around interactively designable 3D objects. Tool will be presented at this year’s prestigious SIGGRAPH conference.

When engineers or designers want to test the aerodynamic properties of the newly designed shape of a car, airplane, or other object, they would normally model...

Im Focus: Robots as 'pump attendants': TU Graz develops robot-controlled rapid charging system for e-vehicles

Researchers from TU Graz and their industry partners have unveiled a world first: the prototype of a robot-controlled, high-speed combined charging system (CCS) for electric vehicles that enables series charging of cars in various parking positions.

Global demand for electric vehicles is forecast to rise sharply: by 2025, the number of new vehicle registrations is expected to reach 25 million per year....

All Focus news of the innovation-report >>>

Anzeige

Anzeige

VideoLinks
Industry & Economy
Event News

LaserForum 2018 deals with 3D production of components

17.08.2018 | Event News

Within reach of the Universe

08.08.2018 | Event News

A journey through the history of microscopy – new exhibition opens at the MDC

27.07.2018 | Event News

 
Latest News

Air pollution leads to cardiovascular diseases

21.08.2018 | Ecology, The Environment and Conservation

Researchers target protein that protects bacteria's DNA 'recipes'

21.08.2018 | Life Sciences

A paper battery powered by bacteria

21.08.2018 | Power and Electrical Engineering

VideoLinks
Science & Research
Overview of more VideoLinks >>>