The New York Genome Center (NYGC) and the New York University (NYU) researchers have developed a 3D-printed, portable, and low-cost microfluidic controller.
The new 3D microfluidic controller provides access to single-cell sequencing.
It helps to demonstrate the use of the device in clinical environments and they have deployed the device to study synovial tissue from patients with Rheumatoid Arthritis (RA) at the Hospital for Special Surgery (HSS).
The specific cause of RA is undetermined and mixed-up by the diversity of cells found in the swollen joints of patients.
The compact, tissue box-sized device performs droplet microfluidics and in particular Drop-seq, a massively parallel technology for single cell RNA-sequencing.
The 3D-printed custom device and its electronic and pneumatic components are easily obtained and assembled.
The researchers have gathered samples from five RA patients totaling 20,837 cells and examined individual gene expression patterns for each cell.
The patient samples can be processed on-site due to the portability of the controller, reduced handling and transport to optimize sample quality, immediately after surgery.
13 groups were identified by analysing the complete dataset and searching for clusters of similar cells. These groups represent both infiltrating immune and inflamed stromal populations.
The presence of these multiple groups was validated using flow cytometry, revealing that they exhibited distinct localisation patterns with the joint tissue as well.
The dataset is a step toward creating a comprehensive “cell atlas” for synovial tissue from RA patients.
The researchers are now collecting data from additional RA patients, and 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.
The device has been fully open-sourced in order to facilitate its widespread use in the scientific and medical community.
Instructions and assembly manuals for this device can be found online at the popular microfluidics repository.
Researchers hope that this device lowers the hurdles associated with performing single-cell transcriptome profiling experiments in basic research and clinical settings.