Liquid Biopsy (LB) Core

Blood Infusion into the Chip

DAPI-stained CTC

Rare cell affinity isolation chip. The chip is made from a plastic via injection molding and consists of a series of sinusoidally-shaped channels. Each channel contains affinity agents that can be tailored to fit the user’s application. This chip can be operated by the robotic platform.

References

1. Capture and Enumeration of Circulating Tumor Cells from Peripheral Blood using Microfluidics, A.A. Adams, P. Okagbare, J. Feng, R.L. McCarley, M.C. Murphy and S.A. Soper, J. Am. Chem. Soc. 130 (2008) 8633-8641.
2. Highly Efficient Capture and Enumeration of Low Abundance Prostate Cancer Cells Using Prostate-Specific Membrane Antigen Aptamers Immobilized to a Polymeric Microfluidic Device. U. Dharmasiri, S. Balamurugan, R.L. McCarley, D. Spivak and S.A. Soper, Electrophoresis 30 (2009) 3289-3300.
3. Microsystems for the Capture of Low Abundant Cells, U. Dharmasiri, A.A. Adams, M. Witek and S.A. Soper, Annual Reviews in Analytical Chemistry 3 (2010) 409-431.
4. High-throughput Selection, Enumeration, Electrokinetic Manipulation, and Molecular Profiling of Low-Abundance Circulating Tumor Cells. U. Dharmisiri, S.A. Soper, Anal. Chem. 83 (2011) 2301-2309.
5. Modular microfluidic system for the high throughput selection, enumeration and phenotyping of circulating tumor cells, J. Kamande, H. Wang, J.J. Yeh, M.L. Hupert and S.A. Soper, Anal. Chem. 85 (2013) 9092-9100.
6. Circulating tumor cells as a possible marker for micrometastatic disease in patients with localized pancreatic cancer, R.D. Aufforth, J.J. Baker, M.A. Witek, J.W. Kamande, H.J. Kim, P. Kuan, S.A. Soper and J.J. Yeh, Annals of Surgical Oncology, 20 (2013) S129.
7. Circulating tumor cells as a biomarker of response to treatment in patient derived xenograft mouse models of pancreatic adenocarcinoma, R.J. Torphy, C.J. Tignanelli, R.A. Moffitt, S.A. Soper, J.J. Yeh, J. Am. College Surgeons, 217 (2013) S30.
8. Arrays of high-aspect ratio microchannels for high-throughput isolation of circulating tumor cells, M.L. Hupert, J.M. Jackson, H. Wang, M.A. Witek, J. Kamande, M.I. Milowsky, Y.E. Whang and S.A. Soper, Microsyst. Technol. (2013; DOI 10.1007/s00542-013-1941-6).
9. Parallel affinity-based isolation of leukocyte subsets using microfluidics: Applications for stroke diagnosis, S.R. Pullagurla, M.A. Witek, J.M. Jackson, M.M. Lindell, M.L. Hupert, I.V. Nesterova, A.E. Baird and S.A. Soper, Anal. Chem. 86 (2014) 4058-4065.
10. Circulating tumor cells as a biomarker of response to treatment in patient-derived xenograft mouse models of pancreatic adenocarcinoma, Trophy, R.J., Tignanelli, C.J., Kamande, J.W., R.A. Moffitt, S.G. Herrera Loeza, S.A. Soper, J.J. Yen, PLOS ONE 9 (2014) e89474.
11. Capture and Enzymatic Release of Circulating Tumor Cells, Soumya Nair, Joshua Jackson, Maggie Witek, V. Bae-Jump, P.A. Gehrig, W.Z. Wysham, P.M. Armistead, P. Voorhees and S.A. Soper, Chemical Communications 51 (2015) 3266-3269.
12. Rapid Assessment of Minimal Residual Acute Myeloid Leukemia from Peripheral Blood Using a Microfluidic Chip, Jackson, JM , Taylor, J , Witek, M , Hunsucker, SA, Waugh, JP , Fedorw, YD , Shea, TC , Soper, SA , Armistead, PM, Blood 126 (2015) 1389.
13. Detection of Minimum Residual Disease in Acute Myeloid Leukemia using Integrated Microfluidic Systems, J.M. Jackson, J. Taylor, S.A. Hunsucker, P.A. Armistead and S.A. Soper, Analyst 141 (2016) 640-651.
14. Improved Clinical Sensitivity Detection of Circulating Tumor Cell Assays using a Dual Selection Strategy in Women with Epithelial Ovarian Cancer, W. Wysham, M. Witek, S.A. Soper, P. Gehrigh, J. Stine and V. Bae-Jump, Gynecologic Oncology, 141 (2016) 138-139.
15. Materials and Microfluidics: Enabling the Efficient Isolation and Analysis of Circulating Tumour Cells, J.M. Jackson, M. Witek, J. Kamande and S.A. Soper, Chem. Soc. Rev. 46 (2017) 4245-4280.
16. Discrete Microfluidics for the Isolation of Circulating Tumor Cell Subpopulations Targeting Fibroblast Activation Protein Alpha and Epithelial Cell Adhesion Molecule, M.A. Witek, R.D. Aufforth, H. Wang, J. Kamande, J.M. Jackson, S. Pullagurla, M. Hupert, J. Usary, W. Wysham, D. Hilliard, S. Montgomery, V. Bae-Jump, L. Carey, P. Gehrig, M. Milowsky, C. Perou, J. Soper, Y. Whang. J.J. Yeh, G. Martin and S.A. Soper, npj Precision Oncology 1 (2017) 24.
17. Isolation of Circulating Plasma Cells from Blood of Patients Diagnosed with Clonal Plasma Cell Disorder using Cell Selection Microfluidics, S.A. Soper, J. Kamande, M. Lindell, M. Witek and P. Voorhees, Integr. Biol. 10 (2018) 82 – 91.

Extracellular Vesicle (EV) Isolation

The Core uses a plastic chip consisting of a high density array of micropillars (each chip has 1.5M pillars) that can be activated to allow for the covalent attachment of affinity agents to each pillar. The high surface area of the chip allows for selecting >10¹¹ particles, and release the EVs in a total volume of 22.4 µ L. The chip is manufactured via injection molding in a high production mode. The chip can recover >80% of the EVs at a volume flow are ~25 µ L/min. The chip can be operated on the fluid handling robot.

• EVs isolated directly from plasma/serum/urine based on affinity interaction of antigens loaded onto the surface of pillars.
• Can be customized to any surface antigen of interest
• EVs can be released intact from chip for downstream applications

Finished Chip




EV affinity isolation chip. The chip is made from a plastic, in this case cyclic olefin copolymer (COC), that can be UV/O3 activated to allow for direct antibody attachment. Each pillar contains surface immobilized affinity agents (any affinity agent can be used to suit the application need). The chip can be operated by the liquid handling robot. Because the chip is made via injection molding, the cost per assay is low and any clinical study can be supported.

References

1. Microfluidic Enrichment of Extracellular Vesicles for Diagnosing Ischemic Stroke, H. N. K. Wijerathne, M. W. Witek, J. M. Jackson, A. E. Baird, and S. A. Soper, Nature Communications – Biology (2020, manuscript under review).
2. Microfluidic Affinity Purification Chip for the Enrichment of Cancer-Associated Exosomes, V. Brown, J.M. Jackson, M.W. Witek, A. K. Godwin, and S.A. Soper, LOC (2020, manuscript under review).

Cell Free DNA (cfDNA), genomic DNA and RNA Isolation

We have developed an inexpensive microfluidic chip that can be used for the solid-phase extraction of DNA (cfDNA, plasmid DNA, genomic DNA) with high efficiency and using a very simple procedure. The chip is made from a plastic that can be injection molded to produce the chip at low cost and in high numbers to support any clinical study. When compared to existing solid-phase extraction techniques (Qiagen, Norgen), it exceeds their recovery values across a large DNA size range (recovery >85%). In addition, the solid-phase extraction chip can be used to extract total RNA as well. The chip can be operated by our fluid handling robot and process 16 samples at any one time and with full automation. Here are the salient features of this solid-phase extraction technique:

• Solid-phase extracted DNA size can be controlled by the immobilization buffer composition (PEG, NaCl, EtOH)
• cfDNA mass load ~2,000 ng per chip
• cfDNA eluted in a small volume, ~20 µL
• Elution buffer of your choice: PCR buffer, water, TE, etc

Ready-to-use Chip


Solid-phase extraction chip for DNA and RNA. The chip is made from a plastic and can accommodate up to 2,000 ng of cfDNA. The chip consists of micropillars to increase provide the high mass load of DNA. By simply changing the composition of the immobilization buffer, which consists of polyethylene glycol (PEG), salt (NaCl or MgCl2), and ethanol (EtOH), the size of DNA preferentially extracted can be selected. Because the chip is made from a plastic, it can be injected molded at very low cost and at high rates. Following molding, the chip requires UV/O3 activation and cover plate bonding and is ready to use for solid-phase extractions.