Sample to Answer System for Isolation and Detection of Circulating Cell Free DNA, RNA, and Exosome Biomarkers for Liquid Biopsy Cancer Diagnostics

Friday, February 26, 2016 - 2:00pm
Fung Auditorium | Powell-Focht Bioengineering Hall
Michael Heller

Departments of Bioengineering and Nanoengineering
UC San Diego

Sample to Answer System for Isolation and Detection of Circulating Cell Free DNA, RNA, and Exosome Biomarkers for Liquid Biopsy Cancer Diagnostics


Circulating cell free (ccf) DNA and RNA are now considered important biomarkers for liquid biopsy cancer diagnostics, and exosome biomarkers hold particular promise for early cancer detection. Nevertheless, the isolation of ccf-DNA, RNA and exosomes from patient samples requires relatively complex, time consuming and expensive procedures which greatly limits their practical use for most cancer diagnostic applications. New AC dielectrophoretic (DEP) microarray/chip devices now allow 15-20-minute isolation of cancer related ccf-DNA, RNA and exosome biomarkers from 20-50ul of blood, plasma or serum. After isolation of the biomarkers, specific fluorescent dyes can be used first to simultaneously detect the different biomarker levels directly on the chip (in-situ). In a subsequent step, immunofluorescent analysis can be carried out to identify specific protein biomarkers on the exosomes. Finally, the ccf-DNA and RNA (mRNAs and miRNAs release from the exosomes) can be eluted from the DEP chip, and PCR and sequencing analysis carried out to identify the cancer-related point mutations and other polymorphisms, as well as to further verify the tissue origin of the biomarkers. In the case of our Chronic Lymphocytic Leukemia clinical studies, final PCR and DNA sequencing results for the CLL related ccf-DNA isolated by DEP were found to be exactly comparable to two much more complex and time consuming “gold standard” procedures. In the case of glioblastoma exosomes isolated from plasma, exosome-specific surface and interior proteins CD63 and TSG101 could be detected by immunofluorescence, and mutated EGFRvlll mRNA was detected by RT-PCR. For cancer diagnostics, the DEP technology is now setting the stage for seamless sample to answer liquid biopsy, cancer patient therapy monitoring and ultimately for early and minimal disease detection. In other clinical areas, DEP is being used for the isolation and detection of exosomes and mRNA biomarkers for traumatic brain injury (TBI), protein aggregate (beta-amyloid, tau, etc.) biomarkers for Alzheimer’s Disease, and for isolating drug delivery nanoparticles from blood. DEP microarray devices and systems are now being developed for commercialization by Biological Dynamics, a new cancer diagnostic’s company founded by Dr. Raj Krishnan, who was a former UCSD Bioengineering student of Dr. Heller.


Michael J. Heller received his Ph.D. in Biochemistry from Colorado State University in 1973. He was an NIH Postdoctoral Fellow at Northwestern University from 1973 to 1976. From 1976 to 1984 he was supervisor of the DNA Technology Group at Amoco Corporation (Standard Oil Indiana) During that time he carried out early bioengineering and recombinant DNA work on plants, algae and photosynthetic bacteria for energy and chemical production, and he developed some of the first fluorescent resonant energy transfer (FRET) and chemiluminescent oligonucleotide probes for DNA hybridization analysis. He also oversaw Amoco’s sponsored energy and chemical research work at Cetus Corporation, which included the cloning of thermophilic enzymes. Dr. Heller was the Director of Molecular Biology at Molecular Biosystems, Inc., from 1984 to 1987. He was a co-founder of Integrated DNA Technologies, and served as President and Chief Operating Officer from 1987 to 1989. He was a co-found of Nanogen, and served as the Chief Technical Officer from 1993 to 2001. Nanogen carried out the successful development and commercialization of electronic DNA microarray technology for clinical diagnostic genotyping applications. Dr. Heller is now a Professor in the Departments of Nanoengineering and Bioengineering at the University California San Diego. He has recently co-founded a new company called Biological Dynamics which is developing new sample to answer cancer diagnostics technology, based on the novel dielectrophoretic (DEP) technology developed at his UCSD lab. Dr. Heller has extensive industrial experience in biotechnology, biomedical and molecular diagnostic devices and nanotechnology, with particular expertise in the areas of DNA probe diagnostics, DC and AC electrokinetic devices, DNA synthesis, FRET/fluorescent-based detection technologies and electric field assisted self-assembly of DNA nanocomponents. Dr. Heller has a respectable publication record, and has been an invited speaker to a large number of scientific conferences, which now include recent meetings on cell free nucleic acid and exosome biomarkers for cancer detection and molecular diagnostics. He also has over 50 issued US patents in the molecular diagnostics, biotechnology and nanotechnology areas.