Adam R. Abate
University of California-San Francisco, CA·Biomedical Engineering
Many infections cause similar symptoms, and drug resistance is rising. That makes it hard to find the right pathogen and pick a treatment quickly.
- Fields
Biomedical Engineering
Microbiology & Immunology
Neuroscience
- Topics
digital PCR
dPCR
gigapixel PCR
- Grants
- 3 known grants, through Jul 2028
What they work on
- Develop gigapixel PCR (gPCR), which pairs microfluidic-free self-assembled droplets with capillary electrophoresis readout, to quantify over 100 pathogen DNA targets in one reaction. Validate it against SeraCare reference standards.
- Apply gPCR to stored respiratory and central nervous system infection samples from UCSF hospitals to measure absolute pathogen loads and identify the causative organism.
- Build gigapixel NGS, which uses double emulsion droplets sorted on standard flow cytometers, to detect, isolate and sequence pathogen genomes from patient samples.
- Develop clinical workflows and bioinformatic tools that search recovered pathogen genomes for virulence factors and drug-resistance genes.
- Develop SEARCH-seq, a cytometry method that detects RNA or DNA markers at single-molecule sensitivity, to isolate rare cells for transcriptomic, genomic or epigenomic analysis.
- Determine how the receptor NR3C2 and corepressor NCOR2 limit XBP1-driven harmful astrocytes in multiple sclerosis, using SEARCH-seq, knockout mice, CRISPR/Cas9 and EAE mouse and human samples.
More about the research
Some important cells in the body are also rare, too rare to study with standard methods. These projects share a toolkit for splitting samples into millions of tiny droplets. Each droplet holds single molecules or single cells, which can then be counted, sorted or sequenced. The lab applies this approach to two problems: faster, more quantitative infection testing, and isolating rare brain cells involved in multiple sclerosis.
Why it matters
Hospital infections must be diagnosed and treated fast. Tests that report exact pathogen amounts for over 100 microbes, or sequence pathogen genomes for drug-resistance genes, could help clinicians pick the true cause and the right drug sooner, such as for brain and respiratory infections. In multiple sclerosis, isolating rare harmful astrocytes may reveal mechanisms that could become treatment targets.
Known grants
From NIH and NSF research grants. Labs often have other funding we can't see.
Identification of Regulatory Mechanisms Operating in Rare Pathogenic Astrocyte Subsets in Multiple Sclerosis with a Novel Genomic Technology
NIH · Aug 2023 – Jul 2028
Next Generation Infectious Disease Diagnostics: Microfluidic-Free Gigapixel PCR with Self-Assembled Partitioning
NIH · Jun 2023 – May 2028
Gigapixel Next-Generation-Sequencing: An Ultra-Sensitive Diagnostic for Infections of the CNS
NIH · Nov 2023 – Oct 2027
Closest labs
Igal Ifergan
University of Cincinnati, OH·Microbiology & Immunology
Characterize mature (CD27- CD11b+) and immature (CD27+ CD11b-) natural killer cell subsets in the brain and spinal cord across stages of relapsing-remitting EAE, a mouse model of MS, using single-cell RNA sequencing.
Booki Min
Northwestern University, IL·Microbiology & Immunology
Determine how Lag3, an inhibitory surface co-receptor, lets Foxp3+ regulatory T cells suppress autoimmune neuroinflammation, using mice with the Lag3 outer domain, cytoplasmic tail or KIEELE motif deleted only in Tregs.
Mingnan Chen
University of Utah, UT·Pharmacology
Determine why a depleting anti-PD-1 antibody delays diabetes in early insulitis but accelerates it in late insulitis in NOD mice, profiling pancreatic islets and systemic immune cells by single-cell RNA sequencing and flow cytometry before and after treatment.
The school
University of California-San Francisco: 89 labs on PI Pages, $2.1B a year on research, 164 research doctorates a year.
Reach out
A start for your email. Fill in the brackets.