Publications

Liquid chromatography purification of multiple recombinant proteins, in parallel, could catalyze research and discovery if the processes are fast and approach the robustness of traditional, “one-protein-at-a-time” purification. Led by Robert Puccinelli and Rafael Gómez-Sjöberg of the BioE team at CZ Biohub San Francisco, we built an automated, four channel chromatography platform for parallelized protein purification at milligram scales. Using our instrument, we purified, in parallel, coronavirus (SARS-CoV-2, HCoV-229E, HCoV-OC43, HCoV-229E) trimeric Spike antigens, and monoclonal antibodies. We include a detailed hardware build guide, and have made the controlling software open source, to allow others to build and customize their own protein purifier systems.

Serology can provide valuable diagnostic and epidemiological data on antibody responses to SARS-CoV-2 infection and vaccination. In this collaborative study, co-led by Shalin Mehta (CZ Biohub SF), Bryan Greenhouse (UCSF), Manu Prakash (Stanford University), and others, we built and validated an open-source platform for multiplex serology imaging and analysis. Built on top of a simple 96-well plate-based ELISA format, we show that our open-source tools for ELISA-array image acquisition and quantification can compete with commercial options, thus lowering the barriers to obtaining high-content, multiplexed serosurveillance data.

In this study, led by Brian Hie and Peter Kim (Stanford University), language-model guided affinity maturation of antibodies was developed and evaluated for seven antibodies. By screening only a small number of variants (20 or fewer), binding affinities were improved despite providing the model with no information about the target antigen. Our contribution to the study was to generate and purify the recombinant antibodies at high throughput.

B cell depletion, using anti-CD20 monoclonal antibodies (mAbs), is a successful treatment for relapsing multiple sclerosis (MS). The ability of chimeric antigen receptor (CAR-) T cells to penetrate the central nervous system, however, may offer a therapeutic benefit over existing mAb therapies. In this study, led by Scott Zamvil (UCSF), anti-CD19 CAR-T cells that target B-cells were shown to ameliorate disease in an experimental autoimmune encephalomyelitis (EAE) mouse model for MS. Our contribution to this study was the recombinant production of myelin oligodendrocyte glycoprotein that was used to immunize mice and induce EAE.

Severe COVID-19 is associated with epithelial and endothelial barrier dysfunction within the lung as well as in distal organs. In this study, led by Eva Harris (UC Berkeley), we report that cell-intrinsic interactions between the Spike (S) glycoprotein of SARS-CoV-2 and epithelial/endothelial cells are sufficient to trigger barrier dysfunction in vitro and vascular leak in vivo. Our contribution to this study was to produce and characterize a panel of SARS-CoV-2 Spike and RBD antigens, for in vitro and in vivo analyses.

The size and complexity of antibody repertoires of B cells can make it difficult to identify convergent immune responses. In this collaborative study with the Data Science platform (Biohub), we developed AIRRscape, an R Shiny-based interactive web browser application that enables B-cell receptor (BCR) and antibody feature discovery through comparisons among multiple repertoires.

Mutations in the SARS-CoV-2 Spike protein can lead to the loss of efficacy of antibody-based treatments. In this study, led by Peter Kim (Stanford/Biohub), broad-spectrum SARS-CoV-2 inhibitors were developed by tethering ACE2 to non-neutralizing antibodies that target highly conserved epitopes in the viral spike protein. Our contribution to this study was to perform phylogenetic analyses of anti-SARS-CoV antibody sequences, to identify candidate antibodies for tethering to ACE2.

Many existing protein detection strategies depend on highly functionalized antibody reagents. In this study, led by Alice Ting (Stanford/Biohub), a single-component, recombinant, luminescent biosensor that can be expressed in E. coli and S. cerevisiae is described. Our contribution to this study was to produce SARS-CoV-2 Spike and RBD proteins, which were used to performance test the assay.

COVID-19 vaccines and many clinical diagnostics are based on the structure and function of the SARS-CoV-2 Spike ectodomain. In this study, led by Susan Marqusee (UC Berkeley/Biohub), hydrogen deuterium exchange mass spectrometry was used to discover a new, open-trimer conformation that is distinct from known structures. Our contribution to this study was to produce and biophysically characterize the SARS-CoV-2 Spike protein under a variety of conditions.

Severe COVID-19 is associated with epithelial and endothelial barrier dysfunction within the lung as well as in distal organs. In this study, led by Eva Harris (UC Berkeley), we report that cell-intrinsic interactions between the Spike (S) glycoprotein of SARS-CoV-2 and epithelial/endothelial cells are sufficient to trigger barrier dysfunction in vitro and vascular leak in vivo. Our contribution to this study was to produce and characterize a panel of SARS-CoV-2 Spike and RBD antigens, for in vitro and in vivo analyses.

Interpretation of SARS-CoV-2 serosurveillance studies is limited by poorly defined performance of antibody assays over time in individuals with different clinical presentations. In this study, led by Bryan Greenhouse (UCSF/Biohub), antibody responses in plasma samples from 128 individuals over 160 days were measured using 14 assays. Our contribution to this study was to produce SARS-CoV-2 Spike and Nucleocapsid proteins, for use in serology assays.

Serosurveillance provides a unique opportunity to quantify the proportion of the population that has been exposed to pathogens. In this study, led by Isabel Rodriguez-Barraquer (UCSF/Biohub), remnant blood draws from two major hospital networks in San Francisco were tested for SARS-CoV-2 antibodies. Our contribution to this study was to produce SARS-CoV-2 Spike and Nucleocapsid proteins, for use in serology assays.

Individuals with COVID-19 frequently develop neurological symptoms, but the cause of this neurologic sequelae is unclear. In this study, led by Shelli Farhadian (Yale University), CNS-specific T cell activation and B cell responses were identified from COVID-19 individuals with neurological symptoms. Our contribution to this study was to measure the binding kinetics and affinity of cerebrospinal fluid-derived antibodies for SARS-CoV-2 Spike.

Serology has provided valuable diagnostic and epidemiological data on antibody responses to SARS-CoV-2 in diverse patient cohorts. In this study, a collaborative effort across several groups at the Biohub, we report multiSero, an open platform for multiplex serology with up to 48 antigens in a 96-well format.

The Abbott BInaxNOW rapid assay is a popular, lateral flow assay that detects SARS-CoV-2 N protein directly from nasal swab samples. In this study, led by Diane Havlir (UCSF) and Joseph DeRisi (UCSF/Biohub), the performance characteristics of the Binax test in a community screening setting was examined. Our contribution to this study was to produce SARS-CoV-2 N protein, for use in measuring the lot-to-lot variability of the tests in detecting N.

It is critical to develop tools for rapid and accessible diagnosis of individuals actively infected with SARS-CoV-2. In this study, led by Markita Landry (UC Berkeley/Biohub), single-walled carbon nanotubes were functionalized with ACE2 and evaluated as a nanosensor for detecting SARS-CoV-2 Spike. Our contribution to this study was to produce SARS-CoV-2 Spike protein, for use in measuring the sensitivity of the nanosensor.

Protein subunit vaccines are an attractive option for an accessible SARS-CoV-2 vaccine for reasons including safety, scalability, and ease of distribution. This study, led by Peter Kim (Stanford/Biohub), showed that ferratin nanoparticles that display a truncated SARS-CoV-2 Spike can elicit neutralizing antibodies at higher levels than Spike or RBD alone. Our group contributed to this study by assisting with the biophysical characterization of the homogeneity and oligomeric state of the Spike ferratin nanoparticles.

In July 2020, the COVID-19 diagnostic laboratory (CLIAHUB) at the Biohub identified 40+ samples from Madera Country, California that exhibited poor N-gene assay performance, due to a genetic polymorphism in N. Our group contributed to this study by mapping this polymorphism onto the three-dimensional structure of N, to estimate functional significance. In unpublished work, we also purified N protein with this polymorphism and showed that it was biophysically indistinguishable from wild type N.

At the onset of the COVID-19 pandemic, there was little known about the human antibody response to SARS-CoV-2. This study, led by Michel Nussenzweig (Rockefeller University), reported on the antibody responses to SARS-CoV-2 in 149 COVID-19 convalescent individuals, showing that potent neutralizing antibodies were found in all individuals, and which suggested that vaccines designed to elicit such antibodies could be broadly effective. Our group contributed to this study by designing and producing biotinylated SARS-CoV-2 Spike and RBD antigens, which were used to isolate antigen specific B cells from convalescent plasma.

In 2016, Catalonia experienced a pediatric brainstem encephalitis outbreak caused by enterovirus A71. This study, led by Michael Wilson (UCSF) and Joseph DeRisi (Biohub/UCSF), significantly increased the detection of enterovirus in the cerebrospinal fluid, relative to conventional qRT-PCR testing. Our group contributed to this study by producing EV71 antigens, which were used to profile the specificity of antibodies in the cerebrospinal fluid of affected children.

An important goal of vaccine design for Dengue fever is to elicit broadly neutralizing antibodies against the four dengue virus serotypes (DENV1-4). This study, led by Leslie Goo (Biohub), uncovered antibodies from DENV-infected individuals that exhibited potent, pan-DENV neutralization. Our group contributed to this study by biophysically characterizing the homogeneity and oligomeric state of these antibodies.

Acute flaccid myelitis (AFM) is an uncommon but serious polio-like illness that affects the spinal cord of children. This study, led by Michael Wilson (UCSF) and Joseph DeRisi (Biohub/UCSF), uncovered evidence for a causal role of non-polio enterovirus in AFM. Our group contributed to this study by producing a panel on enterovirus antigens, which were used to profile the specificity of antibodies in the cerebrospinal fluid of children with AFM.