See background of NCD 32985. 

The identifcation of high-affinity peptide epitopes displayed on MHC-I molecules is an important first step in understanding cell-mediated immune responses and in the development of targeted immunotherapies to treat infections or cancer. This task is typically addressed through the useof highly sensitive mass-spectroscopy approaches and machine learning algorithms. However, this approach is hampered by peptide loss during the upstream purification step. The approach is also hampered by a lack of specificity in purification.  This technology involves the use of peptide-receptive MHC-I molecules in complex made using the TAPBPR chaperone. The peptide receptive MHC-I can be immobilized on chromatography columns or magnetic beads. They can provide unprecedented levels of highly specific peptide recovery 

Tech ID 32985/Case number 2018-408 describes the generation of E. coli expressed, peptide receptive MHC-I monomers and multimers using the TAPBPR chaperone. In this case, the technology was improved based upon the surprising discovery that the TAPBPR chaperone acts catalytically on MHC-I-placeholder peptide complexes to create peptide receptive MHC-I species. 

Typically, peptide receptive MHC-I multimer reagents are prepared in bacterial (E. coli) culture. While this is efficient, it does not result in glycosylation of the MHC-I peptide fragments as is done in mammalian cells. As a result, if such reagents are produced in mammalian cells, proper glycosylation would result and the reagents would have a potentially more accurate representation of the natural T-cell target.  

MHC Class I multimers are key reagents that are used in the identification of antigen specific T cells + an antigenic peptide. The most useful form of such a reagent involves a Class I MHC molecule that is provided ready to be loaded with an antigenic peptide of interest. However, such molecules are inherently unstable. Potential solutions to the instability have major drawbacks. Some MHC Class I molecules are provided with a conditional ligand that can be cleaved by exposure to UV light. These constructs are prone to aggregation and precipitation, must be stored and worked with in the dark, and they can have relatively poor peptide exchange efficiency. Other peptide receptive MHC class I molecules are engineered to have disulfide links holding the peptide to the MHC-I binding groove. In addition to altering natural peptide-MHC-I binding, such molecules are diffficult to express in bacterial vectors.UC Santa Cruz researchers and the Office of Innovation Transfer have collaborated to produce a robust patent portfolio around a new method of producing peptide receptive class I MHC multimers that produce MHC-I molecules at a high yield with highly efficient peptide exchange. A description of the original system (2018-408) is below. Related inventions include: 2019-975 - a system that uses peptide receptive MHC-I made using TAPBPR to purify a antigenic peptides from a peptide library. The peptides bind to immobilized peptide receptive MHC-I conjugated to a column, then are later eluted. 2020-284 - specific placeholder peptides and methods for creating peptide receptive HLA-A*68:02 and HLA*A24:022020-297 -  an invention resulting from the surprising result that TAPBPR acts catalytically on MHC-I/placeholder peptide complexes to form peptide receptive MHC-I. A 1:10,000 ration of TAPBPR:MHC-I placeholder peptide produces peptide receptive MHC-I as efficiently as a 1:1 ratio. 2020-251 - co-expression of TAPBPR with MHC-I in mammalian cells. This has the following advantages: (a) placeholder peptides are not needed, (b) peptide receptive MHC-I can be purified directly from the culture, (c) the MHC-I molecules are glycosylated as they would be in a mammalian immune system.  

Prof. Min Xue from the University of California, Riverside and Prof. Wei Wei from the Institute for Systems Biology have developed materials and  methods to detect and measure FA uptake alone or simultaneously with protein detection in multiplex down to single-cell resolution. FA analogs with an azide functional group mimics natural FAs. Specially designed small polymers are used to efficiently assay the FA analogs and produce fluorescent or chemical signals upon binding. The technology is compatible with protein analysis and generally applicable to other metabolites and proteins. Fig 1: Schematic of the UCR-ISB method for detecting fatty acid uptake from single cells.  

New chemistries are emerging for the direct attachment of complex molecules to cell surfaces. Chemistries that modify cells must perform under a narrow set of conditions in order to maintain cell viability. They must proceed in buffered aqueous media at the optimal physiological pH—typically pH 7.4—and within a temperature range of 4 – 37 ºC. Furthermore, these reactions must have sufficiently rapid kinetics to achieve high conversion even when confronted with the limits of surface diffusion characteristics. Due to these requirements, few chemistries exist that can attach molecules and proteins to live cells.  There is a need for improved methods of attaching proteins to living cells.   UC researchers have developed a convenient enzymatic strategy for the modification of cell surfaces for targeted immunotherapy applications.  

Researchers at the University of California, Davis, have developed an environmentally friendly one-pot multienzyme (OPME) method for synthesizing sialidase reagents, probes, and inhibitors.

RNA-binding proteins (RBPs) play essential roles in gene expression and other cellular functions. Thus their identification and the understanding of their mechanisms of action and regulation is key to unraveling physiology and disease. To measure translation efficiency and different steps of ribosome recruitment, the state of the art is ribosome profiling (or Ribo‐seq) and polysome profiling which uses millions of cells, sucrose gradients, centrifugation and often requires the removal of ribosomal RNA as part of the sequencing library preparation as it contaminates more than 50% of most ribosome/polysome libraries. Also, we cannot distinguish full length isoforms here, as the ribosome‐fragments are short.

The number of color channels that can be concurrently probed in fluorescence microscopy is severely limited by the broad fluorescence spectral width. Spectral imaging offers potential solutions, yet typical approaches to disperse the local emission spectra notably impede the attainable throughput.    UC Berkeley researchers have discovered methods and systems for simultaneously imaging up to 6 subcellular targets, labeled by common fluorophores of substantial spectral overlap, in live cells at low (~1%) crosstalks and high temporal resolutions (down to ~10 ms), using a single, fixed fluorescence emission detection band. 

Prof. Talbot and her colleagues from the University of California, Riverside have developed a research tool to prolong the viability and pluripotency of stem cells in culture. The culture medium is supplemented with an additive that includes a source of acetate ions, a carboxylic acid, or a salt of the carboxylic acid, or a combination of these substances. Results have shown that this substrate medium allows for less stem cell death, faster colony growth, and causes cells to attach to and spread faster on the substrate. This provides tremendous advantages in stem cell colony morphology, growth, survival, maintenance of pluripotency, and dynamic behavior when compared to existing media.  Fig 1: Images of stem cells in culture before and after treatment  

Nonalcoholic fatty liver disease (NAFLD) is the most common cause of chronic liver disease in the United States. It can be broadly sub-classified into nonalcoholic fatty liver (NAFL), which is thought to have minimal risk of progression to cirrhosis, and nonalcoholic steatohepatitis (NASH), which is thought to have an increased risk of progression to cirrhosis. The current diagnostic gold standard for differentiating whether a patient with NAFLD has NAFL versus NASH is liver biopsy. However, liver biopsy is an invasive procedure, which is limited by sampling variability, cost, and may be complicated by morbidity and even death, although rare. Accurate, non-invasive, biomarkers for the detection of liver disease and liver disease progression e.g., progression to NASH, are currently also not available.

Researchers at the University of California, Davis have developed monoclonal antibodies with multiple applications relevant to canine PD-1 and PD-L1.

Researchers at UCSF and Chan Zuckerberg Biohub have discovered a novel biomarker for an autoimmune disease that affects patients with testicular cancer.  The disease, known as “testicular cancer-associated paraneoplastic encephalitis,” can cause severe neurological symptoms.  The symptoms include loss of limb control, eye movement, and in some cases, speech.  The disease begins with testicular cancer, which in some cases causes the immune system to attack the brain.  Affected patients are often misdiagnosed and appropriate treatment is delayed. 

UCLA researchers in the Department of Medicine have developed small molecule ENPP1 inhibitors and monoclonal antibodies for treating myocardial infarction and ocular calcification.

UCLA researchers in the Department of Medicine have developed small molecule ENPP1 inhibitors and monoclonal antibodies for treating myocardial infarction and ocular calcification.

Control of gene expression is a general approach to treat diseases where there is too much or too little of a gene product. However, while there are many methods which are available to downregulate the expression of messenger RNA transcripts, very few strategies can upregulate the endogenous gene product. The vast majority of gene regulatory drugs which are commercially available or being developed are designed to knockdown gene expression (i.e. siRNAs, miRNAs, anti-sense, etc.). There exist some methods to enhance gene expression, such as the delivery of messenger RNAs; although, therapeutic delivery of such large and charged RNA molecules is technically challenging, inefficient, and may not be practical. There are also classical gene therapy approaches where a gene product is delivered as viral-encoded products (AAV or lentivirus-packaged). However, these methods suffer from not being able to accurately reproduce the correct alternatively spliced isoforms in the right ratios in cells.  

UCLA researchers in the Department of Chemistry and Biochemistry have developed a new chemical reaction that combines ozone, an iron salt, and a hydrogen atom donor to enable hydrodealkenylative cleavage of C(sp3)–C(sp2) bonds in a widely applicable manner.

UCLA researchers in the Department of Medicine and the Department of Molecular and Medicinal Pharmacology have identified several small molecule reagents to treat Cushing disease.

Puromycin is an aminonucleoside antibiotic produced by the bacterium Streptomyces alboniger. Its mode of action is to inhibit protein synthesis by disrupting peptide transfer on ribosomes, leading to premature chain termination during protein translation. Puromycin blocks protein synthesis in both eukaryotes and prokaryotes and is routinely used as a research tool in cell culture. The native Puromycin is also used assays such as mRNA display. As such, derivatives have been synthesized in which the amino acid of the 3' end of adenosine based antibiotics is altered to change the compound's antibiotic activity. Other compounds have been synthesized with differing amino acids and functionalities to examine the effect it has on bacterial viability. The majority do not show useful absorption or emission profiles. What is needed is a method to track the compounds in biological systems.

UCLA Researchers at the California NanoSystems Institute have developed a methodology that permits PCR-based detection of nucleic acid sequences in soil that does not require the isolation of DNA.

Researchers in the UCLA Department of Chemistry and Biochemistry and the University of Texas-Medical Center, Houston Department of Microbiology and Molecular Genetics have modified the Corynebacterium diphtheriae (C. diphtheriae) sortase enzyme so that it can be used as a bioconjugation reagent in vitro.

Researchers led by Saman Sadeghi from the Department of Molecular & Medical Pharmacology at UCLA have developed a new and simple process to make fluorinated organic compounds.

Single-cell analysis offers powerful capabilities of identification of rare sub-populations of cells, understanding heterogeneity of cancerous tumors, and tracking cell differentiation and reprogramming. Despite great potentials for uncovering new biological systems and targeting diseases with precision medicine, single-cell approaches are composed of complex device processes that can cause bias in measurement.  In deep sequencing, technical variation in single cell expression data occurs during capture and pre-amplification steps. Similarly, in single-cell protein assays, technical variability can obscure functionally relevant variance.    To better control protein measurement quality in single-cell assays, researchers at the University of California, Berkeley developed a novel method to loading and release protein standard. This method utilizes the surface of modified and functionalized microparticles as vehicles to capture target proteins with desired concentrations. Chelation-assisted click chemistry is applied to demonstrate that protein standards with different molecular masses can be loaded and bounded in a single-cell protein assay. Microparticles are introduced into single-cell devices by either passive gravity, magnetic attraction, or other physicochemical forces. These protein standards from microparticles provide a reference to measure protein mass sizes from individual cells and a quality control for any biases in device fabrication, cell lysis, protein solubility, protein capture, and protein readouts (i.e. antibody probing).   

Clinical treatment for scar-less wound healing remains a highly desired, yet unmet need. UCI researchers have developed a method to minimize scarring during wound healing through cellular reprograming that encourages formation of new skin fat cells. This novel therapy is non-surgical and applicable to multiple types of scars and aging skin.