Faculty Bibliography

Understanding antibody responses to SARS-CoV-2 is indispensable for the development of containment measures to overcome the current COVID-19 pandemic. Recent studies showed that serum from convalescent patients can display variable neutralization capacities. Still, it remains unclear whether there are specific signatures that can be used to predict neutralization. Here, we performed a detailed analysis of sera from a cohort of 101 recovered healthcare workers and we addressed their SARS-CoV-2 antibody response by ELISA against SARS-CoV-2 Spike receptor binding domain and nucleoprotein. Both ELISA methods detected sustained levels of serum IgG against both antigens. Yet, the majority of individuals from our cohort generated antibodies with low neutralization capacity and only 6% showed high neutralizing titers against both authentic SARS-CoV-2 virus and the Spike pseudotyped virus. Interestingly, higher neutralizing sera correlate with detection of -IgG, IgM and IgA antibodies against both antigens, while individuals with positive IgG alone showed poor neutralization response. These results suggest that having a broader repertoire of antibodies may contribute to more potent SARS-CoV-2 neutralization. Altogether, our work provides a cross sectional snapshot of the SARS-CoV-2 neutralizing antibody response in recovered healthcare workers and provides preliminary evidence that possessing multiple antibody isotypes can play an important role in predicting SARS-CoV-2 neutralization.

Background: Glioblastoma (GBM) is the most common and deadly primary brain malignancy in adults. Tumor propagation, brain invasion, and resistance to therapy critically depend on GBM stem-like cells (GSCs). Given the aggressiveness and poor prognosis of GBM, it is imperative to find biomarkers that could also translate into novel drug targets. Along these lines, we have identified a cell surface antigen, CD97 (ADGRE5), an adhesion G proteincoupled receptor (GPCR), that is expressed on GBM cells but is absent from non-neoplastic brain tissue.
Design(s): We assessed CD97 mRNA and protein expression in patient-derived GBM samples and cultures using publicly available RNA-sequencing datasets and flow cytometry, respectively. To assess CD97 function, we utilized shRNA lentiviral constructs that target CD97 or scrambled shRNA (scr) with no predicted targets in the genome. We evaluated CD97 shRNA lentivirally transduced GBM cells for proliferation, apoptosis, and their ability to selfrenew using clonogenic tumorsphere formation assays. Further, we utilized synthetic Abs (sAbs) generated against the extacellular domain (ECD) of CD97 to test for potential antitumor effects using patient-derived GBM cell lines.
Result(s): CD97 mRNA was expressed at high levels in all GBM's in the TCGA cohort. We found high levels of surface CD97 protein expression in 6/6 patient-derived GBM cell cultures, but not human neural stem cells. CD97 KD(knockdown) induced a significant reduction in cell growth in 3 independent GBM cell lines representing mesenchymal and proneural subtypes, which was accompanied by reduced (~20%) Ki67 staining and increased (~30%) apoptosis. Using three unique GBM patient-derived cultures, we found that CD97 KD attenuated the ability of GBM cells to initiate sphere formation by over 300 fold, consistent with an impairment in GSC self-renewal. Incubation of GBM cells with sAbs (20 mg/ ml) against the ECD of CD97 for 3 days induced GSC differentiation, as determined by the expression of GFAP and tubulin.
Conclusion(s): Loss of CD97 expression in patient-derived GBM cells markedly decreased proliferation, induced cell death, and reduced tumorsphere formation. sAbs against the ECD of CD97 induced differentiation, suggesting that sAbs that inhibit CD97 function will exhibit anti-tumor activity. Collectively, these findings indicate that CD97 is necessary to support the maintenance of human GBM cells and identify CD97 as a promising therapeutically targetable vulnerability in GBM

KRAS is the most frequently mutated human oncogene, and KRAS inhibition has been a longtime goal. Recently, inhibitors were developed that bind KRASG12C-GDP and react with Cys-12 (G12C-Is). Using new affinity reagents to monitor KRASG12C activation and inhibitor engagement, we found that an SHP2 inhibitor (SHP2-I) increases KRAS-GDP occupancy, enhancing G12C-I efficacy. The SHP2-I abrogated RTK feedback signaling and adaptive resistance to G12C-Is in vitro, in xenografts, and in syngeneic KRASG12C-mutant pancreatic ductal adenocarcinoma (PDAC) and non-small cell lung cancer (NSCLC). SHP2-I/G12C-I combination evoked favorable but tumor site-specific changes in the immune microenvironment, decreasing myeloid suppressor cells, increasing CD8+ T cells, and sensitizing tumors to PD-1 blockade. Experiments using cells expressing inhibitor-resistant SHP2 showed that SHP2 inhibition in PDAC cells is required for PDAC regression and remodeling of the immune microenvironment but revealed direct inhibitory effects on tumor angiogenesis and vascularity. Our results demonstrate that SHP2-I/G12C-I combinations confer a substantial survival benefit in PDAC and NSCLC and identify additional potential combination strategies.

The ability to quantify protein-ligand interactions in an accurate and high-throughput manner is important in diverse areas of biology and medicine. Multiplex bead binding assays (MBBAs) are powerful methods that allow for simultaneous analysis of many protein-ligand interactions. Although there are a number of well-established MBBA platforms, there are few platforms suitable for research and development that offer rapid experimentation at low costs and without the need for specialized reagents or instruments dedicated for MBBA. Here, we describe a MBBA method that uses low-cost reagents and standard cytometers. The key innovation is the use of the essentially irreversible biotin-streptavidin interaction. We prepared a biotin-conjugated fluorescent dye and used it to produce streptavidin-coated magnetic beads that are labeled at distinct levels of fluorescence. We show the utility of our method in characterization of phage-displayed antibodies against multiple antigens of SARS-CoV-2, which substantially improves the throughput and dramatically reduces antigen consumption compared with conventional phage ELISA methods. This approach will make MBBAs more broadly accessible.

The COVID-19 pandemic remains a global threat, and host immunity remains the main mechanism of protection against the disease. The spike protein on the surface of SARS-CoV-2 is a major antigen and its engagement with human ACE2 receptor plays an essential role in viral entry into host cells. Consequently, antibodies targeting the ACE2-interacting surface (ACE2IS) located in the receptor-binding domain (RBD) of the spike protein can neutralize the virus. However, the understanding of immune responses to SARS-CoV-2 is still limited, and it is unclear how the virus protects this surface from recognition by antibodies. Here, we designed an RBD mutant that disrupts the ACE2IS and used it to characterize the prevalence of antibodies directed to the ACE2IS from convalescent sera of 94 COVID19-positive patients. We found that only a small fraction of RBD-binding antibodies targeted the ACE2IS. To assess the immunogenicity of different parts of the spike protein, we performed in vitro antibody selection for the spike and the RBD proteins using both unbiased and biased selection strategies. Intriguingly, unbiased selection yielded antibodies that predominantly targeted regions outside the ACE2IS, whereas ACE2IS-binding antibodies were readily identified from biased selection designed to enrich such antibodies. Furthermore, antibodies from an unbiased selection using the RBD preferentially bound to the surfaces that are inaccessible in the context of whole spike protein. These results suggest that the ACE2IS has evolved less immunogenic than the other regions of the spike protein, which has important implications in the development of vaccines against SARS-CoV-2.

The COVID-19 pandemic remains a global threat, and host immunity remains the main mechanism of protection against the disease. The spike protein on the surface of SARS-CoV-2 is a major antigen and its engagement with human ACE2 receptor plays an essential role in viral entry into host cells. Consequently, antibodies targeting the ACE2-interacting surface (ACE2IS) located in the receptor-binding domain (RBD) of the spike protein can neutralize the virus. However, the understanding of immune responses to SARS-CoV-2 is still limited, and it is unclear how the virus protects this surface from recognition by antibodies. Here, we designed an RBD mutant that disrupts the ACE2IS and used it to characterize the prevalence of antibodies directed to the ACE2IS from convalescent sera of 94 COVID19-positive patients. We found that only a small fraction of RBD-binding antibodies targeted the ACE2IS. To assess the immunogenicity of different parts of the spike protein, we performed in vitro antibody selection for the spike and the RBD proteins using both unbiased and biased selection strategies. Intriguingly, unbiased selection yielded antibodies that predominantly targeted regions outside the ACE2IS, whereas ACE2IS-binding antibodies were readily identified from biased selection designed to enrich such antibodies. Furthermore, antibodies from an unbiased selection using the RBD preferentially bound to the surfaces that are inaccessible in the context of whole spike protein. These results suggest that the ACE2IS has evolved less immunogenic than the other regions of the spike protein, which has important implications in the development of vaccines against SARS-CoV-2.

Recent advances in biotechnology have enabled the rapid identification of peptides that bind to inorganic materials. Here, we aimed to identify peptides that bind to indium tin oxide (ITO) nanoparticles via different binding mechanisms, using phage display and biopanning, under five different buffer conditions. Three types of ITO-binding peptides (ITOBPs) were selected from 10 types of identified peptide candidates for characterization. These included ITOBP8, which had an acidic isoelectric point, and was identified when a buffer containing guanidine was used, and ITOBP6 and ITOBP7, which contained a His-His-Lys sequence at their N-termini, and were identified when a highly concentrated phosphate elution buffer with a low ionic strength was used. Among these peptides, ITOBP6 exhibited the strongest ITO-binding affinity (dissociation constant, 585 nmol/L; amount of protein bound at saturation, 17.5 nmol/m2-ITO particles). These results indicate that peptides with specific binding properties can be obtained through careful selection of the buffer conditions in which the biopanning procedure is performed. Further examination is needed to determine the suitability of this approach for the rapid identification of metal oxide-binding peptides.

Recent advances in biotechnology have enabled the generation of antibodies with high affinity for the surfaces of specific inorganic materials. Herein, we report the synthesis of functional materials from multiple nanomaterials by using a small bispecific antibody recombinantly constructed from gold-binding and ZnO-binding antibody fragments. The bispecific antibody-mediated spontaneous linkage of gold and ZnO nanoparticles forms a binary gold-ZnO nanoparticle composite membrane. The relatively low melting point of the gold nanoparticles and the solubility of ZnO in dilute acidic solution then allowed for the bottom-up synthesis of a nanoporous gold membrane by means of a low-energy, low-environmental-load protocol. The nanoporous gold membrane showed high catalytic activity for the reduction of p-nitrophenol to p-aminophenol by sodium borohydride. Here, we show the potential utility of nanoparticle pairing mediated by bispecific antibodies for the bottom-up construction of nanostructured materials from multiple nanomaterials.

Background Targeting and engineering gammadelta T cells has recently emerged as an orthogonal therapeutic approach in oncology with capacity to modulate both innate and adaptive immune properties. In solid tumors such as pancreatic ductal adenocarcinoma (PDA), melanoma, glioblastoma, ovarian, and breast cancer, gammadelta1 T cells express immunosuppression-related molecules and possess a protumorigenic capacity. We have shown that intra-tumoral gammadelta T cells from PDA, colorectal cancer (CRC) and hepatocellular carcinoma (HCC) potently suppress patients' alphabeta T cells. To harness the therapeutic potential of gammadelta1 T cell blockade, we developed highly specific, fully human antibodies against delta1-subset of gammadeltaT cell receptor (gammadelta1- TCR). Methods We determined the amino acid sequences of tumor specific delta1-TCR chains from primary PDA, CRC and gastric cancer samples. Multiple gammadelta-TCR proteins were produced and used to screen a proprietary synthetic, human antibody library using phage display. Surface plasmon resonance and bead-based assays were used to measure binding affinity and specificity. Affinity maturation was performed to improve cross-reactivity to monkey gammadelta1-TCR. Cell based assays were used to evaluate antibody-dependent cell cytotoxicity and phagocytosis (ADCC and ADCP). The levels of gammadelta1-T cell infiltration was measured in patient tumors. Efficacy in reversing immunesuppression was assayed using patient-derived organotypic tumor spheroids (PDOTS, n = 32), which recapitulate complex tumor architecture. Results Because the tumor-derived delta1 chains showed diverse CDR3 sequences, we developed antibodies that bind diverse delta1 TCRs. Our first-in-class anti-delta1 antibodies had low nanomolar affinity to delta1 TCRs and showed no binding to delta2 TCRs. Our lead clinical candidate showed no preference for the gamma chains of the TCR, which enables it to target diverse set of gammadelta1-TCRs. It had equivalent affinity for the human and cynomolgus monkey gammadelta1-TCRs and was potent in mediating cell based ADCC and ADCP. We showed that patient tumors can have a high delta1 T cell infiltration (up to 40% of the total T cell infiltrate). Our lead candidate achieved reproducible and robust efficacy in the up-regulation of pro-inflammatory T cell activation markers in PDOTS from a diverse set of gastrointestinal tumors. Furthermore, gammadelta knockout mice had an improved response to checkpoint inhibitors, anti-PD1 and anti-CTLA4, in melanoma and lung cancer models. Conclusions We have defined a novel therapeutic immuno-oncology strategy and translated it to develop a lead clinical candidate anti-delta1 monoclonal antibody. Our efficacious, novel immunotherapy has the potential to be transformative for the treatment of cancers where gammadelta1 T cells drive a pro-tumorigenic, immunosuppressive environment