Receptor Specificity Engineering of TNF Superfamily Ligands

The tumor necrosis factor (TNF) ligand family has nine ligands that show promiscuity in binding multiple receptors. As different receptors transduce into diverse pathways, the study on the functional role of natural ligands is very complex. In this review, we discuss the TNF ligands engineering for receptor specificity and summarize the performance of the ligand variants in vivo and in vitro. Those variants have an increased binding affinity to specific receptors to enhance the cell signal conduction and have reduced side effects due to a lowered binding to untargeted receptors. Refining receptor specificity is a promising research strategy for improving the application of multi-receptor ligands. Further, the settled variants also provide experimental guidance for engineering receptor specificity on other proteins with multiple receptors.

Systematic discovery of receptor-ligand biology by engineered cell entry and single-cell genomics

Cells communicate with each other via receptor-ligand interactions on the cell surface. Here we describe a technology for lentiviral-mediated cell entry by engineered receptor- ligand interaction (ENTER) to decode receptor specificity. Engineered lentiviral particles displaying specific ligands deliver fluorescent proteins into target cells upon cognate receptor-ligand interaction, without genome integration or transgene transcription. We optimize ENTER to decode interactions between T cell receptor (TCR)-MHC peptides, antibody-antigen, and other receptor-ligand pairs. We develop an effective presentation strategy to capture interactions between B cell receptor (BCR) and intracellular antigen epitopes. Single-cell readout of ENTER by RNA sequencing (ENTER-seq) enables multiplexed enumeration of TCR-antigen specificities, clonality, cell type, and cell states of individual T cells. ENTER-seq of patient blood samples after CMV infection reveals the viral epitopes that drive human effector memory T cell differentiation and inter-clonal phenotypic diversity that targets the same epitope. ENTER enables systematic discovery of receptor specificity, linkage to cell fates, and cell-specific delivery of gene or protein payloads.

A glucagon analogue decreases body weight in mice via signalling in the liver

Glucagon receptor agonists show promise as components of next generation metabolic syndrome pharmacotherapies. However, the biology of glucagon action is complex, controversial, and likely context dependent. As such, a better understanding of chronic glucagon receptor (GCGR) agonism is essential to identify and mitigate potential clinical side-effects. Herein we present a novel, long-acting glucagon analogue (GCG104) with high receptor-specificity and potent in vivo action. It has allowed us to make two important observations about the biology of sustained GCGR agonism. First, it causes weight loss in mice by direct receptor signalling at the level of the liver. Second, subtle changes in GCG104-sensitivity, possibly due to interindividual variation, may be sufficient to alter its effects on metabolic parameters. Together, these findings confirm the liver as a principal target for glucagon-mediated weight loss and provide new insights into the biology of glucagon analogues.

For whom the T cells troll? Bispecific T-cell engagers in glioblastoma

Glioblastoma is the the most common primary brain tumor in adults. Onset of disease is followed by a uniformly lethal prognosis and dismal overall survival. While immunotherapies have revolutionized treatment in other difficult-to-treat cancers, these have failed to demonstrate significant clinical benefit in patients with glioblastoma. Obstacles to success include the heterogeneous tumor microenvironment (TME), the immune-privileged intracranial space, the blood–brain barrier (BBB) and local and systemic immunosuppressions. Monoclonal antibody-based therapies have failed at least in part due to their inability to access the intracranial compartment. Bispecific T-cell engagers are promising antibody fragment-based therapies which can bring T cells close to their target and capture them with a high binding affinity. They can redirect the entire repertoire of T cells against tumor, independent of T-cell receptor specificity. However, the multiple challenges posed by the TME, immune privilege and the BBB suggest that a single agent approach may be insufficient to yield durable, long-lasting antitumor efficacy. In this review, we discuss the mechanism of action of T-cell engagers, their preclinical and clinical developments to date. We also draw comparisons with other classes of multispecific antibodies and potential combinations using these antibody fragment therapies.

Molecular reconstruction of recurrent evolutionary switching in olfactory receptor specificity

Olfactory receptor repertoires exhibit remarkable functional diversity, but how these proteins have evolved is poorly understood. Through analysis of extant and ancestrally-reconstructed drosophilid olfactory receptors from the Ionotropic receptor (Ir) family, we investigated evolution of two organic acid-sensing receptors, Ir75a and Ir75b. Despite their low amino acid identity, we identify a common 'hotspot' in their ligand-binding pocket that has a major effect on changing the specificity of both Irs, as well as at least two distinct functional transitions in Ir75a during evolution. Moreover, we show that odor specificity is refined by changes in additional, receptor-specific sites, including those outside the ligand-binding pocket. Our work reveals how a core, common determinant of ligand-tuning acts within epistatic and allosteric networks of substitutions to lead to functional evolution of olfactory receptors.

Characterization of changes in the hemagglutinin that accompanied the emergence of H3N2/1968 pandemic influenza viruses

The hemagglutinin (HA) of A/H3N2 pandemic influenza viruses (IAVs) of 1968 differed from its inferred avian precursor by eight amino acid substitutions. To determine their phenotypic effects, we studied recombinant variants of A/Hong Kong/1/1968 virus containing either human-type or avian-type amino acids in the corresponding positions of HA. The precursor HA displayed receptor binding profile and high conformational stability typical for duck IAVs. Substitutions Q226L and G228S, in addition to their known effects on receptor specificity and replication, marginally decreased HA stability. Substitutions R62I, D63N, D81N and N193S reduced HA binding avidity. Substitutions R62I, D81N and A144G promoted viral replication in human airway epithelial cultures. Analysis of HA sequences revealed that substitutions D63N and D81N accompanied by the addition of N-glycans represent common markers of avian H3 HA adaptation to mammals. Our results advance understanding of genotypic and phenotypic changes in IAV HA required for avian-to-human adaptation and pandemic emergence.

Isolation and characterizations of a novel H6N1 avian influenza virus from Von Schrenck's Bittern (Ixobrychus eurhythmus) in Jiangxi province, China

In June 2013, the first case of human infection with an avian H6N1 virus was reported in a Taiwanese woman. Although this was a single non-fatal case, the virus continues to circulate in Taiwanese poultry. As with any emerging avian virus that infects humans, there is concern that acquisition of human-type receptor specificity could enable transmission in the human population. Despite mutations in the receptor-binding pocket of the human H6N1 isolate, it has retained avian-type (NeuAca2-3Gal) receptor specificity. An H6N1 AIV was isolated from a Von Schrenck's Bittern during national active surveillance project for avian influenza viruses (AIVs) in wild birds in Jiangxi province, China 2018. Phylogenetic analysis showed that this strain received its genes from H1, H2, H3, H4, H6 and H10 AIVs in different places. This strain was found to be minimally pathogenic in mice and was able to replicate in mice without prior adaptation. Considering that the reassorted H6N1 virus was isolated from Von Schrenck's Bittern in this study, it is possible that this bird can play an important role in the generation of novel reassorted H6 AIVs. In this study, H6N1 virus is a wild virus migration brought from different regions of the AIV gene into the natural gene pool, resulting in the production of a recombinant new virus. The H6N1 virus can be seen as a link in the evolution of the virus and the evolution of other viruses.

In Silico Perspectives on Gonadotropin Crosstalk

The pivotal role of the gonadotropins (GtHs) luteinizing hormone (LH) and follicle stimulating hormone (FSH) in vertebrate reproduction is well documented. LH and FSH bind to the leucine-rich repeats of the extracellular domains of their cognate receptors (R) in the gonads to actuate steroidogenesis and gametogenesis. Though these GtHs specifically bind only to their cognate receptors in mammals, this interaction becomes inconsistent in the case of fish. Whilst in some fish species the gonadotropins show receptor specificity much like their mammalian homologs, FSH and LH have demonstrated mutual and/or singular cross-activation of the FSH and/or LH receptors in several fish species. These complications regarding receptor specificity are further magnified by cross activation by orthologous GtHs from different species. So far no consistent pattern has been established to chart or predict this cross-talk in specific species or higher taxonomic orders. In the current study, we strived to understand the promiscuous nature of FSH and LH through in silico perspectives. While our studies in Russian sturgeon (Acipenser gueldenstaedtii) have shown FSH and LH to exhibit mutual promiscuity but of varying magnitude, in common carp (Cyprinus carpio) only LH showed singular cross-activation of FSHR. In Nile tilapia (Oreochromis niloticus) these gonadotropins exhibited strict specificity towards their cognate receptors similar to humans. Taking these species as representatives of varying degrees of cognate binding shown by the gonadotropins, we have generated docked models of these hormones and the extracellular domain of these receptors using in silico tools. We have further tried to compare these models, their docked poses, and key residues involved in the binding of these hormone-receptor complexes. We have further tried to compare parameters such as phosphorylation sites, N-linked glycosylation motifs, surface charge, etc. of these models to better understand the docking of these complexes. Our results suggest that in cases of cross activation by FSH and/or LH within or across the species, though binding sites are present at the leucine rich repeats on concaved face of the receptor extracellular domain, the docked position and residues involved in binding may vary significantly. Furthermore, though the seatbelt loop and GTHβ loop-2 (gonadotropin hormone subunit- beta) of the gonadotropin hormones act as the key players in binding, the docking of the hormone may vary in conformation. Due the large size and flexibility of these hormones and the receptor binding interface, it seems apparent that there are multiple binding sites that activate the resulting signaling pathway. Our study aspires to provide better insights towards the promiscuous nature of these hormones and attempt to overcome the handicap of lack of individual physical models using in silico tools.

Characterization of changes in the hemagglutinin that accompanied the emergence of H3N2/1968 pandemic influenza viruses

The hemagglutinin (HA) of A/H3N2 pandemic influenza viruses (IAVs) of 1968 differed from its inferred avian precursor by eight amino acid substitutions. To determine their phenotypic effects, we studied recombinant variants of A/Hong Kong/1/1968 virus containing either human-type or avian-type amino acids in the corresponding positions of HA. The precursor HA displayed receptor binding profile and high conformational stability typical for duck IAVs. Substitutions Q226L and G228S, in addition to their known effects on receptor specificity and replication, marginally decreased HA stability. Substitutions R62I, D63N, D81N and N193S reduced HA binding avidity. Substitutions R62I, D63N, D81N and A144G promoted virus replication in human airway epithelial cultures. Analysis of HA sequences revealed that substitutions D63N and D81N accompanied by the addition of N-glycans represent common markers of avian H3 HA adaptation to mammals. Our results advance understanding of genotypic and phenotypic changes in IAV HA required for avian-to-human adaptation and pandemic emergence.