Yunje Cho

Tumor-intrinsic adaptations with emerging resistant clones following T cell-targeted immunotherapies pose a major barrier to durable remissions in multiple myeloma. Through integrated genomic, transcriptomic and epigenomic interrogation of clonal plasma cells, we observed antigenic drift in 68.4% of relapsed cases following anti-GPRC5D T cell-engager (TCE) therapy (n = 21). These escape events were driven by three distinct mutational mechanisms involving (1) focal to large biallelic deletions at the GPRC5D gene locus; (2) monoallelic deletion coupled with GPRC5D single-nucleotide variants or insertions/deletions (indels) on the remaining allele; as well as (3) epigenetic GPRC5D promoter/enhancer silencing. Beyond biallelic deletions resulting in complete antigenic loss, we demonstrate that GPRC5D single-nucleotide variants and indels mutate anti-GPRC5D TCE-binding epitopes or more commonly affect G-protein-coupled receptor family conserved motifs critical for protein membrane trafficking resulting in endoplasmic reticulum GPRC5D trapping. Multiple subclones bearing distinct genomic alterations at GPRC5D locus co-emerged within individual cases, depicting their convergent evolutionary trajectories. Of note, anti-GPRC5D TCEs with varying epitope specificity, affinity and valency differentially targeted mutant subclones, underscoring their nonredundant functional roles in overcoming resistance.

Insulin binding to the insulin receptor (IR) triggers signaling pathways that regulate glucose uptake and cell growth. In previous work, we identified a DNA aptamer, A62, which partially activates the IR. During engineering aptamers for improved in vivo stability, we discovered that crosslinking two A62 aptamers with linkers of varying lengths led to full phosphorylation of the IR, although activation remained selective to the AKT pathway. Here, to elucidate the mechanism behind this aptamer-induced full activation of the IR, we determined the structure of the IR in complex with a dimeric form of A62 (A62D) linked by an eight-nucleotide connector. We identified three distinct conformations of the IR: arrowhead-shaped, pseudo-arrowhead-shaped and pseudo-gamma-shaped. The pseudo-gamma-shaped conformation closely resembles the structure of a fully active IR bound by a single insulin molecule. In these configurations, only one A62 monomer (A62M) within the A62D dimer binds to the IR dimer. This binding brings the IR monomers into close proximity, promoting intermolecular trans-phosphorylation. Our findings provide valuable structural insights for the development of novel therapeutic strategies targeting the IR.

Insulin binding to the insulin receptor (IR) triggers signaling pathways that regulate glucose uptake and cell growth. In previous work, we identified a DNA aptamer, A62, which partially activates the IR. During engineering aptamers for improved in vivo stability, we discovered that crosslinking two A62 aptamers with linkers of varying lengths led to full phosphorylation of the IR, though activation remained selective to the AKT pathway. To elucidate the mechanism behind this aptamer-induced full activation of the IR, we determined the structure of the IR in complex with a dimeric form of A62 (A62D) linked by an 8-nucleotide connector. We identified three distinct conformations of the IR: arrowhead-shaped, pseudo-arrowhead-shaped, and pseudo-gamma-shaped. The pseudo-gamma-shaped conformation closely resembles the structure of a fully active IR bound by a single insulin molecule. In these configurations, only one A62 monomer (A62M) within the A62D dimer binds to the IR dimer. This binding brings the IR monomers into close proximity, promoting intermolecular trans-phosphorylation. Our findings provide valuable structural insights for the development of novel therapeutic strategies targeting the IR.

Alanine racemase (Alr) catalyzes the pyridoxal 5′-phosphate (PLP)-dependent racemization between l- and d-alanine in bacteria. Owing to the potential interest in targeting Alr for antibacterial drug development, several studies have determined the structures of Alr from different species, proposing models for the reaction mechanism. Insights into its reaction dynamics may be conducive to a better understanding of the Alr reaction mechanism. In this study, we determined the structures of the apo and reaction states of Bacillus subtilis Alr (BsAlr) at room temperature using a fixed-target based X-ray free-electron laser. The 2.3 Å resolution structures revealed the alanine substrate or intermediate in various positions at the active site. Conformational change between the N- and C-terminal domains of BsAlr expanded the entryway for substrate binding. In the reaction state of BsAlr, two main alanine binding states were observed: one alanine molecule is positioned away from PLP, whereas the other alanine molecule is covalently bonded to PLP. These structures might represent the dynamic states of the substrate for entrance into, reaction with, or exit from the active site. Our approach provides a simple and rapid method for elucidating the intermediate structure of Alr, which can be expanded to other enzymes.

Class C G-protein-coupled receptors (GPCRs) are activated through binding of agonists to the large extracellular domain (ECD) followed by rearrangement of the transmembrane domains (TMDs). GPR156, a class C orphan GPCR, is unique because it lacks an ECD and exhibits constitutive activity. Impaired GPR156–G_i signaling contributes to loss of hearing. Here we present the cryo-electron microscopy structures of human GPR156 in the G_o-free and G_o-coupled states. We found that an endogenous phospholipid molecule is located within each TMD of the GPR156 dimer. Asymmetric binding of Gα to the phospholipid-bound GPR156 dimer restructures the first and second intracellular loops and the carboxy-terminal part of the elongated transmembrane 7 (TM7) without altering dimer conformation. Our findings reveal that GPR156 is a transducer for phospholipid signaling. Constant binding of abundant phospholipid molecules and the G-protein-induced reshaping of the cytoplasmic face provide a basis for the constitutive activation of GPR156.

Microcrystal delivery instruments are pivotal to performing serial femtosecond crystallography experiments at the XFEL facilities. We present a novel sample delivery technique based on a micro-tubing reeling system (MRS). Despite the tiny size of the micro-tubing, the MRS device has the advantage of operating without real-time position adjustment of the tube to match with the XFEL pulses. Moreover, the applicable repetition rate is more flexible than the previously reported chip-based one-dimensional fixed target system.

Microcrystal delivery instruments are pivotal to perform serial femtosecond crystallography experiments at the XFEL facilities. We present a novel sample delivery technique based on a micro-tubing reeling system (MRS). Even though the tiny size of the micro-tubing, the MRS device has an advantage of operation without real-time position adjustment of the tube to match with the XFEL pulses. Moreover, the applicable repetition rate is more flexible than the previously reported chip-based one-dimensional fixed target system.

Cyanase plays a vital role in the detoxification of cyanate and supplies a continuous nitrogen source for soil microbes by converting cyanate to ammonia and carbon dioxide in a bicarbonate-dependent reaction. The structures of cyanase complexed with dianion inhibitors, in conjunction with biochemical studies, suggest putative binding sites for substrates. However, the substrate-recognition and reaction mechanisms of cyanase remain unclear. Here, crystal structures of cyanase from Escherichia coli were determined in the native form and in complexes with cyanate, bicarbonate and intermediates at 1.5–1.9 Å resolution using synchrotron X-rays and an X-ray free-electron laser. Cyanate and bicarbonate interact with the highly conserved Arg96, Ser122 and Ala123 in the active site. In the presence of a mixture of cyanate and bicarbonate, three different electron densities for intermediates were observed in the cyanase structures. Moreover, the observed electron density could explain the dynamics of the substrate or product. In addition to conformational changes in the substrate-binding pocket, dynamic movement of Leu151 was observed, which functions as a gate for the passage of substrates or products. These findings provide a structural mechanism for the substrate-binding and reaction process of cyanase.