Extracellular Segment Research Articles

Epithelial sodium channel (ENaC) in GtoPdb v.2023.1

Epithelial sodium channel (ENaC) in GtoPdb v.2023.1

A procedure for producing an anti-AXL nanobody in E. coli

As one of the receptors of the TAM family, AXL plays a vital role in stem cell maintenance, angiogenesis, immune escape of viruses and drug resistance against tumors. In this study, the truncated extracellular segment containing two immunoglobulin-like domains of human AXL (AXL-IG), which has been confirmed to bind growth arrest specific 6 (GAS6) by structural studies [1], was expressed in a prokaryotic expression system and then purified. Immunizing camelid with the purified AXL-IG as antigen could lead to the production of unique nanobodies composed of only variable domain of heavy chain of heavy-chain antibody (VHH), which are around 15 kD and stable. We screened out a nanobody A-LY01 specific binding to AXL-IG. We further determined the affinity of A-LY01 to AXL-IG and revealed that A-LY01 could specifically recognize full-length AXL on the surface of HEK 293T/17 cells. Our study provides appropriate support for the development of diagnostic reagents and antibody therapeutics targeting AXL.

Abstract 561: Development of competing and non-competing fully human internalizing anti-Her2 monoclonal antibodies

Abstract The human epidermal growth factor receptor (HER) family of receptors has been implicated in several human cancers. Among them, HER2 is overexpressed in several cancers with or without gene amplification with prognostic and predictive implications. In 15-30% of breast cancers, HER2 overexpression and amplification are associated with shorter disease-free and overall survivals along with resistance to hormonal agents as well as increased risk of brain metastasis. Two types of HER2 targeting have been developed: anti-HER2 monoclonal antibodies and small molecule tyrosine kinase inhibitors. Trastuzumab is a humanized anti-HER2 monoclonal antibody that binds to domain IV of HER2 extracellular segment and blocks its signaling. It is the first therapeutic antibody targeting Her2 overexpression approved by the FDA. More recently, two antibody drug conjugates using trastuzumab have been approved: Ado-Trastuzumab-Emtansine (Kadcyla) consisting of trastuzumab conjugated to the drug mertansine DM1 and fam-trastuzumab-deruxtecan-nhki (Enhertu to deliver the topoisomerase inhibitor deruxtecan. We are reporting here the development of fully human internalizing anti-Her2 antibodies that compete or not with trastuzumab for binding to Her2. These antibodies have been developed by immunizing fully human (TC-Mab mouse) mice with recombinant Her2 protein. After production of hybridoma secreting fully human immunoglobulins, the screening process included inhibition of binding of trastuzumab to Her2 by enzyme linked immunoassay and by Octet epitope binning as well as internalization assay. Several internalizing antibodies able to compete or not with trastuzumab and with high affinity (Kd ranging from 10−9 M to 10−12 M) were selected. They were next investigated for their ability to deliver a cytotoxic payload in HER2 overexpressing cells breast cancer cells such as SKBR3, BT474 and AU565. Two antibodies: one competing with trastuzumab and the other one non-competing were further characterized. Data related to these antibodies’ biochemical characteristics as well as their ability to inhibit proliferation in vitro and in vivo in mouse xenografts studies will be presented here. In conclusion, the use of fully human mice in our laboratory provides a powerful and attractive approach to develop fully human monoclonal antibodies against cancer targets allowing to by-pass the need for humanization and affinity maturation of antibodies. Citation Format: Ginette Serrero, Binbin Yue, Jianping Dong, Chun Dong, Jun Hayashi. Development of competing and non-competing fully human internalizing anti-Her2 monoclonal antibodies [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 561.

Abstract P2-19-01: Characterization of fully human internalizing anti-HER2 monoclonal antibodies that compete with Trastuzumab for binding to HER2

Abstract The human epidermal growth factor receptor (HER) family of receptors plays a significant role in the pathogenesis of several human cancers. Among them, HER2 is overexpressed in several cancers. In particular, overexpression with or without gene amplification occurs in 15-30% of breast cancers and this has both prognostic and predictive implications. HER2 overexpression and amplification is associated with shorter disease-free and overall survivals and with resistance to certain hormonal agents as well as increased risk of metastasis to the brain. Two types of treatment targeting HER2 biological activity have been developed: anti-Her2 monoclonal antibodies and small molecule tyrosine kinase inhibitors such as lapatinib and neratinib targeting HER2 and EGFR and Afatinib targeting all HER family members. Trastuzumab is a humanized anti-HER2 monoclonal antibody that binds to domain IV of HER2 extracellular segment and blocks its signaling. It is the first therapeutic antibody targeting Her2 overexpression approved by the FDA. It is administered in combination with standard of care chemotherapy. More recently, since it was shown that Trastuzumab was an internalizing antibody, two antibody drug conjugates using trastuzumab have been approved and used in the standard of care: Ado-Trastuzumab-Emtansine (Kadcyla) consisting of trastuzumab conjugated to the drug mertansine DM1 and fam-trastuzumab-deruxtecan-nhki (Enhertu). Enhertu is another antibody drug conjugate using Trastuzumab to deliver a topoisomerase inhibitor deruxtecan. Our laboratory has been focused in developing fully human internalizing anti-Her2 antibodies that compete or not with trastuzumab for binding to Her2. These antibodies have been developed by immunizing fully human mice with recombinant Her2 protein. Human Ab producing Tc mice (TC-mAb mice) stably maintain a mouse-derived engineered chromosome containing the entire human Ig heavy and kappa chain loci in a mouse Ig knockout background. After production of hybridoma secreting fully human immunoglobulins, the screening process included inhibition of binding of trastuzumab to Her2 by enzyme linked immunoassay and by Octet epitope binning as well as internalization assay. Several internalizing antibodies with Kd ranging from 10-9 M to 10-12 M were selected. They were stratified by their ability to compete or not with trastuzumab. They were further characterized for their ability to deliver a cytotoxic payload in Her2 overexpressing cells as well as for their efficacy to inhibit proliferation, signaling and migration of Her2 overexpressing breast cancer cells. Data related to these antibodies will be presented here. In conclusion, the use of fully human TC mice in our laboratory represents an attractive approach to develop fully human monoclonal antibodies to high value cancer targets that can by-pass the need for humanization and affinity maturation of antibodies. Citation Format: Ginette Serrero, Jianping Dong, Binbin Yue, Udaya Yerramalla, Jun Hayashi. Characterization of fully human internalizing anti-HER2 monoclonal antibodies that compete with Trastuzumab for binding to HER2 [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr P2-19-01.

Targeting LAYN inhibits colorectal cancer metastasis and tumor-associated macrophage infiltration induced by hyaluronan oligosaccharides

The accumulation of hyaluronan oligosaccharides (oHA) in colorectal cancer (CRC) is closely related to tumor metastasis, but the underlying mechanism remains unclear. In this study, we first described that LAYN, a novel HA receptor, was upregulated in CRC tissue. Aberrant LAYN expression correlated with CRC metastasis and poor prognosis and positively correlated with tumor-associated macrophage (TAM) infiltration and M2 macrophage polarization in the tumor environment. Both in vitro and in vivo studies demonstrated that LAYN is activated by oHA and subsequently induces CRC metastasis and macrophage infiltration. Mechanistic studies demonstrated that oHA activates LAYN by binding to the 60–68th amino acid region of the extracellular segment. oHA-induced LAYN activation promoted metastasis and CCL20 secretion through the NF-kB pathway in CRC cells. Furthermore, targeting LAYN using a blocking antibody prevented oHA-mediated tumor metastasis, TAM infiltration and M2 polarization. This study revealed the LAYN activation mechanism and identified a potential target for the treatment of CRC tumor exhibiting high oHA levels.

Glucose-mediated N-glycosylation of RPTPα affects its subcellular localization and Src activation.

Receptor-type protein tyrosine phosphatase α (RPTPα) is one of the typical PTPs that play indispensable roles in many cellular processes associated with cancers. It has been considered as the most powerful regulatory oncogene for Src activation, however it is unclear how its biological function is regulated by post-translational modifications. Here, we show that the extracellular segment of RPTPα is highly N-glycosylated precisely at N21, N36, N68, N80, N86, N104 and N124 sites. Such N-glycosylation modifications mediated by glucose concentration alter the subcellular localization of RPTPα from Golgi apparatus to plasma membrane, enhance the interaction of RPTPα with Src, which in turn enhances the activation of Src and ultimately promotes tumor development. Our results identified the N-glycosylation modifications of RPTPα, and linked it to glucose starvation and Src activation for promoting tumor development, which provides new evidence for the potential antitumor therapy.

Structural dynamics of the activation loop in the kinase domain of E.faecalis IreK.

IreK is a transmembrane Ser/Thr PASTA kinase found in Enterococcus faecalis, as well as most other Gram-positive bacteria, and plays a key role in resistance to cell wall-active antibiotics such as cephalosporins. IreK belongs to a family of bacterial transmembrane kinases that include multiple PASTA (Penicillin-and Ser/Thr-kinase Associated) domains in the extracellular segment and are ubiquitous in nearly all Gram-positive bacteria. PASTA kinases have conserved functions across Gram-positive bacteria involving monitoring and regulating processes associated with the cell wall. Enterococci are frequently found in the human gut and are a common cause of severe and difficult to treat hospital acquired infections, due to their intrinsic drug resistance. The underlying mechanisms of antibiotic resistance in enterococci are not well understood and are an excellent target for the creation of preventative treatments to eliminate the growth opportunity of resistant E. faecalis in the gut and transfer to other parts of the body. Based on the crystal structures of IreK kinase domain homologs, the activation loop structure is unknown and the phosphorylation sites within this loop are proposed to play a key regulatory role in IreK kinase activity. IreB has also been identified as one of the targets for phosphorylation by IreK. Here, continuous wave electron paramagnetic resonance (CW EPR) spectroscopy was applied to study the dynamics of the IreK activation loop, including the effects of phosphorylation and IreB binding on activation loop structure and dynamics. In addition, new functionally important non-phosphorylation sites in the activation loop that regulate IreK function in vivo were identified and characterized. This comprehensive investigation into the IreK activation loop structure and functional dynamics characterizes the role of this loop as a key regulatory domain in kinase function.

Claudin-10b cation channels in tight junction strands: Octameric-interlocked pore barrels constitute paracellular channels with low water permeability

Claudin proteins constitute the backbone of tight junctions (TJs) regulating paracellular permeability for solutes and water. The molecular mechanism of claudin polymerization and paracellular channel formation is unclear. However, a joined double-rows architecture of claudin strands has been supported by experimental and modeling data. Here, we compared two variants of this architectural model for the related but functionally distinct cation channel-forming claudin-10b and claudin-15: tetrameric-locked-barrel vs octameric-interlocked-barrels model. Homology modeling and molecular dynamics simulations of double-membrane embedded dodecamers indicate that claudin-10b and claudin-15 share the same joined double-rows architecture of TJ-strands. For both, the results indicate octameric-interlocked-barrels: Sidewise unsealed tetrameric pore scaffolds interlocked with adjacent pores via the β1β2 loop of the extracellular segment (ECS) 1. This loop mediates hydrophobic clustering and, together with ECS2, cis- and trans-interaction between claudins of the adjacent tetrameric pore scaffolds. In addition, the β1β2 loop contributes to lining of the ion conduction pathway. The charge-distribution along the pore differs between claudin-10b and claudin-15 and is suggested to be a key determinant for the cation- and water permeabilities that differ between the two claudins. In the claudin-10b simulations, similar as for claudin-15, the conserved D56 in the pore center is the main cation interaction site. In contrast to claudin-15 channels, the claudin-10b-specific D36, K64 and E153 are suggested to cause jamming of cations that prevents efficient water passage. In sum, we provide novel mechanistic information about polymerization of classic claudins, formation of embedded channels and thus regulation of paracellular transport across epithelia.

Comprehensive Discovery of the Accessible Primary Amino Group-Containing Segments from Cell Surface Proteins by Fine-Tuning a High-Throughput Biotinylation Method

Cell surface proteins, including transmembrane and other surface-anchored proteins, play a key role in several critical cellular processes and have a strong diagnostic value. The development of quick and robust experimental methods remains vital for the accurate and comprehensive characterization of the cell surface subproteome of individual cells. Here we present a high-throughput technique which relies on the biotinylation of the accessible primary amino groups in the extracellular segments of the proteins, using HL60 as a model cell line. Several steps of the method have been thoroughly optimized to capture labeled surface proteins selectively and in larger quantities. These include the following: improving the efficiency of the cell surface biotinylation; reducing the endogen protease activity; applying an optimal amount of affinity column and elution steps for labeled peptide enrichment; and examining the effect of various solid-phase extraction methods, different HPLC gradients, and various tandem mass spectrometry settings. Using the optimized workflow, we identified at least 1700 surface-associated individual labeled peptides (~6000-7000 redundant peptides) from the model cell surface in a single nanoHPLC-MS/MS run. The presented method can provide a comprehensive and specific list of the cell surface available protein segments that could be potential targets in various bioinformatics and molecular biology research.

Genomic and Transcriptomic Profiling Reveal the Mechanism and Risk Factors of CD19-Negative Relapse after CAR-T Cell Therapy

Objection: To explore the relationship of mutation or alternative splicing events in CD19 coding region of patients underwent CD19-negative relapse after CAR-T cell therapy, as well as the predictive factors associated with relapse based on WES and RNA-seq, in the hope of explaining the mechanism of CD19-negativerelapse and improving the effect of CAR-T cell therapy. Methods: In this part of study, we collected bone marrow samples from R/R B-ALL patients underwent CD19 CAR-T cell therapy at baseline (T1) and relapse time (T2), then subjecting samples for WES and RNA-seq. Mutect and ANNOVAR software were used to detect single nucleotide variations (SNV) and indel mutations. Alphafold2 was used to predict the protein structure of CD19 after mutation. DESeq2 was used to compare the gene expression level between different groups; ssGSEA method was used to evaluate immunocyte infiltration level in each sample. Therefore, we displayed the potential mechanism of CD19-negative relapse from the aspects of leukemia cells and tumor microenvironment. Results:CD19 exon2-4 mutations were detected in CD19-negative relapse patients at relapse time, which lead to the change of protein structure of CD19 extracellular segment (Figure 1A). The combined analysis of WES and RNA-seq revealed common mutations of OBSCN at baseline and relapse (Figure 1D), which was associated with its continued lower expression in negative-relapse group (Figure 1B-C). Meanwhile, OBSCN was enriched in positive regulation of apoptosis pathway through GO enrichment (Figure 1E). OBSCN low-expression group had poorer 1-year leukemia free survival (LFS) rate (0% vs 44.4%, P=0.016) and long-term OS rate (P=0.027) than high-expression group (Figure 1G). Moreover, RHOH, a related gene of OBSCN, which expressed lower in CD19-negative relapse patients (Figure 1B-C). The 1-year LFS rate of RHOH high-expression group was significantly better than the compared group (44.4% vs 0%, P=0.001) (Figure 1H), and the infiltration level of TN, CD8+ effector memory T cells (TEM), memory T cells (TM) and tumor infiltrating lymphocytes (TILs) were increased in RHOH high-expression group (Figure 1F). Conclusion: Mutations of CD19 exon2-4 leads to the variation on protein structure, which hindered targeted killing process of CAR-T cells and finally resulted in CD19-negative relapse. On the other hand, OBSCN and RHOHmay play a role in promoting leukemia proliferation and decreasing apoptosis, and the lower expression of OBSCN and RHOH may be risk factors associated with CD19-negative relapse. In addition, lower expression of RHOH was unfavourable for the infiltration of TN, TEM, TM and TILs in tumor microenvironment, which lead to the weakening anti-tumor effect of immunocytes. Figure 1View largeDownload PPTFigure 1View largeDownload PPT Close modal

Novel Sirpα-Fc Fusion Protein IMM01 Exhibits Dual Anti-Tumor Activities By Targeting CD47/Sirpα Signal Pathway

Background: This study aims to evaluate the anti-tumor mechanism of IMM01, a novel recombinant SIRPα-Fc fusion protein targeting CD47-SIRPα pathway. Methods: IMM01 was a recombinant fusion protein of SIRPα (V2) extracellular segment domain 1 and human IgG1 Fc, with the N glycosylation site N80 mutated to A (Alanine) in D1 region. IMM01 fusion proteins were produced using in house developed CHO-K1 cell expression system. IMM01 blocking activities on Jurkat-CSR (Jurkat-CD47KO-CARSIRPα) cells, antibody-dependent cellular phagocytosis (ADCP), antibody-dependent cell-mediated cytotoxicity (ADCC) and complement-dependent cytotoxicity (CDC) assays were done by flow cytometry. Detection of cytokines of IL-1β, IL-2, IL-4, IL-5, IL-6, GM-CSF, IFN-γ, IL-10 and TNF production by PBMC was done CBA assay. In vivo mechanism of action study was done in different mouse models including HL-60 CB17-SCID, Daudi CB17-SCID, SNU-1 CB17-SCID, Raji CB17-SCID and CT26-hPDL1(Tg) hCD47(Tg) mPDL1(KO) mCD47(KO). In addition, human red blood cells binding and erythrocyte agglutination of IMM01 were also evaluated. Results:In vitro binding assay revealed that IMM01 has a strong binding affinity to CD47 with lowest EC50 at 0.4967 nM. The removal of N-glycosylation modification improves the consistence and purity of the IMM01 protein expression, and the potential mitigation of immunogenicity. Using a chimeric SIRPα receptor protein expressing cell line, IMM01 not only can block the CD47 at the protein level, but also block the signal transduction at the cellular levels. Compared to negative (hIgG1-Fc) controls, IMM01 stimulated secretion of minimal amount of IL-10 and TNF but inhibited IL-8 production by PBMC. IMM01 can induce strong ADCP and moderate ADCC, but not the CDC activities. The strong phagocytosis against tumor cells is dependent on interaction of Fc with activating FcγRs on the presence of macrophages. Mechanism of action studies demonstrated that IMM01 induced strong phagocytosis against tumor cells was attributed to dual activities of blocking "don't eat me" signal and activating "eat me" signal. IMM01 has strong and robust in vivo anti-tumor activities in different mouse tumor models either as monotherapy on hematological malignancies, or in combination therapy with PD-L1 mAb, PD-1 mAb, CD33 mAb, and HER-2 mAb, respectively. The in vivo therapeutic efficacy of IMM01 was done in HL-60 xenograft model showed that 100% of the mice achieved CR after administration of IMM01 at 5mg/kg for 2 weeks. Also, 100% of mice achieved CR after IMM01 combined with the above mentioned mAbs in different mouse models, respectively. This illustrated that IMM01 has a great therapeutic potential in combination with these commonly used immunotherapy or targeted therapy agents to be used in the treatment of solid tumors and hematological malignancies. Finally, IMM01 demonstrated a favorable safety profile with no human RBC binding, nor hemagglutination induction. Conclusion: Our study results demonstrated that, as a novel bi-functional SIRPα-Fc recombinant protein, IMM01 has very strong anti-tumor activities with a good curative effect on mouse xenograft tumor models with dual anti-tumor activities by blocking CD47 "don't eat me" signal and activating the phagocytosis "eat me" signal. Furthermore, IMM01 demonstrated a well synergistic effect when combined with different immunotherapeutic agents. Importantly, our results revealed that IMM01 has a favorable safety profile with no human RBC binding activity and no hemagglutination induction. Phase I clinical study is ongoing, and the clinical trial results will be reported soon. Figure 1View largeDownload PPTFigure 1View largeDownload PPT Close modal

Mechanistic basis of GPCR activation explored by ensemble refinement of crystallographic structures.

G protein‐coupled receptors (GPCRs) are important drug targets characterized by a canonical seven transmembrane (TM) helix architecture. Recent advances in X‐ray crystallography and cryo‐EM have resulted in a wealth of GPCR structures that have been used in drug design and formed the basis for mechanistic activation hypotheses. Here, ensemble refinement (ER) of crystallographic structures is applied to explore the impact of binding of agonists and antagonist/inverse agonists to selected structures of cannabinoid receptor 1 (CB1R), β2 adrenergic receptor (β2AR), and A2A adenosine receptor (A2AAR). To assess the conformational flexibility and its role in GPCR activation, hydrogen bond (H‐bond) networks are analyzed by calculating and comparing H‐bond propensities. Mapping pairwise propensity differences between agonist‐ and inverse agonist/antagonist‐bound structures for CB1R and β2AR shows that agonist binding destabilizes H‐bonds in the intracellular parts of TM 5–7, forming the G protein binding cavity, while H‐bonds of the extracellular segment of TMs surrounding the orthosteric site are conversely stabilized. Certain class A GPCRs, for example, A2AAR, bind an allosteric sodium ion that negatively modulates agonist binding. The impact of sodium‐excluding mutants (D522.50N, S913.39A) of A2AAR on agonist binding is examined by applying ER analysis to structures of wildtype and the two mutants in complex with a full agonist. While S913.39A exhibits normal activity, D522.50N quenches the downstream signaling. The mainchain H‐bond pattern of the latter is stabilized in the intracellular part of TM 7 containing the NPxxY motif, indicating that an induced rigidity of the mutation prevents conformational selection of G proteins resulting in receptor inactivation.

KL-6 in ARDS and COVID-19 Patients

The Acute Respiratory Distress Syndrome (ARDS) is a common, devastating clinical pattern characterized by life-threatening respiratory failure. In ARDS there is an uncontrolled inflammatory response that results in alveolar damage, with the exudation of protein-rich pulmonary-edema fluid in the alveolar space. Although severe COVID-19 lung failure (CARDS) often meets diagnostic criteria of traditional ARDS, additional features have been reported, such as delayed onset, binary pulmonary compliant states, and hypercoagulable profile. Increased levels of Krebs von den Lungen 6 (KL-6, also known as MUC1) have been reported in both ARDS and CARDS. KL-6 is a transmembrane protein expressed on the apical membrane of most mucosal epithelial cells and it plays a critical role in lining the airway lumen. Abnormalities in mucus production contribute to severe pulmonary complications and death from respiratory failure in patients with diseases such as cystic fibrosis, chronic obstructive pulmonary disease, and acute lung injury due to viral pathogens. Nevertheless, it is not clear what role KL-6 plays in ARDS/CARDS pathophysiology. KL-6 may exert anti-inflammatory effects through the intracellular segment, as proven in animal models of ARDS, while its extracellular segment will enter the blood circulation through the alveolar space when the alveolar epithelial cells are damaged. Therefore, changes in plasma KL-6 levels may be useful in ARDS and CARDS phenotyping, and KL-6 might guide future clinical trials in ‘personalized medicine’ settings.

Functions of G protein-coupled receptor 56 in health and disease.

Human G protein-coupled receptor 56 (GPR56) is encoded by gene ADGRG1 from chromosome 16q21 and is homologously encoded in mice, at chromosome 8. Both 687 and 693 splice forms are present in humans and mice. GPR56 has a 381 amino acid-long N-terminal extracellular segment and a GPCR proteolysis site upstream from the first transmembrane domain. GPR56 is mainly expressed in the heart, brain, thyroid, platelets, and peripheral blood mononuclear cells. Accumulating evidence indicates that GPR56 promotes the formation of myelin sheaths and the development of oligodendrocytes in the cerebral cortex of the central nervous system. Moreover, GPR56 contributes to the development and differentiation of hematopoietic stem cells, induces adipogenesis, and regulates the function of immune cells. The lack of GPR56 leads to nervous system dysfunction, platelet disorders, and infertility. Abnormal expression of GPR56 is related to the malignant transformation and tumor metastasis of several cancers including melanoma, neuroglioma, and gastrointestinal cancer. Metabolic disorders and cardiovascular diseases are also associated with dysregulation of GPR56 expression, and GPR56 is involved in the pharmacological resistance to some antidepressant and cancer drug treatments. In this review, the molecular structure, expression profile, and signal transduction of GPR56 are introduced, and physiological and pathological functions of GRP56 are comprehensively summarized. Attributing to its significant biological functions and its long N-terminal extracellular region that interacts with multiple ligands, GPR56 is becoming an attractive therapeutic target in treating neurological and hematopoietic diseases.

A short amphipathic alpha helix in scavenger receptor BI facilitates bidirectional HDL-cholesterol transport

During reverse cholesterol transport, high-density lipoprotein (HDL) carries excess cholesterol from peripheral cells to the liver for excretion in bile. The first and last steps of this pathway involve the HDL receptor, scavenger receptor BI (SR-BI). While the mechanism of SR-BI-mediated cholesterol transport has not yet been established, it has long been suspected that cholesterol traverses through a hydrophobic tunnel in SR-BI’s extracellular domain. Confirmation of a hydrophobic tunnel is hindered by the lack of a full-length SR-BI structure. Part of SR-BI’s structure has been resolved, encompassing residues 405 to 475, which includes the C-terminal transmembrane domain and its adjacent extracellular region. Within the extracellular segment is an amphipathic helix (residues 427–436, referred to as AH(427–436)) that showed increased protection from solvent in NMR-based studies. Homology models predict that hydrophobic residues in AH(427–436) line a core cavity in SR-BI’s extracellular region that may facilitate cholesterol transport. Therefore, we hypothesized that hydrophobic residues in AH(427–436) are required for HDL cholesterol transport. Here, we tested this hypothesis by mutating individual residues along AH(427–436) to a charged residue (aspartic acid), transiently transfecting COS-7 cells with plasmids encoding wild-type and mutant SR-BI, and performing functional analyses. We found that mutating hydrophobic, but not hydrophilic, residues in AH(427–436) impaired SR-BI bidirectional cholesterol transport. Mutating phenylalanine-430 was particularly detrimental to SR-BI’s functions, suggesting that this residue may facilitate important interactions for cholesterol delivery within the hydrophobic tunnel. Our results support the hypothesis that a hydrophobic tunnel within SR-BI mediates cholesterol transport.

Soluble Receptor for Advanced Glycation End Product Is Involved in the Inflammatory Response of Human Adenovirus-Infected Patients.

Human adenovirus (HAdV) infection causes excessive inflammation associated with severe tissue injury, such as pneumonia. The molecules involved in the underlying inflammatory mechanisms remain to be elucidated. Receptor for advanced glycation end product (RAGE) is mainly expressed on immune cells and lung tissues, and it is a key factor in the initiation and development of inflammation. RAGE can be cleaved by metalloprotease 9 (MMP9) to release the extracellular segment, which is named soluble RAGE (sRAGE), into the intercellular space, where it can bind to RAGE ligands and block RAGE activation and subsequent inflammation. In our study, we enrolled HAdV-infected patients and their contacts to examine the relationship between sRAGE and inflammation induced by HAdV infection. The results showed that HAdV infection stimulated inflammatory cytokine secretion, increased such as high mobility group box 1 (HMGB1) levels, and suppressed sRAGE expression. sRAGE levels were significantly different between patients with or without pneumonia. We also found that MMP9 was significantly lower in patients with pneumonia, and it was positively correlated with sRAGE levels over 7 days after disease onset. The mitogen-activated protein kinase (MAPK) pathway is an important immune activation signaling pathway that is regulated by RAGE. We observed the activation of the MAPK pathway in the peripheral blood mononuclear cells (PBMCs) of patients. Negative correlations between sRAGE and phosphorylated JNK and p38 were observed. These results suggest that sRAGE is involved in HAdV-induced inflammatory responses, and might be a potential therapeutic target to alleviate the HAdV-induced excessive inflammation.

Genome-wide analysis of PTR transporters in Candida species and their functional characterization in Candida auris.

The peptide transport (PTR) or proton-dependent oligopeptide transporter (POT) family exploits the inwardly directed proton motive force to facilitate the cellular uptake of di/tripeptides. Interestingly, some representatives are also shown to import peptide-based antifungals in certain Candida species. Thus, the identification and characterization of PTR transporters serve as an essential first step for their potential usage as antifungal peptide uptake systems. Herein, we present a genome-wide inventory of the PTR transporters in five prominent Candida species. Our study identifies 2 PTR transporters each in C. albicans and C. dubliniensis, 1 in C. glabrata, 4 in C. parapsilosis, and 3 in C. auris. Notably, despite all representatives retaining the conserved features seen in the PTR family, there exist two distinct classes of PTR transporters that differ in terms of their sequence identities and lengths of certain extracellular and intracellular segments. Further, we also evaluated the contribution of each PTR protein of the newly emerged multi-drug-resistant C. auris in di/tripeptide uptake. Notably, deletion of two PTR genes BNJ08_003830 and BNJ08_005124 led to a marked reduction in the transport capabilities of several tested di/tripeptides. However, all three genes could complement the role of native PTR2 gene of Saccharomyces cerevisiae, albeit to varied levels. Besides, BNJ08_005124 deletion also resulted in increased resistance toward the peptide-nucleoside drug Nikkomycin Z as well as the glucosamine-6-phosphate synthase inhibitor, L-norvalyl-N3-(4-methoxyfumaroyl)-L-2,3-diaminopropionoic acid (Nva-FMDP), pointing toward its predominant role in their uptake mechanism. Altogether, the study provides an important template for future structure-function investigations of PTR transporters in Candida species. KEY POINTS: • Candida genome encodes for two distinct classes of PTR transporters. • Candida auris encodes for 3 PTR transporters with different specificities. • BNJ08_005124 in C. auris is involved in the uptake of Nikkomycin Z and Nva-FMDP.

Structural insights into the non-inhibitory mechanism of the anti-EGFR EgB4 nanobody

BackgroundThe epidermal growth factor receptor (EGFR) is involved in various developmental processes, and alterations of its extracellular segment are associated with several types of cancers, in particular glioblastoma multiforme (GBM). The EGFR extracellular region is therefore a primary target for therapeutic agents, such as monoclonal antibodies and variable domains of heavy chain antibodies (VHH), also called nanobodies. Nanobodies have been previously shown to bind to EGFR, and to inhibit ligand-mediated EGFR activation.ResultsHere we present the X-ray crystal structures of the EgB4 nanobody, alone (to 1.48 Å resolution) and bound to the full extracellular EGFR-EGF complex in its active conformation (to 6.0 Å resolution). We show that EgB4 binds to a new epitope located on EGFR domains I and II, and we describe the molecular mechanism by which EgB4 plays a non-inhibitory role in EGFR signaling.ConclusionThis work provides the structural basis for the application of EgB4 as a tool for research, for targeted therapy, or as a biomarker to locate EGFR-associated tumors, all without affecting EGFR activation.

KL-6 in ARDS and COVID-19 Patients.

The Acute Respiratory Distress Syndrome (ARDS) is a common, devastating clinical pattern characterized by life-threatening respiratory failure. In ARDS there is an uncontrolled inflammatory response that results in alveolar damage, with the exudation of protein-rich pulmonary-edema fluid in the alveolar space. Although severe COVID-19 lung failure (CARDS) often meets diagnostic criteria of traditional ARDS, additional features have been reported, such as delayed onset, binary pulmonary compliant states, and hypercoagulable profile. Increased levels of Krebs von den Lungen 6 (KL-6, also known as MUC1) have been reported in both ARDS and CARDS. KL-6 is a transmembrane protein expressed on the apical membrane of most mucosal epithelial cells and it plays a critical role in lining the airway lumen. Abnormalities in mucus production contribute to severe pulmonary complications and death from respiratory failure in patients with diseases such as cystic fibrosis, chronic obstructive pulmonary disease, and acute lung injury due to viral pathogens. Nevertheless, it is not clear what role KL-6 plays in ARDS/CARDS pathophysiology. KL-6 may exert anti-inflammatory effects through the intracellular segment, as proven in animal models of ARDS, while its extracellular segment will enter the blood circulation through the alveolar space when the alveolar epithelial cells are damaged. Therefore, changes in plasma KL-6 levels may be useful in ARDS and CARDS phenotyping, and KL-6 might guide future clinical trials in 'personalized medicine' settings.

Recognition of the ligand-induced spatiotemporal residue pair pattern of β2-adrenergic receptors using 3-D residual networks trained by the time series of protein distance maps

G protein-coupled receptors (GPCRs) are promising drug targets because they play a large role in physiological processes by modulating diverse signaling pathways in the human body. The GPCR-mediated signaling pathways are regulated by four types of ligands—agonists, neutral antagonists, partial agonists, and inverse agonists. Once each type of ligand is bound to the binding site, it activates, deactivates, or does not perturb signaling by shifting the conformational ensemble of GPCRs. Predicting the ligand's effect on the conformation at the binding moment could be a powerful screening tool for rational GPCR drug design. Here, we detected conformational differences by capturing the spatiotemporal residue pair pattern of the ligand-bound β2-adrenergic receptor (β2AR) using a 3-dimensional residual network, 3D-ResNets. The network was trained with the time series of protein distance maps extracted from hundreds of molecular dynamics (MD) simulation trajectories of ten β2AR-ligand complexes. The MD system was constructed with a lipid bilayer embedded in an inactive β2AR X-ray crystal structure and solvated with explicit water molecules. To train the network, three hyperparameters were tested, and it was found that the number of MD trajectories in the training set significantly affected the model's accuracy. The classification of agonists and neutral antagonists was successful, but inverse agonists were not. Between the agonists and antagonists, different residue pair patterns were spotted on the extracellular loop segment. This result demonstrates the potential application of a 3-D neural network in GPCR drug screening, as well as an analysis tool for protein functional dynamics