Pair Of Ligands Research Articles

Combining crystallographic and binding affinity data towards a novel dataset of small molecule overlays

Although small molecule superposition is a standard technique in drug discovery, a rigorous performance assessment of the corresponding methods is currently challenging. Datasets in this field are sparse, small, tailored to specific applications, unavailable, or outdated. The newly developed LOBSTER set described herein offers a publicly available and method-independent dataset for benchmarking and method optimization. LOBSTER stands for “Ligand Overlays from Binding SiTe Ensemble Representatives”. All ligands were derived from the PDB in a fully automated workflow, including a ligand efficiency filter. So-called ligand ensembles were assembled by aligning identical binding sites. Thus, the ligands within the ensembles are superimposed according to their experimentally determined binding orientation and conformation. Overall, 671 representative ligand ensembles comprise 3583 ligands from 3521 proteins. Altogether, 72,734 ligand pairs based on the ensembles were grouped into ten distinct subsets based on their volume overlap, for the benefit of introducing different degrees of difficulty for evaluating superposition methods. Statistics on the physicochemical properties of the compounds indicate that the dataset represents drug-like compounds. Consensus Diversity Plots show predominantly high Bemis–Murcko scaffold diversity and low median MACCS fingerprint similarity for each ensemble. An analysis of the underlying protein classes further demonstrates the heterogeneity within our dataset. The LOBSTER set offers a variety of applications like benchmarking multiple as well as pairwise alignments, generating training and test sets, for example based on time splits, or empirical software performance evaluation studies. The LOBSTER set is publicly available at https://doi.org/10.5281/zenodo.12658320, representing a stable and versioned data resource. The Python scripts are available at https://github.com/rareylab/LOBSTER, open-source, and allow for updating or recreating superposition sets with different data sources. Graphical abstractSimplified illustration of the LOBSTER dataset generation.

A collection of split-Gal4 drivers targeting conserved signaling ligands in Drosophila.

Communication between cells in metazoan organisms is mediated by a remarkably small number of highly conserved signaling pathways. Given this small number of signaling pathways, the existence of multiple related ligands for many of these pathways represents a key evolutionary innovation for encoding complexity into cell-cell signaling. Relatedly, crosstalk between pathways is another critical feature which allows a modest number pathways to ultimately generate an enormously diverse range of outcomes. It would thus be useful to have genetic tools to identify and manipulate not only those cells which express a given signaling ligand, but also those cells that specifically co-express pairs of signaling ligands. We present a collection of split-Gal4 knock-in lines targeting many of the ligands for highly conserved signaling pathways in Drosophila (Notch, Hedgehog, FGF, EGF, TGFβ, JAK/STAT, JNK, and PVR). We demonstrate that these lines faithfully recapitulate the endogenous expression pattern of their targets, and that they can be used to identify cells and tissues that co-express pairs of ligands. As a proof of principle, we demonstrate that the 4th chromosome TGFβ ligands myoglianin and maverick are broadly co-expressed in muscles and other tissues of both larva and adults, and that the JAK/STAT ligands upd2 and upd3 are partially co-expressed from cells of the midgut following gut damage. Together with our previously collection of split-Gal4 lines targeting the seven Wnt ligands, this resource allows Drosophila researchers to identify and genetically manipulate cells that specifically express pairs of conserved ligands from nearly all the major intercellular signaling pathways.

A Combined Experimental and Computational Exploration of Heteroleptic cis-Pd2L2L'2 Coordination Cages through Geometric Complementarity.

Heteroleptic (mixed-ligand) coordination cages are of interest as host systems with more structurally and functionally complex cavities than homoleptic architectures. The design of heteroleptic cages, however, is far from trivial. In this work, we experimentally probed the self-assembly of Pd(II) ions with binary ligand combinations in a combinatorial fashion to search for new cis-Pd2L2L'2 heteroleptic cages. A hierarchy of computational analyses was then applied to these systems with the aim of elucidating key factors for rationalising self-assembly outcomes. Simple and inexpensive geometric analyses were shown to be effective in identifying complementary ligand pairs. Preliminary results demonstrated the viability of relatively rapid semi-empirical calculations for predicting the topology of thermodynamically favoured assemblies with rigid ligands, whilst more flexible systems proved challenging. Stemming from this, key challenges were identified for future work developing effective computational forecasting tools for self-assembled metallo-supramolecular systems.

Orientational Compatibility Modulation of Ligands in Low-Symmetry Multi-Cavity Discrete Coordination Cages by Neighbouring Cage Participation.

Complexation of Pd(II) with a designer unsymmetrical bis-monodentate ligand (2 : 4 ratio) yielded a specific Pd2L4 type "single-cavity discrete coordination cage" (SCDCC), from a pool of 4 isomeric structures. The observed selctivity is attributed to inherent orientational preference of the ligand strands around the metal centers. Crafting a short coordinating arm at either ends of the bis-monodentate ligand (i.e the longer-arm) produced a pair of unsymmetrical isomeric tris-monodentate ligands; whereas crafting the same short-arm at both ends of the ligand gives an unsymmetrical tetrakis-monodentate ligand. Complexation of Pd(II) with either of the isomeric tris-monodenate ligands (3 : 4 ratio) resulted in corresponding low-symmetry "multi-cavity discrete coordination cage" MCDCC having two conjoined cavities, though the inherent relative orientational preference of the longer arms is not achievable in these cages. The enforced orientation is sustained by "Neighbouring Cage Participation" (NCP). However, one-pot combination of Pd(II), with a mixture of isomeric tris-monodentate ligands in 3 : 2 : 2 ratio produced an integratively self-sorted mixed-ligated MCDCC from a pool of 31 structures. Also, mixing Pd(II) with the tetrakis-monodentate ligand produced a MCDCC having three conjoined cavities. The inherent orientational preference of longer-arm of the ligand strands is retained in the mixed-ligated double-cavity and the homo-ligated triple cavity cages.

Abstract PR007: To the tumor and beyond: Tales of a holistic miRNA delivery vehicle

Abstract Like the challenges and skepticism that faced the antibody therapeutics field over a decade ago, RNA therapeutics is facing the same. And, like the antibody therapeutics field, we are beginning to realize the clinical impact of RNA therapeutics amiss these challenges. This is most clearly highlighted with the recent approval of mRNA vaccines and RNAi drugs targeted to the liver. Unfortunately, RNA-based drugs targeted to tumors is lagging behind, even with countless years of work that has revealed the power of using RNAi for treating oncological diseases. Lack of success is attributed to inability to deliver RNAi safely and effectively. A successful delivery agent requires multiple features. First, the agent must deliver the RNA specifically to the intended cells. Second, the agent must have a large therapeutic window, meaning that toxicity, if observed, should occur at doses that are orders of magnitude higher than the therapeutic dose. Third, if delivery of the RNA is by way of a specific ligand and receptor pair, as is the case herein, the RNA must successfully escape the endosome. Simply swelling the endosome is not enough if noncovalent interactions between the ligand and the receptor cannot be disrupted. Fourth, the RNA should include appropriate stabilizing modifications to increase intracellular half-life that will reduce dosing and cost. Through hard work and dedication, we have come up with an inclusive, easily synthesized, intramolecular molecule that achieves all of these essential features. Here, the challenges we face, the hurdles we have overcome, and the barriers that still remain with achieving success in reveling the clinical potential of miRNAs as anti-cancer therapeutics will be presented. Citation Format: Andrea L Kasinski. To the tumor and beyond: Tales of a holistic miRNA delivery vehicle [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: RNAs as Drivers, Targets, and Therapeutics in Cancer; 2024 Nov 14-17; Bellevue, Washington. Philadelphia (PA): AACR; Mol Cancer Ther 2024;23(11_Suppl):Abstract nr PR007.

Single-cell analyses reveal metastasis mechanism and microenvironment remodeling of lymph node in intrahepatic cholangiocarcinoma

Background and AimsLymph node metastasis (LNM) is a major determinant of recurrence and prognosis in intrahepatic cholangiocarcinoma (iCCA). LNM disrupts T-cell-mediated cytotoxicity, promotes tumor-specific immune tolerance, and facilitates distant metastasis. Despite its importance, extensive research on LMN in iCCA is lacking. This study aimed to systematically explore the heterogeneity of the LNM-associated microenvironment in iCCA by integrating single-cell and multiomics analyses, identifying metastasis-associated cell subgroups, and validating these findings through multiple cohorts. MethodsWe analyzed single-cell transcriptomics data from primary tumors, cancer-adjacent liver tissues, and tumor-draining lymph nodes of four iCCA patients who underwent radical surgery. Additionally, we collected 81 tumor and matched lymph node tissue sections from iCCA patients. We performed single-cell RNA sequencing and multiplex immunohistochemistry (mIHC), followed by differential gene expression analysis, functional enrichment analysis, single-cell copy number variation assessment, and pseudotime analysis. ResultsOur analysis revealed the complex heterogeneity of the iCCA LNM-associated microenvironment. We found a significant increase in stromal and mature immune cells in the metastatic lymph nodes. T cells constitute the predominant component, with diverse functional subtypes. We identified CD36+ macrophages and SAA1+ tumor cells as key players in the metastatic process. The SAA1-CD36 receptor‒ligand pair may be crucial in forming the LNM-associated microenvironment. ConclusionWe identified several metastasis-associated cell subgroups. These findings provide new insights into the mechanisms underlying LNM in iCCA and lay the groundwork for the development of novel therapeutic strategies. Our study highlights the importance of single-cell technologies in understanding tumor microenvironment complexity and offers valuable resources for future research. Impact and implicationsThe lack of single-cell transcriptome analysis of iCCA lymph node metastases has prevented us from understanding the underlying mechanisms of disease progression. To fill this knowledge gap, we elucidated the unique ecosystem of iCCA lymph node metastases, which is an important advance in clarifying the impact of the immune environment on the development of this disease. The results of this study identified several LNM-related therapeutic targets, which will not only be helpful to basic researchers but also provide potential diagnostic and treatment ideas for physicians, thereby helping patients and their caregivers develop more personalized treatment plans. This finding is highly important for improving the prognosis of patients with advanced iCCA in the future.

A collection of split-Gal4 drivers targeting conserved signaling ligands in Drosophila.

Communication between cells in metazoan organisms is mediated by a remarkably small number of highly conserved signaling pathways. Given the relatively small number of signaling pathways, the existence of multiple related ligands for many of these pathways is thought to represent a key evolutionary innovation for encoding complexity into cell-cell signaling. Relatedly, crosstalk and other interactions between pathways is another critical feature which allows a modest number pathways to ultimately generate an enormously diverse range of outcomes. It would thus be useful to have genetic tools to identify and manipulate not only those cells which express a given signaling ligand, but also those cells that specifically co-express pairs of signaling ligands. Here, we present a collection of split-Gal4 knock-in lines targeting many of the ligands for highly conserved signaling pathways in Drosophila (Notch, Hedgehog, FGF, EGF, TGF β , JAK/STAT, JNK, and PVR). We demonstrate that these lines faithfully recapitulate the endogenous expression pattern of their targets, and that they can be used to specifically identify the cells and tissues that co-express pairs of signaling ligands. As a proof of principle, we demonstrate that the 4th chromosome TGF β ligands myoglianin and maverick are broadly co-expressed in muscles and other tissues of both larva and adults, and that the JAK/STAT ligands upd2 and upd3 are partially co-expressed from cells of the midgut following gut damage. Together with our previously collection of split-Gal4 lines targeting the seven Wnt ligands, this resource allows Drosophila researchers to identify and genetically manipulate cells that specifically express pairs of conserved ligands from nearly all the major intercellular signaling pathways.

Synthesis and Local Characterization of CoO Nanoparticles in Distinct Phases: Unveiling Polymorphic Structures.

The advancement of functional nanomaterials has become a major focus of recent research, driven by the exceptional properties these materials display compared to their macroscopic (bulk) counterparts. Cobalt oxide nanoparticles (CoO-NPs) stand out primarily for their catalytic and magnetic properties, which can enable a range of technological applications, such as advanced catalysts, drug delivery systems, implants, prosthetics, sensors. However, in addition to the dependence on factors such as size, morphology, and functionalization, the properties of CoO-NPs are significantly influenced by the crystal structure. Therefore, local investigation into the polymorphic structures of CoO at the nanometric scale may provide new insights into the local structural and magnetic characteristics of these systems. In this report, we address the synthesis and local characterization of cobalt oxide (CoO) nanoparticles in the rock-salt cubic fcc-CoO and Wurtzite hpc-CoO phases, obtained through thermal decomposition. We analyze the influence of oleylamine and oleic acid ligands on the structural and morphological control of these systems. The obtained nanoparticles were characterized using conventional techniques such as X-ray diffraction (XRD), transmission electron microscopy, Raman spectroscopy, and Fourier-transform infrared spectroscopy. Local characterization was carried out by the perturbed angular correlation (PAC) nuclear technique using the radioactive tracer 111In(111Cd). Measurements were conducted at 295 and 10 K to investigate possible magnetic phase transitions in these systems. XRD results confirmed the formation of fcc-CoO and hcp-CoO phases. The phase fcc was obtained with the pair of oleylamine and oleic acid ligands, while the phase hcp phase was synthesized using only oleylamine. Additionally, nanoparticles synthesized with oleylamine and oleic acid exhibited better morphological control compared to those produced with only oleylamine. Raman spectroscopy analyses suggest a phase transformation process resulting in Co3O4. PAC results for hyperfine interactions at the 111In(111Cd) probe nucleus, indicate that the hcp-CoO phase shows smaller hyperfine magnetic interactions (B hf = 1 T) compared to the fcc-CoO phase (B hf = 17 T). This suggests the mechanism of superexchange interactions, which are strongly influenced by the Co-O-Co bond angle, which is 110° for the hpc-CoO phase and 180° for the fcc-CoO phase due to the geometries of the systems.

Modulating Immune Responses: The Double-Edged Sword of Platelet CD40L.

The CD40-CD40L receptor ligand pair plays a fundamental role in the modulation of the innate as well as the adaptive immune response, regulating monocyte, T and B cell activation, and antibody isotype switching. Although the expression and function of the CD40-CD40L dyad is mainly attributed to the classical immune cells, the majority of CD40L is expressed by activated platelets, either in a membrane-bound form or shed as soluble molecules in the circulation. Platelet-derived CD40L is involved in the communication with different immune cell subpopulations and regulates their functions effectively. Thus, platelet CD40L contributes to the containment and clearance of bacterial and viral infections, and additionally guides leukocytes to sites of infection. However, platelet CD40L promotes inflammatory cellular responses also in a pathophysiological context. For example, in HIV infections, platelet CD40L is supportive of neuronal inflammation, damage, and finally HIV-related dementia. In sepsis, platelet CD40L can induce extensive endothelial and epithelial damage resulting in barrier dysfunction of the gut, whereby the translocation of microbiota into the circulation further aggravates the uncontrolled systemic inflammation. Nevertheless, a distinct platelet subpopulation expressing CD40L under septic conditions can attenuate systemic inflammation and reduce mortality in mice. This review focuses on recent findings in the field of platelet CD40L biology and its physiological and pathophysiological implications, and thereby highlights platelets as vital immune cells that are essential for a proper immune surveillance. In this context, platelet CD40L proves to be an interesting target for various inflammatory diseases. However, either an agonism or a blockade of CD40L needs to be well balanced since both the approaches can cause severe adverse events, ranging from hyperinflammation to immune deficiency. Thus, an interference in CD40L activities should be likely done in a context-dependent and timely restricted manner.

Facile microwave synthesis of various-shaped magnetite/ reduced graphene oxide heterostructures and their magnetization properties

Heterostructures of magnetite (Fe3O4) nanoparticles and reduced graphene oxide (RGO) sheets are very common composite materials for different applications such as catalysis, energy storage, and biomedicine. Developing methods for the facile control of the size and shape of both freestanding Fe3O4 nanoparticles and those anchored onto RGO sheets is in demand. Herein, we report on the rapid and facile microwave synthesis (MWS) of Fe3O4 nanoparticles and Fe3O4/RGO with various sizes and shapes using the oleylamine (OAm)/oleic acid (OAc) ligand pair. The solvothermal synthesis using microwave irradiation (MWI) resulted in the concurrent conversion of graphene oxide (GO) into RGO and the in-situ formation of various-shaped Fe3O4 on RGO sheets. Freestanding Fe3O4 nanoparticles of various shapes were prepared using MWS for comparison. The morphological, structural, and surface properties of the samples were studied using different characterization techniques. The magnetization properties of the prepared samples were determined using a vibrating sample magnetometer. Various-shaped standalone and RGO-supported Fe3O4 nanoparticles including nanospheres, nanocubes, and nanotriangles were synthesized via MWI at 1000 W for 20 min by changing the ratios of the iron precursor and the OAm/OAc ligand pair. Interestingly, the MWI using OAm/OAc ligand pair of a molar ratio of 3:4 resulted in the in-situ formation of large hexagonal Fe3O4/RGO. The X-ray diffraction (XRD) and X-ray photoelectron spectroscopy (XPS) results confirm the crystallinity and spinel structure of the prepared Fe3O4 samples and prove the concurrent conversion of GO into RGO with assemblies of Fe3O4 nanoparticles. The magnetization measurements further emphasized the role of size and shape in affecting the magnetic properties of Fe3O4 and Fe3O4/RGO heterostructures. The results identify the qualities of the prepared samples and prove the MWS as a facile one-pot method for the preparation of Fe3O4 and Fe3O4/RGO heterostructures.

Dynamic responses of human lung innate and adaptive immune cells highlight the roles of genes at asthma risk loci.

The lung is a unique immunological niche with diverse immune cell types. The effects of stimulation through innate and adaptive immune receptors on human lung immune cells has largely been extrapolated from studies of blood immune cells. While multiple immune cell types and many genes have been implicated as contributing to asthma, the dynamics of these in human lung immune cells following activation will yield insights into asthma pathogenesis and lung immunity more broadly. Human lung immune cells from 6 donors were isolated. Mixed leukocytes were treated separately with lipopolysaccharide (LPS), F(ab)2-anti-human-IgM/IgG + IL4 and anti-CD3/CD28 for 4 and 18 hours and underwent single cell RNA sequencing (scRNAseq). Lung immune cell types were annotated, and gene expression compared across conditions. Genes at prior asthma-associated genetic loci were characterized across cell types, treatments and timepoints. Expression of non-classical class II genes associated with asthma, HLA-DQA2 and HLA-DQB2, and their protein products was characterized with immunohistochemistry. We characterized gene expression in 116,697 lung immune cells. Cell-, treatment-, and timepoint-specific effects on gene expression were detected in all lung immune cell populations. Correlation of gene expression between lung and blood lymphocyte populations decreased following stimulation. Among the genes that were differentially expressed, 97 receptor:ligand pairs had changes with treatments. 96.0% of genes at asthma risk loci demonstrated differential expression in at least one cell type and at least one treatment. B cells were the cell type with the highest expression of HLA-DQA2 and HLA-DQB2 which increased with anti-IgM/IgG treatment and the HLA-DQB2 protein was identified in lung B cells from a donor with asthma. Human lung immune activation elicits a broad range of cellular responses that deviate from those of blood immune cells and are relevant to asthma. Lung B cells expressing HLA-DQA2 and HLA-DQB2 appear to be involved in a novel antigen presentation pathway that contributes to asthma risk.

In Search of Covalency Measure of Gd(III)-Ligand Interactions.

Experimental electron density distribution of the [C(NH2)3]3[Gd(EDTA)F2]·H2O crystal was determined. The derived experimental and theoretical (DFT) topological parameters such as ∇2ρc, ρc, bond degree (BD), kinetics, and potential energy were used to study the nature of Gd-O, Gd-F, and Gd-N interactions. The natural charge of the Gd is 1.86; the natural configuration of the cation is [Xe]6s0.134f7.105d0.83, and the covalency of the Gd-L bond is mainly connected with the transfer of charge from the spx ligand orbitals onto the 5d orbitals of the Gd cation. Simultaneously, the donation of charge onto the 6s and 4f orbitals occurs to a lesser extent. Moreover it was found that the donation of the ligand charges onto the Gd(III) is larger for compounds with a lower coordination number. The obtained topological parameters were analyzed in the context of the Gd(III) f-f transition properties, i.e., energy of the excited 2S+1LJ states, Judd-Ofelt intensity parameters, and luminescence lifetimes, of 18 Gd(III) compounds with various O, N, and F donor ligands (DOTA, EDTA, CDTA, DTPA, NTA, EGTA, ODA, F-, H2O, and CO32-). The calculated nephelauxetic β parameter may reflect the penetration degree of electron lone pairs of ligands inside the metal basin. Finally, it was found for the first time that the sum of the Gd(III)-L bond energy (∑EGdL) is correlated with the position of the gravity center of the 8S7/2 → 2S+1LJ transitions and increase of covalency of the Gd(III)-L bonds is associated with decrease of their bond energy. The obtained results may shed light on chemical bonding in systems containing f-elements. Such subtle differences in the covalent contribution to the Ln-L or An-L bond may tune the selectivity of the partitioning processes of lanthanides and actinides.

A Reduced-Symmetry Pd2L4 Cage from a Heterotopic Dipyridyl Ligand.

Two dipyridyl ligands, L3,3 and L3,4, have been used in combination with palladium(II) in the construction of metallosupramolecular species that show anion-dependent behavior in solution. A rare example of a low-symmetry (C2h) lantern-type cage is formed in one instance, [Pd2(L3,3)4]4+, while the isomeric ligand yields a larger double-walled square complex, [Pd4(L3,4)8]8+. [Pd2(L3,3)4](NO3)4 was isolated in crystalline form revealing two anions within the interior of the C2h-symmetry cage. The cage itself is held together by hydrogen bonding between "head-to-tail" pairs of ligands that reinforces the symmetry generated by the ditopic ligands. In solution, the cage with NO3- has sharp 1H nuclear magnetic resonance (NMR) signals at room temperature, while the BF4- analogue has broad signals that sharpen at higher temperatures or upon addition of (Bu4N)(NO3), highlighting the importance of the anion in templating or otherwise influencing self-assembly in solution. Altering the substitution position of one of the pyridyl rings yields a more "open" complex, with [Pd4(L3,4)8](NO3)8 being isolated as a crystalline solid. The double-walled square complex has a greater Pd···Pd separation due to the increased angle that the pyridyl groups subtend at the core of the ligand. NMR spectroscopy and mass spectrometry studies suggest a single species in the presence of nitrate but multiple species with tetrafluoroborate.

Stable and Highly Emissive Infrared Yb-Doped Perovskite Quantum Cutters Engineered by Machine Learning.

Quantum cutting (QC) allows the conversion of high-energy photons into lower-energy photons, exhibiting great potential for infrared communications. Yb-doped perovskite nanocrystals can achieve an efficient QC process with extremely high photoluminescence quantum yield (PLQY) thanks to the favorable Yb3+ incorporation in the perovskite structure. However, conventionally used oleic acid-oleylamine-based ligand pairs cause instability issues due to highly dynamic binding to surface states that have curbed their potential applications. Herein, zwitterionic type C3-sulfobetaine 3-(N,N-Dimethylpalmitylammonio)propanesulfonate molecule is utilized to build a strong binding state on the nanocrystals' surface through a new phosphine oxide synthesis route. Leveraging machine learning and Bayesian Optimization workflow to determine optimal synthesis conditions, near-infrared PLQY above 190% is achieved. The high PLQY is well maintained after over three months of aging, under high-flux continuous UV irradiation, and long continuous annealing. This is the first report of highly efficient and stable perovskite quantum cutters, which will drive the study of fundamental physics phenomena and near-infrared quantum communications.

Crystal structure of polymeric bis-(3-amino-1H-pyrazole)-cadmium diiodide.

The reaction of cadmium iodide with 3-amino-pyrazole (3-apz) in ethano-lic solution leads to tautomerization of the ligand and the formation of crystals of the title compound, catena-poly[[di-iodido-cadmium(II)]-bis-(μ-3-amino-1H-pyrazole)-κ2 N 2:N 3;κ2 N 3:N 2], [CdI2(C3H5N3)2] n or [CdI2(3-apz)2] n . Its asymmetric unit consists of a half of a Cd2+ cation, an iodide anion and a 3-apz mol-ecule. The Cd2+ cations are coordinated by two iodide anions and two 3-apz ligands, generating trans-CdN4I2 octa-hedra, which are linked into chains by pairs of the bridging ligands. In the crystal, the ligand mol-ecules and iodide anions of neighboring chains are linked through inter-chain hydrogen bonds into a di-periodic network. The inter-molecular contacts were qu-anti-fied using Hirshfeld surface analysis and two-dimensional fingerprint plots, revealing the relative qu-anti-tative contributions of the weak inter-molecular contacts.

TGF-β ligand cross-subfamily interactions in the response of Caenorhabditis elegans to a bacterial pathogen.

The Transforming Growth Factor beta (TGF-β) family consists of numerous secreted peptide growth factors that play significant roles in cell function, tissue patterning, and organismal homeostasis, including wound repair and immunity. Typically studied as homodimers, these ligands have the potential to diversify their functions through ligand interactions that may enhance, repress, or generate novel functions. In the nematode Caenorhabditis elegans, there are only five TGF-β ligands, providing an opportunity to dissect ligand interactions in fewer combinations than in vertebrates. As in vertebrates, these ligands can be divided into bone morphogenetic protein (BMP) and TGF-β/Activin subfamilies that predominantly signal through discrete signaling pathways. The BMP subfamily ligand DBL-1 has been well studied for its role in the innate immune response in C. elegans. Here we show that all five TGF-β ligands play a role in survival on bacterial pathogens. We also demonstrate that multiple TGF-β ligand pairs act nonredundantly as part of this response. We show that the two BMP-like ligands-DBL-1 and TIG-2 -function independently of each other in the immune response, while TIG2/BMP and the TGF-β/Activin-like ligand TIG-3 function together. Structural modeling supports the potential for TIG-2 and TIG-3 to form heterodimers. Additionally, we identify TIG-2 and TIG-3 as members of a rare subset of TGF-β ligands lacking the conserved cysteine responsible for disulfide linking mature dimers. Finally, we show that canonical DBL1/BMP receptor and Smad signal transducers function in the response to bacterial pathogens, while components of the DAF7 TGF-β/Activin signaling pathway do not play a major role in survival. These results demonstrate a novel potential for BMP and TGF-β/Activin subfamily ligands to interact and may provide a mechanism for distinguishing the developmental and homeostatic functions of these ligands from an acute response such as the innate immune response to bacterial pathogens.

Asymmetric allostery in estrogen receptor-α homodimers drives responses to the ensemble of estrogens in the hormonal milieu

The estrogen receptor-α (ER) is thought to function only as a homodimer but responds to a variety of environmental, metazoan, and therapeutic estrogens at subsaturating doses, supporting binding mixtures of ligands as well as dimers that are only partially occupied. Here, we present a series of flexible ER ligands that bind to receptor dimers with individual ligand poses favoring distinct receptor conformations-receptor conformational heterodimers-mimicking the binding of two different ligands. Molecular dynamics simulations showed that the pairs of different ligand poses changed the correlated motion across the dimer interface to generate asymmetric communication between the dimer interface, the ligands, and the surface binding sites for epigenetic regulatory proteins. By examining the binding of the same ligand in crystal structures of ER in the agonist vs. antagonist conformers, we also showed that these allosteric signals are bidirectional. The receptor conformer can drive different ligand binding modes to support agonist vs. antagonist activity profiles, a revision of ligand binding theory that has focused on unidirectional signaling from the ligand to the coregulator binding site. We also observed differences in the allosteric signals between ligand and coregulator binding sites in the monomeric vs. dimeric receptor, and when bound by two different ligands, states that are physiologically relevant. Thus, ER conformational heterodimers integrate two different ligand-regulated activity profiles, representing different modes for ligand-dependent regulation of ER activity.

Genomic characteristics of adipose-derived stromal cells induced into neurons based on single-cell RNA sequencing

Adipose-derived stromal cells (ADSCs) can be induced to differentiate into neurons, representing the most promising avenue for cell therapy. However, the molecular mechanism and genomic characteristics of the differentiation of ADSCs into neurons remain poorly understood. In this study, cells from the adult ADSCs group, induction 1h, 3h, 5h, 6h, and 8h groups were selected for single-cell RNA sequencing (scRNA-Seq). Samples from these seven-time points were sequenced and analyzed. The expression of neuron marker genes, including NES, MAP2, TMEM59L, PTK2B, CHN1, DNM1, NRSN2, FBLN2, SCAMP1, SLC1A1, DLG4, CDK5, and ENO2, was found to be low in the ADSCs group, but highly expressed in differentiated cell clusters. The expression of stem cell marker genes, including CCND1, IL1B, MMP1, MMP3, MYO10, and BMP2, was the highest in the ADSCs cluster. This expression decreased significantly with the extension of induction time. Gene ontology (GO) enrichment analysis of upregulated genes in the induced samples showed that the biological processes related to neuronal differentiation and development, such as neuronal differentiation, projection, and apoptosis, were significantly upregulated with a longer induction time during cell cluster differentiation. The results of the cell communication analysis demonstrated the gradual formation of complex neural network connections between ADSC-derived neurons through receptor and ligand pairs at 5h after the induction of differentiation.

Mendelian randomization and single-cell expression analyses identify the causal relationship between depression and chronic rhinosinusitis.

The causative relationship between chronic rhinosinusitis (CRS) and depression remains unclear. Herein we employed Mendelian randomization (MR) coupled with single-cell analysis to investigate the causality between CRS and depression. Data pertaining to CRS and depression were mined from the genome-wide association study database, and a single-cell dataset was sourced from the literature. To explore causality, we conducted bidirectional MR analysis using MR-Egger, weighted median, inverse variance weighted (IVW), simple mode, and weighted mode, with IVW representing the most important method. Further, sensitivity analysis was performed to evaluate the robustness of MR analysis results. Candidate genes were analyzed via single-cell combined MR analysis. Forward MR analysis indicated depression as a risk factor for CRS when depression was the exposure factor and CRS was the outcome (OR = 1.425, P < 0.001). Reverse MR analysis revealed the same positive relationship between CRS and depression when CRS was the exposure factor and depression was the outcome (OR = 1.012, P = 0.038). Sensitivity analysis validated the robustness of bidirectional MR analysis results. Ten cell types (endothelial, ciliated, basal, myeloid, mast, apical, plasma, glandular, fibroblast, and T cells) were identified in the single-cell dataset. The network of receptor-ligand pairs showed that in normal samples, cell-cell interactions were present among various cell types, such as epithelial, mast, myeloid, and endothelial cells. In contrast, CRS samples featured only one specific receptor-ligand pair, confined to myeloid cells. TCF4 and MEF2C emerged as potentially crucial for CRS-associated depression development. Our findings suggest a bidirectional causal relationship between CRS and depression, offering a new perspective on the association between CRS and depression.

Synthesis of cationic lanthanoid tetraphenylborate crown ether complexes

The efficacy of Me3NHBPh4 as a protolytic agent in the generation of reactive lanthanoid cations has been further explored. Reaction of [Nd(BH4)3(thf)4] with Me3NHBPh4 in a 1:3 mole ratio, and dibenzo-18-crown-6 (DB18C6) in thf did not yield [Nd(thf)n][BPh4]3, but [Nd(BH4)2(DB18C6)][BPh4]⋅2THF (1), a complex primed for further functionalisation, was isolated. The structure has an eight coordinate Nd atom with two trans tridentate BH4− ligands. Redox transmetallation/protolysis (RTP) reactions between Yb metal, PhHgC6F5, and Me3NHBPh4 in the presence of 18-crown-6 (18C6) or DB18C6 in MeCN or in thf followed by work up with MeCN yields [Yb(CE)(MeCN)3][BPh4]2⋅nMeCN (CE = 18C6, n = 0 (2), and DB18C6 n = 3 (3)), the structures of which have nine coordinate Yb atoms. Two pairs of MeCN ligands are transoid, whereas the third pair have a small cis NYbN angle. In the absence of a crown ether ligand, the RTP reaction in MeCN yields the known [Yb(MeCN)8] [BPh4]2.