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We consider wavefunctions built from antisymmetrized products of two-electron wavefunctions (geminals), which is arguably the simplest extension of the antisymmetrized product of one-electron wavefunctions (orbitals) (i.e., a Slater determinant). Extensive use of geminals in wavefunctions has been limited by their high cost stemming from the many combinations of the two-electron basis functions (orbital pairs) used to build the geminals. When evaluating the overlap of the APG wavefunction with an orthogonal Slater determinant, this cost can be interpreted as the cost of evaluating the permanent, resulting from the symmetry with respect to the interchange of orbital pairs, and the cost of assigning the occupied orbitals to the orbital pairs of the wavefunction. Focusing on the latter, we present a graphical interpretation of the Slater determinant and utilize the maximum weighted matching algorithm to estimate the combination of orbital pairs with the largest contribution to the overlap. Then, the cost due to partitioning the occupied orbitals in the overlap is reduced from 𝒪 ( ( N - 1 ) ! ! ) to 𝒪 ( N 3 log N ) . Computational results show that many of these combinations are not necessary to obtain an accurate solution to the wavefunction. Because the APG wavefunction is the most general of the geminal wavefunctions, this approach can be applied to any of the simpler geminal wavefunction ansätze. In fact, this approach may even be extended to generalized quasiparticle wavefunctions, opening the door to tractable wavefunctions built using components of arbitrary numbers of electrons, not just two electrons., Competing Interests: The authors declare no potential conflicts of interest., (© 2024 The Author(s). International Journal of Quantum Chemistry published by Wiley Periodicals LLC.)

ErbB3 is markedly overexpressed in breast cancer cells and is associated with resistance and metastasis. Additionally, ErbB3 expression levels are positively correlated with low densities of tumor-infiltrating lymphocytes, a marker of poor prognosis. Consequently, ErbB3 is a promising therapeutic target for cancer immunotherapy. Here, we report the generation of ErbB3-targeted chimeric antigen receptor (CAR)-modified natural killer (NK) cells by transducing cord blood-derived primary NK cells using vsv-g envelope-pseudotyped lentiviral vectors. Transduced cells displayed stable CAR-expressing activity and increased cytotoxicity against ErbB3-positive breast cancer cell lines. Furthermore, anti-ErbB3 (aErbB3) CAR-NK cells strongly reduced the tumor burden in the SK-BR-3 xenograft mouse model without observable side effects. These findings underscore the potential of aErbB3 CAR-NK cells as targeted immunotherapy for ErbB3-positive breast cancer, suggesting a promising alternative to conventional treatments., Competing Interests: Declarations. Conflict of interest: The authors declare no competing interests., (© 2024. The Author(s).)

V(D)J recombination secures the production of functional immunoglobulin (Ig) genes and antibody diversity during the early stages of B-cell development through long-distance interactions mediated by cis-regulatory elements and trans-acting factors. O-GlcNAcylation is a dynamic and reversible posttranslational modification of nuclear and cytoplasmic proteins that regulates various protein functions, including DNA-binding affinity and protein-protein interactions. However, the effects of O-GlcNAcylation on proteins involved in V(D)J recombination remain largely unknown. To elucidate this relationship, we downregulated O-GlcNAcylation in a mouse model by administering an O-GlcNAc inhibitor or restricting the consumption of a regular diet. Interestingly, the inhibition of O-GlcNAcylation in mice severely impaired Ig heavy-chain (IgH) gene rearrangement. We identified several factors crucial for V(D)J recombination, including YY1, CTCF, SMC1, and SMC3, as direct targets of O-GlcNAc modification. Importantly, O-GlcNAcylation regulates the physical interaction between SMC1 and SMC3 and the DNA-binding patterns of YY1 at the IgH gene locus. Moreover, O-GlcNAc inhibition downregulated DDX5 protein expression, affecting the functional association of CTCF with its DNA-binding sites at the IgH locus. Our results showed that locus contraction and long-range interactions throughout the IgH locus are disrupted in a manner dependent on the cellular O-GlcNAc level. In this study, we established that V(D)J recombination relies on the O-GlcNAc status of stage-specific proteins during early B-cell development and identified O-GlcNAc-dependent mechanisms as new regulatory components for the development of a diverse antibody repertoire., Competing Interests: Competing interests: The authors declare no competing interests., (© 2024. The Author(s), under exclusive licence to CSI and USTC.)

Transfection of plasmid DNA (pDNA) encoding target genes is a routine tool in gene function studies and therapeutic applications. However, nucleic acid-sensing-mediated innate immune responses influence multiple intracellular signaling pathways. The stimulator of interferon genes (STING) is a crucial adapter protein for DNA sensors in mammalian cells. In this study, we explored the molecular mechanisms underlying DNA sensing by investigating the relationship between mRNA and protein expression levels and the STING pathway using single-cell analysis. We observed that reporter gene expression was dose-nonlinear after transfection of pDNA in cells with intact DNA-sensing pathways. Moreover, blocking the STING pathway in THP-1 cells significantly downregulated innate immune responses, upregulated exogenous gene expression, and mitigated the effects of innate immune responses on cell and gene function, but did not affect the proportion of reporter protein-positive cells. We elucidated the mechanisms of DNA sensing-induced innate immune response and cell death by analyzing heterozygous cellular responses to DNA transfection and transcriptome changes in positive cells. These findings suggest that the regulation of STING-mediated nucleic acid-sensing pathways is crucial for the accuracy of gene function studies and could enhance the efficacy of gene therapy., Competing Interests: Declaration of competing interest The authors declare no competing interests., (Copyright © 2024 The Authors. Published by Elsevier B.V. All rights reserved.)

Background: Natural killer (NK) cells are a subset of innate lymphoid cells that are inherently capable of recognizing and killing infected or tumour cells. This has positioned NK cells as a promising live drug for tumour immunotherapy, but limited success suggests incomplete knowledge of their killing mechanism. NK cell-mediated killing involves a complex decision-making process based on integrating activating and inhibitory signals from various ligand-receptor repertoires. However, the relative importance of the different activating ligand-receptor interactions in triggering NK killing remains unclear., Methods: We employed a systematic approach combining clinical, in silico, in vitro, and in vivo data analysis to quantify the impact of various activating ligands. Clinical data analysis was conducted using massive pan-cancer data (n = 10,595), where patients with high NK cell levels were stratified using CIBERSORT. Subsequently, multivariate Cox regression and Kaplan-Meier (KM) survival analysis were performed based on activating ligand expression. To examine the impact of ligand expression on NK killing at the cellular level, we assessed surface expression of five major activating ligands (B7H6, MICA/B, ULBP1, ULBP2/5/6, and ULBP3) of human tumour cell lines of diverse origins (n = 33) via flow cytometry (FACs) and their NK cell-mediated cytotoxicity on by calcein-AM assay using human primary NK cells and NK-92 cell lines. Based on this data, we quantified the contribution of each activating ligand to the NK killing activity using mathematical models and Bayesian statistics. To further validate the results, we performed calcein-AM assays upon ligand knockdown and overexpression, conjugation assays, and co-culture assays in activating ligand-downregulated/overexpressed in liquid tumour (LT) cell lines. Moreover, we established LT-xenograft mouse models to assess the efficacy of NK cell targeting toward tumours with dominant ligands., Findings: Through the clinical analysis, we discovered that among nearly all 18 activating ligands, only patients with LT who were NK cell-rich and specifically had higher B7H6 level exhibited a favorable survival outcome (p = 0.0069). This unexpected dominant role of B7H6 was further confirmed by the analysis of datasets encompassing multiple ligands and a variety of tumours, which showed that B7H6 exhibited the highest contribution to NK killing among five representative ligands. Furthermore, LT cell lines (acute myeloid leukemia (AML), B cell lymphoma, and T-acute lymphocytic leukemia (ALL)) with lowered B7H6 demonstrated decreased susceptibility to NK cell-mediated cytotoxicity compared to those with higher levels. Even within the same cell line, NK cells selectively targeted cells with higher B7H6 levels. Finally, LT-xenograft mouse models (n = 24) confirmed that higher B7H6 results in less tumour burden and longer survival in NK cell-treated LT mice (p = 0.0022)., Interpretation: While NK cells have gained attention for their potent anti-tumour effects without causing graft-versus-host disease (GvHD), thus making them a promising off-the-shelf therapy, our limited understanding of NK killing mechanisms has hindered their clinical application. This study illuminates the crucial role of the activating ligand B7H6 in driving NK cell killing, particularly in the context of LT. Therefore, the expression level of B7H6 could serve as a prognostic marker for patients with LT. Moreover, for the development of NK cell-based immunotherapy, focusing on increasing the level of B7H6 on its cognate receptor, NKp30, could be the most effective strategy., Funding: This work was supported by the National Research Council of Science & Technology (NST) grant (CAP-18-02-KRIBB, GTL24021-000), a National Research Foundation grant (2710012258, 2710004815), and an Institute for Basic Science grant (IBS-R029-C3)., Competing Interests: Declaration of interests All authors declare no competing interests., (Copyright © 2024 The Author(s). Published by Elsevier B.V. All rights reserved.)

Cell-based immunotherapies have emerged as promising cancer treatment modalities, demonstrating remarkable clinical efficacy. As interest in applying immune cell-based therapies to solid tumors has gained momentum, experimental models that enable long-term monitoring and mimic clinical administration are increasingly necessary. This study explores the potential of scaffold-based cell culture technologies, specifically three-dimensional (3D) extracellular matrix (ECM)-like frameworks, as promising solutions. These frameworks facilitate unhindered immune cell growth and enable continuous cancer cell culture. The three-dimensional (3D) cell culture model was developed using tailored scaffolds for natural killer (NK) cell culture. Within this framework, A549 lung cancer cells were cocultured with NK cells, allowing real-time monitoring for up to 28 days. The expression of critical markers associated with anticancer drug resistance and epithelial-mesenchymal transition (EMT) was evaluated in cancer cells within this 3D culture context. Compared to conventional 2D monolayer cultures, this 3D scaffold-based culture revealed that solid tumor cells, specifically A549 cells, exhibited heightened resistance to anticancer drugs. Additionally, the 3D culture environment upregulated the expression of EMT markers namely vimentin, N-cadherin, and fibronectin, while NK and zEGFR-CAR-NK cells displayed anticancer effects. In the two-dimensional (2D) coculture, only zEGFR-CAR-NK cells exhibited such effects in the 3D coculture system, highlighting an intriguing inconsistency with the 2D culture model, further confirmed by in vivo experiments. This in vitro 3D cell culture model reliably predicts outcomes in NK immunotherapy experiments. Thus, it represents a valuable tool for investigating drug resistance mechanisms and assessing the efficacy of immune cell-based therapies. By bridging the gap between in vitro and in vivo investigations, this model effectively translates potential treatments into animal models and facilitates rigorous preclinical evaluations.

Importance: Most youths receiving palliative care undergo many surgical interventions over their lifetimes. The intended purposes of interventions in the context of goals of care are not commonly articulated., Objective: To describe the goals and purposes of surgical intervention in youths receiving palliative care and propose a framework discussing intervention using goal-oriented language., Design, Setting, and Participants: This retrospective cohort analysis was conducted among a subset of patients enrolled between April 2017 and March 2021 in a prospective multicenter cohort study of youths receiving palliative care (the Pediatric Palliative Care Research Network's Shared Data and Research [SHARE] Study). Patients younger than 30 years receiving palliative care services were eligible for inclusion in SHARE, and all enrolled at Boston Children's Hospital/Dana Farber Cancer Institute, a SHARE site, were included in this study. Goals and purposes of all surgical interventions from the time of diagnosis through the present were abstracted from patient records. A goal and purpose framework was generated using a hybrid deductive-inductive approach based on established goals-of-care frameworks and the clinical context of surgical interventions. Data were analyzed in September 2023., Main Outcomes and Measures: Primary outcomes included goals and purposes of surgical interventions performed in the study population., Results: Among 197 youths receiving palliative care (mean [SD] age at palliative care start, 8.01 [7.53] years; 108 male [54.8%]; 6 Asian [3.0%], 12 Black [6.1%], 129 White [65.5%], and 16 with >1 race [8.1%]; 27 Hispanic [13.7%] and 142 not Hispanic [72.1%]), almost all individuals (189 youths [95.9%]) underwent at least 1 surgical intervention (mean [SD] 17.5 [16.3] interventions; median [IQR] 13 [5-22] interventions). Of 3331 surgical interventions, there were 878 interventions (26.5%) conducted with the goal of life extension, 1229 interventions (37.1%) conducted for life enhancement, and 79 interventions (2.4%) conducted for both goals; the remaining 1130 interventions (34.1%) held neither goal. Most interventions were performed with the purpose of diagnosis (1092 interventions [32.9%]) or cure and repair (1055 interventions [31.8%]), with fewer performed for the purpose of placing or maintaining assistive technology (696 interventions [21.0%]) or for supportive (434 interventions [13.1%]) or temporizing (39 interventions [1.2%]) purposes. Patients with cardiovascular disease and cancers constituted approximately half (592 patients [56.1%]) of those undergoing curative or repair interventions, whereas youths with neurologic or genetic conditions constituted approximately half (244 patients [56.2%]) of those undergoing supportive interventions., Conclusions and Relevance: In this cohort study, nearly all youths underwent surgical intervention, and the purposes of intervention differed by serious illness type. These findings suggest that conversations centered on a proposed framework concerning goals and purposes of surgical intervention may facilitate goal-concordant, high-quality care for youths with serious illness.

PyCI is a free and open-source Python library for setting up and running arbitrary determinant-driven configuration interaction (CI) computations, as well as their generalizations to cases where the coefficients of the determinant are nonlinear functions of optimizable parameters. PyCI also includes functionality for computing the residual correlation energy, along with the ability to compute spin-polarized one- and two-electron (transition) reduced density matrices. PyCI was originally intended to replace the ab initio quantum chemistry functionality in the HORTON library but emerged as a standalone research tool, primarily intended to aid in method development, while maintaining high performance so that it is suitable for practical calculations. To this end, PyCI is written in Python, adopting principles of modern software development, including comprehensive documentation, extensive testing, continuous integration/delivery protocols, and package management. Computationally intensive steps, notably operations related to generating Slater determinants and computing their expectation values, are delegated to low-level C++ code. This article marks the official release of the PyCI library, showcasing its functionality and scope., (© 2024 Author(s). Published under an exclusive license by AIP Publishing.)

Photosynthesis-the conversion of energy from sunlight into chemical energy-is essential for life on Earth. Yet there is much we do not understand about photosynthetic energy conversion on a fundamental level: how it evolved and the extent of its diversity, its dynamics, and all the components and connections involved in its regulation. In this commentary, researchers working on fundamental aspects of photosynthesis including the light-dependent reactions, photorespiration, and C4 photosynthetic metabolism pose and discuss what they view as the most compelling open questions in their areas of research., Competing Interests: Conflict of interest statement. None declared., (© The Author(s) 2024. Published by Oxford University Press on behalf of American Society of Plant Biologists.)

Natural killer (NK) cells play a crucial role in immunotherapy for cancer due to their natural ability to target and destroy cancer cells. However, current methods to visualize NK cells' activity against tumors in live organisms are limited. We introduce an imaging method that non-invasively tracks NK cell activation by cancer cells through the STAT1 protein. To achieve this, we modified NK cells to include a specific genetic sequence that binds to STAT1 when activated. These engineered NK cells (GAS-NK) demonstrate their functionality through various biological tests and analysis. Observations of changes in cancer environments and patient-derived cancer organoid models further confirm the effectiveness of this approach. Our method provides a way to monitor NK cell activity, which could improve the prediction and effectiveness of NK cell-based cancer therapies, contributing to advances in cancer treatment., (© 2024. The Author(s).)

Cancer therapies have evolved from traditional chemotherapy to more precise molecular-targeted immunotherapies, which have been associated with improved side effects and outcomes. These modern strategies rely on cancer-specific biomarkers that differentiate malignant from normal cells. The B7 family of immune checkpoint molecules is crucial for cancer immune evasion and a prime therapeutic target. B7-H6, a recently identified member of the B7 family, has emerged as a promising therapeutic target. Unlike other B7 proteins, B7-H6 is not expressed in healthy tissues but is upregulated in several cancers. It binds to NKp30, activating natural killer (NK) cells and triggering immune responses against cancer cells. This review explores the expression of B7-H6 in different cancers, the factors that regulate its expression, and its intrinsic and extrinsic pathways. Additionally, we discuss potential anticancer therapies targeting B7-H6, highlighting its significance in advancing precision medicine. Understanding the role of B7-H6 in cancer immunity may inform the development of appropriate therapies that exploit its cancer-specific expression.

Background/purpose: Despite the prevalence of surgical intervention in seriously ill children, data is scarce regarding interventions performed based on type of serious illness. We therefore sought to evaluate the surgical interventions performed from the time of serious illness diagnosis to the present in a cohort of children receiving palliative care, including identification of the surgical specialists involved in these procedures., Methods: We conducted a retrospective cohort analysis of surgical interventions in 197 children enrolled in a multicenter prospective cohort study (Pediatric Palliative Care Research Network SHARE Study). All surgical interventions were abstracted via clinical record review., Results: 189 (of 197, 96%) patients (45% female) with an average of 5.3 complex, chronic conditions (CCC) underwent 3331 surgical interventions (median = 13) by 21 specialist teams (most commonly general surgeons). Those with hematologic malignancies underwent intervention most frequently, followed by children with respiratory, genetic/metabolic, and gastrointestinal/genitourinary (GI/GU) diagnoses. Children with cardiovascular disease, malignancies, and prematurity had the shortest time between diagnosis and first intervention and between diagnosis and pediatric palliative care (PPC) services. By contrast, those with genetic, neurologic, and respiratory diagnoses had significantly longer intervals between diagnosis and intervention., Conclusions: Nearly all seriously ill children receiving PPC undergo surgical intervention, and many undergo tens of interventions by a variety of subspecialist teams. Surgical intervention differs by serious illness type, with children with more acutely life-limiting illnesses undergoing high-volume, high-risk interventions in the immediate post-diagnosis period. Those with chronic, life-limiting illnesses undergo a higher lifetime volume of interventions that are relatively lower risk and more evenly distributed over time., Level of Evidence: N/A., Competing Interests: Conflicts of interest The authors have no competing interests to declare., (Copyright © 2024 Elsevier Inc. All rights reserved.)

Perceptual decision-making is the process by which an animal uses sensory stimuli to choose an action or mental proposition. This process is thought to be mediated by neurons organized as attractor networks 1,2 . However, whether attractor dynamics underlie decision behavior and the complex neuronal responses remains unclear. Here we use an unsupervised, deep learning-based method to discover decision-related dynamics from the simultaneous activity of neurons in frontal cortex and striatum of rats while they accumulate pulsatile auditory evidence. We found that trajectories evolved along two sequential regimes, the first dominated by sensory inputs, and the second dominated by the autonomous dynamics, with flow in a direction (i.e., "neural mode") largely orthogonal to that in the first regime. We propose that the second regime corresponds to decision commitment. We developed a simplified model that approximates the coupled transition in dynamics and neural mode and allows precise inference, from each trial's neural activity, of a putative internal decision commitment time in that trial. The simplified model captures diverse and complex single-neuron temporal profiles, such as ramping and stepping 3-5 . It also captures trial-averaged curved trajectories 6-8 , and reveals distinctions between brain regions. The putative neurally-inferred commitment times ("nTc") occurred at times broadly distributed across trials, and not time-locked to stimulus onset, offset, or response onset. Nevertheless, when trials were aligned to nTc, behavioral analysis showed that, as predicted by a decision commitment time, sensory evidence before nTc affected the subjects' decision, but evidence after nTc did not. Our results show that the formation of a perceptual choice involves a rapid, coordinated transition in both the dynamical regime and the neural mode of the decision process, and suggest the moment of commitment to be a useful entry point for dissecting mechanisms underlying rapid changes in internal state.

GBasis is a free and open-source Python library for molecular property computations based on Gaussian basis functions in quantum chemistry. Specifically, GBasis allows one to evaluate functions expanded in Gaussian basis functions (including molecular orbitals, electron density, and reduced density matrices) and to compute functionals of Gaussian basis functions (overlap integrals, one-electron integrals, and two-electron integrals). Unique features of GBasis include supporting evaluation and analytical integration of arbitrary-order derivatives of the density (matrices), computation of a broad range of (screened) Coulomb interactions, and evaluation of overlap integrals of arbitrary numbers of Gaussians in arbitrarily high dimensions. For circumstances where the flexibility of GBasis is less important than high performance, a seamless Python interface to the Libcint C package is provided. GBasis is designed to be easy to use, maintain, and extend following many standards of sustainable software development, including code-quality assurance through continuous integration protocols, extensive testing, comprehensive documentation, up-to-date package management, and continuous delivery. This article marks the official release of the GBasis library, outlining its features, examples, and development., (© 2024 Author(s). Published under an exclusive license by AIP Publishing.)

The UV resistance of bacterial endospores is an important quality supporting their survival in inhospitable environments and therefore constitutes an essential driver of the ecological success of spore-forming bacteria. Nevertheless, the variability and evolvability of this trait are poorly understood. In this study, directed evolution and genetics approaches revealed that the Bacillus cereus pdaA gene (encoding the endospore-specific peptidoglycan-N-acetylmuramic acid deacetylase) serves as a contingency locus in which the expansion and contraction of short tandem repeats can readily compromise (PdaA OFF ) or restore (PdaA ON ) the pdaA open reading frame. Compared with B. cereus populations in the PdaA ON state, populations in the PdaA OFF state produced a lower yield of viable endospores but endowed them with vastly increased UV resistance. Moreover, selection pressures based on either quantity (i.e., yield of viable endospores) or quality (i.e., UV resistance of viable endospores) aspects could readily shift populations between PdaA ON and PdaA OFF states, respectively. Bioinformatic analysis also revealed that pdaA homologs within the Bacillus and Clostridium genera are often equipped with several short tandem repeat regions, suggesting a wider implementation of the pdaA-mediated phase variability in other sporeformers as well. These results for the first time reveal (1) pdaA as a phase-variable contingency locus in the adaptive evolution of endospore properties and (2) bet-hedging between what appears to be a quantity versus quality trade-off in endospore crops., Competing Interests: Declaration of interests The authors declare no competing interests., (Copyright © 2024 Elsevier Inc. All rights reserved.)

Wet heat treatment is a commonly applied method in the food and medical industries for the inactivation of microorganisms, and bacterial spores in particular. While many studies have delved into the mechanisms underlying wet heat killing and spore resistance, little attention has so far been dedicated to the capacity of spore-forming bacteria to tune their resistance through adaptive evolution. Nevertheless, a recent study from our group revealed that a psychrotrophic strain of the Bacillus cereus sensu lato group (i.e. Bacillus weihenstephanensis LMG 18989) could readily and reproducibly evolve to acquire enhanced spore wet heat resistance without compromising its vegetative cell growth ability at low temperatures. In the current study, we demonstrate that another B. cereus strain (i.e. the mesophilic B. cereus sensu stricto ATCC 14579) can acquire significantly increased spore wet heat resistance as well, and we subjected both the previously and currently obtained mutants to whole genome sequencing. This revealed that five out of six mutants were affected in genes encoding regulators of the spore coat and exosporium pathway (i.e. spoIVFB, sigK and gerE), with three of them being affected in gerE. A synthetically constructed ATCC 14579 ΔgerE mutant likewise yielded spores with increased wet heat resistance, and incurred a compromised spore coat and exosporium. Further investigation revealed significantly increased spore DPA levels and core dehydration as the likely causes for the observed enhanced spore wet heat resistance. Interestingly, deletion of gerE in Bacillus subtilis 168 did not impose increased spore wet heat resistance, underscoring potentially different adaptive evolutionary paths in B. cereus and B. subtilis., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interest or personal relationships that could have appeared to influence the work reported in this article., (Copyright © 2024 Elsevier B.V. All rights reserved.)

Recently, mRNA-based therapeutics, including vaccines, have gained significant attention in the field of gene therapy for treating various diseases. Among the various mRNA delivery vehicles, lipid nanoparticles (LNPs) have emerged as promising vehicles for packaging and delivering mRNA with low immunogenicity. However, while mRNA delivery has several advantages, the delivery efficiency and stability of LNPs remain challenging for mRNA therapy. In this study, an ionizable helper cholesterol analog, 3β[L-histidinamide-carbamoyl] cholesterol (Hchol) lipid is developed and incorporated into LNPs instead of cholesterol to enhance the LNP potency. The pK a values of the Hchol-LNPs are ≈6.03 and 6.61 in MC3- and SM102-based lipid formulations. Notably, the Hchol-LNPs significantly improve the delivery efficiency by enhancing the endosomal escape of mRNA. Additionally, the Hchol-LNPs are more effective in a red blood cell hemolysis at pH 5.5, indicating a synergistic effect of the protonated imidazole groups of Hchol and cholesterol on endosomal membrane destabilization. Furthermore, mRNA delivery is substantially enhanced in mice treated with Hchol-LNPs. Importantly, LNP-encapsulated SARS-CoV-2 spike mRNA vaccinations induce potent antigen-specific antibodies against SARS-CoV-2. Overall, incorporating Hchol into LNP formulations enables efficient endosomal escape and stability, leading to an mRNA delivery vehicle with a higher delivery efficiency., (© 2024 Wiley‐VCH GmbH.)

The quantification of molecular similarity has been present since the beginning of cheminformatics. Although several similarity indices and molecular representations have been reported, all of them ultimately reduce to the calculation of molecular similarities of only two objects at a time. Hence, to obtain the average similarity of a set of molecules, all the pairwise comparisons need to be computed, which demands a quadratic scaling in the number of computational resources. Here we propose an exact alternative to this problem: iSIM (instant similarity). iSIM performs comparisons of multiple molecules at the same time and yields the same value as the average pairwise comparisons of molecules represented by binary fingerprints and real-value descriptors. In this work, we introduce the mathematical framework and several applications of iSIM in chemical sampling, visualization, diversity selection, and clustering., Competing Interests: There are no conflicts to declare., (This journal is © The Royal Society of Chemistry.)

We propose a new perturbation theory framework that can be used to help with the projective solution of the Schrödinger equation for arbitrary wave functions. This Flexible Ansatz for N -body Perturbation Theory (FANPT) is based on our previously proposed Flexible Ansatz for the N -body Configuration Interaction (FANCI). We derive recursive FANPT expressions, including arbitrary orders in the perturbation hierarchy. We show that the FANPT equations are well-behaved across a wide range of conditions, including static correlation-dominated configurations and highly nonlinear wave functions.

HORTON is a free and open-source electronic-structure package written primarily in Python 3 with some underlying C++ components. While HORTON's development has been mainly directed by the research interests of its leading contributing groups, it is designed to be easily modified, extended, and used by other developers of quantum chemistry methods or post-processing techniques. Most importantly, HORTON adheres to modern principles of software development, including modularity, readability, flexibility, comprehensive documentation, automatic testing, version control, and quality-assurance protocols. This article explains how the principles and structure of HORTON have evolved since we started developing it more than a decade ago. We review the features and functionality of the latest HORTON release (version 2.3) and discuss how HORTON is evolving to support electronic structure theory research for the next decade., (© 2024 Author(s). Published under an exclusive license by AIP Publishing.)

Recently, interest in cancer immunotherapy has increased over traditional anti-cancer therapies such as chemotherapy or targeted therapy. Natural killer (NK) cells are part of the immune cell family and essential to tumor immunotherapy as they detect and kill cancer cells. However, the disadvantage of NK cells is that cell culture is difficult. In this study, porous microgels have been fabricated using microfluidic channels to effectively culture NK cells. Microgel fabrication using microfluidics can be mass-produced in a short time and can be made in a uniform size. Microgels consist of photo cross-linkable polymers such as methacrylic gelatin (GelMa) and can be regulated via controlled GelMa concentrations. NK92 cell-laden three-dimensional (3D) microgels increase mRNA expression levels, NK92 cell proliferation, cytokine release, and anti-tumor efficacy, compared with two-dimensional (2D) cultures. In addition, the study confirms that 3D-cultured NK92 cells enhance anti-tumor effects compared with enhancement by 2D-cultured NK92 cells in the K562 leukemia mouse model. Microgels containing healthy NK cells are designed to completely degrade after 5 days allowing NK cells to be released to achieve cell-to-cell interaction with cancer cells. Overall, this microgel system provides a new cell culture platform for the effective culturing of NK cells and a new strategy for developing immune cell therapy., Competing Interests: The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (© 2024 The Authors.)

Electron pairs have an illustrious history in chemistry, from powerful concepts to understanding structural stability and reactive changes to the promise of serving as building blocks of quantitative descriptions of the electronic structure of complex molecules and materials. However, traditionally, two-electron wavefunctions (geminals) have not enjoyed the popularity and widespread use of the more standard single-particle methods. This has changed recently, with a renewed interest in the development of geminal wavefunctions as an alternative to describing strongly correlated phenomena. Hence, there is a need to find geminal methods that are accurate, computationally tractable, and do not demand significant input from the user (particularly via cumbersome and often ill-behaved orbital optimization steps). Here, we propose new families of geminal wavefunctions inspired by the pair coupled cluster doubles ansatz. We present a new hierarchy of two-electron wavefunctions that extends the one-reference orbital idea to other geminals. Moreover, we show how to incorporate single-like excitations in this framework without leaving the quasiparticle picture. We explore the role of imposing seniority restrictions on these wavefunctions and benchmark these new methods on model strongly correlated systems., (© 2024 Author(s). Published under an exclusive license by AIP Publishing.)

Background: Disparities in obstetric care have been well documented, but disparities in the within-hospital population have not been as extensively explored. The objective is to assess cesarean delivery rate disparities at the hospital level in a nationally recognized low risk of cesarean delivery group., Methods: An observational study using a national population-based database, Nationwide Inpatient Sample, from 2008 to 2011 was conducted. All patients with nulliparous, term, singleton, vertex pregnancies from Black and White patients were included. The primary outcome was delivery mode (cesarean vs vaginal). The primary independent variable was race (Black vs White)., Results: A total of 1,064,351 patients were included and the overall nulliparous, term, singleton, and vertex pregnancies cesarean delivery rate was 14.1%. The within-hospital disparities of cesarean delivery rates were lower in minority-serving hospitals (OR: 1.20 95% CI: 1.12-1.28), rural hospitals (OR 1.11 95% CI: 1.02-1.20), and the South (OR 1.24 95% CI 1.19-1.30) compared to their respective counterparts. Non-minority serving hospitals (OR: 1.20 95% CI 0.12-1.25), and urban hospitals (OR1.32 95% CI 1.28-1.37), the Northeast (OR 1.41 95% CI 1.30-1.53) or West (OR 1.52 95% CI 1.38-1.67), had higher within-hospital racial disparities of cesarean delivery rates. The odds ratios reported are comparing within-hospital cesarean delivery rates in Black and White patients., Discussion: Significant within-hospital disparities of cesarean delivery rates across hospitals highlight the importance of facility-level factors. Policies aimed at advancing health equity must address hospital-level drivers of disparities in addition to structural racism., Competing Interests: Declaration of Conflicting InterestsThe author(s) declared no potential conflicts of interest with respect to the research, authorship, and/or publication of this article.

Understanding the evolutionary dynamics of foodborne pathogens throughout our food production chain is of utmost importance. In this study, we reveal that Salmonella Typhimurium can readily and reproducibly acquire vastly increased heat shock resistance upon repeated exposure to heat shock. Counterintuitively, this boost in heat shock resistance was invariantly acquired through loss-of-function mutations in the dnaJ gene, encoding a heat shock protein that acts as a molecular co-chaperone of DnaK and enables its role in protein folding and disaggregation. As a trade-off, however, the acquisition of heat shock resistance inevitably led to attenuated growth at 37°C and higher temperatures. Interestingly, loss of DnaJ also downregulated the activity of the master virulence regulator HilD, thereby lowering the fraction of virulence-expressing cells within the population and attenuating virulence in mice. By connecting heat shock resistance evolution to attenuation of HilD activity, our results confirm the complex interplay between stress resistance and virulence in Salmonella Typhimurium., Importance: Bacterial pathogens such as Salmonella Typhimurium are equipped with both stress response and virulence features in order to navigate across a variety of complex inhospitable environments that range from food-processing plants up to the gastrointestinal tract of its animal host. In this context, however, it remains obscure whether and how adaptation to one environment would obstruct fitness in another. In this study, we reveal that severe heat stress counterintuitively, but invariantly, led to the selection of S. Typhimurium mutants that are compromised in the activity of the DnaJ heat shock protein. While these mutants obtained massively increased heat resistance, their virulence became greatly attenuated. Our observations, therefore, reveal a delicate balance between optimal tuning of stress response and virulence features in bacterial pathogens., Competing Interests: The authors declare no conflict of interest.

Background: Platelets are generated from megakaryocytes (MKs), mainly located in the bone marrow (BM). Megakaryopoiesis can be affected by genetic disorders, metabolic diseases, and aging. The molecular mechanisms underlying platelet count regulation have not been fully elucidated., Objectives: In the present study, we investigated the role of thioredoxin-interacting protein (TXNIP), a protein that regulates cellular metabolism in megakaryopoiesis, using a Txnip -/- mouse model., Methods: Wild-type (WT) and Txnip -/- mice (2-27-month-old) were studied. BM-derived MKs were analyzed to investigate the role of TXNIP in megakaryopoiesis with age. The global transcriptome of BM-derived CD41 + megakaryocyte precursors (MkPs) of WT and Txnip -/- mice were compared. The CD34 + hematopoietic stem cells isolated from human cord blood were differentiated into MKs., Results: Txnip -/- mice developed thrombocytopenia at 4 to 5 months that worsened with age. During ex vivo megakaryopoiesis, Txnip -/- MkPs remained small, with decreased levels of MK-specific markers. Critically, Txnip -/- MkPs exhibited reduced mitochondrial reactive oxygen species, which was related to AKT activity. Txnip -/- MkPs also showed elevated glycolysis alongside increased glucose uptake for ATP production. Total RNA sequencing revealed enrichment for oxidative stress- and apoptosis-related genes in differentially expressed genes between Txnip -/- and WT MkPs. The effects of TXNIP on MKs were recapitulated during the differentiation of human cord blood-derived CD34 + hematopoietic stem cells., Conclusion: We provide evidence that the megakaryopoiesis pathway becomes exhausted with age in Txnip -/- mice with a decrease in terminal, mature MKs that response to thrombocytopenic challenge. Overall, this study demonstrates the role of TXNIP in megakaryopoiesis, regulating mitochondrial metabolism., Competing Interests: Declaration of competing interest The authors declare no competing interests., (Copyright © 2023 The Author(s). Published by Elsevier Inc. All rights reserved.)

Efforts to treat cancer using chimeric antigen receptor (CAR)-T therapy have made astonishing progress and clinical trials against hematopoietic malignancies have demonstrated their use. However, there are still disadvantages which need to be addressed: high costs, and side effects such as Graft-versus-Host Disease (GvHD) and Cytokine Release Syndrome (CRS). Therefore, recent efforts have been made to harness the properties of certain immune cells to treat cancer-not just T cells, but also natural killer (NK) cells, macrophages (Mφ), dendritic cells (DC), etc. In this paper, we will introduce immune cell-based cellular therapies that use various immune cells and describe their characteristics and their clinical situation. The development of immune cell-based cancer therapy fully utilizing the unique advantages of each and every immune cell is expected to enhance the survival of tumor patients owing to their high efficiency and fewer side effects.

Objectives: Jumonji C domain-containing (JMJD) 2B (JMJD2B) is a transcriptional cofactor and histone demethylase that is involved in prostate cancer formation. However, how its function is regulated by posttranslational modification has remained elusive. Hence, we examined if JMJD2B would be regulated by lysine methylation., Methods: Through in vitro methylation assays and Western blotting with methyl-lysine specific antibodies, we analyzed lysine methylation within JMJD2B. Identified methylated lysine residues were mutated to arginine residues and the respective impact on JMJD2B transcriptional activity measured with a reporter gene assay in human LNCaP prostate cancer cells., Results: We discovered that JMJD2B is methylated on up to six different lysine residues. Further, we identified the suppressor of variegation 3-9/enhancer of zeste/trithorax (SET) domain-containing protein 7/9 (SET7/9) as the methyltransferase being responsible for this posttranslational modification. Mutating the methylation sites in JMJD2B to arginine residues led to diminished coactivation of the Ju-nana (JUN) transcription factor, which is a known oncogenic protein in prostate tumors. In contrast, methylation of JMJD2B had no impact on its ability to coactivate another transcription factor associated with prostate cancer, the DNA-binding protein E26 transformation-specific (ETS) variant 1 (ETV1). Consistent with a potential joint action of JMJD2B, SET7/9 and JUN in prostate cancer, the expression of JMJD2B in human prostate tumors was positively correlated with both SET7/9 and JUN levels., Conclusions: The identified SET7/9-mediated methylation of JMJD2B appears to impact its cooperation with selected interacting transcription factors in prostate cancer cells. Given the implicated roles of JMJD2B beyond prostate tumorigenesis, SET7/9-mediated methylation of JMJD2B possibly also influences the development of other cancers, while its impairment might have relevance for obesity or a global developmental delay that can be elicited by reduced JMJD2B activity., Competing Interests: None., (IJBMB Copyright © 2023.)

How the function of the JMJD2D epigenetic regulator is regulated or whether it plays a role in prostate cancer has remained elusive. We found that JMJD2D was overexpressed in prostate tumors, stimulated prostate cancer cell growth and became methylated by SET7/9 on K427. Mutation of this lysine residue in JMJD2D reduced the ability of DU145 prostate cancer cells to grow, invade and form tumors and elicited extensive transcriptomic changes. This included downregulation of CBLC, a ubiquitin ligase gene with hitherto unknown functions in prostate cancer, and upregulation of PLAGL1, a transcription factor with reported tumor suppressive characteristics in the prostate. Bioinformatic analyses indicated that CBLC expression was elevated in prostate tumors. Further, downregulation of CBLC largely phenocopied the effects of the K427 mutation on DU145 cells. In sum, these data have unveiled a novel mode of regulation of JMJD2D through lysine methylation, illustrated how this can affect oncogenic properties by influencing expression of the CBLC gene, and established a pro-tumorigenic role for CBLC in the prostate. A corollary is that JMJD2D and CBLC inhibitors could have therapeutic benefits in the treatment of prostate and possibly other cancers., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2023 Gu, Kim, Jiang, Shin, Oh and Janknecht.)

Nucleic acid sensing is involved in viral infections, immune response-related diseases, and therapeutics. Based on the composition of nucleic acids, nucleic acid sensors are defined as DNA or RNA sensors. Pathogen-associated nucleic acids are recognized by membrane-bound and intracellular receptors, known as pattern recognition receptors (PRRs), which induce innate immune-mediated antiviral responses. PRR activation is tightly regulated to eliminate infections and prevent abnormal or excessive immune responses. Nucleic acid sensing is an essential mechanism in tumor immunotherapy and gene therapies that target cancer and infectious diseases through genetically engineered immune cells or therapeutic nucleic acids. Nucleic acid sensing supports immune cells in priming desirable immune responses during tumor treatment. Recent studies have shown that nucleic acid sensing affects the efficiency of gene therapy by inhibiting translation. Suppression of innate immunity induced by nucleic acid sensing through small-molecule inhibitors, virus-derived proteins, and chemical modifications offers a potential therapeutic strategy. Herein, we review the mechanisms and regulation of nucleic acid sensing, specifically covering recent advances. Furthermore, we summarize and discuss recent research progress regarding the different effects of nucleic acid sensing on therapeutic efficacy. This study provides insights for the application of nucleic acid sensing in therapy., (© 2023. The Author(s).)

The histone demethylase JMJD2A/KDM4A facilitates prostate cancer development, yet how JMJD2A function is regulated has remained elusive. Here, we demonstrate that SET7/9-mediated methylation on 6 lysine residues modulated JMJD2A. Joint mutation of these lysine residues suppressed JMJD2A's ability to stimulate the MMP1 matrix metallopeptidase promoter upon recruitment by the ETV1 transcription factor. Mutation of just 3 methylation sites (K505, K506, and K507) to arginine residues (3xR mutation) was sufficient to maximally reduce JMJD2A transcriptional activity and also decreased its binding to ETV1. Introduction of the 3xR mutation into DU145 prostate cancer cells reduced in vitro growth and invasion and also severely compromised tumorigenesis. Consistently, the 3xR genotype caused transcriptome changes related to cell proliferation and invasion pathways, including downregulation of MMP1 and the NPM3 nucleophosmin/nucleoplasmin gene. NPM3 downregulation phenocopied and its overexpression rescued, to a large degree, the 3xR mutation in DU145 cells, suggesting that NPM3 was a seminal downstream effector of methylated JMJD2A. Moreover, we found that NPM3 was overexpressed in prostate cancer and might be indicative of disease aggressiveness. SET7/9-mediated lysine methylation of JMJD2A may aggravate prostate tumorigenesis in a manner dependent on NPM3, implying that the SET7/9→JMJD2A→NPM3 axis could be targeted for therapy.

Trauma elicits various adaptive and maladaptive responses among all exposed people. There may be distinctively different patterns of adaptation/maladaptation or types according to neurobiological predisposition. The present study aims to dissect the heterogeneity of posttraumatic conditions in order to identify clinically meaningful subtypes in recently traumatized individuals and evaluate their neurobiological correlates and long-term prognosis. We implemented a data-driven classification approach in both discovery (n = 480) and replication (n = 220) datasets of trauma-exposed and trauma-unexposed individuals based on the clinical data across a wide range of assessments. Subtype-specific patterns of functional connectivity in higher-order cortical networks, longitudinal clinical outcomes, and changes in functional connectivity were also evaluated. We identified four distinct and replicable subtypes for trauma-exposed individuals according to posttraumatic stress symptoms. Each subtype was distinct in clinical characteristics, brain functional organization, and long-term trajectories for posttraumatic symptoms. These findings help enhance current understanding of mechanisms underlying the human-specific heterogeneous responses to trauma. Furthermore, this study contributes data towards the development of improved interventions, including targeting of subtype-specific characteristics, for trauma-exposed individuals and those with PTSD., (© 2023. The Author(s), under exclusive licence to Springer Nature Limited.)

Understanding structure-activity landscapes is essential in drug discovery. Similarly, it has been shown that the presence of activity cliffs in compound data sets can have a substantial impact not only on the design progress but also can influence the predictive ability of machine learning models. With the continued expansion of the chemical space and the currently available large and ultra-large libraries, it is imperative to implement efficient tools to analyze the activity landscape of compound data sets rapidly. The goal of this study is to show the applicability of the n-ary indices to quantify the structure-activity landscapes of large compound data sets using different types of structural representation rapidly and efficiently. We also discuss how a recently introduced medoid algorithm provides the foundation to finding optimum correlations between similarity measures and structure-activity rankings. The applicability of the n-ary indices and the medoid algorithm is shown by analyzing the activity landscape of 10 compound data sets with pharmaceutical relevance using three fingerprints of different designs, 16 extended similarity indices, and 11 coincidence thresholds., (© 2023 The Authors. Molecular Informatics published by Wiley-VCH GmbH.)

Background: Patients face a serious threat if a solid tumor leaves behind partial residuals or cannot be completely removed after surgical resection. Immunotherapy has attracted attention as a method to prevent this condition. However, the conventional immunotherapy method targeting solid tumors, that is, intravenous injection, has limitations in homing in on the tumor and in vivo expansion and has not shown effective clinical results., Method: To overcome these limitations, NK cells (Natural killer cells) were encapsulated in micro/macropore-forming hydrogels using 3D bioprinting to target solid tumors. Sodium alginate and gelatin were used to prepare micro-macroporous hydrogels. The gelatin contained in the alginate hydrogel was removed because of the thermal sensitivity of the gelatin, which can generate interconnected micropores where the gelatin was released. Therefore, macropores can be formed through bioprinting and micropores can be formed using thermally sensitive gelatin to make macroporous hydrogels., Results: It was confirmed that intentionally formed micropores could help NK cells to aggregate easily, which enhances cell viability, lysis activity, and cytokine release. Macropores can be formed using 3D bioprinting, which enables NK cells to receive the essential elements. We also characterized the functionality of NK 92 and zEGFR-CAR-NK cells in the pore-forming hydrogel. The antitumor effects on leukemia and solid tumors were investigated using an in vitro model., Conclusion: We demonstrated that the hydrogel encapsulating NK cells created an appropriate micro-macro environment for clinical applications of NK cell therapy for both leukemia and solid tumors via 3D bioprinting. 3D bioprinting makes macro-scale clinical applications possible, and the automatic process shows potential for development as an off-the-shelf immunotherapy product. This immunotherapy system could provide a clinical option for preventing tumor relapse and metastasis after tumor resection. Micro/macropore-forming hydrogel with NK cells fabricated by 3D bioprinting and implanted into the tumor site., (© 2023. The Author(s).)

Photosystem II is the water-oxidizing and O 2 -evolving enzyme of photosynthesis. How and when this remarkable enzyme arose are fundamental questions in the history of life that have remained difficult to answer. Here, recent advances in our understanding of the origin and evolution of photosystem II are reviewed and discussed in detail. The evolution of photosystem II indicates that water oxidation originated early in the history of life, long before the diversification of cyanobacteria and other major groups of prokaryotes, challenging and transforming current paradigms on the evolution of photosynthesis. We show that photosystem II has remained virtually unchanged for billions of years, and yet the nonstop duplication process of the D1 subunit of photosystem II, which controls photochemistry and catalysis, has enabled the enzyme to become adaptable to variable environmental conditions and even to innovate enzymatic functions beyond water oxidation. We suggest that this evolvability can be harnessed to develop novel light-powered enzymes with the capacity to carry out complex multistep oxidative transformations for sustainable biocatalysis.

The COVID-19 pandemic is an ongoing global public health threat. COVID-19 is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, and binding of the SARS-CoV-2 spike to its receptor, angiotensin-converting enzyme 2 (ACE2), on host cells is critical for viral infection. Here, we developed a luminescent biosensor that readily detects interactions of the spike receptor-binding domain (RBD) and ACE2 in cell culture medium ('SpACE-CCM'), which was based on bimolecular complementation of the split nanoluciferase-fused spike RBD and ectodomain of ACE2 and further engineered to be efficiently secreted from cells by adding a heterologous secretory signal peptide (SSP). Screening of various SSPs identified 'interferon-α+alanine-aspartate' as the SSP that induced the highest activity. The SpACE-CCM biosensor was validated by observing a marked reduction of the activity caused by interaction-defective mutations or in the presence of neutralizing antibodies, recombinant decoy proteins, or peptides. Importantly, the SpACE-CCM biosensor responded well in assay-validating conditions compared with conventional cell lysate-based NanoLuc Binary Technology, indicating its advantage. We further demonstrated the biosensor's versatility by quantitatively detecting neutralizing activity in blood samples from COVID-19 patients and vaccinated individuals, discovering a small molecule interfering with the spike RBD-ACE2 interaction through high-throughput screening, and assessing the cross-reactivity of neutralizing antibodies against SARS-CoV-2 variants. Because the SpACE-CCM is a facile and rapid one-step reaction biosensor that aptly recapitulates the native spike-ACE2 interaction, it would be advantageous in many experimental and clinical applications associated with this interaction., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023 The Authors. Published by Elsevier B.V. All rights reserved.)

Chronic obstructive pulmonary disease (COPD) is a chronic inflammatory lung disease which causes breathing problems. YPL-001, consisting of six iridoids, has potent inhibitory efficacy against COPD. Although YPL-001 has completed clinical trial phase 2a as a natural drug for COPD treatment, the most effective iridoid in YPL-001 and its mechanism for reducing airway inflammation remain unclear. To find an iridoid most effectively reducing airway inflammation, we examined the inhibitory effects of the six iridoids in YPL-001 on TNF or PMA-stimulated inflammation (IL-6, IL-8, or MUC5AC) in NCI-H292 cells. Here, we show that verproside among the six iridoids most strongly suppresses inflammation. Both TNF/NF-κB-induced MUC5AC expression and PMA/PKCδ/EGR-1-induced IL-6/-8 expression are successfully reduced by verproside. Verproside also shows anti-inflammatory effects on a broad range of airway stimulants in NCI-H292 cells. The inhibitory effect of verproside on the phosphorylation of PKC enzymes is specific to PKCδ. Finally, in vivo assay using the COPD-mouse model shows that verproside effectively reduces lung inflammation by suppressing PKCδ activation and mucus overproduction. Altogether, we propose YPL-001 and verproside as candidate drugs for treating inflammatory lung diseases that act by inhibiting PKCδ activation and its downstream pathways.

N 6 -Methyladenosine (m 6 A) is the most abundant epitranscriptomic mark and plays a fundamental role in almost every aspect of mRNA metabolism. Although m 6 A writers and readers have been widely studied, the roles of m 6 A erasers are not well-understood. Here, we investigate the role of FTO, one of the m 6 A erasers, in natural killer (NK) cell immunity. We observe that FTO-deficient NK cells are hyperactivated. Fto knockout (Fto -/- ) mouse NK cells prevent melanoma metastasis in vivo, and FTO-deficient human NK cells enhance the antitumor response against leukemia in vitro. We find that FTO negatively regulates IL-2/15-driven JAK/STAT signaling by increasing the mRNA stability of suppressor of cytokine signaling protein (SOCS) family genes. Our results suggest that FTO is an essential modulator of NK cell immunity, providing a new immunotherapeutic strategy for allogeneic NK cell therapies., (© 2023 The Authors.)

The formation of an immunological synapse (IS) is essential for natural killer (NK) cells to eliminate target cells. Despite an advanced understanding of the characteristics of the IS and its formation processes, the mechanisms that regulate its stability via the cytoskeleton are unclear. Here, we show that Nogo receptor 1 (NgR1) has an important function in modulating NK cell-mediated killing by destabilization of IS formation. NgR1 deficiency or blockade resulted in improved tumor control of NK cells by enhancing NK-to-target cell contact stability and regulating F-actin dynamics during IS formation. Patients with tumors expressing abundant NgR1 ligand had poor prognosis despite high levels of NK cell infiltration. Thus, our study identifies NgR1 as an immune checkpoint in IS formation and indicates a potential approach to improve the cytolytic function of NK cells in cancer immunotherapy., (© 2023. The Author(s), under exclusive licence to Springer Nature America, Inc.)

Fanpy is a free and open-source Python library for developing and testing multideterminant wavefunctions and related ab initio methods in electronic structure theory. The main use of Fanpy is to quickly prototype new methods by making it easier to convert the mathematical formulation of a new wavefunction ansätze to a working implementation. Fanpy is designed based on our recently introduced Flexible Ansatz for N-electron Configuration Interaction (FANCI) framework, where multideterminant wavefunctions are represented by their overlaps with Slater determinants of orthonormal spin-orbitals. In the simplest case, a new wavefunction ansatz can be implemented by simply writing a function for evaluating its overlap with an arbitrary Slater determinant. Fanpy is modular in both implementation and theory: the wavefunction model, the system's Hamiltonian, and the choice of objective function are all independent modules. This modular structure makes it easy for users to mix and match different methods and for developers to quickly explore new ideas. Fanpy is written purely in Python with standard dependencies, making it accessible for various operating systems. In addition, it adheres to principles of modern software development, including comprehensive documentation, extensive testing, quality assurance, and continuous integration and delivery protocols. This article is considered to be the official release notes for the Fanpy library., (© 2022 Wiley Periodicals LLC.)

Natural killer (NK) cells are immune effector cells with outstanding features for adoptive immunotherapy. Immune effector cells with chimeric antigen receptors (CARs) are promising targeted therapeutic agents for various diseases. Because tumor cells exhibit heterogeneous antigen expression and lose cell surface antigen expression during malignant progression, many CARs fixed against only one antigen have limited efficacy and are associated with tumor relapse. To expand the utility of CAR-NK cells, we designed a split and universal cotinine-CAR (Cot-CAR) system, comprising a Cot-conjugator and NK92 cells (α-Cot-NK92 cells) engineered with a CAR containing an anti-Cot-specific single-chain variable fragment and intracellular signaling domain. The efficacy of the Cot-CAR system was assessed in vitro using a cytolysis assay against various tumor cells, and its single- or multiple- utility potential was demonstrated using an in vivo lung metastasis model by injecting A549-Red-Fluc cells. The α-Cot-NK92 cells could switch targets, logically respond to multiple antigens, and tune cytolytic activation through the alteration of conjugators without re-engineering. Therefore the universal Cot-CAR system is useful for enhancing specificity and diversity of antigens, combating relapse, and controlling cytolytic activity. In conclusion, this universal Cot-CAR system reveals that multiple availability and controllability can be generated with a single, integrated system., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as potential conflicts of interest., (Copyright © 2023 Kang, Lee, Kim, Lee, Lee, Cho, Oh, Kim, Park, Han, Kim, Kim, Yoon, Doh, Chung, Hong, Choi and Kim.)

Background: This study analyzes the association between limited language proficiency and screening for colorectal cancer., Methods: This is a retrospective cohort study from the 2015 sample of the National Health Interview Survey database utilizing univariate and multivariate regression analysis. The study population includes subjects between 50 and 75 years of age. The main outcome analyzed was rates of screening colonoscopies between limited English-language proficiency (LEP) subjects and those fluent in English. Secondary outcomes included analysis of baseline, socioeconomic, access to health care variables, and other modalities for colorectal cancer screening between the groups., Results: Incidence of limited language proficiency was 4.8% (n = 1978, count = 4 453 599). They reported lower rates of screening colonoscopies (61% vs 34%, P < .001), less physician recommendation for a colonoscopy (87 vs 60%, P < .001), fewer polyps removed in the previous 3 years (24% vs 9.1%; P < .001), and fewer fecal occult blood samples overall (P < .001). Additionally, Hispanic non-LEP subjects have higher rates of colonoscopies compared to those with language barriers (50% vs 33%, P < .001). On multivariate analysis, LEP was associated with a lower likelihood to have a screening colonoscopy (OR .67 95% CI .49-.91). A second regression model with "Spanish language" and "other language" variables included, associated Spanish speakers with a lower likelihood for a screening colonoscopy (OR .71 95% CI .52-.97) when controlling for baseline, socioeconomic, and access to health care covariates., Discussion: Patients with limited English-language proficiency are associated with lower rates of screening for colorectal cancer, in particular the Spanish speaking subgroup.

Interleukin-7 (IL-7) is a multipotent cytokine that maintains the homeostasis of the immune system. IL-7 plays a vital role in T-cell development, proliferation, and differentiation, as well as in B cell maturation through the activation of the IL-7 receptor (IL-7R). IL-7 is closely associated with tumor development and has been used in cancer clinical research and therapy. In this review, we first summarize the roles of IL-7 and IL-7Rα and their downstream signaling pathways in immunity and cancer. Furthermore, we summarize and discuss the recent advances in the use of IL-7 and IL-7Rα as cancer immunotherapy tools and highlight their potential for therapeutic applications. This review will help in the development of cancer immunotherapy regimens based on IL-7 and IL-7Rα, and will also advance their exploitation as more effective and safe immunotherapy tools.

The heterotypic CIC structures formed of cancer and immune cells have been observed in tumor tissues. We aimed to assess the feasibility of using heterotypic CICs as a functional biomarker to predict NK susceptibility and drug resistance. The heterotypic CIC-forming cancer cells showed a lower response to NK cytotoxicity and higher proliferative ability than non-CIC cancer cells. After treatment with anticancer drugs, cancer cells that formed heterotypic CICs showed a higher resistance to anticancer drugs than non-CIC cancer cells. We also observed the formation of more CIC structures in cancer cells treated with anticancer drugs than in the non-treated group. Our results confirm the association between heterotypic CIC structures and anticancer drug resistance in CICs formed from NK and cancer cells. These results suggest a mechanism underlying immune evasion in heterotypic CIC cancer cells and provide insights into the anticancer drug resistance of cancer cells., Competing Interests: The authors declare no conflicts of interest or financial interests., (© 2022.)

Aurantii Fructus Immaturus (AFI), extensively used in traditional herbal medicine, is known to have diverse physiological effects against various diseases, including obesity, diabetes, and cardiovascular disease. However, the effects of AFI on the immune system, especially natural killer (NK) cells, remain largely unknown. We aimed to investigate the effect of AFI on NK cell activity in vitro and in vivo and to elucidate the underlying mechanisms. Further, we verified the anticancer efficacy of AFI in a mouse lung metastasis model, underscoring the therapeutic potential of AFI in cancer therapy. Our results revealed that AFI significantly enhanced the cytolytic activity of NK cells in a dose-dependent manner, accompanied by an increase in the expression of NK cell-activating receptors, especially NKp30 and NKp46. AFI treatment also increased the expression of cytolytic granules, including granzyme B and perforin. Furthermore, the expression of CD107a, a degranulation marker, was increased upon treatment with AFI. A signaling study using western blot analysis demonstrated that the phosphorylation of extracellular signal-regulated kinase (ERK) was involved in increasing the NK cell activity following AFI treatment. In the in vivo study performed in mice, oral administration of AFI markedly enhanced the cytotoxic activity of spleen mononuclear cells against YAC-1 cells, which was accompanied by NKp46 upregulation. In addition, we confirmed that cancer metastasis was inhibited in a mouse cancer metastasis model, established using the mouse melanoma B16F10 cell line, by the administration of AFI in vivo. Collectively, these results indicate that AFI enhances NK cell-mediated cytotoxicity in vitro and in vivo via activation of the ERK signaling pathway and suggest that AFI could be a potential supplement for cancer immunotherapy., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Park, Yang, Lee, Jung, Kim, Noh, Lee and Yoon.)

The importance of epigenetic drug and probe discovery is on the rise. This is not only paramount to identify and develop therapeutic treatments associated with epigenetic processes but also to understand the underlying epigenetic mechanisms involved in biological processes. To this end, chemical vendors have been developing synthetic compound libraries focused on epigenetic targets to increase the probabilities of identifying promising starting points for drug or probe candidates. However, the chemical contents of these data sets, the distribution of their physicochemical properties, and diversity remain unknown. To fill this gap and make this information available to the scientific community, we report a comprehensive analysis of eleven libraries focused on epigenetic targets containing more than 50,000 compounds. We used well-validated chemoinformatics approaches to characterize these sets, including novel methods such as automated detection of analog series and visual representations of the chemical space based on Constellation Plots and Chemical Library Networks. This work will guide the efforts of experimental groups working on high-throughput and medium-throughput screening of epigenetic-focused libraries. The outcome of this work can also be used as a reference to design and describe novel focused epigenetic libraries., (© 2021 Wiley-VCH GmbH.)

Ginseng is one of the most widely used herbal remedies for various diseases worldwide. Ginsenoside Rg3 (G-Rg3), the main component of ginseng, possesses several pharmacological properties, including anti-inflammatory, anti-tumor, antioxidant, anti-obesity, and immunomodulatory activities. However, the effect of G-Rg3 on natural killer (NK) cells in humans is not fully understood. Here, we investigated the effect of G-Rg3 on NK cell function and differentiation and elucidated the underlying mechanism. G-Rg3 increased NK cell cytotoxicity and simultaneously increased the expression of NK-activating receptors, NKp44, NKp46, and NKp30. Additionally, G-Rg3 increased the mRNA expression of NK cytolytic molecules, granzyme B and perforin. The expression of CD107a, a marker of NK cell degranulation, also increased in G-Rg3-treated NK cells. We therefore proceeded to identify which MAPK signaling pathway was involved in G-Rg3-mediated cytolytic activity. Treatment with G-Rg3 increased the phosphorylation levels of extracellular signal-regulated kinase (ERK), whereas ERK inhibition eliminated G-Rg3-induced NK cell cytotoxicity, suggesting the involvement of the ERK pathway. G-Rg3 did not affect the rate of differentiation of human cord-blood-derived NK cells; however, it increased the functional maturation of differentiated NK cells and promoted their cytotoxicity. The G-Rg3 isomer, 20(R)-Rg3, effectively activated NK cells via the extracellular signal-regulated kinase (ERK) signaling pathway, whereas 20(S)-Rg3 had no effect on NK cell activity. Altogether, the results demonstrated that 20(R)-Rg3 promoted NK cell activity via activation of the MAPK/ERK pathway, suggesting that 20(R)-Rg3 may be used as an activator of NK cell cytotoxicity for the treatment of diverse types of cancers., (Copyright © 2022 Elsevier B.V. All rights reserved.)

The quantification of chemical diversity has many applications in drug discovery, organic chemistry, food, and natural product chemistry, to name a few. As the size of the chemical space is expanding rapidly, it is imperative to develop efficient methods to quantify the diversity of large and ultralarge chemical libraries and visualize their mutual relationships in chemical space. Herein, we show an application of our recently introduced extended similarity indices to measure the fingerprint-based diversity of 19 chemical libraries typically used in drug discovery and natural products research with over 18 million compounds. Based on this concept, we introduce the Chemical Library Networks (CLNs) as a general and efficient framework to represent visually the chemical space of large chemical libraries providing a global perspective of the relation between the libraries. For the 19 compound libraries explored in this work, it was found that the (extended) Tanimoto index offers the best description of extended similarity in combination with RDKit fingerprints. CLNs are general and can be explored with any structure representation and similarity coefficient for large chemical libraries.