Single-cell functional genomics reveals determinants of sensitivity and resistance to natural killer cells in blood cancers.

Cancer cells can evade natural killer (NK) cell activity, thereby limiting anti-tumor immunity. To reveal genetic determinants of susceptibility to NK cell activity, we examined interacting NK cells and blood cancer cells using single-cell and genome-scale functional genomics screens. Interaction of NK and cancer cells induced distinct activation and type I interferon (IFN) states in both cell types depending on the cancer cell lineage and molecular phenotype, ranging from more sensitive myeloid to less sensitive B-lymphoid cancers. CRISPR screens in cancer cells uncovered genes regulating sensitivity and resistance to NK cell-mediated killing, including adhesion-related glycoproteins, protein fucosylation genes, and transcriptional regulators, in addition to confirming the importance of antigen presentation and death receptor signaling pathways. CRISPR screens with a single-cell transcriptomic readout provided insight into underlying mechanisms, including regulation of IFN-γ signaling in cancer cells and NK cell activation states. Our findings highlight the diversity of mechanisms influencing NK cell susceptibility across different cancers and provide a resource for NK cell-based therapies.

Wavefunction matching for solving quantum many-body problems.

Ab initio calculations have an essential role in our fundamental understanding of quantum many-body systems across many subfields, from strongly correlated fermions1-3 to quantum chemistry4-6 and from atomic and molecular systems7-9 to nuclear physics10-14. One of the primary challenges is to perform accurate calculations for systems where the interactions may be complicated and difficult for the chosen computational method to handle. Here we address the problem by introducing an approach called wavefunction matching. Wavefunction matching transforms the interaction between particles so that the wavefunctions up to some finite range match that of an easily computable interaction. This allows for calculations of systems that would otherwise be impossible owing to problems such as Monte Carlo sign cancellations. We apply the method to lattice Monte Carlo simulations15,16 of light nuclei, medium-mass nuclei, neutron matter and nuclear matter. We use high-fidelity chiral effective field theory interactions17,18 and find good agreement with empirical data. These results are accompanied by insights on the nuclear interactions that may help to resolve long-standing challenges in accurately reproducing nuclear binding energies, charge radii and nuclear-matter saturation in ab initio calculations19,20.

A preoptic neuronal population controls fever and appetite during sickness.

During infection, animals exhibit adaptive changes in physiology and behaviour aimed at increasing survival. Although many causes of infection exist, they trigger similar stereotyped symptoms such as fever, warmth-seeking, loss of appetite and fatigue1,2. Yet exactly how the nervous system alters body temperature and triggers sickness behaviours to coordinate responses to infection remains unknown. Here we identify a previously uncharacterized population of neurons in the ventral medial preoptic area (VMPO) of the hypothalamus that are activated after sickness induced by lipopolysaccharide (LPS) or polyinosinic:polycytidylic acid. These neurons are crucial for generating a fever response and other sickness symptoms such as warmth-seeking and loss of appetite. Single-nucleus RNA-sequencing and multiplexed error-robust fluorescence in situ hybridization uncovered the identity and distribution of LPS-activated VMPO (VMPOLPS) neurons and non-neuronal cells. Gene expression and electrophysiological measurements implicate a paracrine mechanism in which the release of immune signals by non-neuronal cells during infection activates nearby VMPOLPS neurons. Finally, we show that VMPOLPS neurons exert a broad influence on the activity of brain areas associated with behavioural and homeostatic functions and are synaptically and functionally connected to circuit nodes controlling body temperature and appetite. Together, these results uncover VMPOLPS neurons as a control hub that integrates immune signals to orchestrate multiple sickness symptoms in response to infection.

Ab Initio Calculation of the Alpha-Particle Monopole Transition Form Factor.

We present a parameter-free ab initio calculation of the α-particle monopole transition form factor in the framework of nuclear lattice effective field theory. We use a minimal nuclear interaction that was previously used to reproduce the ground state properties of light nuclei, medium-mass nuclei, and neutron matter simultaneously with no more than a few percent error in the energies and charge radii. The results for the monopole transition form factor are in good agreement with recent precision data from Mainz.

Structure Factors for Hot Neutron Matter from Ab Initio Lattice Simulations with High-Fidelity Chiral Interactions.

We present the first ab initio lattice calculations of spin and density correlations in hot neutron matter using high-fidelity interactions at next-to-next-to-next-to-leading order in chiral effective field theory. These correlations have a large impact on neutrino heating and shock revival in core-collapse supernovae and are encapsulated in functions called structure factors. Unfortunately, calculations of structure factors using high-fidelity chiral interactions were well out of reach using existing computational methods. In this Letter, we solve the problem using a computational approach called the rank-one operator (RO) method. The RO method is a general technique with broad applications to simulations of fermionic many-body systems. It solves the problem of exponential scaling of computational effort when using perturbation theory for higher-body operators and higher-order corrections. Using the RO method, we compute the vector and axial static structure factors for hot neutron matter as a function of temperature and density. The ab initio lattice results are in good agreement with virial expansion calculations at low densities but are more reliable at higher densities. Random phase approximation codes used to estimate neutrino opacity in core-collapse supernovae simulations can now be calibrated with ab initio lattice calculations.

Nuclear Charge Radii of Silicon Isotopes.

The nuclear charge radius of ^{32}Si was determined using collinear laser spectroscopy. The experimental result was confronted with ab initio nuclear lattice effective field theory, valence-space in-medium similarity renormalization group, and mean field calculations, highlighting important achievements and challenges of modern many-body methods. The charge radius of ^{32}Si completes the radii of the mirror pair ^{32}Ar-^{32}Si, whose difference was correlated to the slope L of the symmetry energy in the nuclear equation of state. Our result suggests L≤60 MeV, which agrees with complementary observables.

Results of a phase I trial with Haploidentical mbIL-21 ex vivo expanded NK cells for patients with multiply relapsed and refractory AML.

Natural killer (NK)-cells have potent anti-tumor effects, yet it remains unclear if they are effective for patients with relapsed acute myeloid leukemia (AML). In a phase I clinical trial, we treated 12 patients (median age 60 years) with refractory AML (median 5 lines of prior therapy, median bone marrow blast count of 47%) with fludarabine/cytarabine followed by 6 infusions of NK-cells expanded from haploidentical donors using K562 feeder cells expressing membrane-bound IL21 and 4-1BBL. Patients received 106-107/kg/dose. No toxicity or graft-versus-host disease (GVHD) was observed and MTD was not reached. Seven patients (58.3%) responded and achieved a complete remission (CR) with/without count recovery. Median time to best response was 48 days. Five responding patients proceeded to a haploidentical transplant from the same donor. After a median follow-up of 52 months, 1-year overall survival (OS) for the entire group was 41.7%, better for patients who responded with CR/CRi (57.14%), and for patients who responded and underwent transplantation (60%). Persistence and expansion of donor-derived NK-cells were identified in patients' blood, and serum IFNγ levels rose concurrently with NK cell infusions. A higher count-functional inhibitory KIR was associated with higher likelihood of achieving CR/CRi. In conclusion, we observed a significant response to ex vivo expanded NK-cell administration in refractory AML patients without adverse effects.

Cerebral organoids containing an AUTS2 missense variant model microcephaly.

Variants in the AUTS2 gene are associated with a broad spectrum of neurological conditions characterized by intellectual disability, microcephaly, and congenital brain malformations. Here, we use a human cerebral organoid model to investigate the pathophysiology of a heterozygous de novo missense AUTS2 variant identified in a patient with multiple neurological impairments including primary microcephaly and profound intellectual disability. Proband cerebral organoids exhibit reduced growth, deficits in neural progenitor cell (NPC) proliferation and disrupted NPC polarity within ventricular zone-like regions compared to control cerebral organoids. We used CRISPR-Cas9-mediated gene editing to correct this variant and demonstrate rescue of impaired organoid growth and NPC proliferative deficits. Single-cell RNA sequencing revealed a marked reduction of G1/S transition gene expression and alterations in WNT-ß-catenin signalling within proband NPCs, uncovering a novel role for AUTS2 in NPCs during human cortical development. Collectively, these results underscore the value of cerebral organoids to investigate molecular mechanisms underlying AUTS2 syndrome.

Manufacture and Characterization of Good Manufacturing Practice-Compliant SARS-COV-2 Cytotoxic T Lymphocytes.

BACKGROUND: Coronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). SARS-CoV-2 virus-specific cytotoxic T-cell lymphocytes (vCTLs) could provide a promising modality in COVID-19 treatment. We aimed to screen, manufacture, and characterize SARS-CoV-2-vCTLs generated from convalescent COVID-19 donors using the CliniMACS Cytokine Capture System (CCS). METHODS: Donor screening was done by stimulation of convalescent COVID-19 donor peripheral blood mononuclear cells with viral peptides and identification of interferonγ (IFN-γ)+ CD4 and CD8 T cells using flow cytometry. Clinical-grade SARS-CoV-2-vCTLs were manufactured using the CliniMACS CCS. The enriched SARS-CoV-2-vCTLs were characterized by T-cell receptor sequencing, mass cytometry, and transcriptome analysis. RESULTS: Of the convalescent donor blood samples, 93% passed the screening criteria for clinical manufacture. Three validation runs resulted in enriched T cells that were 79% (standard error of the mean 21%) IFN-γ+ T cells. SARS-CoV-2-vCTLs displayed a highly diverse T-cell receptor repertoire with enhancement of both memory CD8 and CD4 T cells, especially in CD8 TEM, CD4 TCM, and CD4 TEMRA cell subsets. SARS-CoV-2-vCTLs were polyfunctional with increased gene expression in T-cell function, interleukin, pathogen defense, and tumor necrosis factor superfamily pathways. CONCLUSIONS: Highly functional SARS-CoV-2-vCTLs can be rapidly generated by direct cytokine enrichment (12 hours) from convalescent donors. CLINICAL TRIALS REGISTRATION: NCT04896606.

Charged-Particle Bound States in Periodic Boxes.

We consider the binding energy of a two-body system with a repulsive Coulomb interaction in a finite periodic volume. We define the finite-volume Coulomb potential as the usual Coulomb potential, except that the distance is defined as the shortest separation between the two bodies in the periodic volume. We investigate this problem in one and three-dimensional periodic boxes and derive the asymptotic behavior of the volume dependence for bound states with zero angular momentum in terms of Whittaker functions. We benchmark our results against numerical calculations and show how the method can be used to extract asymptotic normalization coefficients for charged-particle bound states. The results we derive here have immediate applications for calculations of atomic nuclei in finite periodic volumes for the case where the leading finite-volume correction is associated with two charged clusters.

Floating Block Method for Quantum Monte Carlo Simulations.

Quantum Monte Carlo simulations are powerful and versatile tools for the quantum many-body problem. In addition to the usual calculations of energies and eigenstate observables, quantum Monte Carlo simulations can in principle be used to build fast and accurate many-body emulators using eigenvector continuation or design time-dependent Hamiltonians for adiabatic quantum computing. These new applications require something that is missing from the published literature, an efficient quantum Monte Carlo scheme for computing the inner product of ground state eigenvectors corresponding to different Hamiltonians. In this work, we introduce an algorithm called the floating block method, which solves the problem by performing Euclidean time evolution with two different Hamiltonians and interleaving the corresponding time blocks. We use the floating block method and nuclear lattice simulations to build eigenvector continuation emulators for energies of ^{4}He, ^{8}Be, ^{12}C, and ^{16}O nuclei over a range of local and nonlocal interaction couplings. From the emulator data, we identify the quantum phase transition line from a Bose gas of alpha particles to a nuclear liquid.

Cellular therapy: Adoptive immunotherapy with expanded natural killer cells.

Adoptive immunotherapy with natural killer cells was pioneered 30 years ago in human clinical trials with the development of cytokine-induced killer cells-unfractionated peripheral blood mononuclear cell (PBMC) populations activated overnight with IL-2. Higher doses were subsequently made possible through the advent of steady-state apheresis, allowing the collection of PBMC numbers equivalent to an entire adult blood volume, and increased purity made feasible through magnetic CD3-depletion and/or CD56-selection methods. Still, these approaches rarely achieved clinical dosing above a single infusion of 108 NK cells/kg, except with substantial donor-recipient size mismatch (eg, parents donating cells to children). To address this shortcoming, leukemia cell lines with NK cell-like function or ex vivo expansion approaches centered on the homeostatic cytokine IL-15 were developed. Here, we describe the development of an ex vivo expansion system based on a feeder cell expressing membrane-bound IL-21 that enables log-phase growth of primary NK cells for many weeks without inducing senescence, and describe the biology, correlative science, and translation to clinical trials for patients with leukemia, brain tumors, and solid tumors.

Role of NK-Like CD8+ T Cells during Asymptomatic Borrelia burgdorferi Infection.

Lyme disease (LD) due to Borrelia burgdorferi is the most prevalent vector-borne disease in the United States. There is a poor understanding of how immunity contributes to bacterial control, pathology, or both during LD. Dogs in an area of endemicity were screened for B. burgdorferi and Anaplasma exposure and stratified according to seropositivity, presence of LD symptoms, and doxycycline treatment. Significantly elevated serum interleukin-21 (IL-21) and increased circulating CD3+ CD94+ lymphocytes with an NK-like CD8+ T cell phenotype were predominant in asymptomatic dogs exposed to B. burgdorferi. Both CD94+ T cells and CD3- CD94+ lymphocytes, corresponding to NK cells, from symptomatic dogs expressed gamma interferon (IFN-γ) at a 3-fold-higher frequency upon stimulation with B. burgdorferi than the same subset among endemic controls. Surface expression of activating receptor NKp46 was reduced on CD94+ T cells from LD, compared to cells after doxycycline treatment. A higher frequency of NKp46-expressing CD94+ T cells correlated with significantly increased peripheral blood mononuclear cell (PBMC) cytotoxic activity via calcein release assay. PBMCs from dogs with symptomatic LD showed significantly reduced killing ability compared with endemic control PBMCs. An elevated NK-like CD8+ T cell response was associated with protection against development of clinical LD, while excess IFN-γ was associated with clinical disease.

CD38 deletion of human primary NK cells eliminates daratumumab-induced fratricide and boosts their effector activity.

Multiple myeloma (MM) is a plasma cell neoplasm that commonly expresses CD38. Daratumumab (DARA), a human monoclonal antibody targeting CD38, has significantly improved the outcome of patients with relapsed or refractory MM, but the response is transient in most cases. Putative mechanisms of suboptimal efficacy of DARA include downregulation of CD38 expression and overexpression of complement inhibitory proteins on MM target cells as well as DARA-induced depletion of CD38high natural killer (NK) cells resulting in crippled antibody-dependent cellular cytotoxicity (ADCC). Here, we tested whether maintaining NK cell function during DARA therapy could maximize DARA-mediated ADCC against MM cells and deepen the response. We used the CRISPR/Cas9 system to delete CD38 (CD38KO) in ex vivo expanded peripheral blood NK cells. These CD38KO NK cells were completely resistant to DARA-induced fratricide, showed superior persistence in immune-deficient mice pretreated with DARA, and enhanced ADCC activity against CD38-expressing MM cell lines and primary MM cells. In addition, transcriptomic and cellular metabolic analysis demonstrated that CD38KO NK cells have unique metabolic reprogramming with higher mitochondrial respiratory capacity. Finally, we evaluated the impact of exposure to all-trans retinoic acid (ATRA) on wild-type NK and CD38KO NK cell function and highlighted potential benefits and drawbacks of combining ATRA with DARA in patients with MM. Taken together, these findings provide proof of concept that adoptive immunotherapy using ex vivo expanded CD38KO NK cells has the potential to boost DARA activity in MM.

Perturbative Quantum Monte Carlo Method for Nuclear Physics.

While first order perturbation theory is routinely used in quantum Monte Carlo (QMC) calculations, higher-order terms present significant numerical challenges. We present a new approach for computing perturbative corrections in projection QMC calculations. We demonstrate the method by computing nuclear ground state energies up to second order for a realistic chiral interaction. We calculate the binding energies of several light nuclei up to ^{16}O by expanding the Hamiltonian around the Wigner SU(4) limit and find good agreement with data. In contrast to the natural ordering of the perturbative series, we find remarkably large second-order energy corrections. This occurs because the perturbing interactions break the symmetries of the unperturbed Hamiltonian. Our method is free from the sign problem and can be applied to QMC calculations for many-body systems in nuclear physics, condensed matter physics, ultracold atoms, and quantum chemistry.

The Future of Natural Killer Cell Immunotherapy for B Cell Non-Hodgkin Lymphoma (B Cell NHL).

OPINION STATEMENT: Natural killer (NK) cells have played a critical-if largely unrecognized or ignored-role in the treatment of B cell non-Hodgkin lymphoma (NHL) since the introduction of CD20-directed immunotherapy with rituximab as a cornerstone of therapy over 25 years ago. Engagement with NK cells leading to lysis of NHL targets through antibody-dependent cellular cytotoxicity (ADCC) is a critical component of rituximab's mechanism of action. Despite this important role, the only aspect of B cell NHL therapy that has been adopted as standard therapy that even indirectly augments or restores NK cell function is the introduction of obinutuzumab, a CD20 antibody with enhanced ability to engage with NK cells. However, over the last 5 years, adoptive immunotherapy with effector lymphocytes of B cell NHL has experienced tremendous growth, with five different CAR T cell products now licensed by the FDA, four of which target CD19 and have approved indications for some subtype of B cell NHL-axicabtagene ciloleucel, brexucabtagene autoleucel, lisocabtagene maraleucel, and tisagenlecleucel. These T cell-based immunotherapies essentially mimic the recognition, activation pathway, and cytotoxic machinery of a CD19 antibody engaging NK cells and lymphoma targets. Despite their efficacy, these T cell-based immunotherapies have been difficult to implement because they require 4-6 weeks of manufacture, are costly, and have significant toxicities. This renewed interest in the potential of cellular immunity-and the manufacturing, supply chain, and administration logistics that have been addressed with these new agents-have ignited a new wave of enthusiasm for NK cell-directed therapies in NHL. With high safety profiles and proven anti-lymphoma efficacy, one or more new NK cell-directed modalities are certain to be introduced into the standard toolbox of NHL therapy within the next few years, be it function-enhancing cytokine muteins, multi-domain NK cell engagers, or adoptive therapy with expanded or genetically modified NK cells.

Adoptive immunotherapy with double-bright (CD56bright /CD16bright ) expanded natural killer cells in patients with relapsed or refractory acute myeloid leukaemia: a proof-of-concept study.

Patients with acute myeloid leukaemia (AML) have a five-year survival rate of 28·7%. Natural killer (NK)-cell have anti-leukaemic activity. Here, we report on a series of 13 patients with high-risk R/R AML, treated with repeated infusions of double-bright (CD56bright /CD16bright ) expanded NK cells at an academic centre in Brazil. NK cells from HLA-haploidentical donors were expanded using K562 feeder cells, modified to express membrane-bound interleukin-21. Patients received FLAG, after which cryopreserved NK cells were thawed and infused thrice weekly for six infusions in three dose cohorts (106 -107 cells/kg/infusion). Primary objectives were safety and feasibility. Secondary endpoints included overall response (OR) and complete response (CR) rates at 28-30 days after the first infusion. Patients received a median of five prior lines of therapy, seven with intermediate or adverse cytogenetics, three with concurrent central nervous system (CNS) leukaemia, and one with concurrent CNS mycetoma. No dose-limiting toxicities, infusion-related fever, or cytokine release syndrome were observed. An OR of 78·6% and CR of 50·0% were observed, including responses in three patients with CNS disease and clearance of a CNS mycetoma. Multiple infusions of expanded, cryopreserved NK cells were safely administered after intensive chemotherapy in high-risk patients with R/R AML and demonstrated encouraging outcomes.

Convergence of Eigenvector Continuation.

Eigenvector continuation is a computational method that finds the extremal eigenvalues and eigenvectors of a Hamiltonian matrix with one or more control parameters. It does this by projection onto a subspace of eigenvectors corresponding to selected training values of the control parameters. The method has proven to be very efficient and accurate for interpolating and extrapolating eigenvectors. However, almost nothing is known about how the method converges, and its rapid convergence properties have remained mysterious. In this Letter, we present the first study of the convergence of eigenvector continuation. In order to perform the mathematical analysis, we introduce a new variant of eigenvector continuation that we call vector continuation. We first prove that eigenvector continuation and vector continuation have identical convergence properties and then analyze the convergence of vector continuation. Our analysis shows that, in general, eigenvector continuation converges more rapidly than perturbation theory. The faster convergence is achieved by eliminating a phenomenon that we call differential folding, the interference between nonorthogonal vectors appearing at different orders in perturbation theory. From our analysis we can predict how eigenvector continuation converges both inside and outside the radius of convergence of perturbation theory. While eigenvector continuation is a nonperturbative method, we show that its rate of convergence can be deduced from power series expansions of the eigenvectors. Our results also yield new insights into the nature of divergences in perturbation theory.

Rodeo Algorithm for Quantum Computing.

We present a stochastic quantum computing algorithm that can prepare any eigenvector of a quantum Hamiltonian within a selected energy interval [E-ε,E+ε]. In order to reduce the spectral weight of all other eigenvectors by a suppression factor δ, the required computational effort scales as O[|logδ|/(pε)], where p is the squared overlap of the initial state with the target eigenvector. The method, which we call the rodeo algorithm, uses auxiliary qubits to control the time evolution of the Hamiltonian minus some tunable parameter E. With each auxiliary qubit measurement, the amplitudes of the eigenvectors are multiplied by a stochastic factor that depends on the proximity of their energy to E. In this manner, we converge to the target eigenvector with exponential accuracy in the number of measurements. In addition to preparing eigenvectors, the method can also compute the full spectrum of the Hamiltonian. We illustrate the performance with several examples. For energy eigenvalue determination with error ε, the computational scaling is O[(logε)^{2}/(pε)]. For eigenstate preparation, the computational scaling is O(logΔ/p), where Δ is the magnitude of the orthogonal component of the residual vector. The speed for eigenstate preparation is exponentially faster than that for phase estimation or adiabatic evolution.

Hidden Spin-Isospin Exchange Symmetry.

The strong interactions among nucleons have an approximate spin-isospin exchange symmetry that arises from the properties of quantum chromodynamics in the limit of many colors, N_{c}. However this large-N_{c} symmetry is well hidden and reveals itself only when averaging over intrinsic spin orientations. Furthermore, the symmetry is obscured unless the momentum resolution scale is close to an optimal scale that we call Λ_{large-N_{c}}. We show that the large-N_{c} derivation requires a momentum resolution scale of Λ_{large-N_{c}}∼500 MeV. We derive a set of spin-isospin exchange sum rules and discuss implications for the spectrum of ^{30}P and applications to nuclear forces, nuclear structure calculations, and three-nucleon interactions.