Mitophagy in Intestinal Epithelial Cells Triggers Adaptive Immunity during Tumorigenesis.

In colorectal cancer patients, a high density of cytotoxic CD8+ T cells in tumors is associated with better prognosis. Using a Stat3 loss-of-function approach in two wnt/ß-catenin-dependent autochthonous models of sporadic intestinal tumorigenesis, we unravel a complex intracellular process in intestinal epithelial cells (IECs) that controls the induction of a CD8+ T cell based adaptive immune response. Elevated mitophagy in IECs causes iron(II)-accumulation in epithelial lysosomes, in turn, triggering lysosomal membrane permeabilization. Subsequent release of proteases into the cytoplasm augments MHC class I presentation and activation of CD8+ T cells via cross-dressing of dendritic cells. Thus, our findings highlight a so-far-unrecognized link between mitochondrial function, lysosomal integrity, and MHC class I presentation in IECs and suggest that therapies triggering mitophagy or inducing LMP in IECs may prove successful in shifting the balance toward anti-tumor immunity in colorectal cancer.

RIPK1 regulates RIPK3-MLKL-driven systemic inflammation and emergency hematopoiesis.

Upon ligand binding, RIPK1 is recruited to tumor necrosis factor receptor superfamily (TNFRSF) and Toll-like receptor (TLR) complexes promoting prosurvival and inflammatory signaling. RIPK1 also directly regulates caspase-8-mediated apoptosis or, if caspase-8 activity is blocked, RIPK3-MLKL-dependent necroptosis. We show that C57BL/6 Ripk1(-/-) mice die at birth of systemic inflammation that was not transferable by the hematopoietic compartment. However, Ripk1(-/-) progenitors failed to engraft lethally irradiated hosts properly. Blocking TNF reversed this defect in emergency hematopoiesis but, surprisingly, Tnfr1 deficiency did not prevent inflammation in Ripk1(-/-) neonates. Deletion of Ripk3 or Mlkl, but not Casp8, prevented extracellular release of the necroptotic DAMP, IL-33, and reduced Myd88-dependent inflammation. Reduced inflammation in the Ripk1(-/-)Ripk3(-/-), Ripk1(-/-)Mlkl(-/-), and Ripk1(-/-)Myd88(-/-) mice prevented neonatal lethality, but only Ripk1(-/-)Ripk3(-/-)Casp8(-/-) mice survived past weaning. These results reveal a key function for RIPK1 in inhibiting necroptosis and, thereby, a role in limiting, not only promoting, inflammation.

A molecular threshold for effector CD8(+) T cell differentiation controlled by transcription factors Blimp-1 and T-bet.

T cell responses are guided by cytokines that induce transcriptional regulators, which ultimately control differentiation of effector and memory T cells. However, it is unknown how the activities of these molecular regulators are coordinated and integrated during the differentiation process. Using genetic approaches and transcriptional profiling of antigen-specific CD8(+) T cells, we reveal a common program of effector differentiation that is regulated by IL-2 and IL-12 signaling and the combined activities of the transcriptional regulators Blimp-1 and T-bet. The loss of both T-bet and Blimp-1 leads to abrogated cytotoxic function and ectopic IL-17 production in CD8(+) T cells. Overall, our data reveal two major overlapping pathways of effector differentiation governed by the availability of Blimp-1 and T-bet and suggest a model for cytokine-induced transcriptional changes that combine, quantitatively and qualitatively, to promote robust effector CD8(+) T cell differentiation.

Tumor macrophage functional heterogeneity can inform the development of novel cancer therapies.

Macrophages represent a key component of the tumor microenvironment (TME) and are largely associated with poor prognosis. Therapeutic targeting of macrophages has historically focused on inhibiting their recruitment or reprogramming their phenotype from a protumor (M2-like) to an antitumor (M1-like) one. Unfortunately, this approach has not provided clinical breakthroughs that have changed practice. Emerging studies utilizing single-cell RNA-sequencing (scRNA-seq) and spatial transcriptomics have improved our understanding of the ontogeny, phenotype, and functional plasticity of macrophages. Overlaying the wealth of current information regarding macrophage molecular subtypes and functions has also identified novel therapeutic vulnerabilities that might drive better control of tumor-associated macrophages (TAMs). Here, we discuss the functional profiling of macrophages and provide an update of novel macrophage-targeted therapies in development.

EHF is essential for epidermal and colonic epithelial homeostasis, and suppresses Apc-initiated colonic tumorigenesis.

Ets homologous factor (EHF) is a member of the epithelial-specific Ets (ESE) family of transcription factors. To investigate its role in development and epithelial homeostasis, we generated a series of novel mouse strains in which the Ets DNA-binding domain of Ehf was deleted in all tissues (Ehf-/-) or specifically in the gut epithelium. Ehf-/- mice were born at the expected Mendelian ratio, but showed reduced body weight gain, and developed a series of pathologies requiring most Ehf-/- mice to reach an ethical endpoint before reaching 1 year of age. These included papillomas in the facial skin, abscesses in the preputial glands (males) or vulvae (females), and corneal ulcers. Ehf-/-mice also displayed increased susceptibility to experimentally induced colitis, which was confirmed in intestinal-specific Ehf knockout mice. Gut-specific Ehf deletion also impaired goblet cell differentiation, induced extensive transcriptional reprogramming in the colonic epithelium and enhanced Apc-initiated adenoma development. The Ets DNA-binding domain of EHF is therefore essential for postnatal homeostasis of the epidermis and colonic epithelium, and its loss promotes colonic tumour development.

In vivo MRI of hyperpolarized silicon-29 nanoparticles.

PURPOSE: The objective of the present work was to test the feasibility of in vivo imaging of hyperpolarized 50-nm silicon-29 (29Si) nanoparticles. METHODS: Commercially available, crystalline 50-nm nanoparticles were hyperpolarized using dynamic polarization transfer via the endogenous silicon oxide-silicon defects without the addition of exogenous radicals. Phantom experiments were used to quantify the effect of sample dissolution and various surface coating on T1 and T2 relaxation. The in vivo feasibility of detecting hyperpolarized silicon-29 was tested following intraperitoneal, intragastric, or intratumoral injection in mice and compared with the results obtained with previously reported, large, micrometer-size particles. The tissue clearance of SiNPs was quantified in various organs using inductively coupled plasma optical emission spectroscopy. RESULTS: In vivo images obtained after intragastric, intraperitoneal, and intratumoral injection compare favorably between small and large SiNPs. Improved distribution of small SiNPs was observed after intraperitoneal and intragastric injection as compared with micrometer-size SiNPs. Sufficient clearance of nanometer-size SiNPs using ex vivo tissue sample analysis was observed after 14 days following injection, indicating their safe use. CONCLUSION: In vivo MRI of hyperpolarized small 50-nm SiNPs is feasible with polarization levels and room-temperature relaxation times comparable to large micrometer-size particles.

Pulsed dynamic nuclear polarization: a comprehensive Floquet description.

Dynamic nuclear polarization (DNP) experiments using microwave (mw) pulse sequences are one approach to transfer the larger polarization on the electron spin to nuclear spins of interest. How the result of such experiments depends on the external magnetic field and the excitation power is part of an ongoing debate and of paramount importance for applications that require high chemical-shift resolution. To date numerical simulations using operator-based Floquet theory have been used to predict and explain experimental data. However, such numerical simulations provide only limited insight into parameters relevant for efficient polarization transfer, such as transition amplitudes or resonance offsets. Here we present an alternative method to describe pulsed DNP experiments by using matrix-based Floquet theory. This approach leads to analytical expressions for the transition amplitudes and resonance offsets. We validate the method by comparing computations by these analytical expressions to their numerical counterparts and to experimental results for the XiX, TOP and TPPM DNP sequences. Our results explain the experimental data and are in very good agreement with the numerical simulations. The analytical expressions allow for the discussion of the scaling behaviour of pulsed DNP experiments with respect to the external magnetic field. We find that the transition amplitudes scale inversely with the external magnetic field.

Relaxation enhancement by microwave irradiation may limit dynamic nuclear polarization.

Dynamic nuclear polarization enables the hyperpolarization of nuclear spins beyond the thermal-equilibrium Boltzmann distribution. However, it is often unclear why the experimentally measured hyperpolarization is below the theoretically achievable maximum polarization. We report a (near-) resonant relaxation enhancement by microwave (MW) irradiation, leading to a significant increase in the nuclear polarization decay compared to measurements without MW irradiation. For example, the increased nuclear relaxation limits the achievable polarization levels to around 35% instead of hypothetical 60%, measured in the DNP material TEMPO in 1H glassy matrices at 3.3 K and 7 T. Applying rate-equation models to published build-up and decay data indicates that such relaxation enhancement is a common issue in many samples when using different radicals at low sample temperatures and high Boltzmann polarizations of the electrons. Accordingly, quantification and a better understanding of the relaxation processes under MW irradiation might help to design samples and processes towards achieving higher nuclear hyperpolarization levels.

Continuous Floquet theory in solid-state NMR.

This article presents the application of continuous Floquet theory in solid-state nuclear magnetic resonance (NMR). Continuous Floquet theory extends the traditional Floquet theory to non-continuous Hamiltonians, enabling the description of observable effects not fully captured by the traditional Floquet theory due to its requirement for a periodic Hamiltonian. We present closed-form expressions for computing first- and second-order effective Hamiltonians, streamlining integration with the traditional Floquet theory and facilitating application in NMR experiments featuring multiple modulation frequencies. Subsequently, we show examples of the practical application of continuous Floquet theory by investigating several solid-state NMR experiments. These examples illustrate the importance of the duration of the pulse scheme regarding the width of the resonance conditions and the near-resonance behavior.

Identification of Serum Biomarkers to Monitor Therapeutic Response in Intestinal-Type Gastric Cancer.

There are a limited number of clinically useful serum biomarkers to predict tumor onset or treatment response in gastric cancer (GC). For this reason, we explored the serum proteome of the gp130Y757F murine model of intestinal-type gastric cancer (IGC). We identified 30 proteins with significantly elevated expression in early gp130Y757F IGC and 12 proteins that were significantly elevated in late gp130Y757F IGC compared to age- and gender-matched wild-type mice. Within these signatures, there was an overlap of 10 proteins commonly elevated in both early- and late-stage disease. These results highlight the potential to identify serum biomarkers of disease stage. Since IGC in the gp130Y757F model can be reversed following therapeutic inhibition of Interleukin (IL)-11, we explored whether the protein signatures we identified could be used to monitor tumor regression. We compared two different therapeutic modalities and found 5 proteins to be uniquely differentially expressed between control animals and animals halfway through treatment, with 10 differentially expressed at the end of treatment. Our findings highlight the potential to identify reliable biomarkers to track IGC tumor regression in response to treatment.

Induction of Fibroblast Growth Factor Receptor 4 by Helicobacter pylori via Signal Transducer and Activator of Transcription 3 With a Feedforward Activation Loop Involving SRC Signaling in Gastric Cancer

BACKGROUND & AIMS: Helicobacter pylori (H pylori) infection is the main risk factor for gastric cancer. The role of fibroblast growth factor receptors (FGRFs) in H pylori-mediated gastric tumorigenesis remains largely unknown. This study investigated the molecular and mechanistic links between H pylori, inflammation, and FGFR4 in gastric cancer. METHODS: Cell lines, human and mouse gastric tissue samples, and gastric organoids models were implemented. Infection with H pylori was performed using in vitro and in vivo models. Western blot, real-time quantitative reverse-transcription polymerase chain reaction, flow cytometry, immunofluorescence, immunohistochemistry, chromatin immunoprecipitation, and luciferase reporter assays were used for molecular, mechanistic, and functional studies. RESULTS: Analysis of FGFR family members using The Cancer Genome Atlas data, followed by validation, indicated that FGFR4 messenger (m)RNA was the most significantly overexpressed member in human gastric cancer tissue samples (P < .001). We also detected high levels of Fgfr4 mRNA and protein in gastric dysplasia and adenocarcinoma lesions in mouse models. Infection with J166, 7.13, and PMSS1 cytotoxin-associated gene A (CagA)+ H pylori strains induced FGFR4 mRNA and protein expression in in vitro and in vivo models. This was associated with a concordant activation of signal transducer and activator of transcription 3 (STAT3). Analysis of the FGFR4 promoter suggested several putative binding sites for STAT3. Using chromatin immunoprecipitation assay and an FGFR-promoter luciferase reporter containing putative STAT3 binding sites and their mutants, we confirmed a direct functional binding of STAT3 on the FGFR4 promoter. Mechanistically, we also discovered a feedforward activation loop between FGFR4 and STAT3 where the fibroblast growth factor 19­FGFR4 axis played an essential role in activating STAT3 in a SRC proto-oncogene non-receptor tyrosine kinase dependent manner. Functionally, we found that FGFR4 protected against H pylori-induced DNA damage and cell death. CONCLUSIONS: Our findings demonstrated a link between infection, inflammation, and FGFR4 activation, where a feedforward activation loop between FGFR4 and STAT3 is established via SRC proto-oncogene non-receptor tyrosine kinase in response to H pylori infection. Given the relevance of FGFR4 to the etiology and biology of gastric cancer, we propose FGFR4 as a druggable molecular vulnerability that can be tested in patients with gastric cancer.

IL-17 cuts to the chase in colon cancer.

Although interleukin-17A (IL-17A) facilitates colon cancer development, its target cells remain elusive. In this issue of Immunity, Wang et al. (2014) now demonstrate that IL-17A receptors on the intestinal epithelium promote progression of APC mutant adenomas associated with IL-6 expression and that IL-17A confers chemotherapy resistance.

Residual proton line width under refocused frequency-switched Lee-Goldburg decoupling in MAS NMR.

Despite many decades of research, homonuclear decoupling in solid-state NMR under magic-angle spinning (MAS) has yet to reach a point where the achievable proton line widths become comparable to the resolution obtained in solution-state NMR. This makes the precise determination of isotropic chemical shifts difficult and thus presents a limiting factor in the application of proton solid-state NMR to biomolecules and small molecules. In this publication we analyze the sources of the residual line width in refocused homonuclear-decoupled spectra in detail by comparing numerical simulations and experimental data. Using a hybrid analytical/numerical approach based on Floquet theory, we find that third-order effective Hamiltonian terms are required to realistically characterize the line shape and line width under frequency-switched Lee-Goldburg (FSLG) decoupling under MAS. Increasing the radio-frequency field amplitude enhances the influence of experimental rf imperfections such as pulse transients and the MAS-modulated radial rf-field inhomogeneity. While second- and third-order terms are, as expected, reduced in size at higher rf-field amplitudes, the line width becomes dominated by first-order terms which severely limits the achievable line width. We expect, therefore, that significant improvements in the line width of FSLG-decoupled spectra can only be achieved by reducing the influence of MAS-modulated rf-field inhomogeneity and pulse transients.

The effect of methyl group rotation on 1H-1H solid-state NMR spin-diffusion spectra.

Fast magic-angle spinning (MAS) NMR experiments open the way for proton-detected NMR studies and have been explored in the past years for a broad range of materials, comprising biomolecules and pharmaceuticals. Proton-spin diffusion (SD) is a versatile polarization-transfer mechanism and plays an important role in resonance assignment and structure determination. Recently, the occurrence of negative cross peaks in 2D 1H-1H SD-based spectra has been reported and explained with higher-order SD effects, in which the chemical shifts of the involved quadruple of nuclei need to compensate each other. We herein report negative cross peaks in SD-based spectra observed for a variety of small organic molecules involving methyl groups. We combine experimental observations with numerical and analytical simulations to demonstrate that the methyl groups can give rise to coherent (SD) as well as incoherent (Nuclear Overhauser Enhancement, NOE) effects, both in principle manifesting themselves as negative cross peaks in the 2D spectra. Analytical calculations and simulations however show that higher-order coherent contributions dominate the experimentally observed negative peaks in our systems. Methyl groups are prone to the observation of such higher order coherent effects. Due to their low-frequency shifted 1H resonances, the chemical-shift separation relative to for instance aromatic protons in spatial proximity is substantial (>4.7 ppm in the studied examples) preventing any sizeable second-order spin-diffusion processes, which would mask the negative contribution to the peaks.

The effect of 1H offset and flip-angle on heteronuclear decoupling efficiency in ROSPAC pulsed sequence: A Floquet description.

A new heteronuclear decoupling sequence for solid-state NMR and magic angle spinning faster than 60 kHz was recently introduced [Simion et al., J. Chem. Phys. 157, 014202 (2022)]. It was dubbed ROtor-Synchronized Phase-Alternated Cycles (ROSPAC), and it offers robustness for a large range of chemical shifts and low radio-frequency (RF) powers and is almost independent of the radio-frequency power. Here, we theoretically explore the robustness of the ROSPAC sequence toward 1H offset and RF field inhomogeneities, as well as the spacing effect of the π pulses on the decoupling efficiency. We use a generalized theoretical framework based on the Floquet theory to assess these parameters. The optimum decoupling conditions, where the magnitude of the second-order cross-terms and first-order resonance conditions are small, were identified.

Theoretical description of pulse induced resonances in the homonuclear PIRATE experiment.

Rotor-synchronous π pulses applied to protons (S) enhance homonuclear polarisation transfer between two spins (I) such as 13C or 15N as long as at least a single I-S heteronuclear dipolar-coupling interaction exists. The enhancement is maximum when the chemical-shift difference Δν between two spins equals an integer multiple, n, of the pulse-modulation frequency, which is half the rotor frequency νr. This condition, applied in the Pulse Induced Resonance with Angular dependent Total Enhancement (PIRATE) experiment, can be generalised for any spacing of the pulses k/νr such that Δν=nνr2k . We show, using average Hamiltonian theory (AHT) and Floquet theory, that the resonance conditions promote a second-order recoupling consisting of a cross-term between the homonuclear and heteronuclear dipolar interactions in a three-spin system. The minimum requirement is a coupling between the two I spins and a coupling of one of the I spins to the S spin. The effective Hamiltonian at the resonance conditions contains three-spin operators of the form 2I1±I2∓Sz with a non-zero effective dipolar coupling. Theoretical analysis shows that the effective strength of the resonance conditions decreases with increasing values of k and n. The theory is backed by numerical simulations, and experimental results on fully labelled 13C-glycine demonstrating the efficiency of the different resonance condition for k=1,2 at various spinning frequencies.

Early-onset pulmonary and cutaneous vasculitis driven by constitutively active SRC-family kinase HCK.

BACKGROUND: Inborn errors of immunity are genetic disorders characterized by various degrees of immune dysregulation that can manifest as immune deficiency, autoimmunity, or autoinflammation. The routine use of next-generation sequencing in the clinic has facilitated the identification of an ever-increasing number of inborn errors of immunity, revealing the roles of immunologically important genes in human pathologies. However, despite this progress, treatment is still extremely challenging. OBJECTIVE: We sought to report a new monogenic autoinflammatory disorder caused by a de novo activating mutation, p.Tyr515∗, in hematopoietic cell kinase (HCK). The disease is characterized by cutaneous vasculitis and chronic pulmonary inflammation that progresses to fibrosis. METHODS: Whole-exome sequencing, Sanger sequencing, mass spectrometry, and western blotting were performed to identify and characterize the pathogenic HCK mutation. Dysregulation of mutant HCK was confirmed ex vivo in primary cells and in vitro in transduced cell lines. RESULTS: Mutant HCK lacking the C-terminal inhibitory tyrosine Tyr522 exhibited increased kinase activity and enhanced myeloid cell priming, migration and effector functions, such as production of the inflammatory cytokines IL-1ß, IL-6, IL-8, and TNF-α, and production of reactive oxygen species. These aberrant functions were reflected by inflammatory leukocyte infiltration of the lungs and skin. Moreover, an overview of the clinical course of the disease, including therapies, provides evidence for the therapeutic efficacy of the Janus kinase 1/2 inhibitor ruxolitinib in inflammatory lung disease. CONCLUSIONS: We propose HCK-driven pulmonary and cutaneous vasculitis as a novel autoinflammatory disorder of inborn errors of immunity.

The Rigid Core and Flexible Surface of Amyloid Fibrils Probed by Magic-Angle-Spinning NMR Spectroscopy of Aromatic Residues.

Aromatic side chains are important reporters of the plasticity of proteins, and often form important contacts in protein-protein interactions. We studied aromatic residues in the two structurally homologous cross-ß amyloid fibrils HET-s, and HELLF by employing a specific isotope-labeling approach and magic-angle-spinning NMR. The dynamic behavior of the aromatic residues Phe and Tyr indicates that the hydrophobic amyloid core is rigid, without any sign of "breathing motions" over hundreds of milliseconds at least. Aromatic residues exposed at the fibril surface have a rigid ring axis but undergo ring flips on a variety of time scales from nanoseconds to microseconds. Our approach provides direct insight into hydrophobic-core motions, enabling a better evaluation of the conformational heterogeneity generated from an NMR structural ensemble of such amyloid cross-ß architecture.

Repurposing of drugs as STAT3 inhibitors for cancer therapy.

Drug repurposing is a valuable approach in delivering new cancer therapeutics rapidly into the clinic. Existing safety and patient tolerability data for drugs already in clinical use represent an untapped resource in terms of identifying therapeutic agents for off-label protein targets. The multicellular effects of STAT3 mediated by a range of various upstream signaling pathways make it an attractive therapeutic target with utility in a range of diseases including cancer, and has led to the development of a variety of STAT3 inhibitors. Moreover, heightened STAT3 transcriptional activation in tumor cells and within the cells of the tumor microenvironment contribute to disease progression. Consequently, there are many STAT3 inhibitors in preclinical development or under evaluation in clinical trials for their therapeutic efficacy predominantly in inflammatory diseases and cancer. Despite these advances, many challenges remain in ultimately providing STAT3 inhibitors to patients as cancer treatments, highlighting the need not only for a better understanding of the mechanisms associated with STAT3 activation, but also how various pharmaceutical agents suppress STAT3 activity in various cancers. In this review we discuss the importance of STAT3-dependent functions in cancer, review the status of compounds designed as direct-acting STAT3 inhibitors, and describe some of the strategies for repurposing of drugs as STAT3 inhibitors for cancer therapy.

Solid-State NMR Reveals Asymmetric ATP Hydrolysis in the Multidrug ABC Transporter BmrA.

The detailed mechanism of ATP hydrolysis in ATP-binding cassette (ABC) transporters is still not fully understood. Here, we employed 31P solid-state NMR to probe the conformational changes and dynamics during the catalytic cycle by locking the multidrug ABC transporter BmrA in prehydrolytic, transition, and posthydrolytic states, using a combination of mutants and ATP analogues. The 31P spectra reveal that ATP binds strongly in the prehydrolytic state to both ATP-binding sites as inferred from the analysis of the nonhydrolytic E504A mutant. In the transition state of wild-type BmrA, the symmetry of the dimer is broken and only a single site is tightly bound to ADP:Mg2+:vanadate, while the second site is more 'open' allowing exchange with the nucleotides in the solvent. In the posthydrolytic state, weak binding, as characterized by chemical exchange with free ADP and by asymmetric 31P-31P two-dimensional (2D) correlation spectra, is observed for both sites. Revisiting the 13C spectra in light of these findings confirms the conformational nonequivalence of the two nucleotide-binding sites in the transition state. Our results show that following ATP binding, the symmetry of the ATP-binding sites of BmrA is lost in the ATP-hydrolysis step, but is then recovered in the posthydrolytic ADP-bound state.