Identification of piRNA Binding Sites Reveals the Argonaute Regulatory Landscape of the C. elegans Germline.

piRNAs (Piwi-interacting small RNAs) engage Piwi Argonautes to silence transposons and promote fertility in animal germlines. Genetic and computational studies have suggested that C. elegans piRNAs tolerate mismatched pairing and in principle could target every transcript. Here we employ in vivo cross-linking to identify transcriptome-wide interactions between piRNAs and target RNAs. We show that piRNAs engage all germline mRNAs and that piRNA binding follows microRNA-like pairing rules. Targeting correlates better with binding energy than with piRNA abundance, suggesting that piRNA concentration does not limit targeting. In mRNAs silenced by piRNAs, secondary small RNAs accumulate at the center and ends of piRNA binding sites. In germline-expressed mRNAs, however, targeting by the CSR-1 Argonaute correlates with reduced piRNA binding density and suppression of piRNA-associated secondary small RNAs. Our findings reveal physiologically important and nuanced regulation of individual piRNA targets and provide evidence for a comprehensive post-transcriptional regulatory step in germline gene expression.

MEK guards proteome stability and inhibits tumor-suppressive amyloidogenesis via HSF1.

Signaling through RAS/MAP kinase pathway is central to biology. ERK has long been perceived as the only substrate for MEK. Here, we report that HSF1, the master regulator of the proteotoxic stress response, is a new MEK substrate. Beyond mediating cell-environment interactions, the MEK-HSF1 regulation impacts malignancy. In tumor cells, MEK blockade inactivates HSF1 and thereby provokes proteomic chaos, presented as protein destabilization, aggregation, and, strikingly, amyloidogenesis. Unlike their non-transformed counterparts, tumor cells are particularly susceptible to proteomic perturbation and amyloid induction. Amyloidogenesis is tumor suppressive, reducing in vivo melanoma growth and contributing to the potent anti-neoplastic effects of proteotoxic stressors. Our findings unveil a key biological function of the oncogenic RAS-MEK signaling in guarding proteostasis and suppressing amyloidogenesis. Thus, proteomic instability is an intrinsic feature of malignant state, and disrupting the fragile tumor proteostasis to promote amyloidogenesis may be a feasible therapeutic strategy.

Heat Shock Factor 1 Is a Direct Antagonist of AMP-Activated Protein Kinase.

Through transcriptional control of the evolutionarily conserved heat shock, or proteotoxic stress, response, heat shock factor 1 (HSF1) preserves proteomic stability. Here, we show that HSF1, a physiological substrate for AMP-activated protein kinase (AMPK), constitutively suppresses this central metabolic sensor. By physically evoking conformational switching of AMPK, HSF1 impairs AMP binding to the γ subunits and enhances the PP2A-mediated de-phosphorylation, but it impedes the LKB1-mediated phosphorylation of Thr172, and retards ATP binding to the catalytic α subunits. These immediate and manifold regulations empower HSF1 to both repress AMPK under basal conditions and restrain its activation by diverse stimuli, thereby promoting lipogenesis, cholesterol synthesis, and protein cholesteroylation. In vivo, HSF1 antagonizes AMPK to control body fat mass and drive the lipogenic phenotype and growth of melanomas independently of its intrinsic transcriptional action. Thus, the physical AMPK-HSF1 interaction epitomizes a reciprocal kinase-substrate regulation whereby lipid metabolism and proteomic stability intertwine.

Overexpression of transcription factor TBX5 inhibits the activation of YAP1-TEAD1 pathway to promote ferroptosis in lung cancer cells.

BACKGROUND: Non-small cell lung cancer (NSCLC) accounts for more than 80 % of lung cancer (LC) cases, making it the primary cause of cancer-related mortality worldwide. T-box transcription factor 5 (TBX5) is an important regulator of embryonic and organ development and plays a key role in cancer development. Here, our objective was to investigate the involvement of TBX5 in ferroptosis within LC cells and the underlying mechanisms. METHODS: First, TBX5 expression was examined in human LC cells. Next, overexpression of TBX5 and Yes1-associated transcriptional regulator (YAP1) and knockdown of TEA domain 1 (TEAD1) were performed in A549 and NCI-H1703 cells. The proliferation ability of A549 and NCI-H1703 cells, GSH, MDA, ROS, and Fe2+ levels were measured. Co-immunoprecipitation (Co-IP) was performed to verify whether TBX5 protein could bind YAP1. Then TBX5, YAP1, TEAD1, GPX4, p53, FTH1, SLC7A11 and PTGS2 protein levels were assessed. Finally, we verified the effect of TBX5 on ferroptosis in LC cells in vivo. RESULTS: TBX5 expression was down-regulated in LC cells, especially in A549 and NCI-H1703 cells. Overexpression of TBX5 significantly decreased proliferation ability of A549 and NCI-H1703 cells, downregulated GPX4 and GSH levels, and upregulated MDA, ROS, and Fe2+ levels. Co-IP verified that TBX5 protein could bind YAP1. Moreover, oe-YAP1 promoted proliferation ability of A549 and NCI-H1703 cells transfected with Lv-TBX5, upregulated GPX4 and GSH levels and downregulated MDA, ROS, and Fe2+ levels. Additionally, oe-YAP1 promoted FTH1 and SLC7A11 levels and inhibited p53 and PTGS2 levels in A549 and NCI-H1703 cells transfected with Lv-TBX5. However, transfection with si-TEAD1 further reversed these effects. In vivo experiments further validated that TBX5 promoted ferroptosis in LC cells. CONCLUSIONS: TBX5 inhibited the activation of YAP1-TEAD1 pathway to promote ferroptosis in LC cells.

Dual-loss of PBRM1 and RAD51 identifies hyper-sensitive subset patients to immunotherapy in clear cell renal cell carcinoma.

BACKGROUND: Homologous recombination deficiency (HRD), though largely uncharacterized in clear cell renal cell carcinoma (ccRCC), was found associated with RAD51 loss of expression. PBRM1 is the second most common mutated genes in ccRCC. Here, we introduce a HRD function-based PBRM1-RAD51 ccRCC classification endowed with diverse immune checkpoint blockade (ICB) responses. METHODS: Totally 1542 patients from four independent cohorts were enrolled, including our localized Zhongshan hospital (ZSHS) cohort and Zhongshan hospital metastatic RCC (ZSHS-mRCC) cohort, The Cancer Genome Atlas (TCGA) cohort and CheckMate cohort. The genomic profile and immune microenvironment were depicted by genomic, transcriptome data and immunohistochemistry. RESULTS: We observed that PBRM1-loss ccRCC harbored enriched HRD-associated mutational signature 3 and loss of RAD51. Dual-loss of PBRM1 and RAD51 identified patients hyper-sensitive to immunotherapy. This dual-loss subtype was featured by M1 macrophage infiltration. Dual-loss was, albeit homologous recombination defective, with high chromosomal stability. CONCLUSIONS: PBRM1 and RAD51 dual-loss ccRCC indicates superior responses to immunotherapy. Dual-loss ccRCC harbors an immune-desert microenvironment but enriched with M1 macrophages. Dual-loss ccRCC is susceptible to defective homologous recombination but possesses high chromosomal stability.

Generation of frequency 32-tupling millimeter-wave based on a dual-parallel polarization modulator.

A scheme to generate a frequency 32-tupling millimeter wave (mm-wave) is proposed, enabled by two dual-parallel polarization modulators (DP-PolMs) in cascade. By properly controlling the amplitude and the phase shift of the radio-frequency (RF) driving signal applied to two DP-PolMs, the main optical components at the output of the DP-PolM are ±16th order optical sidebands and the central carrier. After the central carrier is canceled by the polarization multiplexing structure, the ±16th order optical sidebands are beaten in the photodetector; then the frequency 32-tupling mm-wave can be achieved. The optical sideband suppression ratio (OSSR) and the radio-frequency spurious suppression ratio (RFSSR) of the generated signal are 52 and 47 dB in simulation, which are consistent with the theoretical analysis values 53.7 and 47.7 dB. The influence on the OSSR and RFSSR of the generated signal by the key parameters of devices deviating from the theoretical analysis value i are investigated.

Author Correction: Configurable phonon polaritons in twisted α-MoO3.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Configurable phonon polaritons in twisted α-MoO3.

Moiré engineering is being intensively investigated as a method to tune the electronic, magnetic and optical properties of twisted van der Waals materials. Advances in moiré engineering stem from the formation of peculiar moiré superlattices at small, specific twist angles. Here we report configurable nanoscale light-matter waves-phonon polaritons-by twisting stacked α-phase molybdenum trioxide (α-MoO3) slabs over a broad range of twist angles from 0° to 90°. Our combined experimental and theoretical results reveal a variety of polariton wavefront geometries and topological transitions as a function of the twist angle. In contrast to the origin of the modified electronic band structure in moiré superlattices, the polariton twisting configuration is attributed to the electromagnetic interaction of highly anisotropic hyperbolic polaritons in stacked α-MoO3 slabs. These results indicate twisted α-MoO3 to be a promising platform for nanophotonic devices with tunable functionalities.

Author Correction: Ultralow-loss polaritons in isotopically pure boron nitride.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Hyperbolic Phonon Polaritons in Suspended Hexagonal Boron Nitride.

Highly confined and low-loss hyperbolic phonon polaritons in hexagonal boron nitride possess properties analogous to surface plasmon polaritons, but with enhanced confinement and lower loss. Their properties have been so far mostly studied on dielectric substrates, which provide an asymmetric environment for polariton propagation, and add to damping. In this work, we investigate hyperbolic phonon polaritons over suspended hexagonal boron nitride, showing remarkable properties, including elongated polariton wavelength and reduced damping, up to 18% lower compared to dielectric-backed samples. We use real-space nanoimaging of the polaritons in hexagonal boron nitride to demonstrate and visualize these effects. Our results indicate that suspended boron nitride offers better figures of merit for polariton transport, which are generalizable to other polaritonic materials, and they may be explored in heterostructures for advanced nanophotonic applications.

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Chronic kidney disease (CKD) can result in alteration of intestinal flora and damage of intestinal barrier function. Intestinal dysbios is contributes to the generation of colon-derived uremic solutes and the translocation of bacteria and endotoxins from gut lumen into the bloodstream, subsequently increasing uremic toxicity and triggering systemic inflammation, which is related to CKD progression and many complications. Studies have revealed that dietary fiber can reduce uremic toxin levels and systemic inflammation in CKD through targeting the "gut-kidney axis". Dietary fiber seems to be a promising measure for CKD treatment.

Suppression of the HSF1-mediated proteotoxic stress response by the metabolic stress sensor AMPK.

Numerous extrinsic and intrinsic insults trigger the HSF1-mediated proteotoxic stress response (PSR), an ancient transcriptional program that is essential to proteostasis and survival under such conditions. In contrast to its well-recognized mobilization by proteotoxic stress, little is known about how this powerful adaptive mechanism reacts to other stresses. Surprisingly, we discovered that metabolic stress suppresses the PSR. This suppression is largely mediated through the central metabolic sensor AMPK, which physically interacts with and phosphorylates HSF1 at Ser121. Through AMPK activation, metabolic stress represses HSF1, rendering cells vulnerable to proteotoxic stress. Conversely, proteotoxic stress inactivates AMPK and thereby interferes with the metabolic stress response. Importantly, metformin, a metabolic stressor and popular anti-diabetic drug, inactivates HSF1 and provokes proteotoxic stress within tumor cells, thereby impeding tumor growth. Thus, these findings uncover a novel interplay between the metabolic stress sensor AMPK and the proteotoxic stress sensor HSF1 that profoundly impacts stress resistance, proteostasis, and malignant growth.

Ultralow-loss polaritons in isotopically pure boron nitride.

Conventional optical components are limited to size scales much larger than the wavelength of light, as changes to the amplitude, phase and polarization of the electromagnetic fields are accrued gradually along an optical path. However, advances in nanophotonics have produced ultrathin, so-called 'flat' optical components that beget abrupt changes in these properties over distances significantly shorter than the free-space wavelength. Although high optical losses still plague many approaches, phonon polariton (PhP) materials have demonstrated long lifetimes for sub-diffractional modes in comparison to plasmon-polariton-based nanophotonics. We experimentally observe a threefold improvement in polariton lifetime through isotopic enrichment of hexagonal boron nitride (hBN). Commensurate increases in the polariton propagation length are demonstrated via direct imaging of polaritonic standing waves by means of infrared nano-optics. Our results provide the foundation for a materials-growth-directed approach aimed at realizing the loss control necessary for the development of PhP-based nanophotonic devices.

Quantum Control of Graphene Plasmon Excitation and Propagation at Heaviside Potential Steps.

Quantum mechanical effects of single particles can affect the collective plasmon behaviors substantially. In this work, the quantum control of plasmon excitation and propagation in graphene is demonstrated by adopting the variable quantum transmission of carriers at Heaviside potential steps as a tuning knob. First, the plasmon reflection is revealed to be tunable within a broad range by varying the ratio γ between the carrier energy and potential height, which originates from the quantum mechanical effect of carrier propagation at potential steps. Moreover, the plasmon excitation by free-space photos can be regulated from fully suppressed to fully launched in graphene potential wells also through adjusting γ, which defines the degrees of the carrier confinement in the potential wells. These discovered quantum plasmon effects offer a unified quantum-mechanical solution toward ultimate control of both plasmon launching and propagating, which are indispensable processes in building plasmon circuitry.

Internal Nanostructure Diagnosis with Hyperbolic Phonon Polaritons in Hexagonal Boron Nitride.

Imaging materials and inner structures with resolution below the diffraction limit has become of fundamental importance in recent years for a wide variety of applications. We report subdiffractive internal structure diagnosis of hexagonal boron nitride by exciting and imaging hyperbolic phonon polaritons. On the basis of their unique propagation properties, we are able to accurately locate defects in the crystal interior with nanometer resolution. The precise location, size, and geometry of the concealed defects are reconstructed by analyzing the polariton wavelength, reflection coefficient, and their dispersion. We have also studied the evolution of polariton reflection, transmission, and scattering as a function of defect size and photon frequency. The nondestructive high-precision polaritonic structure diagnosis technique introduced here can be also applied to other hyperbolic or waveguide systems and may be deployed in the next-generation biomedical imaging, sensing, and fine structure analysis.

Large Photothermal Effect in Sub-40 nm h-BN Nanostructures Patterned Via High-Resolution Ion Beam.

The controlled nanoscale patterning of 2D materials is a promising approach for engineering the optoelectronic, thermal, and mechanical properties of these materials to achieve novel functionalities and devices. Herein, high-resolution patterning of hexagonal boron nitride (h-BN) is demonstrated via both helium and neon ion beams and an optimal dosage range for both ions that serve as a baseline for insulating 2D materials is identified. Through this nanofabrication approach, a grating with a 35 nm pitch, individual structure sizes down to 20 nm, and additional nanostructures created by patterning crystal step edges are demonstrated. Raman spectroscopy is used to study the defects induced by the ion beam patterning and is correlated to scanning probe microscopy. Photothermal and scanning near-field optical microscopy measure the resulting near-field absorption and scattering of the nanostructures. These measurements reveal a large photothermal expansion of nanostructured h-BN that is dependent on the height to width aspect ratio of the nanostructures. This effect is attributed to the large anisotropy of the thermal expansion coefficients of h-BN and the nanostructuring implemented. The photothermal expansion should be present in other van der Waals materials with large anisotropy and can lead to applications such as nanomechanical switches driven by light.

Efficiency of Launching Highly Confined Polaritons by Infrared Light Incident on a Hyperbolic Material.

We investigated phonon-polaritons in hexagonal boron nitride-a naturally hyperbolic van der Waals material-by means of the scattering-type scanning near-field optical microscopy. Real-space nanoimages we have obtained detail how the polaritons are launched when the light incident on a thin hexagonal boron nitride slab is scattered by various intrinsic and extrinsic inhomogeneities, including sample edges, metallic nanodisks deposited on its top surface, random defects, and surface impurities. The scanned tip of the near-field microscope is itself a polariton launcher whose efficiency proves to be superior to all the other types of polariton launchers we studied. Our work may inform future development of polaritonic nanodevices as well as fundamental studies of collective modes in van der Waals materials.

Faraday Rotation Due to Surface States in the Topological Insulator (Bi1-xSbx)2Te3.

Using magneto-infrared spectroscopy, we have explored the charge dynamics of (Bi,Sb)2Te3 thin films on InP substrates. From the magneto-transmission data we extracted three distinct cyclotron resonance (CR) energies that are all apparent in the broad band Faraday rotation (FR) spectra. This comprehensive FR-CR data set has allowed us to isolate the response of the bulk states from the intrinsic surface states associated with both the top and bottom surfaces of the film. The FR data uncovered that electron- and hole-type Dirac Fermions reside on opposite surfaces of our films, which paves the way for observing many exotic quantum phenomena in topological insulators.

Intrinsic Plasmon-Phonon Interactions in Highly Doped Graphene: A Near-Field Imaging Study.

As a two-dimensional semimetal, graphene offers clear advantages for plasmonic applications over conventional metals, such as stronger optical field confinement, in situ tunability, and relatively low intrinsic losses. However, the operational frequencies at which plasmons can be excited in graphene are limited by the Fermi energy EF, which in practice can be controlled electrostatically only up to a few tenths of an electronvolt. Higher Fermi energies open the door to novel plasmonic devices with unprecedented capabilities, particularly at mid-infrared and shorter-wave infrared frequencies. In addition, this grants us a better understanding of the interaction physics of intrinsic graphene phonons with graphene plasmons. Here, we present FeCl3-intercalated graphene as a new plasmonic material with high stability under environmental conditions and carrier concentrations corresponding to EF > 1 eV. Near-field imaging of this highly doped form of graphene allows us to characterize plasmons, including their corresponding lifetimes, over a broad frequency range. For bilayer graphene, in contrast to the monolayer system, a phonon-induced dipole moment results in increased plasmon damping around the intrinsic phonon frequency. Strong coupling between intrinsic graphene phonons and plasmons is found, supported by ab initio calculations of the coupling strength, which are in good agreement with the experimental data.