Tumor-intrinsic expression of the autophagy gene Atg16l1 suppresses anti-tumor immunity in colorectal cancer.

Microsatellite-stable colorectal cancer (MSS-CRC) is highly refractory to immunotherapy. Understanding tumor-intrinsic determinants of immunotherapy resistance is critical to improve MSS-CRC patient outcomes. Here, we demonstrate that high tumor expression of the core autophagy gene ATG16L1 is associated with poor clinical response to anti-PD-L1 therapy in KRAS-mutant tumors from IMblaze370 (NCT02788279), a large phase III clinical trial of atezolizumab (anti-PD-L1) in advanced metastatic MSS-CRC. Deletion of Atg16l1 in engineered murine colon cancer organoids inhibits tumor growth in primary (colon) and metastatic (liver and lung) niches in syngeneic female hosts, primarily due to increased sensitivity to IFN-γ-mediated immune pressure. ATG16L1 deficiency enhances programmed cell death of colon cancer organoids induced by IFN-γ and TNF, thus increasing their sensitivity to host immunity. In parallel, ATG16L1 deficiency reduces tumor stem-like populations in vivo independently of adaptive immune pressure. This work reveals autophagy as a clinically relevant mechanism of immune evasion and tumor fitness in MSS-CRC and provides a rationale for autophagy inhibition to boost immunotherapy responses in the clinic.

Push-pull photochromic dyes for semi-transparent solar cells with light-adjustable optical properties and high color-rendering index.

We report the design, synthesis and characterization of push-pull photochromic naphthopyran dyes, incorporating different carbazole moieties as the electron-donor group for use in dye-sensitized solar cells. Compared to a reference dye incorporating a diphenylamine-type donor moiety, the introduction of functionalized carbazoles allows for a hypsochromic shift of the absorption of the coloured isomers of the dyes in the visible region and a better tuning of their spectra to the photopic response of the human eye. Under illumination, the molecules exhibit a broad absorption with a maximum comprised between 546 nm and 571 nm in solution and they reveal relatively fast discoloration kinetics. By using these dyes to fabricate photochromic solar cells whose optical and photovoltaic properties vary with the light exposure, we have achieved a PCE of up to 3% in opaque cells. Using these molecules in semi-transparent solar cells with different electrolytes, a PCE of 2.3% was achieved. We also produced a semi-transparent mini-module with an average visible transmittance varying between 66% and 50% and a colour rendering index around 95 in both the uncoloured and coloured states.

Adrenergic nerves regulate intestinal regeneration through IL-22 signaling from type 3 innate lymphoid cells.

The intestinal epithelium has high intrinsic turnover rate, and the precise renewal of the epithelium is dependent on the microenvironment. The intestine is innervated by a dense network of peripheral nerves that controls various aspects of intestinal physiology. However, the role of neurons in regulating epithelial cell regeneration remains largely unknown. Here, we investigated the effects of gut-innervating adrenergic nerves on epithelial cell repair following irradiation (IR)-induced injury. We observed that adrenergic nerve density in the small intestine increased post IR, while chemical adrenergic denervation impaired epithelial regeneration. Single-cell RNA sequencing experiments revealed a decrease in IL-22 signaling post IR in denervated animals. Combining pharmacologic and genetic tools, we demonstrate that ß-adrenergic receptor signaling drives IL-22 production from type 3 innate lymphoid cells (ILC3s) post IR, which in turn promotes epithelial regeneration. These results define an adrenergic-ILC3 axis important for intestinal regeneration.

Obligate role for Rock1 and Rock2 in adult stem cell viability and function.

The ability of stem cells to rapidly proliferate and differentiate is integral to the steady-state maintenance of tissues with high turnover such as the blood and intestine. Mutations that alter these processes can cause primary immunodeficiencies, malignancies and defects in barrier function. The Rho-kinases, Rock1 and Rock2, regulate cell shape and cytoskeletal rearrangement, activities essential to mitosis. Here, we use inducible gene targeting to ablate Rock1 and Rock2 in adult mice, and identify an obligate requirement for these enzymes in the preservation of the hematopoietic and gastrointestinal systems. Hematopoietic cell progenitors devoid of Rho-kinases display cell cycle arrest, blocking the differentiation to mature blood lineages. Similarly, these mice exhibit impaired epithelial cell renewal in the small intestine, which is ultimately fatal. Our data reveal a novel role for these kinases in the proliferation and viability of stem cells and their progenitors, which is vital to maintaining the steady-state integrity of these organ systems.

Disruption of stem cell niche-confined R-spondin 3 expression leads to impaired hematopoiesis.

Self-renewal and differentiation of stem and progenitor cells are tightly regulated to ensure tissue homeostasis. This regulation is enabled both remotely by systemic circulating cues, such as cytokines and hormones, and locally by various niche-confined factors. R-spondin 3 (RSPO3) is one of the most potent enhancers of Wnt signaling, and its expression is usually restricted to the stem cell niche where it provides localized enhancement of Wnt signaling to regulate stem cell expansion and differentiation. Disruption of this niche-confined expression can disturb proper tissue organization and lead to cancers. Here, we investigate the consequences of disrupting the niche-restricted expression of RSPO3 in various tissues, including the hematopoietic system. We show that normal Rspo3 expression is confined to the perivascular niche in the bone marrow. Induction of increased systemic levels of circulating RSPO3 outside of the niche results in prominent loss of early B-cell progenitors and anemia but surprisingly has no effect on hematopoietic stem cells. Using molecular, pharmacologic, and genetic approaches, we show that these RSPO3-induced hematopoietic phenotypes are Wnt and RSPO3 dependent and mediated through noncanonical Wnt signaling. Our study highlights a distinct role for a Wnt/RSPO3 signaling axis in the regulation of hematopoiesis, as well as possible challenges related to therapeutic use of RSPOs for regenerative medicine.

Directed evolution identifies high-affinity cystine-knot peptide agonists and antagonists of Wnt/ß-catenin signaling.

Developing peptide-based tools to fine-tune growth signaling pathways, in particular molecules with exquisite selectivity and high affinities, opens up opportunities for cellular reprogramming in tissue regeneration. Here, we present a library based on cystine-knot peptides (CKPs) that incorporate multiple loops for randomization and selection via directed evolution. Resulting binders could be assembled into multimeric structures to fine-tune cellular signaling. An example is presented for the Wnt pathway, which plays a key role in the homeostasis and regeneration of tissues such as lung, skin, and intestine. We discovered picomolar affinity CKP agonists of the human LPR6 receptor by exploring the limits of the topological manipulation of LRP6 dimerization. Structural analyses revealed that the agonists bind at the first ß-propeller domain of LRP6, mimicking the natural Wnt inhibitors DKK1 and SOST. However, the CKP agonists exhibit a different mode of action as they amplify the signaling of natural Wnt ligands but do not activate the pathway by themselves. In an alveolosphere organoid model, the CKP agonists induced alveolar stem cell activity. They also stimulated growth in primary human intestinal organoids. The approach described here advances the important frontier of next-generation agonist design and could be applied to other signaling pathways to discover tunable agonist ligands.

Inference-Based Quantum Sensing.

In a standard quantum sensing (QS) task one aims at estimating an unknown parameter θ, encoded into an n-qubit probe state, via measurements of the system. The success of this task hinges on the ability to correlate changes in the parameter to changes in the system response R(θ) (i.e., changes in the measurement outcomes). For simple cases the form of R(θ) is known, but the same cannot be said for realistic scenarios, as no general closed-form expression exists. In this Letter, we present an inference-based scheme for QS. We show that, for a general class of unitary families of encoding, R(θ) can be fully characterized by only measuring the system response at 2n+1 parameters. This allows us to infer the value of an unknown parameter given the measured response, as well as to determine the sensitivity of the scheme, which characterizes its overall performance. We show that inference error is, with high probability, smaller than δ, if one measures the system response with a number of shots that scales only as Ω(log^{3}(n)/δ^{2}). Furthermore, the framework presented can be broadly applied as it remains valid for arbitrary probe states and measurement schemes, and, even holds in the presence of quantum noise. We also discuss how to extend our results beyond unitary families. Finally, to showcase our method we implement it for a QS task on real quantum hardware, and in numerical simulations.

Colon tumour cell death causes mTOR dependence by paracrine P2X4 stimulation.

Solid cancers exhibit a dynamic balance between cell death and proliferation ensuring continuous tumour maintenance and growth1,2. Increasing evidence links enhanced cancer cell apoptosis to paracrine activation of cells in the tumour microenvironment initiating tissue repair programs that support tumour growth3,4, yet the direct effects of dying cancer cells on neighbouring tumour epithelia and how this paracrine effect potentially contributes to therapy resistance are unclear. Here we demonstrate that chemotherapy-induced tumour cell death in patient-derived colorectal tumour organoids causes ATP release triggering P2X4 (also known as P2RX4) to mediate an mTOR-dependent pro-survival program in neighbouring cancer cells, which renders surviving tumour epithelia sensitive to mTOR inhibition. The induced mTOR addiction in persisting epithelial cells is due to elevated production of reactive oxygen species and subsequent increased DNA damage in response to the death of neighbouring cells. Accordingly, inhibition of the P2X4 receptor or direct mTOR blockade prevents induction of S6 phosphorylation and synergizes with chemotherapy to cause massive cell death induced by reactive oxygen species and marked tumour regression that is not seen when individually applied. Conversely, scavenging of reactive oxygen species prevents cancer cells from becoming reliant on mTOR activation. Collectively, our findings show that dying cancer cells establish a new dependency on anti-apoptotic programs in their surviving neighbours, thereby creating an opportunity for combination therapy in P2X4-expressing epithelial tumours.

Antibody targeting of E3 ubiquitin ligases for receptor degradation.

Most current therapies that target plasma membrane receptors function by antagonizing ligand binding or enzymatic activities. However, typical mammalian proteins comprise multiple domains that execute discrete but coordinated activities. Thus, inhibition of one domain often incompletely suppresses the function of a protein. Indeed, targeted protein degradation technologies, including proteolysis-targeting chimeras1 (PROTACs), have highlighted clinically important advantages of target degradation over inhibition2. However, the generation of heterobifunctional compounds binding to two targets with high affinity is complex, particularly when oral bioavailability is required3. Here we describe the development of proteolysis-targeting antibodies (PROTABs) that tether cell-surface E3 ubiquitin ligases to transmembrane proteins, resulting in target degradation both in vitro and in vivo. Focusing on zinc- and ring finger 3 (ZNRF3), a Wnt-responsive ligase, we show that this approach can enable colorectal cancer-specific degradation. Notably, by examining a matrix of additional cell-surface E3 ubiquitin ligases and transmembrane receptors, we demonstrate that this technology is amendable for 'on-demand' degradation. Furthermore, we offer insights on the ground rules governing target degradation by engineering optimized antibody formats. In summary, this work describes a strategy for the rapid development of potent, bioavailable and tissue-selective degraders of cell-surface proteins.

Optimal Control of Families of Quantum Gates.

Quantum optimal control (QOC) enables the realization of accurate operations, such as quantum gates, and supports the development of quantum technologies. To date, many QOC frameworks have been developed, but those remain only naturally suited to optimize a single targeted operation at a time. We extend this concept to optimal control with a continuous family of targets, and demonstrate that an optimization based on neural networks can find families of time-dependent Hamiltonians realizing desired classes of quantum gates in minimal time.

Transparent and Colorless Dye-Sensitized Solar Cells Based on Pyrrolopyrrole Cyanine Sensitizers.

The development of transparent solar cells extends the applications of photovoltaics by offering the opportunity to substitute the gigantic surface coverage of windows by solar panels to produce electricity. Herein, we report a new family of NIR-sensitizers based on pyrrolopyrrole cyanine dyes, particularly efficient for the development of fully transparent and colorless dye-sensitized solar cells since a record efficiency of 2.5 % was achieved with an average visible transmittance (AVT) of 76 % and a color rending index (CRI) of 93.

Frequency and Genomic Aspects of Intrinsic Resistance to Vismodegib in Locally Advanced Basal Cell Carcinoma.

PURPOSE: Vismodegib is approved for the treatment of locally advanced basal cell carcinoma (laBCC), but some cases demonstrate intrinsic resistance (IR) to the drug. We sought to assess the frequency of IR to vismodegib in laBCC and its underlying genomic mechanisms. EXPERIMENTAL DESIGN: Response to vismodegib was evaluated in a cohort of 148 laBCC patients. Comprehensive genomic and transcriptomic profiling was performed in a subset of five intrinsically resistant BCC (IR-BCC). RESULTS: We identified that IR-BCC represents 6.1% of laBCC in the studied cohort. Prior treatment with chemotherapy was associated with IR. Genetic events that were previously associated with acquired resistance (AR) in BCC or medulloblastoma were observed in three out of five IR-BCC. However, IR-BCCs were distinct by highly rearranged polyploid genomes. Functional analyses identified hyperactivation of the HIPPO-YAP and WNT pathways at RNA and protein levels in IR-BCC. In vitro assay on the BCC cell line further confirmed that YAP1 overexpression increases the cell proliferation rate. CONCLUSIONS: IR to vismodegib is a rare event in laBCC. IR-BCCs frequently harbor resistance mutations in the Hh pathway, but also are characterized by hyperactivation of the HIPPO-YAP and WNT pathways.

Molecular-Level Insight into Correlation between Surface Defects and Stability of Methylammonium Lead Halide Perovskite Under Controlled Humidity.

Perovskite-based photovoltaics (PVs) have garnered tremendous interest, enabling power conversion efficiencies exceeding 25%. Although much of this success is credited to the exploration of new compositions, defects passivation and process optimization, environmental stability remains an important bottleneck to be solved. The underlying mechanisms of thermal and humidity-induced degradation are still far from a clear understanding, which poses a severe limitation to overcome the stability issues. Herein, in situ X-ray diffraction (XRD), in operando liquid-cell transmission electron microscopy (TEM) and ex situ solid-state (ss)NMR spectroscopy are combined with time-resolved spectroscopies to reveal new insights about the degradation mechanisms of methylammonium lead halide (MAPbI3 ) under 85% relative humidity (RH) at different length scales. Liquid-cell TEM enables the live visualizations from meso-to-nanoscale transformation between the perovskite particles and water molecules, which are corroborated by the changes in local structures at sub-nanometer distances by ssNMR and longer range by XRD. This work clarifies the role of surface defects and the significance of their passivation to prevent hydration and decomposition reactions.

Transparent and Colorless Dye-Sensitized Solar Cells Exceeding 75% Average Visible Transmittance.

Most photovoltaic (PV) technologies are opaque to maximize visible light absorption. However, see-through solar cells open additional perspectives for PV integration. Looking beyond maximizing visible light harvesting, this work considers the human eye photopic response to optimize a selective near-infrared sensitizer based on a polymethine cyanine structure (VG20-C x ) to render dye-sensitized solar cells (DSSCs) fully transparent and colorless. This peculiarity was achieved by conferring to the dye the ability to strongly and sharply absorb beyond 800 nm (S0-S1 transition) while rejecting the upper S0-S n contributions far in the blue where the human retina is poorly sensitive. When associated with an aggregation-free anatase TiO2 photoanode, the selective NIR-DSSC can display 3.1% power conversion efficiency, up to 76% average visible transmittance (AVT), a value approaching the 78% AVT value of a standard double glazing window while reaching a color rendering index (CRI) of 92.1%. The ultrafast and fast charge transfer processes are herein discussed, clarifying the different relaxation channels from the dye monomer excited states and highlighting the limiting steps to provide future directions to enhance the performances of this nonintrusive NIR-DSSC technology.

IL-1R1-dependent signaling coordinates epithelial regeneration in response to intestinal damage.

Repair of the intestinal epithelium is tightly regulated to maintain homeostasis. The response after epithelial damage needs to be local and proportional to the insult. How different types of damage are coupled to repair remains incompletely understood. We report that after distinct types of intestinal epithelial damage, IL-1R1 signaling in GREM1+ mesenchymal cells increases production of R-spondin 3 (RSPO3), a Wnt agonist required for intestinal stem cell self-renewal. In parallel, IL-1R1 signaling regulates IL-22 production by innate lymphoid cells and promotes epithelial hyperplasia and regeneration. Although the regulation of both RSPO3 and IL-22 is critical for epithelial recovery from Citrobacter rodentium infection, IL-1R1-dependent RSPO3 production by GREM1+ mesenchymal cells alone is sufficient and required for recovery after dextran sulfate sodium-induced colitis. These data demonstrate how IL-1R1-dependent signaling orchestrates distinct repair programs tailored to the type of injury sustained that are required to restore intestinal epithelial barrier function.

Tuning the Acceptor Unit of Push-Pull Porphyrazines for Dye-Sensitized Solar Cells.

A family of four push-pull porphyrazines of A3B type, where each unit A contains two peripheral propyl chains and the unit B is endowed with a carboxylic acid, were prepared. The carboxylic acid was attached to the ß-position of the pyrrolic unit, either directly (Pz 10), or through cyanovinyl (Pz 11) and phenyl (Pz 7) groups. The fourth Pz (14) consisted in a pyrazinoporphyrazine wherein the dinitrogenated heterocycle provided intrinsic donor-acceptor character to the macrocycle and contained a carboxyphenyl substituent. The direct attachment of the carboxylic acid functions and their linkers to the porphyrazine core produces stronger perturbation on the electronic properties of the macrocycle, with respect to their connection through fused benzene or pyrazine rings in TT112 and 14, respectively. The HOMO and LUMO energies of the Pzs, which were estimated with DFT calculations, show little variation within the series, except upon introduction of the cyanovinyl spacer, which produces a decrease in both frontier orbital energetic levels. This effective interaction of cyanovinyl substitution with the macrocycle is also evidenced in UV/Vis spectroscopy, where a large splitting of the Q-band indicates strong desymmetrization of the Pz. The performance of the four Pzs as photosensitizers in DSSCs were also investigated.

Gremlin 1+ fibroblastic niche maintains dendritic cell homeostasis in lymphoid tissues.

Fibroblastic reticular cells (FRCs) are specialized stromal cells that define tissue architecture and regulate lymphocyte compartmentalization, homeostasis, and innate and adaptive immunity in secondary lymphoid organs (SLOs). In the present study, we used single-cell RNA sequencing (scRNA-seq) of human and mouse lymph nodes (LNs) to identify a subset of T cell-zone FRCs defined by the expression of Gremlin1 (Grem1) in both species. Grem1-CreERT2 knock-in mice enabled localization, multi-omics characterization and genetic depletion of Grem1+ FRCs. Grem1+ FRCs primarily localize at T-B cell junctions of SLOs, neighboring pre-dendritic cells and conventional dendritic cells (cDCs). As such, their depletion resulted in preferential loss and decreased homeostatic proliferation and survival of resident cDCs and compromised T cell immunity. Trajectory analysis of human LN scRNA-seq data revealed expression similarities to murine FRCs, with GREM1+ cells marking the endpoint of both trajectories. These findings illuminate a new Grem1+ fibroblastic niche in LNs that functions to maintain the homeostasis of lymphoid tissue-resident cDCs.

Modeling Colorectal Cancer Progression Through Orthotopic Implantation of Organoids.

Colorectal cancer (CRC) related death has often been attributed to the presence of metastatic disseminated disease. A concise understanding of the molecular mechanism(s) that drive metastatic progression is therefore needed but has thus far been hampered by the limited number of CRC mouse models that progress toward this disease stage. In addition, preclinical evaluation of therapeutic modalities aimed at managing metastatic disease also rests on the availability of relevant in vivo models that faithfully recapitulate the key molecular features of metastatic human CRC. To overcome these limitations, we have recently developed methodologies that enable the study of CRC progression at relevant orthotopic sites. Here, we provide a detailed methodology that describes the injection of CRC derived cell lines and organoids directly into the colorectal mucosa. This results in the growth of a single tumor mass within the colon, that can spontaneously metastasize to the liver. Furthermore, we also present a surgical procedure to directly inject cells into the portal venous circulation to induce CRC tumor growth in the liver without the requirement of a primary tumor.

Lgr5+ telocytes are a signaling source at the intestinal villus tip.

The intestinal epithelium is a structured organ composed of crypts harboring Lgr5+ stem cells, and villi harboring differentiated cells. Spatial transcriptomics have demonstrated profound zonation of epithelial gene expression along the villus axis, but the mechanisms shaping this spatial variability are unknown. Here, we combine laser capture micro-dissection and single cell RNA sequencing to uncover spatially zonated populations of mesenchymal cells along the crypt-villus axis. These include villus tip telocytes (VTTs) that express Lgr5, a gene previously considered a specific crypt epithelial stem cell marker. VTTs are elongated cells that line the villus tip epithelium and signal through Bmp morphogens and the non-canonical Wnt5a ligand. Their ablation is associated with perturbed zonation of enterocyte genes induced at the villus tip. Our study provides a spatially-resolved cell atlas of the small intestinal stroma and exposes Lgr5+ villus tip telocytes as regulators of the epithelial spatial expression programs along the villus axis.