Multi-omics blood atlas reveals unique features of immune and platelet responses to SARS-CoV-2 Omicron breakthrough infection.

Although host responses to the ancestral SARS-CoV-2 strain are well described, those to the new Omicron variants are less resolved. We profiled the clinical phenomes, transcriptomes, proteomes, metabolomes, and immune repertoires of >1,000 blood cell or plasma specimens from SARS-CoV-2 Omicron patients. Using in-depth integrated multi-omics, we dissected the host response dynamics during multiple disease phases to reveal the molecular and cellular landscapes in the blood. Specifically, we detected enhanced interferon-mediated antiviral signatures of platelets in Omicron-infected patients, and platelets preferentially formed widespread aggregates with leukocytes to modulate immune cell functions. In addition, patients who were re-tested positive for viral RNA showed marked reductions in B cell receptor clones, antibody generation, and neutralizing capacity against Omicron. Finally, we developed a machine learning model that accurately predicted the probability of re-positivity in Omicron patients. Our study may inspire a paradigm shift in studying systemic diseases and emerging public health concerns.

Splicing Activation by Rbfox Requires Self-Aggregation through Its Tyrosine-Rich Domain.

Proteins of the Rbfox family act with a complex of proteins called the Large Assembly of Splicing Regulators (LASR). We find that Rbfox interacts with LASR via its C-terminal domain (CTD), and this domain is essential for its splicing activity. In addition to LASR recruitment, a low-complexity (LC) sequence within the CTD contains repeated tyrosines that mediate higher-order assembly of Rbfox/LASR and are required for splicing activation by Rbfox. This sequence spontaneously aggregates in solution to form fibrous structures and hydrogels, suggesting an assembly similar to the insoluble cellular inclusions formed by FUS and other proteins in neurologic disease. Unlike the pathological aggregates, we find that assembly of the Rbfox CTD plays an essential role in its normal splicing function. Rather than simple recruitment of individual regulators to a target exon, alternative splicing choices also depend on the higher-order assembly of these regulators within the nucleus.

Intercellular Spread of Protein Aggregates in Neurodegenerative Disease.

Most neurodegenerative diseases are characterized by the accumulation of protein aggregates, some of which are toxic to cells. Mounting evidence demonstrates that in several diseases, protein aggregates can pass from neuron to neuron along connected networks, although the role of this spreading phenomenon in disease pathogenesis is not completely understood. Here we briefly review the molecular and histopathological features of protein aggregation in neurodegenerative disease, we summarize the evidence for release of proteins from donor cells into the extracellular space, and we highlight some other mechanisms by which protein aggregates might be transmitted to recipient cells. We also discuss the evidence that supports a role for spreading of protein aggregates in neurodegenerative disease pathogenesis and some limitations of this model. Finally, we consider potential therapeutic strategies to target spreading of protein aggregates in the treatment of neurodegenerative diseases.

Loss of TAX1BP1-Directed Autophagy Results in Protein Aggregate Accumulation in the Brain.

Protein aggregates disrupt cellular homeostasis, causing toxicity linked to neurodegeneration. Selective autophagic elimination of aggregates is critical to protein quality control, but how aggregates are selectively targeted for degradation is unclear. We compared the requirements for autophagy receptor proteins: OPTN, NBR1, p62, NDP52, and TAX1BP1 in clearance of proteotoxic aggregates. Endogenous TAX1BP1 is recruited to and required for the clearance of stress-induced aggregates, whereas ectopic expression of TAX1BP1 increases clearance through autophagy, promoting viability of human induced pluripotent stem cell-derived neurons. In contrast, TAX1BP1 depletion sensitizes cells to several forms of aggregate-induced proteotoxicity. Furthermore, TAX1BP1 is more specifically expressed in the brain compared to other autophagy receptor proteins. In vivo, loss of TAX1BP1 results in accumulation of high molecular weight ubiquitin conjugates and premature lipofuscin accumulation in brains of young TAX1BP1 knockout mice. TAX1BP1 mediates clearance of a broad range of cytotoxic proteins indicating therapeutic potential in neurodegenerative diseases.

Whole genome sequencing based analysis of inflammation biomarkers in the Trans-Omics for Precision Medicine (TOPMed) consortium.

Inflammation biomarkers can provide valuable insight into the role of inflammatory processes in many diseases and conditions. Sequencing based analyses of such biomarkers can also serve as an exemplar of the genetic architecture of quantitative traits. To evaluate the biological insight, which can be provided by a multi-ancestry, whole-genome based association study, we performed a comprehensive analysis of 21 inflammation biomarkers from up to 38 465 individuals with whole-genome sequencing from the Trans-Omics for Precision Medicine (TOPMed) program (with varying sample size by trait, where the minimum sample size was n = 737 for MMP-1). We identified 22 distinct single-variant associations across 6 traits-E-selectin, intercellular adhesion molecule 1, interleukin-6, lipoprotein-associated phospholipase A2 activity and mass, and P-selectin-that remained significant after conditioning on previously identified associations for these inflammatory biomarkers. We further expanded upon known biomarker associations by pairing the single-variant analysis with a rare variant set-based analysis that further identified 19 significant rare variant set-based associations with 5 traits. These signals were distinct from both significant single variant association signals within TOPMed and genetic signals observed in prior studies, demonstrating the complementary value of performing both single and rare variant analyses when analyzing quantitative traits. We also confirm several previously reported signals from semi-quantitative proteomics platforms. Many of these signals demonstrate the extensive allelic heterogeneity and ancestry-differentiated variant-trait associations common for inflammation biomarkers, a characteristic we hypothesize will be increasingly observed with well-powered, large-scale analyses of complex traits.

Intraneuronal ß-amyloid impaired mitochondrial proteostasis through the impact on LONP1.

Mitochondrial dysfunction plays a critical role in the pathogenesis of Alzheimer's disease (AD). Mitochondrial proteostasis regulated by chaperones and proteases in each compartment of mitochondria is critical for mitochondrial function, and it is suspected that mitochondrial proteostasis deficits may be involved in mitochondrial dysfunction in AD. In this study, we identified LONP1, an ATP-dependent protease in the matrix, as a top Aß42 interacting mitochondrial protein through an unbiased screening and found significantly decreased LONP1 expression and extensive mitochondrial proteostasis deficits in AD experimental models both in vitro and in vivo, as well as in the brain of AD patients. Impaired METTL3-m6A signaling contributed at least in part to Aß42-induced LONP1 reduction. Moreover, Aß42 interaction with LONP1 impaired the assembly and protease activity of LONP1 both in vitro and in vivo. Importantly, LONP1 knockdown caused mitochondrial proteostasis deficits and dysfunction in neurons, while restored expression of LONP1 in neurons expressing intracellular Aß and in the brain of CRND8 APP transgenic mice rescued Aß-induced mitochondrial deficits and cognitive deficits. These results demonstrated a critical role of LONP1 in disturbed mitochondrial proteostasis and mitochondrial dysfunction in AD and revealed a mechanism underlying intracellular Aß42-induced mitochondrial toxicity through its impact on LONP1 and mitochondrial proteostasis.

Impairment of the Glial Phagolysosomal System Drives Prion-Like Propagation in a Drosophila Model of Huntington's Disease.

Protein misfolding, aggregation, and spread through the brain are primary drivers of neurodegenerative disease pathogenesis. Phagocytic glia are responsible for regulating the load of pathological proteins in the brain, but emerging evidence suggests that glia may also act as vectors for aggregate spread. Accumulation of protein aggregates could compromise the ability of glia to eliminate toxic materials from the brain by disrupting efficient degradation in the phagolysosomal system. A better understanding of phagocytic glial cell deficiencies in the disease state could help to identify novel therapeutic targets for multiple neurological disorders. Here, we report that mutant huntingtin (mHTT) aggregates impair glial responsiveness to injury and capacity to degrade neuronal debris in male and female adult Drosophila expressing the gene that causes Huntington's disease (HD). mHTT aggregate formation in neurons impairs engulfment and clearance of injured axons and causes accumulation of phagolysosomes in glia. Neuronal mHTT expression induces upregulation of key innate immunity and phagocytic genes, some of which were found to regulate mHTT aggregate burden in the brain. A forward genetic screen revealed Rab10 as a novel component of Draper-dependent phagocytosis that regulates mHTT aggregate transmission from neurons to glia. These data suggest that glial phagocytic defects enable engulfed mHTT aggregates to evade lysosomal degradation and acquire prion-like characteristics. Together, our findings uncover new mechanisms that enhance our understanding of the beneficial and harmful effects of phagocytic glia in HD and other neurodegenerative diseases.

Live 3D imaging and mapping of shear stresses within tissues using incompressible elastic beads.

To investigate the role of mechanical constraints in morphogenesis and development, we have developed a pipeline of techniques based on incompressible elastic sensors. These techniques combine the advantages of incompressible liquid droplets, which have been used as precise in situ shear stress sensors, and of elastic compressible beads, which are easier to tune and to use. Droplets of a polydimethylsiloxane mix, made fluorescent through specific covalent binding to a rhodamin dye, are produced by a microfluidics device. The elastomer rigidity after polymerization is adjusted to the tissue rigidity. Its mechanical properties are carefully calibrated in situ, for a sensor embedded in a cell aggregate submitted to uniaxial compression. The local shear stress tensor is retrieved from the sensor shape, accurately reconstructed through an active contour method. In vitro, within cell aggregates, and in vivo, in the prechordal plate of the zebrafish embryo during gastrulation, our pipeline of techniques demonstrates its efficiency to directly measure the three dimensional shear stress repartition within a tissue.

Amyloid-ß deposits in human astrocytes contain truncated and highly resistant proteoforms.

Alzheimer's disease (AD) is a neurodegenerative disorder that develops over decades. Glial cells, including astrocytes are tightly connected to the AD pathogenesis, but their impact on disease progression is still unclear. Our previous data show that astrocytes take up large amounts of aggregated amyloid-beta (Aß) but are unable to successfully degrade the material, which is instead stored intracellularly. The aim of the present study was to analyze the astrocytic Aß deposits composition in detail in order to understand their role in AD propagation. For this purpose, human induced pluripotent cell (hiPSC)-derived astrocytes were exposed to sonicated Aß42 fibrils and magnetic beads. Live cell imaging and immunocytochemistry confirmed that the ingested Aß aggregates and beads were transported to the same lysosomal compartments in the perinuclear region, which allowed us to successfully isolate the Aß deposits from the astrocytes. Using a battery of experimental techniques, including mass spectrometry, western blot, ELISA and electron microscopy we demonstrate that human astrocytes truncate and pack the Aß aggregates in a way that makes them highly resistant. Moreover, the astrocytes release specifically truncated forms of Aß via different routes and thereby expose neighboring cells to pathogenic proteins. Taken together, our study establishes a role for astrocytes in mediating Aß pathology, which could be of relevance for identifying novel treatment targets for AD.

Visualizing molecular weights differences in supramolecular polymers.

Issues of molecular weight determination have been central to the development of supramolecular polymer chemistry. Whereas relationships between concentration and optical features are established for well-behaved absorptive and emissive species, for most supramolecular polymeric systems no simple correlation exists between optical performance and number-average molecular weight (Mn). As such, the Mn of supramolecular polymers have to be inferred from various measurements. Herein, we report an anion-responsive supramolecular polymer [M1·Zn(OTf)2]n that exhibits monotonic changes in the fluorescence color as a function of Mn Based on theoretical estimates, the calculated average degree of polymerization (DPcal) increases from 16.9 to 84.5 as the monomer concentration increases from 0.08 mM to 2.00 mM. Meanwhile, the fluorescent colors of M1 + Zn(OTf)2 solutions were found to pass from green to yellow and to orange, corresponding to a red shift in the maximum emission band (λmax ). Therefore, a relationship between DPcal and λmax could be established. Additionally, the anion-responsive nature of the present system meant that the extent of supramolecular polymerization could be regulated by introducing anions, with the resulting change in Mn being readily monitored via changes in the fluorescent emission features.

Aggregate fluctuations in adaptive production networks.

To counteract the adverse effects of shocks, such as the global pandemic, on the economy, governments have discussed policies to improve the resilience of supply chains by reducing dependence on foreign suppliers. In this paper, we develop and quantify an adaptive production network model to study network resilience and the consequences of reshoring of supply chains. In our model, firms exit due to exogenous shocks or the propagation of shocks through the network, while firms can replace suppliers they have lost due to exit subject to switching costs and search frictions. Applying our model to a large international firm-level production network dataset, we find that restricting buyer-supplier links via reshoring policies reduces output and increases volatility and that volatility can be amplified through network adaptivity.

Molecularly Detailed View of Strong Coupling in Supramolecular Plexcitonic Nanohybrids.

Plexcitons constitute a peculiar example of light-matter hybrids (polaritons) originating from the (strong) coupling of plasmonic modes and molecular excitations. Here we propose a fully quantum approach to model plexcitonic systems and test it against existing experiments on peculiar hybrids formed by Au nanoparticles and a well-known porphyrin derivative, involving the Q branch of the organic dye absorption spectrum. Our model extends simpler descriptions of polaritonic systems to account for the multilevel structure of the dyes, spatially varying interactions with a given plasmon mode, and the simultaneous occurrence of plasmon-molecule and intermolecular interactions. By keeping a molecularly detailed view, we were able to gain insights into the local structure and individual contributions to the resulting plexcitons. Our model can be applied to rationalize and predict energy funneling toward specific molecular sites within a plexcitonic assembly, which is highly valuable for designing and controlling chemical transformations in the new polaritonic landscapes.

Impacts of cytoplasmic p53 aggregates on the prognosis and the transcriptome in lung squamous cell carcinoma.

The tumor suppressor TP53 gene, the most frequently mutated gene in human cancers, produces the product tumor protein p53, which plays an essential role in DNA damage. p53 protein mutations may contribute to tumorigenesis by loss of tumor suppressive functions and malignancy of cancer cells via gain-of-oncogenic functions. We previously reported that mutant p53 proteins form aggregates and that cytoplasmic p53 aggregates were associated with poor prognosis in human ovarian cancer. However, the prognostic impact of p53 aggregation in other tumors including lung squamous cell carcinoma (SCC) is poorly understood. Here, we demonstrated that lung SCC cases with cytoplasmic p53 aggregates had a significantly poor clinical prognosis. Analysis via patient-derived tumor organoids (PDOs) established from lung SCC patients and possessing cytoplasmic p53 aggregates showed that eliminating cytoplasmic p53 aggregates suppressed cell proliferation. RNA sequencing and transcriptome analysis of p53 aggregate-harboring PDOs indicated multiple candidate pathways involved in p53 aggregate oncogenic functions. With lung SCC-derived cell lines, we found that cytoplasmic p53 aggregates contributed to cisplatin resistance. This study thus shows that p53 aggregates are a predictor of poor prognosis in lung SCC and suggests that detecting p53 aggregates via p53 conventional immunohistochemical analysis may aid patient selection for platinum-based therapy.

Mesoscale Acid-Base Complexes Display Size-Associated Photophysical Property and Photochemical Activity.

The properties of single molecules and molecular aggregates can differ dramatically, leading to a long-standing interest in mesoscale aggregation processes. Herein, a series of acid-base molecular complexes is developed by using a tetraphenylethylene-backboned fluorophore, and investigated the photophysical properties and photochemical activities at different aggregation length scales. This fluorophore, with two basic diethylamine groups and two acidic tetrazole groups, exhibits sparse solubility due to multivalent interactions that cause infinite aggregation. The addition of a third acid leads to the formation of fluorophore/acid complexes with good dispersibility and colloidal stability. This assembly process can be controlled by the use of different acids and their stoichiometry, resulting in aggregates ranging in size from a few to hundreds of nanometers. A crystalline structure is obtained to illustrate the complex properties of the acid-base network. Unlike the single molecule, these complexes show a trend of size-related properties for photoluminescence efficiency and photochemical activity. As the amount of acid added increases, the size of the complexes decreases, the aggregation effect of the complexes on fluorescence emission increases, and the rates of the oxidative photocyclization and photodecomposition slow down. This work may help to understand size-controlled molecular materials at the mesoscale for functional design.

Epitaxially Grown Mechanically Robust 2D Thin Film of Secondary Interactions Led Molecularly Woven Material.

Molecularly woven materials with striking mechanical resilience, and 2D controlled topologies like textiles, fishing nets, and baskets are highly anticipated. Molecular weaving exclusively apprehended by the secondary interactions expanding to laterally grown 2D self-assemblies with retained crystalline arrangement is stimulating. The interlacing entails planar molecules screwed together to form 2D woven thin films. Here, secondary interactions led 2D interlaced molecularly woven material (2°MW) built by 1D helical threads of organic chromophores twisted together via end-to-end CH···O connections, held strongly at inter-crossing by multiple OH···N interactions to prevent slippage is presented. Whereas, 1D helical threads with face-to-face O-H···O connections sans interlacing led the non-woven material (2°NW). The polarity-driven directionality in 2°MW led the water-actuated epitaxial growth of 2D-sheets to lateral thin films restricted to nano-scale thickness. The molecularly woven thin film is self-healing, flexible, and mechanically resilient in nature, while maintaining the crystalline regularity is attributed to the supple secondary interactions (2°).

Stabilisation of soil organic matter with rock dust partially counteracted by plants.

Soil application of Ca- and Mg-rich silicates can capture and store atmospheric carbon dioxide as inorganic carbon but could also have the potential to stabilise soil organic matter (SOM). Synergies between these two processes have not been investigated. Here, we apply finely ground silicate rock mining residues (basalt and granite blend) to a loamy sand in a pot trial at a rate of 4% (equivalent to 50 t ha-1 ) and investigate the effects of a wheat plant and two watering regimes on soil carbon sequestration over the course of 6 months. Rock dust addition increased soil pH, electric conductivity, inorganic carbon content and soil-exchangeable Ca and Mg contents, as expected for weathering. However, it decreased exchangeable levels of micronutrients Mn and Zn, likely related to the elevated soil pH. Importantly, it increased mineral-associated organic matter by 22% due to the supply of secondary minerals and associated sites for SOM sorption. Additionally, in the nonplanted treatments, rock supply of Ca and Mg increased soil microaggregation that subsequently stabilised labile particulate organic matter as organic matter occluded in aggregates by 46%. Plants, however, reduced soil-exchangeable Mg and Ca contents and hence counteracted the silicate rock effect on microaggregates and carbon within. We suggest this cation loss might be attributed to plant exudates released to solubilise micronutrients and hence neutralise plant deficiencies. The effect of enhanced silicate rock weathering on SOM stabilisation could substantially boost its carbon sequestration potential.

Azulene-Containing Bis(squaraine) Dyes: Design, Synthesis and Aggregation Behaviors.

The relationship among chemical structure, physicochemical property and aggregation behavior of organic functional material is an important research topic. Here, we designed and synthesized three bis(squaraine) dyes BSQ1, BSQ2 and BSQ3 through the combination of two kinds of unsymmetrical azulenyl squaraine monomers. Their physicochemical properties were investigated in both molecular and aggregate states. Generally, BSQ1 displayed different assembly behaviors from BSQ2 and BSQ3. Upon fabrication into nanoparticles, BSQ1 tend to form J-aggregates while BSQ2 and BSQ3 tend to form H-aggregates in aqueous medium. When in the form of thin films, three bis(squaraine) dyes all adopted J-aggregation packing modes while only BSQ1 presented the most significant rearrangement of aggregate structures as well as the improvement in the carrier mobilities upon thermal annealing. Our research highlights the discrepancy of aggregation behaviors originating from the molecular structure and surrounding circumstances, providing guidance for the molecular design and functional applications of squaraines.

Boosting Excited-State Energy Transfer by Anchoring Dipole Orientation in Binary Thermally Activated Delayed Fluorescence/J-Aggregate Assemblies.

Förster resonance energy transfer (FRET) has been widely applied in fluorescence imaging, sensing and so on, while developing useful strategy of boosting FRET efficiency becomes a key issue that limits the application. Except optimizing spectral properties, promoting orientation factor (κ2) has been well discussed but rarely utilized for boosting FRET. Herein, we constructed binary nano-assembling of two thermally activated delayed fluorescence (TADF) emitters (2CzPN and DMAC-DPS) with J-type aggregate of cyanine dye (C8S4) as doping films by taking advantage of their electrostatic interactions. Time-resolved spectroscopic measurements indicated that 2CzPN/Cy-J films exhibit an order of magnitude higher kFRET than DMAC-DPS/Cy-J films. Further quantitative analysing on kFRET and kDET indicated higher orientation factor (κ2) in 2CzPN/Cy-J films play a key role for achieving fast kFRET, which was subsequently confirmed by anisotropic measurements. Corresponding DFT/TDDFT calculation revealed strong "two-point" electrostatic anchoring in 2CzPN/Cy-J films that is responsible for highly orientated transitions. We provide a new strategy for boosting FRET in nano-assemblies, which might be inspired for designing FRET-based devices of sensing, imaging and information encryption.

Tuning the Optical Properties Through Hydrogen Bond-assisted H-aggregate Formation: The ODIN Case.

The current work focuses on the investigation of two functionalized naphthyridine derivatives, namely ODIN-EtPh and ODIN-But, to gain insights into the hydrogen bond-assisted H-aggregate formation and its impact on the optical properties of ODIN molecules. By employing a combination of X-ray and electron crystallography, absorption and emission spectroscopy, time resolved fluorescence and ultrafast pump-probe spectroscopy (visible and infrared) we unravel the correlation between the structure and light-matter response, with a particular emphasis on the influence of the polarity of the surrounding environment. Our experimental results and simulations confirm that in polar and good hydrogen-bond acceptor solvents (DMSO), the formation of dimers for ODIN derivatives is strongly inhibited. The presence of a phenyl group linked to the ureidic unit favors the folding of ODIN derivatives (forming an intramolecular hydrogen bond) leading to the stabilization of a charge-transfer excited state which almost completely quenches its fluorescence emission. In solvents with a poor aptitude for forming hydrogen bonds, the formation of dimers is favored and gives rise to H aggregates, with a consequent considerable reduction in the fluorescence emission. The urea-bound phenyl group furtherly stabilizes the dimers in chloroform.

Control of Kinetic Pathways toward Supramolecular Chiral Polymorphs for Tunable Circularly Polarized Luminescence.

An amphiphilic aza-BODIPY dye (S)-1 bearing two chiral hydrophilic side chains with S-stereogenic centers was synthesized. This dye exhibited kinetic-controlled self-assembly pathways and supramolecular chiral polymorphism properties in MeOH/H2O (9/1, v/v) mixed solvent. The (S)-1 monomers first aggregated into a kinetic controlled, off-pathway species Agg. A, which was spontaneously transformed into an on-pathway metastable aggregate (Agg. B) and subsequently into the thermodynamic Agg. C. The three aggregate polymorphs of dye (S)-1 displayed distinct optical properties and nanomorphologies. In particular, chiral J-aggregation characteristics were observed for both Agg. B and Agg. C, such as Davydov-split absorption bands (Agg. B), extremely sharp and intense J-band with large bathochromic shift (Agg. C), non-diminished fluorescence upon aggregation, as well as strong bisignated Cotton effects. Moreover, the AFM and TEM studies revealed that Agg. A had the morphology of nanoparticle while fibril or rod-like helical nanostructures with left-handedness were observed respectively for Agg. B and Agg. C. By controlling the kinetic transformation process from Agg. B to Agg. C, thin films consisting of Agg. B and Agg. C with different ratios were prepared, which displayed tunable CPL with emission maxima at 788-805 nm and g-factors between -4.2×10-2 and -5.1×10-2.