SMARCB1 regulates the hypoxic stress response in sickle cell trait.

Renal medullary carcinoma (RMC) is an aggressive kidney cancer that almost exclusively develops in individuals with sickle cell trait (SCT) and is always characterized by loss of the tumor suppressor SMARCB1. Because renal ischemia induced by red blood cell sickling exacerbates chronic renal medullary hypoxia in vivo, we investigated whether the loss of SMARCB1 confers a survival advantage under the setting of SCT. Hypoxic stress, which naturally occurs within the renal medulla, is elevated under the setting of SCT. Our findings showed that hypoxia-induced SMARCB1 degradation protected renal cells from hypoxic stress. SMARCB1 wild-type renal tumors exhibited lower levels of SMARCB1 and more aggressive growth in mice harboring the SCT mutation in human hemoglobin A (HbA) than in control mice harboring wild-type human HbA. Consistent with established clinical observations, SMARCB1-null renal tumors were refractory to hypoxia-inducing therapeutic inhibition of angiogenesis. Further, reconstitution of SMARCB1 restored renal tumor sensitivity to hypoxic stress in vitro and in vivo. Together, our results demonstrate a physiological role for SMARCB1 degradation in response to hypoxic stress, connect the renal medullary hypoxia induced by SCT with an increased risk of SMARCB1-negative RMC, and shed light into the mechanisms mediating the resistance of SMARCB1-null renal tumors against angiogenesis inhibition therapies.

Syndecan 1 is a critical mediator of macropinocytosis in pancreatic cancer.

Pancreatic ductal adenocarcinoma (PDAC) remains recalcitrant to all forms of cancer treatment and carries a five-year survival rate of only 8%1. Inhibition of oncogenic KRAS (hereafter KRAS*), the earliest lesion in disease development that is present in more than 90% of PDACs, and its signalling surrogates has yielded encouraging preclinical results with experimental agents2-4. However, KRAS*-independent disease recurrence following genetic extinction of Kras* in mouse models anticipates the need for co-extinction strategies5,6. Multiple oncogenic processes are initiated at the cell surface, where KRAS* physically and functionally interacts to direct signalling that is essential for malignant transformation and tumour maintenance. Insights into the complexity of the functional cell-surface-protein repertoire (surfaceome) have been technologically limited until recently and-in the case of PDAC-the genetic control of the function and composition of the PDAC surfaceome in the context of KRAS* signalling remains largely unknown. Here we develop an unbiased, functional target-discovery platform to query KRAS*-dependent changes of the PDAC surfaceome, which reveals syndecan 1 (SDC1, also known as CD138) as a protein that is upregulated at the cell surface by KRAS*. Localization of SDC1 at the cell surface-where it regulates macropinocytosis, an essential metabolic pathway that fuels PDAC cell growth-is essential for disease maintenance and progression. Thus, our study forges a mechanistic link between KRAS* signalling and a targetable molecule driving nutrient salvage pathways in PDAC and validates oncogene-driven surfaceome annotation as a strategy to identify cancer-specific vulnerabilities.

Suppression of alias and replica noises in phase holograms using fractal topologies.

Two-dimensional fractal topologies featuring (scaling) self-similarity, dense set of Bragg (diffraction) peaks, and inherent rotation symmetry, which are not achievable with regular grid-matrix geometries, exhibit optical robustness against structural damage and noise immunity of optical transmission paths. In this work, we numerically and experimentally demonstrate phase holograms using fractal plane-divisions. By taking advantage of the symmetries of the fractal topology, we propose numerical algorithms to design the fractal holograms. This algorithm solves the inapplicability of the conventional iterative Fourier transform algorithm (IFTA) method and enables efficient optimizations of millions of adjustable parameters in the optical element. Experimental samples show that the alias and replica noises in the image plane of fractal holograms are clearly suppressed, facilitating applications for high-accuracy and compact requirements.

K-series approximation of vectorial optical fields for designing diffractive optical elements with subwavelength feature sizes.

Diffractive optical elements (DOEs) are widely applied as compact solutions for desired light manipulations via wavefront shaping. Recent advanced chip applications further require their feature sizes to move down to the subwavelength, which inevitably brings forth vectorial effects of optical fields and makes the typical scalar-based theory invalid. However, simulating and optimizing their vectorial fields, which are associated with billions of adjustable parameters in the optical element, are difficult to do, because of the issues of numerical stability and the highly-demanding computational cost. To address this problem, this research proposes an applicable algorithm by means of a wave-vector (k) series approximation of vectorial optical fields. On the basis of the semi-analytical rigorous coupled wave analysis (RCWA), an adequate selection scheme on k-series enables computationally efficient yet still predictive calculations for DOEs. The performance estimations for exemplary designs by the finite difference time domain (FDTD) method show that the predicted intensity profiles by the proposed algorithm agree with the target by just a fractional error. Together with optimizing the geometrical degrees of freedom (e.g., DOE depth h) as compensation for errors from the truncation of k-series, the algorithm demonstrates its outperformance by one or two orders of magnitude in accuracy versus the scalar-based model, and demands only a reasonable computational resource.

Study of wide-spectrum and high-resolution diffraction optical elements by stacks of binary phase gratings.

This work theoretically investigates wide-spectrum and high-resolution diffraction optical elements that are made of stacks of low-resolution binary phase gratings, whereby the two-dimensional grids in different grating layers are arranged with specified displacements. We remodel the common kinoform algorithm for this multi-scale architecture. Numerical computations show that, by increasing the number of stacking layers, the resolution of the far-field image can be improved and also that the optical elements are more insensitive to variations of incident wavelengths at the cost of part accuracy of the image reconstructions. Practical concern focuses on largely increasing the number of grating layers and efficiency of the optical designs in theory and on the manufacture of stacks of ultra-thin grating films.

Small Artery Elastin Distribution and Architecture-Focus on Three Dimensional Organization.

The distribution of ECM proteins within the walls of resistance vessels is complex both in variety of proteins and structural arrangement. In particular, elastin exists as discrete fibers varying in orientation across the adventitia and media as well as often resembling a sheet-like structure in the case of the IEL. Adding to the complexity is the tissue heterogeneity that exists in these structural arrangements. For example, small intracranial cerebral arteries lack adventitial elastin while similar sized arteries from skeletal muscle and intestinal mesentery exhibit a complex adventitial network of elastin fibers. With regard to the IEL, several vascular beds exhibit an elastin sheet with punctate holes/fenestrae while in others the IEL is discontinuous and fibrous in appearance. Importantly, these structural patterns likely sub-serve specific functional properties, including mechanosensing, control of external forces, mechanical properties of the vascular wall, cellular positioning, and communication between cells. Of further significance, these processes are altered in vascular disorders such as hypertension and diabetes mellitus where there is modification of ECM. This brief report focuses on the three-dimensional wall structure of small arteries and considers possible implications with regard to mechanosensing under physiological and pathophysiological conditions.

Crystallinity effects on scaling properties of photoinduced modes in silver nanoprisms.

The crystallinity effects on scaling properties of photoinduced modes in crystalline silver nanoprisms with C3v symmetry are studied using a realistic atomistic model and group theory. Among all vibrational modes, photoinduced modes can be identified as those vibrational modes which possess larger in-phase radial atomic displacement and can be projected out by the projected density of states method. We found that the properties of vibrations in silver nanoprisms strongly depend on the particle's aspect ratio (bisector length over thickness). By considering crystallinity of silver nanoprisms, the dominant modes with the in-plane oscillation become several closely spaced modes, and become obvious for nanoprisms with a smaller aspect ratio. The oscillation spectra show that the dominant planar modes are insensitive to thickness change. On the contrary, the atomic displacements show significantly different patterns for nanoprisms of different thicknesses. We also found that, for nanoprisms with same aspect ratio that is larger than 4, the vibrational properties of dominant modes exhibit scaling similarity. By using a simple linear transformation, the vibration frequencies for large-sized nanoprisms of aspect ratio 6 can be obtained by a corresponding scaling factor. The calculated results are in good agreement with experimental data.

Activation of endogenous retroviruses and induction of viral mimicry by MEK1/2 inhibition in pancreatic cancer.

While pancreatic ductal adenocarcinomas (PDACs) are addicted to KRAS-activating mutations, inhibitors of downstream KRAS effectors, such as the MEK1/2 kinase inhibitor trametinib, are devoid of therapeutic effects. However, the extensive rewiring of regulatory circuits driven by the attenuation of the KRAS pathway may induce vulnerabilities of therapeutic relevance. An in-depth molecular analysis of the transcriptional and epigenomic alterations occurring in PDAC cells in the initial hours after MEK1/2 inhibition by trametinib unveiled the induction of endogenous retroviruses (ERVs) escaping epigenetic silencing, leading to the production of double-stranded RNAs and the increased expression of interferon (IFN) genes. We tracked ERV activation to the early induction of the transcription factor ELF3, which extensively bound and activated nonsilenced retroelements and synergized with IRF1 (interferon regulatory factor 1) in the activation of IFNs and IFN-stimulated genes. Trametinib-induced viral mimicry in PDAC may be exploited in the rational design of combination therapies in immuno-oncology.

Clonal dominance defines metastatic dissemination in pancreatic cancer.

Tumors represent ecosystems where subclones compete during tumor growth. While extensively investigated, a comprehensive picture of the interplay of clonal lineages during dissemination is still lacking. Using patient-derived pancreatic cancer cells, we created orthotopically implanted clonal replica tumors to trace clonal dynamics of unperturbed tumor expansion and dissemination. This model revealed the multifaceted nature of tumor growth, with rapid changes in clonal fitness leading to continuous reshuffling of tumor architecture and alternating clonal dominance as a distinct feature of cancer growth. Regarding dissemination, a large fraction of tumor lineages could be found at secondary sites each having distinctive organ growth patterns as well as numerous undescribed behaviors such as abortive colonization. Paired analysis of primary and secondary sites revealed fitness as major contributor to dissemination. From the analysis of pro- and nonmetastatic isogenic subclones, we identified a transcriptomic signature able to identify metastatic cells in human tumors and predict patients' survival.

WRAD core perturbation impairs DNA replication fidelity promoting immunoediting in pancreatic cancer.

It is unclear how cells counteract the potentially harmful effects of uncoordinated DNA replication in the context of oncogenic stress. Here, we identify the WRAD (WDR5/RBBP5/ASH2L/DPY30) core as a modulator of DNA replication in pancreatic ductal adenocarcinoma (PDAC) models. Molecular analyses demonstrated that the WRAD core interacts with the replisome complex, with disruption of DPY30 resulting in DNA re-replication, DNA damage, and chromosomal instability (CIN) without affecting cancer cell proliferation. Consequently, in immunocompetent models, DPY30 loss induced T cell infiltration and immune-mediated clearance of highly proliferating cancer cells with complex karyotypes, thus improving anti-tumor efficacy upon anti-PD-1 treatment. In PDAC patients, DPY30 expression was associated with high tumor grade, worse prognosis, and limited response to immune checkpoint blockade. Together, our findings indicate that the WRAD core sustains genome stability and suggest that low intratumor DPY30 levels may identify PDAC patients who will benefit from immune checkpoint inhibitors.

Ether phospholipids are required for mitochondrial reactive oxygen species homeostasis.

Mitochondria are hubs where bioenergetics, redox homeostasis, and anabolic metabolism pathways integrate through a tightly coordinated flux of metabolites. The contributions of mitochondrial metabolism to tumor growth and therapy resistance are evident, but drugs targeting mitochondrial metabolism have repeatedly failed in the clinic. Our study in pancreatic ductal adenocarcinoma (PDAC) finds that cellular and mitochondrial lipid composition influence cancer cell sensitivity to pharmacological inhibition of electron transport chain complex I. Profiling of patient-derived PDAC models revealed that monounsaturated fatty acids (MUFAs) and MUFA-linked ether phospholipids play a critical role in maintaining ROS homeostasis. We show that ether phospholipids support mitochondrial supercomplex assembly and ROS production; accordingly, blocking de novo ether phospholipid biosynthesis sensitized PDAC cells to complex I inhibition by inducing mitochondrial ROS and lipid peroxidation. These data identify ether phospholipids as a regulator of mitochondrial redox control that contributes to the sensitivity of PDAC cells to complex I inhibition.

Approximate scheme by the coupled-wave theory to efficiently analyze the influences of moiré phenomena in liquid-crystal devices.

This work studies an approximate scheme by coupled-wave theory to analyze quickly the large-scale moiré phenomena as seen in common liquid-crystal devices. The moiré phenomena are considered to be caused by two periodic structures (with lattice vectors γ[combininb arrow](1) and γ[combininb arrow](2) and show an interference pattern spanning over a length γ(m)=|γ[combininb arrow](1)|·|γ[combininb arrow](2)|/|γ[combininb arrow](1)-γ[combininb arrow](2)| (with γ[combininb arrow](1)=/~γ[combininb arrow](2)). With the coupled-wave theory, the complete analysis of the moiré optics includes at least 2γ(m)/λ (λ: wavelength in vacuum) Fourier components and presents an ineffective computation. This work applies a cos(τ) type approximation for the openings of unpatterned liquid-crystal pixels, and considers the first-order coupling between the Fourier components of pixels and other (periodic) optical structures. We hence arrive at an effective evaluation, including 4τ|γ[combininb arrow](1)|/λ (or 4τ|γ[combininb arrow](2)|/λ) Fourier components, and are able to go back to a complete analysis when considering higher-order couplings at an appropriate τ integer value.

ZNRF1 Mediates Epidermal Growth Factor Receptor Ubiquitination to Control Receptor Lysosomal Trafficking and Degradation.

Activation of the epidermal growth factor receptor (EGFR) is crucial for development, tissue homeostasis, and immunity. Dysregulation of EGFR signaling is associated with numerous diseases. EGFR ubiquitination and endosomal trafficking are key events that regulate the termination of EGFR signaling, but their underlying mechanisms remain obscure. Here, we reveal that ZNRF1, an E3 ubiquitin ligase, controls ligand-induced EGFR signaling via mediating receptor ubiquitination. Deletion of ZNRF1 inhibits endosome-to-lysosome sorting of EGFR, resulting in delayed receptor degradation and prolonged downstream signaling. We further demonstrate that ZNRF1 and Casitas B-lineage lymphoma (CBL), another E3 ubiquitin ligase responsible for EGFR ubiquitination, mediate ubiquitination at distinct lysine residues on EGFR. Furthermore, loss of ZNRF1 results in increased susceptibility to herpes simplex virus 1 (HSV-1) infection due to enhanced EGFR-dependent viral entry. Our findings identify ZNRF1 as a novel regulator of EGFR signaling, which together with CBL controls ligand-induced EGFR ubiquitination and lysosomal trafficking.

Epithelial memory of inflammation limits tissue damage while promoting pancreatic tumorigenesis.

Inflammation is a major risk factor for pancreatic ductal adenocarcinoma (PDAC). When occurring in the context of pancreatitis, KRAS mutations accelerate tumor development in mouse models. We report that long after its complete resolution, a transient inflammatory event primes pancreatic epithelial cells to subsequent transformation by oncogenic KRAS. Upon recovery from acute inflammation, pancreatic epithelial cells display an enduring adaptive response associated with sustained transcriptional and epigenetic reprogramming. Such adaptation enables the reactivation of acinar-to-ductal metaplasia (ADM) upon subsequent inflammatory events, thereby limiting tissue damage through a rapid decrease of zymogen production. We propose that because activating mutations of KRAS maintain an irreversible ADM, they may be beneficial and under strong positive selection in the context of recurrent pancreatitis.

Excitation transport in quasi-one-dimensional quantum devices: a multiscale approach with analytical time-dependent non-equilibrium Green's function.

Under the wide-band limit approximation for electrodes, this research proposes analytical time-dependent non-equilibrium Green's function (TD-NEGF) formulae to investigate dynamical functionalities of quasi-one-dimensional quantum devices, especially for (microwave) photon-assisted transports. Together with a multiscale approach by lumped element model, we also study the effects of transiently-transferring charges to reflect the non-conservation of charges in open quantum systems, and implement numerical calculations in hetero-junction systems composed of functional quantum devices and electrode-contacts (to the environment). The results show that (i) the current calculation by the analytical algorithms, versus those by conventional numerical integrals, presents superior numerical stability on a large-time scale, (ii) the correction of charge transfer effects can better clarify non-physical transport issues, e.g. the blocking of AC signaling under the assumption of conventional constant hamiltonian, (iii) the current in the long-time limit validly converges to the steady value obtained by standard time-independent density functional calculations, and (iv) the occurrence of the photon-assisted transport is well-identified.

Energy conversion from environmental fluctuations to coherent fields by Cooper-pair box quantum meta-materials.

Electromagnetic waves propagating in open Cooper-pair boxes (CPBs) system is studied by using Maxwell-Bloch equations and Lindblad master equation. The results demonstrate an ensemble of CPBs as highly non-linear meta-material for electromagnetic waves. Incorporating the CPBs in a ring resonator or a Fabry-Perot cavity, one finds that: (1) With weak environmental couplings and CPBs in superconducting phase dominant regime, the non-linearity is enhanced and the system exhibits regular optical hysteresis. (2) With finite environmental couplings and CPBs in charge dominant regime, the Josephson effect and environmental effect can constructively interplay to produce a gain. In the later case, the electromagnetic field would be amplified by the CPB medium, indicating energy conversion from the environment to coherent fields mediated by CPBs.

Pooled library screening with multiplexed Cpf1 library.

Capitalizing on the inherent multiplexing capability of AsCpf1, we developed a multiplexed, high-throughput screening strategy that minimizes library size without sacrificing gene targeting efficiency. We demonstrated that AsCpf1 can be used for functional genomics screenings and that an AsCpf1-based multiplexed library performs similarly as compared to currently available monocistronic CRISPR/Cas9 libraries, with only one vector required for each gene. We construct the smallest whole-genome CRISPR knock-out library, Mini-human, for the human genome (n = 17,032 constructs targeting 16,977 protein-coding genes), which performs favorably compared to conventional Cas9 libraries.

Pre-existing Functional Heterogeneity of Tumorigenic Compartment as the Origin of Chemoresistance in Pancreatic Tumors.

Adaptive drug-resistance mechanisms allow human tumors to evade treatment through selection and expansion of treatment-resistant clones. Here, studying clonal evolution of tumor cells derived from human pancreatic tumors, we demonstrate that in vitro cultures and in vivo tumors are maintained by a common set of tumorigenic cells that can be used to establish clonal replica tumors (CRTs), large cohorts of animals bearing human tumors with identical clonal composition. Using CRTs to conduct quantitative assessments of adaptive responses to therapeutics, we uncovered a multitude of functionally heterogeneous subpopulations of cells with differential degrees of drug sensitivity. High-throughput isolation and deep characterization of unique clonal lineages showed genetic and transcriptomic diversity underlying functionally diverse subpopulations. Molecular annotation of gemcitabine-naive clonal lineages with distinct responses to treatment in the context of CRTs generated signatures that can predict the response to chemotherapy, representing a potential biomarker to stratify patients with pancreatic cancer.

Real-time circulating tumor cells detection via highly sensitive needle-like cytosensor-demonstrated by a blood flow simulation.

The concept of rapid detection of circulating tumor cells (CTCs) has always been the focal point of modern and future medicine. However, the dispersity and rarity of CTCs in the bloodstream makes it hard to detect metastasis. Herein, our newly designed needle-like cytosensor demonstrates that the capture and analysis of CTCs are a much less laborious process and have more potential than ever. Our aim is to detect and capture CTCs directly in the bloodstream without altering the genetic information; further benefit of current cytosensor is allows for the whole circulation of blood to run through the cytosensor, giving a much better sensitivity and chance of detecting CTCs. Our functionalized needle-like cytosensor has been modified with 3-aminopropyltriethoxysilane, 1-ethyl-3-(3-dimethylaminopropyl) carbodiimide, N-hydroxysuccinimide and conjugated streptavidin to allow the binding of the biotinylated-antibody of epithelial cell adhesion molecules, which captures targeted colon cancer CTC. The capability of our needle-like cytosensor to detect CTCs spanned from 102 to 106 cells/mL. Beyond this, the needle-like cytosensor avoids the distortion of the cell information. In addition, we constructed a blood flow simulation that mimics human circulating system about 10 mL/min speed; by using cyclic voltammetry we could detect significant signals from captured cancer CTCs more than 21 cells/mL without delay; the fluorescence dye detection was further performed for data confirmation. The future of biosensors begins with this, by providing early monitoring quality care in cancer therapy.

Inherent rhythm of smooth muscle cells in rat mesenteric arterioles: An eigensystem formulation.

On the basis of experimental data and mathematical equations in the literature, we remodel the ionic dynamics of smooth muscle cells (SMCs) as an eigensystem formulation, which is valid for investigating finite variations of variables from the equilibrium such as in common experimental operations. This algorithm provides an alternate viewpoint from frequency-domain analysis and enables one to probe functionalities of SMCs' rhythm by means of a resonance-related mechanism. Numerical results show three types of calcium oscillations of SMCs in mesenteric arterioles: spontaneous calcium oscillation, agonist-dependent calcium oscillation, and agonist-dependent calcium spike. For simple single and double SMCs, we demonstrate properties of synchronization among complex signals related to calcium oscillations, and show different correlation relations between calcium and voltage signals for various synchronization and resonance conditions. For practical cell clusters, our analyses indicate that the rhythm of SMCs could (1) benefit enhancements of signal communications among remote cells, (2) respond to a significant calcium peaking against transient stimulations for triggering globally oscillating modes, and (3) characterize the globally oscillating modes via frog-leap (non-molecular-diffusion) calcium waves across inhomogeneous SMCs.