NUP43 promotes PD-L1/nPD-L1/PD-L1 feedback loop via TM4SF1/JAK/STAT3 pathway in colorectal cancer progression and metastatsis.

Programmed cell death-ligand 1 (PD-L1) has a significant role in tumor progression and metastasis, facilitating tumor cell evasion from immune surveillance. PD-L1 can be detected in the tumor cell nucleus and exert an oncogenic effect by nuclear translocation. Colorectal cancer (CRC) progression and liver metastasis (CCLM) are among the most lethal diseases worldwide, but the mechanism of PD-L1 nuclear translocation in CRC and CCLM remains to be fully understood. In this study, using CRISPR-Cas9-based genome-wide screening combined with RNA-seq, we found that the oncogenic factor NUP43 impacted the process of PD-L1 nuclear translocation by regulating the expression level of the PD-L1 chaperone protein IPO5. Subsequent investigation revealed that this process could stimulate the expression of tumor-promoting factor TM4SF1 and further activate the JAK/STAT3 signaling pathway, which ultimately enhanced the transcription of PD-L1, thus establishing a PD-L1-nPD-L1-PD-L1 feedback loop that ultimately promoted CRC progression and CCLM. In conclusion, our study reveals a novel role for nPD-L1 in CRC, identifies the PD-L1-nPD-L1-PD-L1 feedback loop in CRC, and provides a therapeutic strategy for CRC patients.

Rational design of wettability-patterned microchips for high-performance attomolar surface-enhanced Raman detection.

Recent progress in wettability-patterned microchips has facilitated the development of ultra-trace detection in multiple biomedical and food safety fields. The existence of a superhydrophilic trap can realize targeted deposition of the analyte. However, the wetting transition from the Cassie-Baxter state to the Wenzel state usually occurs during evaporation and leads to a larger deposition footprint, which has a strong impact on the detection sensitivity and uniformity. In this paper, we report an integrated design, fabrication, and evaporation strategy to avoid the transition for high-performance attomolar surface-enhanced Raman scattering (SERS) detection. An improved force balance model was proposed to design the microstructures of wettability-patterned microchips, which were fabricated by nanosecond laser direct writing and surface fluorination. The microchips were composed of superhydrophobic micro-grooves and superhydrophilic traps, by which the targeted deposition of Au nanoparticles and rhodamine 6G (R6G) onto a minimal area of ∼70 × 70 µm2 was realized after a two-step heated evaporation. Accordingly, the detection limit was down to the attomolar level (5 × 10-18 M) with SERS enhancement factors (EFs) exceeding 1010. More importantly, the Raman signals showed good uniformity (RSD of 11.5%) for the concentration of 2 × 10-17 M. A good linear relationship was obtained in the quantitative concentration range of 10-12 M to 5 × 10-18 M with a high correlation coefficient (R2) of 0.996. These wettability-patterned microchips exhibit high performance (that is, both good sensitivity and good uniformity) in the detection of ultra-trace molecules in aqueous solutions, avoiding the need for expensive equipment and considerable skill in operations. The proposed strategy could also be applied to other microfluidic devices for rapid and simple analyte pre-concentration.

Comprehensive Analysis of VCAN Expression Profiles and Prognostic Values in HCC.

Background: Hepatocellular carcinoma (HCC) is the world's most common cause of cancer death. Therefore, more molecular mechanisms need to be clarified to meet the urgent need to develop new detection and treatment strategies. Methods: We used TCGAportal, Kaplan-Meier Plotter, the Cistrome DB Toolkit Database, MExpress, GEPIA2, and other databases to discuss the expression profiles, possible biological function, and potential prognostic value of versican (VCAN) in HCC. We conducted cell experiments such as Transwell migration and invasion assays, wound healing assay, and CCK8 experiment to explore the function of VCAN in HCC. Result: We selected three HCC transcriptome databases GSE124535, GSE136247, and GSE144269 and analyzed the overexpressed genes contained in them. The overlapping genes were found by the Venn map, and two interacting network modules were found by Mcode. Module 1 was mainly related to mitosis and cell cycle, and module 2 was mainly related to EMT, angiogenesis, glycolysis, and so on. We found that the seed gene in module 2 is VCAN. Data from TCGAportal showed that compared with normal tissues, the expression of VCAN was up-regulated in HCC tissues. The patients with high expression of VCAN had shorter distant recurrence-free survival and overall survival. Multiple possible VCAN interactions had also been identified. These results revealed that the level of VCAN was higher in the subtypes of HCC with higher malignant degree and was connected to the poor prognosis. In addition, the treatment of VCAN with DNA methyltransferase inhibitors and transcription factor inhibitors may improve the prognosis of patients with HCC. Conclusion: Our findings systematically elucidated the expression profile and different prognostic values of VCAN in HCC, which may provide new therapeutic targets and potential prognostic biomarkers for HCC patients.

METTL3-Mediated ADAMTS9 Suppression Facilitates Angiogenesis and Carcinogenesis in Gastric Cancer.

The role of methyltransferase-like 3 (METTL3), which participates in catalyzing N-methyladenosine (m6A) RNA modification, in gastric cancer (GC) is unclear. Here, we found that METTL3 was overexpressed in human GC. Functionally, we verified that METTL3 promoted tumor cell proliferation and angiogenesis through a series of phenotypic experiments. Subsequently, ADAMTS9 was identified as the downstream effector of METTL3 in GC, which could be degraded by the YTHDF2-dependent pathway. Finally, the data suggested that METTL3 might facilitate GC progression through the ADAMTS9-mediated PI3K/AKT pathway. Our study unveiled the fundamental mechanisms of METTL3 in GC progression. The clinical value of METTL3 in GC deserves further exploration.

Treatment of patients with cancer using PD­1/PD­L1 antibodies: Adverse effects and management strategies (Review).

In 2020, there were an estimated 19.3 million new cancer cases and close to 10 million cancer deaths worldwide. Cancer remains one of the leading causes of death. In recent years, with the continuous improvement of our understanding of tumor immunotherapy, immunotherapeutics, such as immune checkpoint inhibitors, have gradually become a hot spot for tumor treatment. Amongst these, programmed cell death protein 1/programmed cell death protein ligand 1 (PD­1/PD­L1) related inhibitors, such as nivolumab and pembrolizumab, atezolizumab, avelumab and durvalumab have been shown to exhibit a high level of efficacy in several types of tumors. It has been confirmed that these inhibitors play an important role in the anti­tumor process, significantly improving the survival rate of patients and delaying the progress of the underlying cancer. However, its method of therapeutic interference and potential for damaging the immune system has caused concern regarding its suitability. As these adverse effects are caused by an immune response to endogenous tissues, they are designated as immune­related adverse events (irAEs). In this review, the typical irAEs reported in recent years and the management strategies adopted are highlighted, to serve as a reference in assessing the clinical response to these adverse reactions.

Single-cell RNA sequencing in cancer: Applications, advances, and emerging challenges.

Cancer has become one of the greatest threats to human health, and new technologies are urgently needed to further clarify the mechanisms of cancer so that better detection and treatment strategies can be developed. At present, extensive genomic analysis and testing of clinical specimens shape the insights into carcinoma. Nevertheless, carcinoma of humans is a complex ecosystem of cells, including carcinoma cells and immunity-related and stroma-related subsets, with accurate characteristics obscured by extensive genome-related approaches. A growing body of research shows that sequencing of single-cell RNA (scRNA-seq) is emerging to be an effective way for dissecting human tumor tissue at single-cell resolution, presenting one prominent way for explaining carcinoma biology. This review summarizes the research progress of scRNA-seq in the field of tumors, focusing on the application of scRNA-seq in tumor circulating cells, tumor stem cells, tumor drug resistance, the tumor microenvironment, and so on, which provides a new perspective for tumor research.

WNT5a in Colorectal Cancer: Research Progress and Challenges.

Despite the clinical development of new adjuvant and neoadjuvant chemotherapy drugs, colorectal cancer is still one of the leading causes of cancer-related death in human beings. WNT5a, an autocrine and paracrine ß-catenin independent ligand, has been shown to induce tumor inhibition and carcinogenic signals, depending on the type of cancer. In patients with colorectal cancer, WNT5a triggers a variety of downstream signaling pathways, which mainly affect the migration and invasion of tumor cells. This article reviews the mechanism and therapeutic potential of WNT5a in colorectal cancer. In short, an in-depth understanding of the role of WNT5a in colorectal cancer is very helpful to better deal with this disease.

EDSSA: An Encoder-Decoder Semantic Segmentation Networks Accelerator on OpenCL-Based FPGA Platform.

Visual semantic segmentation, which is represented by the semantic segmentation network, has been widely used in many fields, such as intelligent robots, security, and autonomous driving. However, these Convolutional Neural Network (CNN)-based networks have high requirements for computing resources and programmability for hardware platforms. For embedded platforms and terminal devices in particular, Graphics Processing Unit (GPU)-based computing platforms cannot meet these requirements in terms of size and power consumption. In contrast, the Field Programmable Gate Array (FPGA)-based hardware system not only has flexible programmability and high embeddability, but can also meet lower power consumption requirements, which make it an appropriate solution for semantic segmentation on terminal devices. In this paper, we demonstrate EDSSA-an Encoder-Decoder semantic segmentation networks accelerator architecture which can be implemented with flexible parameter configurations and hardware resources on the FPGA platforms that support Open Computing Language (OpenCL) development. We introduce the related technologies, architecture design, algorithm optimization, and hardware implementation of the Encoder-Decoder semantic segmentation network SegNet as an example, and undertake a performance evaluation. Using an Intel Arria-10 GX1150 platform for evaluation, our work achieves a throughput higher than 432.8 GOP/s with power consumption of about 20 W, which is a 1.2× times improvement the energy-efficiency ratio compared to a high-performance GPU.

The structural ensemble of a Holliday junction determined by X-ray scattering interference.

The DNA four-way (Holliday) junction is the central intermediate of genetic recombination, yet key aspects of its conformational and thermodynamic properties remain unclear. While multiple experimental approaches have been used to characterize the canonical X-shape conformers under specific ionic conditions, the complete conformational ensemble of this motif, especially at low ionic conditions, remains largely undetermined. In line with previous studies, our single-molecule Förster resonance energy transfer (smFRET) measurements of junction dynamics revealed transitions between two states under high salt conditions, but smFRET could not determine whether there are fast and unresolvable transitions between distinct conformations or a broad ensemble of related states under low and intermediate salt conditions. We therefore used an emerging technique, X-ray scattering interferometry (XSI), to directly probe the conformational ensemble of the Holliday junction across a wide range of ionic conditions. Our results demonstrated that the four-way junction adopts an out-of-plane geometry under low ionic conditions and revealed a conformational state at intermediate ionic conditions previously undetected by other methods. Our results provide critical information to build toward a full description of the conformational landscape of the Holliday junction and underscore the utility of XSI for probing conformational ensembles under a wide range of solution conditions.

Computational design of three-dimensional RNA structure and function.

RNA nanotechnology seeks to create nanoscale machines by repurposing natural RNA modules. The field is slowed by the current need for human intuition during three-dimensional structural design. Here, we demonstrate that three distinct problems in RNA nanotechnology can be reduced to a pathfinding problem and automatically solved through an algorithm called RNAMake. First, RNAMake discovers highly stable single-chain solutions to the classic problem of aligning a tetraloop and its sequence-distal receptor, with experimental validation from chemical mapping, gel electrophoresis, solution X-ray scattering and crystallography with 2.55 Å resolution. Second, RNAMake automatically generates structured tethers that integrate 16S and 23S ribosomal RNAs into single-chain ribosomal RNAs that remain uncleaved by ribonucleases and assemble onto messenger RNA. Third, RNAMake enables the automated stabilization of small-molecule binding RNAs, with designed tertiary contacts that improve the binding affinity of the ATP aptamer and improve the fluorescence and stability of the Spinach RNA in cell extracts and in living Escherichia coli cells.

Coaxial Printing of Silicone Elastomer Composite Fibers for Stretchable and Wearable Piezoresistive Sensors.

Despite the tremendous efforts dedicated to developing various wearable piezoresistive sensors with sufficient stretchability and high sensitivity, challenges remain pertaining to fabrication scalability, cost, and efficiency. In this study, a facile, scalable, and low-cost coaxial printing strategy is employed to fabricate stretchable and flexible fibers with a core-sheath structure for wearable strain sensors. The highly viscous silica-modified silicone elastomer solution is used to print the insulating sheath layer, and the silicone elastomer solutions containing multi-walled carbon nanotubes (CNTs) are used as the core inks to print the conductive inner layer. With the addition of silica powders as viscosifiers, silica-filled silicone ink (sheath ink) converts to printable ink. The dimensions of the printed coaxial fibers can be flexibly controlled via adjusting the extrusion pressure of the inks. In addition, the electro-mechanical responses of the fiber-shaped strain sensors are investigated. The printed stretchable and wearable fiber-like CNT-based strain sensor exhibits outstanding sensitivities with gauge factors (GFs) of 1.4 to 2.5 × 106, a large stretchability of 150%, and excellent waterproof performance. Furthermore, the sensor can detect a strain of 0.1% and showed stable responses for over 15,000 cycles (high durability). The printed fiber-shaped sensor demonstrated capabilities of detecting and differentiating human joint movements and monitoring balloon inflation. These results obtained demonstrate that the one-step printed fiber-like strain sensors have potential applications in wearable devices, soft robotics, and electronic skins.

Recording and Analyzing Nucleic Acid Distance Distributions with X-Ray Scattering Interferometry (XSI).

Most structural techniques provide averaged information or information about a single predominant conformational state. However, biological macromolecules typically function through series of conformations. Therefore, a complete understanding of macromolecular structures requires knowledge of the ensembles that represent probabilities on a conformational free energy landscape. Here we describe an emerging approach, X-ray scattering interferometry (XSI), a method that provides instantaneous distance distributions for molecules in solution. XSI uses gold nanocrystal labels site-specifically attached to a macromolecule and measures the scattering interference from pairs of heavy metal labels. The recorded signal can directly be transformed into a distance distribution between the two probes. We describe the underlying concepts, present a detailed protocol for preparing samples and recording XSI data, and provide a custom-written graphical user interface to facilitate XSI data analysis. © 2018 by John Wiley & Sons, Inc.

Gold nanocrystal labels provide a sequence-to-3D structure map in SAXS reconstructions.

Small-angle x-ray scattering (SAXS) is a powerful technique to probe the structure of biological macromolecules and their complexes under virtually arbitrary solution conditions, without the need for crystallization. While it is possible to reconstruct molecular shapes from SAXS data ab initio, the resulting electron density maps have a resolution of ~1 nm and are often insufficient to reliably assign secondary structure elements or domains. We show that SAXS data of gold-labeled samples significantly enhance the information content of SAXS measurements, allowing the unambiguous assignment of macromolecular sequence motifs to specific locations within a SAXS structure. We first demonstrate our approach for site-specifically internally and end-labeled DNA and an RNA motif. In addition, we present a protocol for highly uniform and site-specific labeling of proteins with small (~1.4 nm diameter) gold particles and apply our method to the signaling protein calmodulin. In all cases, the position of the small gold probes can be reliably identified in low-resolution electron density maps. Enhancing low-resolution measurements by site-selective gold labeling provides an attractive approach to aid modeling of a large range of macromolecular systems.

Shape-Controllable Gold Nanoparticle-MoS2 Hybrids Prepared by Tuning Edge-Active Sites and Surface Structures of MoS2 via Temporally Shaped Femtosecond Pulses.

Edge-active site control of MoS2 is crucial for applications such as chemical catalysis, synthesis of functional composites, and biochemical sensing. This work presents a novel nonthermal method to simultaneously tune surface chemical (edge-active sites) and physical (surface periodic micro/nano structures) properties of MoS2 using temporally shaped femtosecond pulses, through which shape-controlled gold nanoparticles are in situ and self-assembly grown on MoS2 surfaces to form Au-MoS2 hybrids. The edge-active sites with unbound sulfurs of laser-treated MoS2 drive the reduction of gold nanoparticles, while the surface periodic structures of laser-treated MoS2 assist the shape-controllable growth of gold nanoparticles. The proposed novel method highlights the broad application potential of MoS2; for example, these Au-MoS2 hybrids exhibit tunable and highly sensitive SERS activity with an enhancement factor up to 1.2 × 107, indicating the marked potential of MoS2 in future chemical and biological sensing applications.

Determination of the conformational ensemble of the TAR RNA by X-ray scattering interferometry.

The conformational ensembles of structured RNA's are crucial for biological function, but they remain difficult to elucidate experimentally. We demonstrate with HIV-1 TAR RNA that X-ray scattering interferometry (XSI) can be used to determine RNA conformational ensembles. X-ray scattering interferometry (XSI) is based on site-specifically labeling RNA with pairs of heavy atom probes, and precisely measuring the distribution of inter-probe distances that arise from a heterogeneous mixture of RNA solution structures. We show that the XSI-based model of the TAR RNA ensemble closely resembles an independent model derived from NMR-RDC data. Further, we show how the TAR RNA ensemble changes shape at different salt concentrations. Finally, we demonstrate that a single hybrid model of the TAR RNA ensemble simultaneously fits both the XSI and NMR-RDC data set and show that XSI can be combined with NMR-RDC to further improve the quality of the determined ensemble. The results suggest that XSI-RNA will be a powerful approach for characterizing the solution conformational ensembles of RNAs and RNA-protein complexes under diverse solution conditions.

The solution structural ensembles of RNA kink-turn motifs and their protein complexes.

With the growing number of crystal structures of RNA and RNA-protein complexes, a critical next step is understanding the dynamic solution behavior of these entities in terms of conformational ensembles and energy landscapes. To this end, we have used X-ray scattering interferometry (XSI) to probe the ubiquitous RNA kink-turn motif and its complexes with the canonical kink-turn binding protein L7Ae. XSI revealed that the folded kink-turn is best described as a restricted conformational ensemble. The ions present in solution alter the nature of this ensemble, and protein binding can perturb the kink-turn ensemble without collapsing it to a unique state. This study demonstrates how XSI can reveal structural and ensemble properties of RNAs and RNA-protein complexes and uncovers the behavior of an important RNA-protein motif. This type of information will be necessary to understand, predict and engineer the behavior and function of RNAs and their protein complexes.

Femtosecond laser rapid fabrication of large-area rose-like micropatterns on freestanding flexible graphene films.

We developed a simple, scalable and high-throughput method for fabrication of large-area three-dimensional rose-like microflowers with controlled size, shape and density on graphene films by femtosecond laser micromachining. The novel biomimetic microflower that composed of numerous turnup graphene nanoflakes can be fabricated by only a single femtosecond laser pulse, which is efficient enough for large-area patterning. The graphene films were composed of layer-by-layer graphene nanosheets separated by nanogaps (~10-50 nm), and graphene monolayers with an interlayer spacing of ~0.37 nm constituted each of the graphene nanosheets. This unique hierarchical layering structure of graphene films provides great possibilities for generation of tensile stress during femtosecond laser ablation to roll up the nanoflakes, which contributes to the formation of microflowers. By a simple scanning technique, patterned surfaces with controllable densities of flower patterns were obtained, which can exhibit adhesive superhydrophobicity. More importantly, this technique enables fabrication of the large-area patterned surfaces at centimeter scales in a simple and efficient way. This study not only presents new insights of ultrafast laser processing of novel graphene-based materials but also shows great promise of designing new materials combined with ultrafast laser surface patterning for future applications in functional coatings, sensors, actuators and microfluidics.

Quantifying Nucleic Acid Ensembles with X-ray Scattering Interferometry.

The conformational ensemble of a macromolecule is the complete description of the macromolecule's solution structures and can reveal important aspects of macromolecular folding, recognition, and function. However, most experimental approaches determine an average or predominant structure, or follow transitions between states that each can only be described by an average structure. Ensembles have been extremely difficult to experimentally characterize. We present the unique advantages and capabilities of a new biophysical technique, X-ray scattering interferometry (XSI), for probing and quantifying structural ensembles. XSI measures the interference of scattered waves from two heavy metal probes attached site specifically to a macromolecule. A Fourier transform of the interference pattern gives the fractional abundance of different probe separations directly representing the multiple conformation states populated by the macromolecule. These probe-probe distance distributions can then be used to define the structural ensemble of the macromolecule. XSI provides accurate, calibrated distance in a model-independent fashion with angstrom scale sensitivity in distances. XSI data can be compared in a straightforward manner to atomic coordinates determined experimentally or predicted by molecular dynamics simulations. We describe the conceptual framework for XSI and provide a detailed protocol for carrying out an XSI experiment.

Nanopillar arrays with nanoparticles fabricated by a femtosecond laser pulse train for highly sensitive SERRS.

This work presents a novel method for fabricating repeatable, uniform, large-area, highly sensitive, surface-enhanced resonance Raman scattering (SERRS) substrates combined with silicon nanopillar arrays and silver nanoparticles. The proposed method consists of two steps: (1) induce periodic ripples in deionized water using a linearly polarized femtosecond laser; and (2) generate dense 80-nm-diameter nanopillar arrays with silver nanoparticles in silver nitrate solution with a 90° rotated polarization, femtosecond double-pulse train. As the pulse delay increases from 0 to 1000 fs, the mean size of the silver nanoparticles reduces, and the average number of nanoparticles increases, which, in turn, increases the enhancement factor of SERRS signals up to 1.1×10(9). Furthermore, melamine (down to 125 ppb) was detected by the fabricated SERRS substrates.

Production rate enhancement of size-tunable silicon nanoparticles by temporally shaping femtosecond laser pulses in ethanol.

This paper proposes an efficient approach for production-rate enhancement and size reduction of silicon nanoparticles produced by femtosecond (fs) double-pulse ablation of silicon in ethanol. Compared with a single pulse, the production rate is ~2.6 times higher and the mean size of the NPs is reduced by ~1/5 with a delay of 2 ps. The abnormal enhancement in the production rate is obtained at pulse delays Δt > 200 fs. The production-rate enhancement is mainly attributed to high photon absorption efficiency. It is caused by an increase in localized transient electron density, which results from the first sub-pulse ionization of ethanol molecules before the second sub-pulse arrives. The phase-change mechanism at a critical point might reduce nanoparticle size.