Complementary Alu sequences mediate enhancer-promoter selectivity.

Enhancers determine spatiotemporal gene expression programs by engaging with long-range promoters1-4. However, it remains unknown how enhancers find their cognate promoters. We recently developed a RNA in situ conformation sequencing technology to identify enhancer-promoter connectivity using pairwise interacting enhancer RNAs and promoter-derived noncoding RNAs5,6. Here we apply this technology to generate high-confidence enhancer-promoter RNA interaction maps in six additional cell lines. Using these maps, we discover that 37.9% of the enhancer-promoter RNA interaction sites are overlapped with Alu sequences. These pairwise interacting Alu and non-Alu RNA sequences tend to be complementary and potentially form duplexes. Knockout of Alu elements compromises enhancer-promoter looping, whereas Alu insertion or CRISPR-dCasRx-mediated Alu tethering to unregulated promoter RNAs can create new loops to homologous enhancers. Mapping 535,404 noncoding risk variants back to the enhancer-promoter RNA interaction maps enabled us to construct variant-to-function maps for interpreting their molecular functions, including 15,318 deletions or insertions in 11,677 Alu elements that affect 6,497 protein-coding genes. We further demonstrate that polymorphic Alu insertion at the PTK2 enhancer can promote tumorigenesis. Our study uncovers a principle for determining enhancer-promoter pairing specificity and provides a framework to link noncoding risk variants to their molecular functions.

RIC-seq for global in situ profiling of RNA-RNA spatial interactions.

Highly structured RNA molecules usually interact with each other, and associate with various RNA-binding proteins, to regulate critical biological processes. However, RNA structures and interactions in intact cells remain largely unknown. Here, by coupling proximity ligation mediated by RNA-binding proteins with deep sequencing, we report an RNA in situ conformation sequencing (RIC-seq) technology for the global profiling of intra- and intermolecular RNA-RNA interactions. This technique not only recapitulates known RNA secondary structures and tertiary interactions, but also facilitates the generation of three-dimensional (3D) interaction maps of RNA in human cells. Using these maps, we identify noncoding RNA targets globally, and discern RNA topological domains and trans-interacting hubs. We reveal that the functional connectivity of enhancers and promoters can be assigned using their pairwise-interacting RNAs. Furthermore, we show that CCAT1-5L-a super-enhancer hub RNA-interacts with the RNA-binding protein hnRNPK, as well as RNA derived from the MYC promoter and enhancer, to boost MYC transcription by modulating chromatin looping. Our study demonstrates the power and applicability of RIC-seq in discovering the 3D structures, interactions and regulatory roles of RNA.

Light-Emitting Microfibers from Lotus Root for Eco-Friendly Optical Waveguides and Biosensing.

Optical biosensors based on micro/nanofibers are highly valuable for probing and monitoring liquid environments and bioactivity. Most current optical biosensors, however, are still based on glass, semiconductors, or metallic materials, which might not be fully suitable for biologically relevant environments. Here, we introduce biocompatible and flexible microfibers from lotus silk as microenvironmental monitors that exhibit waveguiding of intrinsic fluorescence as well as of coupled light. These features make single-filament monitors excellent building blocks for a variety of sensing functions, including pH probing and detection of bacterial activity. These results pave the way for the development of new and entirely eco-friendly, potentially multiplexed biosensing platforms.

A review on CRISPR/Cas: a versatile tool for cancer screening, diagnosis, and clinic treatment.

Cancer is one of the leading causes of death worldwide and it has the trend of increase incidence. However, in the past decades, as quickly developed new technologies and modified old techniques for cancer screening, diagnosis, and treatment, the cancer-caused mortality rates dropped quickly, and the survival times of cancer patients are enhanced. However, the current death rate is still about 50% and the survival patients always suffer from the side effect of current cancer treatments. Recently developed Nobel Prize-winning CRISPR/Cas technology provides new hope on cancer screening, early diagnosis, and clinic treatment as well as new drug development. Currently, four major CRISPR/Cas9-derived genome editors, CRISPR/Cas9 nucleotide sequence editor, CRISPR/Cas base editor (BE), CRISPR prime editor (PE), and CRISPR interference (CRISPRi) (including both CRISPRa and CRISPRr), were well developed and used to various research and applications, including cancer biology study and cancer screening, diagnosis, and treatment. Additionally, CRISPR/Cas12 and CRISPR/Cas13 genome editors were also widely used in cancer-related basic and applied research as well as treatment. Cancer-associated SNPs and genetic mutations as well as both oncogenes and tumor suppressor genes are perfect targets for CRISPR/Cas-based gene therapy for cancer treatment. CRISPR/Cas is also employed to modify and generate new Chimeric antigen receptor (CAR) T-cells for improving its safety, efficiency, and longer-time last for treating various cancers. Currently, there are many clinic trails of CRISPR-based gene therapy for cancer treatments. Although all CRISPR/Cas-derived genome and epigenome tools are promising methods for cancer biology study and treatment, the efficiency and long term-safety are still the major concerns for CRISPR-based gene therapy. Developing new CRISPR/Cas delivery methods and reducing the potential side effects, including off-target impacts, will enhance CRISPR/Cas application in cancer-related research, diagnosis, and therapeutical treatment.

Cellular retinol-binding protein 1: a therapeutic and diagnostic tumor marker.

Cellular Retinol Binding Protein 1 (CRBP1) gene is a protein coding gene located on human chromosome 3q21, which codifies a protein named CRBP1. CRBP1 is widely expressed in many tissues as a chaperone protein to regulate the uptake, subsequent esterification and bioavailability of retinol. CRBP1 combines retinol and retinaldehyde with high affinity to protect retinoids from non-specific oxidation, and transports retinoids to specific enzymes to promote the biosynthesis of retinoic acid. The vital role of CRBP1 in retinoids metabolism has been gradually discovered, which has been implicated in tumorigenesis. However, the precise functions of CRBP1 in different diseases are still poorly understood. The purpose of this review is to provide an overview of the role of CRBP1 in various diseases, especially in both the promotion and inhibition of cancers, which may also offer a novel biomarker and potential therapeutic target for human diseases.

Assessment of immune status of laryngeal squamous cell carcinoma can predict prognosis and guide treatment.

BACKGROUND: In the past few years, immunotherapy has changed the way we treat solid tumors. People pay more and more attention to the immune microenvironment of laryngeal squamous cell carcinoma (LSCC). In this study, our immunotherapy research took advantage of the clinical database and focused our in-depth analysis on the tumor microenvironment (TME). METHODS: This study evaluated the relationship between the clinical outcome and the local tissue and overall immune status in 412 patients with primary LSCC. We constructed and validated a risk model that could predict prognosis, assess immune status, identify high-risk patients, and develop personalized treatment plans through bioinformatics. In addition, through immunohistochemical analysis, we verified the differential expression of CTSL and KDM5D genes with the largest weight coefficients in the model in LSCC tissues and their influence on the prognosis and tumor-infiltrating lymphocytes (TILs). RESULTS: We found that interstitial tumor-infiltrating lymphocytes, tumor parenchymal-infiltrating lymphocyte volume, tumor infiltrates lymphocytes of frontier invasion, and the platelet-to-lymphocyte ratio (PLR) were independent factors affecting the prognosis of patients with LSCC. A novel risk model can guide clinicians to accurately predict prognosis, identify high-risk patients, and formulate personalized treatment plans. The differential expression of genes such as CTSL and KDM5D has a significant correlation with the TILs of LSCC and the prognosis of patients. CONCLUSION: Local and systemic inflammatory markers in patients with laryngeal squamous cell carcinoma are reliable prognostic factors. The risk model and CTSL, KDM5D gene have important potential research value.

Point-Source Geometric Metasurface Holography.

Geometric metasurfaces have shown great potential in holography due to their straightforward geometric nature of phase control. The incident angles, spins, and wavelengths of the light provide various degrees of freedom to multiplex metasurface holographic images, which, however, are usually interrelated and hence challenging to be fully decoupled. Here, we report a synergetic recipe to break such seemingly inevitable interrelation by incorporating an effective point source (a pinhole), with which the spin, wavelength, and coordinate of the point source can be fully decoupled in meta-holograms. We experimentally demonstrate spin-decoupled, full-colored metasurface holography and dynamic holography controlled with the position of the point source. The significance of this work is not merely to offer an alternative approach to break the interrelation limitations of the geometric metasurface, but more importantly, it provides a promising route for point sources in reality to realize advanced functionalities with meta-optics, such as single-photon holography, fluorescence holography, etc.

Prognostic value of platelet distribution width and mean platelet volume in patients with laryngeal cancer.

Aims: To investigate the prognostic relevance of platelet volume indices for survival in laryngeal cancer. Patients & methods: The study included 640 patients with laryngeal cancer. We analyzed the optimal cutoff values through receiver operating characteristic analysis, then analyzed the univariate factor and multivariate variables. Kaplan-Meier curves and log-rank tests were conducted to compare the overall survival (OS) and recurrence-free survival rates between the groups. Results: In multivariate analysis, elevated platelet distribution width (PDW) and PDW/platelet count ratio were significantly correlated with poor prognosis for OS; however, elevated mean platelet volume (MPV) and MPV/platelet count ratio suggested a notable correlation with favorable prognosis for OS. Meanwhile, elevated PDW and decreased MPV were significantly correlated with poor prognosis for recurrence-free survival. Conclusions: Our findings indicate that elevated PDW and decreased MPV could serve as independent biomarkers for worse survival in laryngeal cancer.

High Iodine Nutrition May Be a Risk Factor for Cervical Lymph Node Metastasis in Papillary Thyroid Cancer Patients.

PURPOSE: The aim of this study was to retrospectively identify the effect of iodine on the papillary thyroid cancer (PTC) process and investigate the risk clinicopathologic characteristics of cervical lymph node metastasis (CLNM) for achieving a better preventive strategy of PTC. METHODS: Totally 187 patients with CLNM and 279 without CLNM (NCLNM) were enrolled, and their urinary iodine concentration (UIC) and serum iodine concentration (SIC) were measured. Logistic regressions were used to reveal the effects of iodine nutrition on the CLNM status of PTC. RESULTS: The levels of thyroid-stimulating hormone (TSH) and thyroglobulin (TG) were higher in the CLNM group than in the NCLNM group. UIC and SIC were positively correlated, and both of them were correlated with TSH, free thyroxine, and TG. The proportions of UIC >300 µg/L and of SIC >90 µg/L were higher in the CLNM than in the NCLNM. Logistic analysis showed that SIC >90 µg/L was an independent predictor for CLNM in PTC. Additionally, age ≥45, female, TG, multifocality, and diameter of cancer invasion >1 cm also affected CLNM status in PTC, and their logistic regression model showed a certain diagnostic accuracy (area under the receiver-operating characteristic curve = 0.72). CONCLUSIONS: Relatively high iodine nutrition seemed to be a significant risk factor for the occurrence of CLNM in PTC and may promote lymphatic metastasis in PTC.

Long noncoding RNA LINC01194 enhances the malignancy of laryngeal squamous cell carcinoma by sponging miR-655 to increase SOX18 expression.

Long noncoding RNAs (lncRNAs) have undergone a comprehensive study for their involvements in tumor treatments. The purpose of our study was to explore the biological effects and regulatory mechanisms of lncRNA LINC01194 (LINC01194) in laryngeal squamous cell carcinoma (LSCC). The levels of LINC01194 in 105 LSCC patients were detected by RT-qPCR. The diagnostic and prognostic value of LINC01194 in LSCC patients were statistically analyzed. The potential functions of LINC01194 in proliferation, apoptosis, and metastasis of LSCC cells were evaluated. The interaction among LINC01194, miR-655 and SOX18 was explored by bioinformatics analysis, luciferase reporter assays and biotinylated RNA pull-down. We found that the expression levels of LINC01194 were highly expressed in LSCC, which was negatively correlated with the clinical outcome of LSCC patients. The area under the ROC curve for LINC01194 was up to 0.8388. Functional assays indicated that LINC01194 knockdown distinctly inhibited LSCC cells proliferation, induced apoptosis, and also attenuated LSCC cells migration and invasion in vitro. Furthermore, we elucidated that LINC01194 promoted SOX18 expression in LSCC cells via functioning as a molecular sponge for miR-655. Overall, based on our findings, LINC01194 served as a tumor promoter and potentially represents a novel prognostic indicator and therapeutic target in LSCC.

Prognostic Significance of Lactate Dehydrogenase in Patients Undergoing Surgical Resection for Laryngeal Squamous Cell Carcinoma.

The aim is to estimate the prognostic value of lactate dehydrogenase (LDH) in patients undergoing surgical resection for laryngeal squamous cell carcinoma (LSCC). A total of 640 resected LSCC patients were included. Preoperative lactate dehydrogenase (LDH) was assessed. Kaplan-Meier survival analysis and Cox regression analysis were conducted for overall survival (OS) and recurrence-free survival (RFS). Kaplan-Meier analysis, univariate analysis and multivariate analysis demonstrated significant prognostic value for preoperative LDH. Although LDH was predictor of OS, it failed to be a predictor of RFS. The univariate HR and 95% CI of LDH were 0.484 and 0.357-0.658 (P < 0.0001). The multivariate analysis showed that LDH (HR = 0.518, 95% CI: 0.380-0.705, p < 0.0001) was related to OS. Elevated preoperative LDH >132 IU/L was significantly associated with better survival. Preoperative LDH might be an independent prognostic marker of OS in LSCC patients undergoing surgical resection.

Comparative Analysis of Regulatory Role of Notch Signaling Pathway in 8 Types Liver Cell During Liver Regeneration.

Notch signaling is closely related to cell proliferation, cell apoptosis, cell fate decisions, DNA damage repair, and so on. However, the exactly regulatory mechanism of Notch signaling pathway in liver regeneration (LR) remains unclear. To reveal the role of Notch signaling pathway in rat liver regeneration, Ingenuity Pathway Analysis (IPA) software and related pathway database were firstly used to construct the Notch signaling pathway in this study. Next, eight type cells with high purity were obtained by Percoll density centrifugation and immunomagnetic beads sorting. Then, the expression profiles of Notch signaling pathway-related genes in eight type cells were checked by using Rat Genome 230 2.0 Array, and the results showed that the expression of 42 genes were significantly regulated. H-cluster results showed that the hepatic stellate cells are attributed to one cluster; hepatocyte cell, oval cell, sinusoidal endothelial cell, and Kupffer cell are clustered together; and biliary epithelial cell, pit cell, and dendritic cell are one cluster. IPA software and Expression analysis systematic explorer analysis indicated that Notch signaling pathway-related genes were involved in cell proliferation, apoptosis, cell cycle, DNA damage repair, etc. In conclusion, Notch signaling pathway might regulate various physiological activities of LR through multiple pathways.

Krüppel-like factor 5: a novel biomarker for lymph node metastasis and recurrence in supraglottic squamous cell laryngeal carcinoma.

Krüppel-like factor 5 (KLF5), a zinc finger-containing transcription factor, is involved in important biological processes including cell transformation, proliferation, and carcinogenesis. However, its clinical significance has remained largely unknown in laryngeal cancer. Here, specimens from 144 patients with laryngeal tumors were investigated by immunohistochemical staining for KLF5, integrin-linked kinase (ILK), and E-cadherin expressions. A clinicopathological study revealed that the KLF5 expression level in tumor cells was significantly correlated with lymph node metastasis (P < 0.05) and local recurrence (P < 0.05). In addition, KLF5, ILK, and E-cadherin (epithelial-mesenchymal transition (EMT) biomarker) expressions were correlated with each other. These findings suggest that KLF5 may be an epithelial-mesenchymal transition-associated biomarker in human laryngeal carcinomas and play important roles in the progression of laryngeal carcinomas. KLF5 immunoreactivity is therefore considered a potential lymph node metastasis and recurrence factor in human laryngeal cancers. In addition, the KLF5-mediated pathway is a potential target for elimination of laryngeal cancer in the future.

Optical color routing enabled by deep learning.

Nano-color routing has emerged as an immensely popular and widely discussed subject in the realms of light field manipulation, image sensing, and the integration of deep learning. The conventional dye filters employed in commercial applications have long been hampered by several limitations, including subpar signal-to-noise ratio, restricted upper bounds on optical efficiency, and challenges associated with miniaturization. Nonetheless, the advent of bandpass-free color routing has opened up unprecedented avenues for achieving remarkable optical spectral efficiency and operation at sub-wavelength scales within the area of image sensing applications. This has brought about a paradigm shift, fundamentally transforming the field by offering a promising solution to surmount the constraints encountered with traditional dye filters. This review presents a comprehensive exploration of representative deep learning-driven nano-color routing structure designs, encompassing forward simulation algorithms, photonic neural networks, and various global and local topology optimization methods. A thorough comparison is drawn between the exceptional light-splitting capabilities exhibited by these methods and those of traditional design approaches. Additionally, the existing research on color routing is summarized, highlighting a promising direction for forthcoming development, delivering valuable insights to advance the field of color routing and serving as a powerful reference for future endeavors.

Detection of dsRNA with Fluorescence In Situ Hybridization (FISH).

Fluorescence in situ hybridization (FISH) is a powerful technique used for detecting and localizing specific nucleic acid sequences in cells or tissues. Double-stranded RNA (dsRNA) is a type of RNA with complementary strands, highly produced during the replication cycle of RNA viruses. dsRNA plays an essential role in many biological processes, including the activation of RNA silencing. Here, we present an overview of how FISH can be employed to detect and locate dsRNA. The detection and localization of dsRNA through FISH provide valuable insights into RNA-mediated processes and their roles in various biological phenomena.

Tumor keratin 15 expression links with less extent of invasion and better prognosis in papillary thyroid cancer patients receiving tumor resection.

OBJECTIVE: Keratin 15 (KRT15) is identified as a useful biomarker in several solid tumors, while its clinical role in papillary thyroid cancer (PTC) remains unknown. Herein, this study is intended to explore the correlation of tumor KRT15 with clinical features and survival in PTC patients who received tumor resection. METHODS: This study retrospectively screened 350 PTC patients who received tumor resection and 50 thyroid benign lesions (TBL) patients. KRT15 in formalin-fixed paraffin-embedded lesion specimens of all subjects was detected by immunohistochemistry (IHC). RESULTS: KRT15 was reduced in PTC patients compared to TBL patients (P < 0.001). Furthermore, KRT15 was negatively associated with tumor size (P = 0.017), extrathyroidal invasion (P = 0.007), pathological tumor (pT) stage (P < 0.001), and postoperative radioiodine application (P = 0.008) in PTC patients. Regarding prognostic value, high KRT15 (cut-off by an IHC value of 3) is linked with prolonged accumulating disease-free survival (DFS) (P = 0.008) and overall survival (OS) (P = 0.008) in PTC patients. Also, the multivariate Cox regression model showed that high KRT15 (vs. low) was an independent factor for longer DFS (hazard ratio = 0.433, P = 0.049), but not for OS (P > 0.050) in PTC patients. Subgroup analyses revealed that KRT15 possessed a better prognostic value in PTC patients with age ≥ 55 years, tumor size > 4 cm, pathological node stage 1, or pathological tumor-node-metastasis stage ≤ 2 (all P < 0.050). CONCLUSION: Increased tumor KRT15 associates with a lower invasive degree, prolonged DFS, and OS, revealing its prognostic utility in PTC patients undergoing tumor resection.

Elucidation of the key therapeutic targets and potential mechanisms of Andrographolide multi-targets against osteoarthritis via network pharmacological analysis and experimental validation.

OBJECTIVE: Our purpose is to unveil Andrographolide's potential multi-target and multi-mechanism therapeutic effects in treating OA via systematic network pharmacological analysis and cell experimental validation. MATERIALS AND METHODS: Initially, we gathered data from Andrographolide and OA-related databases to obtain information on Andrographolide's biological properties and the targets linked with OA. We developed a bioinformatic network about Andrographolide and OA, whereby we analyzed the network to identify potential therapeutic targets and mechanisms of action of Andrographolide. Subsequently, we used molecular docking to analyze the binding sites of Andrographolide to the target proteins. At the same time, SDF-1 was used to construct an OA cell model to verify the therapeutic effect of Andrographolide on OA and its effect on target proteins. RESULTS: Our experimental results show that Andrographolide has excellent pharmaceutical properties, by Lipinski's rules for drugs, suggesting that this compound can be considered to have a high therapeutic potential in drug development. 233 targets were preliminarily investigated, the mechanisms through which Andrographolide targets OA primarily involve the TNF signaling pathway, PI3K-AKT signaling pathway, IL-17 signaling pathway, and TLR signaling pathway. These mechanisms target OA by influencing immune and inflammatory responses in the joints, regulating apoptosis to prevent chondrocyte death. Finally, TNF-α, STAT3, TP53, IL-6, JUN, IL-1ß, HIF-1α, TGF-ß1, and AKT1 were identified as 9 key targets of Andrographolide anti-OA. In addition, our molecular docking analyzes with cell experimental validation further confirm the network pharmacology results. According to our molecular docking results, Andrographolide can bind to all the hub target proteins and has a good binding ability (binding energy < -5 kcal/mol), with the strongest binding affinity to AKT1 of -9.2 kcal/ mol. The results of cell experiments showed that Andrographolide treatment significantly increased the cell viability and the expression of COL2A1 and ACAN proteins. Moreover, 30 µM Andrographolide significantly reversed SDF-1-induced increases in the protein expression of TNF-α, STAT3, TP53, IL-6, JUN, IL-1ß, HIF-1α, and TGF-ß1, and decreases in the protein expression of AKT1. CONCLUSION: This study provides a comprehensive understanding of the potential therapeutic targets and mechanisms of action of Andrographolide in OA treatment. Our findings suggest that Andrographolide is a promising candidate for drug development in the management of OA.

Clinical efficacy and kinematic analysis of Chinese knotting technique-assisted posterior cruciate ligament reconstruction: A retrospective analysis.

To investigate the clinical efficacy and knee joint kinematic changes of posterior cruciate ligament (PCL) reconstruction assisted by Chinese knotting technique (CKT). A retrospective analysis was conducted on 88 cases of PCL reconstructive surgery admitted between September 2016 and September 2020. All patients were operated on by the same senior doctor and his team. The patients were divided into 2 groups according to whether the CKT was applied, with 44 cases in each group. Both groups received active rehabilitation treatment after surgery. All patients were followed up for more than 2 years. International knee documentation committee, hospital for special surgery (HSS), and Lysholm scores were used to evaluate the clinical efficacy of the 2 methods at 3, 12, and 24 months after surgery. The motion cycle and kinematic indices of the knee joint were measured by the Opti_Knee three-dimensional motion measurement system before surgery and at 3, 12, and 24 months after surgery. A secondary arthroscopic examination was performed at 12 months after surgery, MAS score was used to evaluate the secondary endoscopic examination of PCL. All the patients had wound healing in stage I without infection. International Knee in both sets Documentation Committee scores, HSS scores and Lysholm scores were gradually improved at all time points (P < .05); compared with the traditional group, the HSS score was higher in the reduction group 12 months after surgery (P < .05), but there was no significant difference at 24 months after surgery. 12 months and 24 months after 3 dimensional motion measurement system using Opti_Knee showed a reduction group before and after displacement and displacement of upper and lower range than the traditional group (P < 0. 05). One year after surgery, the good and good rate of MAS score reduction group was higher than traditional group. CKT assisted PCL reconstruction can improve the subjective function score of the affected knee joint and the results of secondary microscopy. Satisfactory knee kinematic function can be obtained in the early stage, and the anteroposteric relaxation of the knee joint can be reduced.

RH20, a phase-separated RNA helicase protein, facilitates plant resistance to viruses.

RNA silencing, a conserved gene regulatory mechanism, is critical for host resistance to viruses. Liquid-liquid phase separation (LLPS) is an important mechanism in regulating various biological processes. Emerging studies suggest RNA helicases play important roles in microRNA (miRNA) production through LLPS. In this study, we investigated the functional role of RNA helicase 20 (RH20), a DDX5 homolog in Arabidopsis thaliana, in RNA silencing and plant resistance to viruses. Our findings reveal that RH20 localizes in both the cytoplasm and nucleus, with puncta formation in the cytoplasm exhibiting liquid-liquid phase separation behavior. We demonstrate that RH20 plays positive roles in plant immunity against viruses. Further study showed that RH20 interacts with Argonaute 2 (AGO2), a key component of the RNA silencing pathway. Moreover, RH20 promotes the accumulation of both endogenous and exogenous small RNAs (sRNAs). Overall, our study identifies RH20 as a novel phase separation protein that interacting with AGO2, influencing sRNAs accumulation, and enhancing plant resistance to viruses.