HBV-associated hepatocellular carcinomas inhibit antitumor CD8 T cell via the long noncoding RNA HDAC2-AS2.

Hepatocellular carcinoma (HCC) is one of the most common malignancies worldwide. Extracellular vesicles (EV) are critical mediators of intercellular communication within the tumor microenvironment, and cancer-cell-secreted EVs often facilitate cancer progression. Here we show that in HBV-associated HCC, tumor-cell-derived EVs contain a TGFβ-inducible long noncoding RNA, termed HDAC2-AS2.

Analysis of Hepatic Lentiviral Vector Transduction: Implications for Preclinical Studies and Clinical Gene Therapy Protocols.

Lentiviral vector-transduced T cells were approved by the FDA as gene therapy anti-cancer medications. Little is known about the effects of host genetic variation on the safety and efficacy of the lentiviral vector gene delivery system. To narrow this knowledge gap, we characterized hepatic gene delivery by lentiviral vectors across the Collaborative Cross (CC) mouse genetic reference population.

The effect of hot air treatment on volatile compounds in nectarine fruit and the regulation of glycosidically bound compounds by sugar.

In order to investigate the impact of hot air (HA) treatment on the sugars and volatiles in postharvest nectarine fruit, nectarines were treated with HA at 40 °C for 4 h and stored at 1 °C for 35 days. Changes of sugars, free and glycosidically bound volatiles, β-glucosidase (β-Glu) activity, and the gene expression of UGT (UDP-glucosyltransferase) in nectarine fruit were determined. The results showed that compared with CK, HA treatment delayed the firmness decline of 48.

Computed tomography enterography radiomics and machine learning for identification of Crohn's disease.

Background: Crohn's disease is a severe chronic and relapsing inflammatory bowel disease. Although contrast-enhanced computed tomography enterography is commonly used to evaluate crohn's disease, its imaging findings are often nonspecific and can overlap with other bowel diseases. Recent studies have explored the application of radiomics-based machine learning algorithms to aid in the diagnosis of medical images.

Analysis of hepatic lentiviral vector transduction; implications for preclinical studies and clinical gene therapy protocols.

Lentiviral vector-transduced T-cells were approved by the FDA as gene therapy anti-cancer medications. Little is known about the host genetic variation effects on the safety and efficacy of the lentiviral vector gene delivery system. To narrow this knowledge-gap, we characterized hepatic gene delivery by lentiviral vectors across the Collaborative Cross (CC) mouse genetic reference population.

KIF2A correlates with lymphovascular invasion and higher tumor stage, and can be used to predict worse prognosis in patients with endometrial carcinoma.

Kinesin family protein 2A (KIF2A) is a microtubule depolymerase that participates in the progression of various cancers; however, its clinical utility in endometrial carcinoma (EC) remains unclear. The aim of the present study was to assess KIF2A expression and its relationship with prognosis in patients with EC. Data from 230 patients with EC who underwent tumor resection were reviewed in the current, retrospective study.

Optimizing calibration of modern skeletal maturity systems.

Purpose: Greulich and Pyle is the most used system to estimate skeletal maturity but has significant drawbacks, prompting the development of newer skeletal maturity systems, such as the modified Fels skeletal maturity systems based on knee radiographs. To create a new skeletal maturity system, an outcome variable, termed a "skeletal maturity standard," must be selected for calibration of the system. Peak height velocity and 90% of final height are both considered reasonable skeletal maturity standards for skeletal maturity system development.

Probabilistic activity driven model of temporal simplicial networks and its application on higher-order dynamics.

Network modeling characterizes the underlying principles of structural properties and is of vital significance for simulating dynamical processes in real world. However, bridging structure and dynamics is always challenging due to the multiple complexities in real systems. Here, through introducing the individual's activity rate and the possibility of group interaction, we propose a probabilistic activity-driven (PAD) model that could generate temporal higher-order networks with both power-law and high-clustering characteristics, which successfully links the two most critical structural features and a basic dynamical pattern in extensive complex systems.

Exploring the Possibility of RNA in Diverse Biological Processes.

The total amount of RNA in a cell is 5 to 10 times greater than that of DNA [...

NDRG1 facilitates self-renewal of liver cancer stem cells by preventing EpCAM ubiquitination.

Background: Portal vein tumour thrombus (PVTT) is the main pathway of HCC intrahepatic metastasis and is responsible for the poor prognosis of patients with HCC. However, the molecular mechanisms underlying PVTT vascular metastases have not been fully elucidated.

Methods: NDRG1 expression was assessed by immunohistochemistry and immunoblotting in clinical specimens obtained from curative surgery.

LncRNA CCTT-mediated RNA-DNA and RNA-protein interactions facilitate the recruitment of CENP-C to centromeric DNA during kinetochore assembly.

Kinetochore assembly on centromeres is central for chromosome segregation, and defects in this process cause mitotic errors and aneuploidy. Besides the well-established protein network, emerging evidence suggests the involvement of regulatory RNA in kinetochore assembly; however, it has remained elusive about the identity of such RNA, let alone its mechanism of action in this critical process. Here, we report CCTT, a previously uncharacterized long non-coding RNA (lncRNA) transcribed from the arm of human chromosome 17, which plays a vital role in kinetochore assembly.

RUNX1 deficiency cooperates with SRSF2 mutation to induce multilineage hematopoietic defects characteristic of MDS.

Myelodysplastic syndromes (MDSs) are a heterogeneous group of hematologic malignancies with a propensity to progress to acute myeloid leukemia. Causal mutations in multiple classes of genes have been identified in patients with MDS with some patients harboring more than 1 mutation. Interestingly, double mutations tend to occur in different classes rather than the same class of genes, as exemplified by frequent cooccurring mutations in the transcription factor RUNX1 and the splicing factor SRSF2.

Local-Forest Method for Superspreaders Identification in Online Social Networks.

Identifying the most influential spreaders in online social networks plays a prominent role in affecting information dissemination and public opinions. Researchers propose many effective identification methods, such as k-shell. However, these methods are usually validated by simulating propagation models, such as epidemic-like models, which rarely consider the Push-Republish mechanism with attenuation characteristic, the unique and widely-existing spreading mechanism in online social media.

Inadvertent Transfer of Murine VL30 Retrotransposons to CAR-T Cells.

For more than a decade, genetically engineered autologous T-cells have been successfully employed as immunotherapy drugs for patients with incurable blood cancers. The active components in some of these game-changing medicines are autologous T-cells that express viral vector-delivered chimeric antigen receptors (CARs), which specifically target proteins that are preferentially expressed on cancer cells. Some of these therapeutic CAR expressing T-cells (CAR-Ts) are engineered via transduction with -retroviral vectors (-RVVs) produced in a stable producer cell line that was derived from murine PG13 packaging cells (ATCC CRL-10686).

ZetaSuite: computational analysis of two-dimensional high-throughput data from multi-target screens and single-cell transcriptomics.

Two-dimensional high-throughput data have become increasingly common in functional genomics studies, which raises new challenges in data analysis. Here, we introduce a new statistic called Zeta, initially developed to identify global splicing regulators from a two-dimensional RNAi screen, a high-throughput screen coupled with high-throughput functional readouts, and ZetaSuite, a software package to facilitate general application of the Zeta statistics. We compare our approach with existing methods using multiple benchmarked datasets and then demonstrate the broad utility of ZetaSuite in processing public data from large-scale cancer dependency screens and single-cell transcriptomics studies to elucidate novel biological insights.

Mapping R-Loops Using Catalytically Inactive RNaseH1 (R-ChIP).

R-loops, three-stranded structures containing double-stranded DNA invaded by single-stranded RNA, have been linked to diverse biological processes. They play important roles in regulating gene regulation and DNA repair, contributing to a wide range of diseases. Understanding the formation and dynamic regulation of R-loops is thus a gateway to address many fundamental questions in regulatory biology, which requires the elucidation of the R-loop landscape at the genome scale.

Whole exome sequencing identified a homozygous novel mutation in SUOX gene causes extremely rare autosomal recessive isolated sulfite oxidase deficiency.

Background: Isolated sulfite oxidase deficiency (ISOD) is a rare type of life-threatening neurometabolic disorders characterized by neonatal intractable seizures and severe developmental delay with an autosomal recessive mode of inheritance. Germline mutation in SUOX gene causes ISOD. Till date, only 32 mutations of SUOX gene have been identified and reported to be associated with ISOD.

Burn Pit Exposure Is Associated With Increased Sinonasal Disease.

Objective: The aim of this study was to determine whether self-reported burn pit exposure is associated with increased subjective and objective sinus disease.

Design: A cross-sectional study was performed evaluating consecutive adult patients presenting to a US Military rhinology clinic. Demographics, medical histories, sinonasal quality-of-life scores, and nasal endoscopy examinations were obtained.

The long noncoding RNA Malat1 regulates CD8+ T cell differentiation by mediating epigenetic repression.

During an immune response to microbial infection, CD8+ T cells give rise to short-lived effector cells and memory cells that provide sustained protection. Although the transcriptional programs regulating CD8+ T cell differentiation have been extensively characterized, the role of long noncoding RNAs (lncRNAs) in this process remains poorly understood. Using a functional genetic knockdown screen, we identified the lncRNA Malat1 as a regulator of terminal effector cells and the terminal effector memory (t-TEM) circulating memory subset.

ADAR1-mediated RNA editing links ganglioside catabolism to glioblastoma stem cell maintenance.

Glioblastoma (GBM) is the most common and lethal primary malignant brain tumor, containing GBM stem cells (GSCs) that contribute to therapeutic resistance and relapse. Exposing potential GSC vulnerabilities may provide therapeutic strategies against GBM. Here, we interrogated the role of adenosine-to-inosine (A-to-I) RNA editing mediated by adenosine deaminase acting on RNA 1 (ADAR1) in GSCs and found that both ADAR1 and global RNA editomes were elevated in GSCs compared with normal neural stem cells.

SmProt: A Reliable Repository with Comprehensive Annotation of Small Proteins Identified from Ribosome Profiling.

Small proteins specifically refer to proteins consisting of less than 100 amino acids translated from small open reading frames (sORFs), which were usually missed in previous genome annotation. The significance of small proteins has been revealed in current years, along with the discovery of their diverse functions. However, systematic annotation of small proteins is still insufficient.