Nomogram prediction of vessels encapsulating tumor clusters in small hepatocellular carcinoma ≤ 3 cm based on enhanced magnetic resonance imaging.

BACKGROUND: Vessels encapsulating tumor clusters (VETC) represent a recently discovered vascular pattern associated with novel metastasis mechanisms in hepatocellular carcinoma (HCC). However, it seems that no one have focused on predicting VETC status in small HCC (sHCC). This study aimed to develop a new nomogram for predicting VETC positivity using preoperative clinical data and image features in sHCC (≤ 3 cm) patients. AIM: To construct a nomogram that combines preoperative clinical parameters and image features to predict patterns of VETC and evaluate the prognosis of sHCC patients. METHODS: A total of 309 patients with sHCC, who underwent segmental resection and had their VETC status confirmed, were included in the study. These patients were recruited from three different hospitals: Hospital 1 contributed 177 patients for the training set, Hospital 2 provided 78 patients for the test set, and Hospital 3 provided 54 patients for the validation set. Independent predictors of VETC were identified through univariate and multivariate logistic analyses. These independent predictors were then used to construct a VETC prediction model for sHCC. The model's performance was evaluated using the area under the curve (AUC), calibration curve, and clinical decision curve. Additionally, Kaplan-Meier survival analysis was performed to confirm whether the predicted VETC status by the model is associated with early recurrence, just as it is with the actual VETC status and early recurrence. RESULTS: Alpha-fetoprotein_lg10, carbohydrate antigen 199, irregular shape, non-smooth margin, and arterial peritumoral enhancement were identified as independent predictors of VETC. The model incorporating these predictors demonstrated strong predictive performance. The AUC was 0.811 for the training set, 0.800 for the test set, and 0.791 for the validation set. The calibration curve indicated that the predicted probability was consistent with the actual VETC status in all three sets. Furthermore, the decision curve analysis demonstrated the clinical benefits of our model for patients with sHCC. Finally, early recurrence was more likely to occur in the VETC-positive group compared to the VETC-negative group, regardless of whether considering the actual or predicted VETC status. CONCLUSION: Our novel prediction model demonstrates strong performance in predicting VETC positivity in sHCC (≤ 3 cm) patients, and it holds potential for predicting early recurrence. This model equips clinicians with valuable information to make informed clinical treatment decisions.

Optimizing predictions: improved performance of preoperative gadobenate-enhanced MRI hepatobiliary phase features in predicting vessels encapsulating tumor clusters in hepatocellular carcinoma-a multicenter study.

BACKGROUND: Vessels Encapsulating Tumor Clusters (VETC) are now recognized as independent indicators of recurrence and overall survival in hepatocellular carcinoma (HCC) patients. However, there has been limited investigation into predicting the VETC pattern using hepatobiliary phase (HBP) features from preoperative gadobenate-enhanced MRI. METHODS: This study involved 252 HCC patients with confirmed VETC status from three different hospitals (Hospital 1: training set with 142 patients; Hospital 2: test set with 64 patients; Hospital 3: validation set with 46 patients). Independent predictive factors for VETC status were determined through univariate and multivariate logistic analyses. Subsequently, these factors were used to construct two distinct VETC prediction models. Model 1 included all independent predictive factors, while Model 2 excluded HBP features. The performance of both models was assessed using the Area Under the Curve (AUC), Decision Curve Analysis, and Calibration Curve. Prediction accuracy between the two models was compared using Net Reclassification Improvement (NRI) and Integrated Discriminant Improvement (IDI). RESULTS: CA199, IBIL, shape, peritumoral hyperintensity on HBP, and arterial peritumoral enhancement were independent predictors of VETC. Model 1 showed robust predictive performance, with AUCs of 0.836 (training), 0.811 (test), and 0.802 (validation). Model 2 exhibited moderate performance, with AUCs of 0.813, 0.773, and 0.783 in the respective sets. Calibration and decision curves for both models indicated consistent predictions between predicted and actual VETC, benefiting HCC patients. NRI showed Model 1 increased by 0.326, 0.389, and 0.478 in the training, test, and validation sets compared to Model 2. IDI indicated Model 1 increased by 0.036, 0.028, and 0.025 in the training, test, and validation sets compared to Model 2. CONCLUSION: HBP features from preoperative gadobenate-enhanced MRI can enhance the predictive performance of VETC in HCC.

Validation of Enhancer Regions in Primary Human Neural Progenitor Cells using Capture STARR-seq.

Genome-wide association studies (GWAS) and expression analyses implicate noncoding regulatory regions as harboring risk factors for psychiatric disease, but functional characterization of these regions remains limited. We performed capture STARR-sequencing of over 78,000 candidate regions to identify active enhancers in primary human neural progenitor cells (phNPCs). We selected candidate regions by integrating data from NPCs, prefrontal cortex, developmental timepoints, and GWAS. Over 8,000 regions demonstrated enhancer activity in the phNPCs, and we linked these regions to over 2,200 predicted target genes. These genes are involved in neuronal and psychiatric disease-associated pathways, including dopaminergic synapse, axon guidance, and schizophrenia. We functionally validated a subset of these enhancers using mutation STARR-sequencing and CRISPR deletions, demonstrating the effects of genetic variation on enhancer activity and enhancer deletion on gene expression. Overall, we identified thousands of highly active enhancers and functionally validated a subset of these enhancers, improving our understanding of regulatory networks underlying brain function and disease.

The EN-TEx resource of multi-tissue personal epigenomes & variant-impact models.

Understanding how genetic variants impact molecular phenotypes is a key goal of functional genomics, currently hindered by reliance on a single haploid reference genome. Here, we present the EN-TEx resource of 1,635 open-access datasets from four donors (∼30 tissues × âˆ¼15 assays). The datasets are mapped to matched, diploid genomes with long-read phasing and structural variants, instantiating a catalog of >1 million allele-specific loci. These loci exhibit coordinated activity along haplotypes and are less conserved than corresponding, non-allele-specific ones. Surprisingly, a deep-learning transformer model can predict the allele-specific activity based only on local nucleotide-sequence context, highlighting the importance of transcription-factor-binding motifs particularly sensitive to variants. Furthermore, combining EN-TEx with existing genome annotations reveals strong associations between allele-specific and GWAS loci. It also enables models for transferring known eQTLs to difficult-to-profile tissues (e.g., from skin to heart). Overall, EN-TEx provides rich data and generalizable models for more accurate personal functional genomics.

Propofol mediates bone metastasis by regulating PC-derived exosomal miR-142-3p.

In this study we investigated the role of propofol in mediating prostate cancer (PCa) bone metastasis through regulating exosomal factors derived from PCa. We isolated exosomes from PCa cells and co-cultured them with mesenchymal stem cells (MSCs). PCa-derived exosomes increased calcium deposition of MSCs and upregulated ALPL'Alkaline phosphatase, tissue-nonspecific isozyme) and BGLAP (Bone Gamma-Carboxyglutamate Protein) expression. Propofol treatment reduced alkaline phosphatase (ALP) activity, and ALPL and BGLAP expression that was induced by PCa-derived exosomes in MSCs. miRNAs present in cancer cell-derived exosomes increased osteogenesis in these cells. We evaluated miRNA expression in PCa cells after treatment with propofol, and found that miR-142-3p was upregulated in PCa cells. Furthermore, we transfected MSCs with miR-142-3p mimics or inhibitors and revealed that miR-142-3p mimics reduced calcium deposition and downregulated ALP activity, and ALPL and BGLAP levels, while miR-142-3p inhibitors increased calcium deposition and increased ALP activity, and ALPL and BGLAP levels. Finally, we determined that MSCs co-cultured with PCa-derived exosomes and transfected with miR-142-3p mimic exhibited reduced calcium deposition and lower ALP activity, and expression of ALPL and BGLAP. These data demonstrate that propofol inhibits osteogenic differentiation and mineralization of MSCs induced by PCa-derived exosomes by regulation of miR-142-3p levels.

Sestrin2 prevents neonatal incision pain and re-incision enhanced hyperalgesia in adult rats.

BACKGROUND: Improving the methods for recognizing pain is important for infants admitted to the neonatal intensive care unit. Sestrin2 is a novel stress-inducible protein with a neuroprotective role that functions as a molecular mediator of hormesis. Nevertheless, the role of sestrin2 in the pain process is still unclear. The following study examined the role of sestrin2 on mechanical hypersensitivity after pups incision, as well as enhanced pain hyperalgesia after adulthood re-incision in rats. METHODS: The experiment was divided into two parts: (1) studying the effect of sestrin2 in the neonatal incision; (2) studying the priming effect in adulthood re-incision. An animal model was established in seven-day-old rat pups with a right hind paw incision. Pups were intrathecally administrated rh-sestrin2 (exogenous sestrin2). Paw withdrawal threshold testing was performed to assay mechanical allodynia; tissue was analyzed in ex vivo using Western blot and immunofluorescence. SB203580 was further used to inhibit microglial function and evaluate the sex-dependent effect in adulthood. RESULTS: Sestrin2 expression increased transitorily in the spinal dorsal horn in pups after incision. Administration of rh-sestrin2 improved pups' mechanical hypersensitivity by regulating the AMPK/ERK pathway and alleviated re-incision-induced enhanced hyperalgesia in male and female adult rats. After administration of SB203580 in pups, the mechanical hyperalgesia following re-incision in adult rats was prevented in males but not females; however, the protective effect of SB203580 in males was counteracted by silencing sestrin2. CONCLUSIONS: These data suggest that sestrin2 prevents neonatal incision pain and re-incision enhanced hyperalgesia in adult rats. Moreover, microglia inhibition affects enhanced hyperalgesia only in adult males, which may be regulated through the sestrin2 mechanism. To sum up, these sestrin2 data may be a potential common molecular target for treating re-incision hyperalgesia in different sexes.

Analgesic Effect of Ropivacaine Combined with Hydromorphone following Surgery for Mixed Hemorrhoids: A Pilot Study.

BACKGROUND: Postoperative pain is a major adverse effect of surgery for mixed hemorrhoids. We evaluated whether spinal anesthesia with ropivacaine and hydromorphone provided safe and effective analgesia after surgery for mixed hemorrhoids. METHODS: This single-center, double-blind pilot study included patients with mixed hemorrhoids who underwent a procedure for prolapse and hemorrhoids (PPH) and external hemorrhoidectomy under spinal anesthesia at Zhejiang Hospital, China (October 2020 to December 2020). Patients were randomized to a hydromorphone group (spinal anesthesia with 0.5% ropivacaine and 75 µg hydromorphone) or morphine group (spinal anesthesia with 0.5% ropivacaine and 150 µg morphine). Pain scores (numerical rating scale), incidences of vomiting and itching, and length of hospital stay (LoS) were recorded at 6, 12, 18, and 24 hours after surgery. RESULTS: The analysis included 40 patients in each group. Median (interquartile range) pain score in the hydromorphone group was higher than that in the morphine group at 12 hours (1 (0-2] vs. 0 (0-2), p=0.044) but not significantly different between groups at 6 hours (0 (0-1) vs. 0 (0-0) p=0.228), 18 hours (2 (2-3) vs. 2 (1-3) p=0.060) or 24 hours (2 (2-3) vs. 2 (1-3) p=0.081). The hydromorphone group had a lower incidence of pruritus than the morphine group (47.5% vs. 67.5%, p=0.018). There were no significant differences between groups in vomiting incidence or LoS. CONCLUSION: In patients with mixed hemorrhoids, spinal anesthesia with ropivacaine/hydromorphone has a comparable analgesic effect and a lower incidence of pruritus during the first 24 hours after surgery than spinal anesthesia with ropivacaine/morphine.

Supervised enhancer prediction with epigenetic pattern recognition and targeted validation.

Enhancers are important non-coding elements, but they have traditionally been hard to characterize experimentally. The development of massively parallel assays allows the characterization of large numbers of enhancers for the first time. Here, we developed a framework using Drosophila STARR-seq to create shape-matching filters based on meta-profiles of epigenetic features. We integrated these features with supervised machine-learning algorithms to predict enhancers. We further demonstrated that our model could be transferred to predict enhancers in mammals. We comprehensively validated the predictions using a combination of in vivo and in vitro approaches, involving transgenic assays in mice and transduction-based reporter assays in human cell lines (153 enhancers in total). The results confirmed that our model can accurately predict enhancers in different species without re-parameterization. Finally, we examined the transcription factor binding patterns at predicted enhancers versus promoters. We demonstrated that these patterns enable the construction of a secondary model that effectively distinguishes enhancers and promoters.

An integrative ENCODE resource for cancer genomics.

ENCODE comprises thousands of functional genomics datasets, and the encyclopedia covers hundreds of cell types, providing a universal annotation for genome interpretation. However, for particular applications, it may be advantageous to use a customized annotation. Here, we develop such a custom annotation by leveraging advanced assays, such as eCLIP, Hi-C, and whole-genome STARR-seq on a number of data-rich ENCODE cell types. A key aspect of this annotation is comprehensive and experimentally derived networks of both transcription factors and RNA-binding proteins (TFs and RBPs). Cancer, a disease of system-wide dysregulation, is an ideal application for such a network-based annotation. Specifically, for cancer-associated cell types, we put regulators into hierarchies and measure their network change (rewiring) during oncogenesis. We also extensively survey TF-RBP crosstalk, highlighting how SUB1, a previously uncharacterized RBP, drives aberrant tumor expression and amplifies the effect of MYC, a well-known oncogenic TF. Furthermore, we show how our annotation allows us to place oncogenic transformations in the context of a broad cell space; here, many normal-to-tumor transitions move towards a stem-like state, while oncogene knockdowns show an opposing trend. Finally, we organize the resource into a coherent workflow to prioritize key elements and variants, in addition to regulators. We showcase the application of this prioritization to somatic burdening, cancer differential expression and GWAS. Targeted validations of the prioritized regulators, elements and variants using siRNA knockdowns, CRISPR-based editing, and luciferase assays demonstrate the value of the ENCODE resource.

Shaping the nebulous enhancer in the era of high-throughput assays and genome editing.

Since the 1st discovery of transcriptional enhancers in 1981, their textbook definition has remained largely unchanged in the past 37 years. With the emergence of high-throughput assays and genome editing, which are switching the paradigm from bottom-up discovery and testing of individual enhancers to top-down profiling of enhancer activities genome-wide, it has become increasingly evidenced that this classical definition has left substantial gray areas in different aspects. Here we survey a representative set of recent research articles and report the definitions of enhancers they have adopted. The results reveal that a wide spectrum of definitions is used usually without the definition stated explicitly, which could lead to difficulties in data interpretation and downstream analyses. Based on these findings, we discuss the practical implications and suggestions for future studies.

Genomics and data science: an application within an umbrella.

Data science allows the extraction of practical insights from large-scale data. Here, we contextualize it as an umbrella term, encompassing several disparate subdomains. We focus on how genomics fits as a specific application subdomain, in terms of well-known 3 V data and 4 M process frameworks (volume-velocity-variety and measurement-mining-modeling-manipulation, respectively). We further analyze the technical and cultural "exports" and "imports" between genomics and other data-science subdomains (e.g., astronomy). Finally, we discuss how data value, privacy, and ownership are pressing issues for data science applications, in general, and are especially relevant to genomics, due to the persistent nature of DNA.

MicroRNA-dependent regulation of biomechanical genes establishes tissue stiffness homeostasis.

Vertebrate tissues exhibit mechanical homeostasis, showing stable stiffness and tension over time and recovery after changes in mechanical stress. However, the regulatory pathways that mediate these effects are unknown. A comprehensive identification of Argonaute 2-associated microRNAs and mRNAs in endothelial cells identified a network of 122 microRNA families that target 73 mRNAs encoding cytoskeletal, contractile, adhesive and extracellular matrix (CAM) proteins. The level of these microRNAs increased in cells plated on stiff versus soft substrates, consistent with homeostasis, and suppressed targets via microRNA recognition elements within the 3' untranslated regions of CAM mRNAs. Inhibition of DROSHA or Argonaute 2, or disruption of microRNA recognition elements within individual target mRNAs, such as connective tissue growth factor, induced hyper-adhesive, hyper-contractile phenotypes in endothelial and fibroblast cells in vitro, and increased tissue stiffness, contractility and extracellular matrix deposition in the zebrafish fin fold in vivo. Thus, a network of microRNAs buffers CAM expression to mediate tissue mechanical homeostasis.

Comprehensive functional genomic resource and integrative model for the human brain.

Despite progress in defining genetic risk for psychiatric disorders, their molecular mechanisms remain elusive. Addressing this, the PsychENCODE Consortium has generated a comprehensive online resource for the adult brain across 1866 individuals. The PsychENCODE resource contains ~79,000 brain-active enhancers, sets of Hi-C linkages, and topologically associating domains; single-cell expression profiles for many cell types; expression quantitative-trait loci (QTLs); and further QTLs associated with chromatin, splicing, and cell-type proportions. Integration shows that varying cell-type proportions largely account for the cross-population variation in expression (with >88% reconstruction accuracy). It also allows building of a gene regulatory network, linking genome-wide association study variants to genes (e.g., 321 for schizophrenia). We embed this network into an interpretable deep-learning model, which improves disease prediction by ~6-fold versus polygenic risk scores and identifies key genes and pathways in psychiatric disorders.

Dynamic RNA-protein interactions underlie the zebrafish maternal-to-zygotic transition.

During the maternal-to-zygotic transition (MZT), transcriptionally silent embryos rely on post-transcriptional regulation of maternal mRNAs until zygotic genome activation (ZGA). RNA-binding proteins (RBPs) are important regulators of post-transcriptional RNA processing events, yet their identities and functions during developmental transitions in vertebrates remain largely unexplored. Using mRNA interactome capture, we identified 227 RBPs in zebrafish embryos before and during ZGA, hereby named the zebrafish MZT mRNA-bound proteome. This protein constellation consists of many conserved RBPs, some of which are potential stage-specific mRNA interactors that likely reflect the dynamics of RNA-protein interactions during MZT. The enrichment of numerous splicing factors like hnRNP proteins before ZGA was surprising, because maternal mRNAs were found to be fully spliced. To address potentially unique roles of these RBPs in embryogenesis, we focused on Hnrnpa1. iCLIP and subsequent mRNA reporter assays revealed a function for Hnrnpa1 in the regulation of poly(A) tail length and translation of maternal mRNAs through sequence-specific association with 3' UTRs before ZGA. Comparison of iCLIP data from two developmental stages revealed that Hnrnpa1 dissociates from maternal mRNAs at ZGA and instead regulates the nuclear processing of pri-mir-430 transcripts, which we validated experimentally. The shift from cytoplasmic to nuclear RNA targets was accompanied by a dramatic translocation of Hnrnpa1 and other pre-mRNA splicing factors to the nucleus in a transcription-dependent manner. Thus, our study identifies global changes in RNA-protein interactions during vertebrate MZT and shows that Hnrnpa1 RNA-binding activities are spatially and temporally coordinated to regulate RNA metabolism during early development.

MicroRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos.

Proper functioning of an organism requires cells and tissues to behave in uniform, well-organized ways. How this optimum of phenotypes is achieved during the development of vertebrates is unclear. Here, we carried out a multi-faceted and single-cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single and multi-gene microRNA (miRNA) families. We found that embryos lacking particular miRNA-dependent signaling pathways develop a vascular trait similar to wild-type, but with a profound increase in phenotypic heterogeneity. Aberrant trait variance in miRNA mutant embryos uniquely sensitizes their vascular system to environmental perturbations. We discovered a previously unrecognized role for specific vertebrate miRNAs to protect tissue development against phenotypic variability. This discovery marks an important advance in our comprehension of how miRNAs function in the development of higher organisms.