Brain Chimeroids reveal individual susceptibility to neurotoxic triggers.

Interindividual genetic variation affects the susceptibility to and progression of many diseases1,2. However, efforts to study how individual human brains differ in normal development and disease phenotypes are limited by the paucity of faithful cellular human models, and the difficulty of scaling current systems to represent multiple people. Here we present human brain Chimeroids, a highly reproducible, multidonor human brain cortical organoid model generated by the co-development of cells from a panel of individual donors in a single organoid. By reaggregating cells from multiple single-donor organoids at the neural stem cell or neural progenitor cell stage, we generate Chimeroids in which each donor produces all cell lineages of the cerebral cortex, even when using pluripotent stem cell lines with notable growth biases. We used Chimeroids to investigate interindividual variation in the susceptibility to neurotoxic triggers that exhibit high clinical phenotypic variability: ethanol and the antiepileptic drug valproic acid. Individual donors varied in both the penetrance of the effect on target cell types, and the molecular phenotype within each affected cell type. Our results suggest that human genetic background may be an important mediator of neurotoxin susceptibility and introduce Chimeroids as a scalable system for high-throughput investigation of interindividual variation in processes of brain development and disease.

Synaptotagmin-1 is a bidirectional Ca2+ sensor for neuronal endocytosis.

Exocytosis and endocytosis are tightly coupled. In addition to initiating exocytosis, Ca2+ plays critical roles in exocytosis­endocytosis coupling in neurons and nonneuronal cells. Both positive and negative roles of Ca2+ in endocytosis have been reported; however, Ca2+ inhibition in endocytosis remains debatable with unknown mechanisms. Here, we show that synaptotagmin-1 (Syt1), the primary Ca2+ sensor initiating exocytosis, plays bidirectional and opposite roles in exocytosis­endocytosis coupling by promoting slow, small-sized clathrin-mediated endocytosis but inhibiting fast, large-sized bulk endocytosis. Ca2+-binding ability is required for Syt1 to regulate both types of endocytic pathways, the disruption of which leads to inefficient vesicle recycling under mild stimulation and excessive membrane retrieval following intense stimulation. Ca2+-dependent membrane tubulation may explain the opposite endocytic roles of Syt1 and provides a general membrane-remodeling working model for endocytosis determination. Thus, Syt1 is a primary bidirectional Ca2+ sensor facilitating clathrin-mediated endocytosis but clamping bulk endocytosis, probably by manipulating membrane curvature to ensure both efficient and precise coupling of endocytosis to exocytosis.

Salt-Inducing Assembly Polymorphism Strategy for Cytotoxicity Differentiation of Phenol-Soluble Modulin α3 Assemblies.

Phenol-soluble modulin α3 (PSMα3) can self-assemble into fibrous assemblies with a unique "cross-α" sheet structure, which serves as a key virulence factor in the infection of Staphylococcus aureus. However, the structure-cytotoxicity relationships of PSMα3 still remain elusive. Herein, we utilized the strategy of salt-inducing assembly polymorphism to controllably prepare three PSMα3 assemblies with morphological and structural distinctions, including amorphous aggregates (AAs), rigid fibrils (RFs), and oligomers/curvilinear fibrils (OCFs), which provided a convincing method to facilitate the structure-cytotoxicity investigation of PSMα3 assemblies. Our results affirmed that amyloid fibrillation was essential for the enhancement of PSMα3 cytotoxicity, which was proved based on the evidence that RFs and OCFs both triggered more obvious cytotoxicity than AAs. Furthermore, our study also demonstrated that the cytotoxicity was severely dependent on the size and structure of PSMα3 fibrils. In detail, smaller OCFs rich in α-helices exhibited stronger virulence than RFs with larger sizes and low α-helical contents. The cytotoxicity caused by such fibrils was achieved via a membrane-disrupting mechanism, in which RFs and OCFs might be prone to membrane thinning and perforation, respectively. This strategy of salt-inducing PSMα3 assembly polymorphism facilitated the comprehension of the relationship between the characteristics of PSMα3 assemblies and their cytotoxicity and was also helpful to understanding the intrinsic assembly mechanism of the PSMα3.

Pine (Pinus sylvestris L.) bark proanthocyanidins affords prevention of peroxynitrite-induced l-tyrosine nitration, DNA damage and hydroxyl radical formation.

Peroxynitrite is known as a strong deleterious species that may readily trigger several geriatric diseases via injuring cellular constituents. Proanthocyanidins, a biological flavonoids constituent of Pinus sylvestris L. bark, has been attributed a large variety of pharmacological functions to its antioxidant potential. The results revealed that peroxynitrite could cause the generation of hydroxyl radical, the breakage of φX-174 plasmid DNA brand as well as the nitration of L-tyrosine. However, pine (Pinus sylvestris L.) bark proanthocyanidins extracts at low concentration range markedly inhibited the peroxynitrite -induced the formation of open circular DNA form (IC50 = 5.03±0.39 mg/mL). The 3-Nitro-L-tyrosine generated by the reaction of peroxynitrite with L-tyrosine was reduced by PBP (IC50 = 1.01±0.01 mg/mL). Besides, electron spin resonance spectroscopy data indicates that the intensive signal of dimethyl pyridine N-oxide hydroxyl radical adduct from peroxynitrite was reversed by pine bark proanthocyanidins extracts (IC50 =1.02±0.04 mg/mL). Moreover, the obtained data shows that PBP provides more efficient protection against peroxynitrite than that of ascorbic acid. Together, the present study suggests that pine bark proanthocyanidins could exert potent preventive activity against peroxynitrite -elicited cytotoxicity on the biomacromolecules, a study-worthy finding with pharmacological importance.

CylinGCN: Cylindrical structures segmentation in 3D biomedical optical imaging by a contour-based graph convolutional network.

Cylindrical organs, e.g., blood vessels, airways, and intestines, are ubiquitous structures in biomedical optical imaging analysis. Image segmentation of these structures serves as a vital step in tissue physiology analysis. Traditional model-driven segmentation methods seek to fit the structure by constructing a corresponding topological geometry based on domain knowledge. Classification-based deep learning methods neglect the geometric features of the cylindrical structure and therefore cannot ensure the continuity of the segmentation surface. In this paper, by treating the cylindrical structures as a 3D graph, we introduce a novel contour-based graph neural network for 3D cylindrical structure segmentation in biomedical optical imaging. Our proposed method, which we named CylinGCN, adopts a novel learnable framework that extracts semantic features and complex topological relationships in the 3D volumetric data to achieve continuous and effective 3D segmentation. Our CylinGCN consists of a multiscale 3D semantic feature extractor for extracting inter-frame multiscale semantic features, and a residual graph convolutional network (GCN) contour generator that combines the semantic features and cylindrical topological priors to generate segmentation contours. We tested the CylinGCN framework on two types of optical tomographic imaging data, small animal whole body photoacoustic tomography (PAT) and endoscopic airway optical coherence tomography (OCT), and the results show that CylinGCN achieves state-of-the-art performance. Code will be released at https://github.com/lzc-smu/CylinGCN.git.

Mixed Systems of Quaternary Ammonium Foam Drainage Agent with Carbon Quantum Dots and Silica Nanoparticles for Improved Gas Field Performance.

Foam drainage agents enhance gas production by removing wellbore liquids. However, due to the ultra-high salinity environments of the Hechuan gas field (salinity up to 32.5 × 104 mg/L), no foam drainage agent is suitable for this gas field. To address this challenge, we developed a novel nanocomposite foam drainage system composed of quaternary ammonium and two types of nanoparticles. This work describes the design and synthesis of a quaternary ammonium foam drainage agent and nano-engineered stabilizers. Nonylphenol polyoxyethylene ether sulfosuccinate quaternary ammonium foam drainage agent was synthesized using maleic anhydride, sodium chloroacetate, N,N-dimethylpropylenediamine, etc., as precursors. We employed the Stöber method to create hydrophobic silica nanoparticles. Carbon quantum dots were then prepared and functionalized with dodecylamine. Finally, carbon quantum dots were incorporated into the mesopores of silica nanoparticles to enhance stability. Through optimization, the best performance was achieved with a (quaternary ammonium foam drainage agents)-(carbon quantum dots/silica nanoparticles) ratio of 5:1 and a total dosage of 1.1%. Under harsh conditions (salinity 35 × 104 mg/L, condensate oil 250 cm3/m3, temperature 80 °C), the system exhibited excellent stability with an initial foam height of 160 mm, remaining at 110 mm after 5 min. Additionally, it displayed good liquid-carrying capacity (160 mL), low surface tension (27.91 mN/m), and a long half-life (659 s). These results suggest the effectiveness of nanoparticle-enhanced foam drainage systems in overcoming high-salinity challenges. Previous foam drainage agents typically exhibited a salinity resistance of no more than 25 × 104 mg/L. In contrast, this innovative system demonstrates a superior salinity tolerance of up to 35 × 104 mg/L, addressing a significant gap in available agents for high-salinity gas fields. This paves the way for future development of advanced foam systems for gas well applications with high salinity.

Effects of drug-induced liver injury on the in vivo fate of liposomes.

Liposomes represent one of the most extensively studied nano-carriers due to their potential in targeted drug delivery. However, the complex in vivo fate, particularly under pathological conditions, presents challenges for clinical translation of liposomal therapeutics. Liver serves as the most important organ for liposome accumulation and metabolism. Unfortunately, the fate of liposomes under pathological liver conditions has been significantly overlooked. This study aimed to investigate the in vivo pharmacokinetic profile and biodistribution profile of liposomes under drug-induced liver injury (DILI) conditions. Two classic DILI animal models, i.e. acetaminophen-induced acute liver injury (AILI) and triptolide-induced subacute liver injury (TILI), were established to observe the effect of pathological liver conditions on the in vivo performance of liposomes. The study revealed significant changes in the in vivo fate of liposomes following DILI, including prolonged blood circulation and enhanced hepatic accumulation of liposomes. Changes in the composition of plasma proteins and mononuclear phagocyte system (MPS)-related cell subpopulations collectively led to the altered in vivo fate of liposomes under liver injury conditions. Despite liver injury, macrophages remained the primary cells responsible for liposomes uptake in liver, with the recruited monocyte-derived macrophages exhibiting enhanced ability to phagocytose liposomes under pathological conditions. These findings indicated that high capture of liposomes by the recruited hepatic macrophages not only offered potential solutions for targeted delivery, but also warned the clinical application of patients under pathological liver conditions.

Safety, efficacy, and pharmacokinetics of nirmatrelvir and ritonavir in patients with severe COVID-19 and renal impairment: A case report.

Nirmatrelvir/ritonavir (N/r) has received emergency use authorization for mild-to-moderate COVID-19 treatment in adult and pediatric patients (aged and weighing at least 12 years and 40 kg, respectively) presenting positive direct SARS-CoV-2 viral testing results and a high risk of disease progression to severe COVID-19. However, information remains limited concerning the corresponding drug safety, efficacy, and pharmacokinetics in patients with severe renal impairment. In this study, we present the case of a 91-year-old Chinese man who, despite exhibiting recurrent positive SARS-CoV-2 results and progression to severe COVID-19, was treated with N/r. Due to severe renal impairment and concurrent administration of continuous renal replacement therapy (continuous venovenous hemofiltration) during medication, we aimed to determine the serum N/r drug concentration in the patient. Our analysis revealed Cmax values of 12.42 and 2.001 µg/mL for nirmatrelvir and ritonavir, respectively. Despite the particularly high serum N/r concentration in this patient, the clinical and laboratory test analyses confirmed that the treatment was safe and effective. Nevertheless, N/r should be used with caution and at lower doses in patients with severe renal impairment to avoid potential high N/r concentration-related adverse reactions and events.

STED Imaging of Vesicular Endocytosis in the Synapse.

Endocytosis is a fundamental biological process that couples exocytosis to maintain the homeostasis of the plasma membrane and sustained neurotransmission. Super-resolution microscopy enables optical imaging of exocytosis and endocytosis in live cells and makes an essential contribution to understanding molecular mechanisms of endocytosis in neuronal somata and other types of cells. However, visualization of exo-endocytic events at the single vesicular level in a synapse with optical imaging remains a great challenge to reveal mechanisms governing the synaptic exo-endocytotic coupling. In this protocol, we describe the technical details of stimulated emission depletion (STED) imaging of synaptic endocytosis at the single-vesicle level, from sample preparation and microscopy calibration to data acquisition and analysis.

An ACC-VTA-ACC positive-feedback loop mediates the persistence of neuropathic pain and emotional consequences.

The central mechanisms underlying pain chronicity remain elusive. Here, we identify a reciprocal neuronal circuit in mice between the anterior cingulate cortex (ACC) and the ventral tegmental area (VTA) that mediates mutual exacerbation between hyperalgesia and allodynia and their emotional consequences and, thereby, the chronicity of neuropathic pain. ACC glutamatergic neurons (ACCGlu) projecting to the VTA indirectly inhibit dopaminergic neurons (VTADA) by activating local GABAergic interneurons (VTAGABA), and this effect is reinforced after nerve injury. VTADA neurons in turn project to the ACC and synapse to the initial ACCGlu neurons to convey feedback information from emotional changes. Thus, an ACCGlu-VTAGABA-VTADA-ACCGlu positive-feedback loop mediates the progression to and maintenance of persistent pain and comorbid anxiodepressive-like behavior. Disruption of this feedback loop relieves hyperalgesia and anxiodepressive-like behavior in a mouse model of neuropathic pain, both acutely and in the long term.

Evaluation of Lipid Droplet Size and Fusion in Bovine Hepatic Cells.

Lipid droplets (LDs) are organelles that play an important role in lipid metabolism and neutral lipid storage in cells. They are associated with a variety of metabolic diseases, such as obesity, fatty liver disease, and diabetes. In hepatic cells, the sizes and numbers of LDs are signs of fatty liver disease. Moreover, the oxidative stress reaction, cell autophagy, and apoptosis are often accompanied by changes in the sizes and numbers of LDs. As a result, the dimensions and quantity of LDs are the basis of the current research regarding the mechanism of LD biogenesis. Here, in fatty acid-induced bovine hepatic cells, we describe how to use oil red O to stain LDs and to investigate the sizes and numbers of LDs. The size distribution of LDs is statistically analyzed. The process of small LDs fusing into large LDs is also observed by a live cell imaging system. The current work provides a way to directly observe the size change trend of LDs under different physiological conditions.

Prediction of Synaptically Localized RNAs in Human Neurons Using Developmental Brain Gene Expression Data.

In the nervous system, synapses are special and pervasive structures between axonal and dendritic terminals, which facilitate electrical and chemical communications among neurons. Extensive studies have been conducted in mice and rats to explore the RNA pool at synapses and investigate RNA transport, local protein synthesis, and synaptic plasticity. However, owing to the experimental difficulties of studying human synaptic transcriptomes, the full pool of human synaptic RNAs remains largely unclear. We developed a new machine learning method, called PredSynRNA, to predict the synaptic localization of human RNAs. Training instances of dendritically localized RNAs were compiled from previous rodent studies, overcoming the shortage of empirical instances of human synaptic RNAs. Using RNA sequence and gene expression data as features, various models with different learning algorithms were constructed and evaluated. Strikingly, the models using the developmental brain gene expression features achieved superior performance for predicting synaptically localized RNAs. We examined the relevant expression features learned by PredSynRNA and used an independent test dataset to further validate the model performance. PredSynRNA models were then applied to the prediction and prioritization of candidate RNAs localized to human synapses, providing valuable targets for experimental investigations into neuronal mechanisms and brain disorders.

Safety Evaluation of Antituberculosis Drugs During Pregnancy: A Systematic Review and Meta-Analysis.

Background: Pregnant women are a common group of people with tuberculosis,especially in patients infected with HIV at the same time. Antituberculosis drug prophylaxis is effective in reducing tuberculosis infection in pregnant women and fetuses after pregnancy, but its safety is still worthy of in-depth discussion. In this study, we conducted a systematic review and meta-analysis of reports on the use of antituberculosis drugs during pregnancy in recent years to provide evidence for clinical diagnosis and treatment. Methods: The PubMed, Embase, Web of Science databases, Ovid, and clinicaltrials.gov were searched. Search for clinical randomized controlled studies and cohort studies on the use of antituberculosis drugs during pregnancy published in the databases from January 2000 to September 2021 was performed using the Stata 16.0 software after screening qualified bodies of literature. Results: On the basis of the initial search of 408 articles, this study included a total of 8 articles and 2,563 patients after screening; meta-analysis results showed that preventive treatment with antituberculosis drugs did not increase the incidence of serious maternal adverse events [RR = 0.99, 95% CI (.88, 1.12), Z = -0.108, P = 0.914], did not increase drug hepatotoxicity [RR = 1.13, 95% CI (.9, 1.43), Z = 1.071, P = 0.284], did not increase the incidence of peripheral nerve disease [RR = 1.52, 95% CI (.85, 2.71), Z = 1.412, P = 0.158], did not increase maternal mortality [RR = 0.67, 95% CI (.27, 1.7), Z = -0.84, P = 0.401], and could significantly reduce adverse pregnancy outcomes [RR = 0.78, 95% CI (0.68, 0.89), Z = -3.581, P < 0.0001]. Discussion: The use of antituberculosis drugs for preventive treatment during pregnancy is safe and can obtain better pregnancy outcomes.

Sappanwood-derived polyphenolic antidote of amyloidal toxins achieved detoxification via inhibition/reversion of amyloidal fibrillation.

The formidable virulence of methicillin-resistant staphylococcus aureus (MRSA) have thrown great challenges to biomedicine, which mainly derives from their autocrine phenol-soluble modulins (PSMs) toxins, especially the most toxic member termed phenol-soluble modulins α3 (PSMα3). PSMα3 cytotoxicity is attributed to its amyloidal fibrillation and subsequent formation of cross-α sheet fibrils. Inspired by the multiple biological activity of Sappanwood, herein, we adopted brazilin, a natural polyphenolic compound originated from Caesalpinia sappan, as a potential antidote of PSMα3 toxins, and attempted to prove that the regulation of PSMα3 fibrillation was an effective alexipharmic way for MRSA infections. In vitro results revealed that brazilin suppressed PSMα3 fibrillation and disassembled preformed amyloidal fibrils in a dose-dependent manner, in which molar ratio (brazilin: PSMα3) of efficient inhibition and disassembly were both 1:1. These desired regulations dominated by brazilin benefited from its bonding to core fibrils-forming residues of PSMα3 monomers urged by hydrogen bonding and pi-pi stacking, and such binding modes facilitated brazilin-mediated inhibition or disruption of interactions between neighboring PSMα3 monomers. In this context, these inhibited and disassembled PSMα3 assemblies could not easily insert into cell membrane and subsequent penetration, and thus alleviating the membrane disruption, cytoplasmic leakage, and reactive oxygen species (ROS) generation in normal cells. As such, brazilin dramatically decreased the cytotoxicity borne by toxic PSMα3 fibrils. In addition, in vivo experiments affirmed that brazilin relieved the toxicity of PSMα3 toxins and thus promoted the skin wound healing of mice. This study provides a new antidote of PSMα3 toxins, and also confirms the feasibility of the assembly-regulation strategy in development of antidotes against supramolecular fibrillation-dependent toxins.

Traumatic Brain Injury Induces Gastrointestinal Dysfunction and Dysbiosis of Gut Microbiota Accompanied by Alterations of Bile Acid Profile.

Gastrointestinal dysfunction is a common peripheral organ complication after traumatic brain injury (TBI), yet the underlying mechanism remains unknown. TBI has been demonstrated to cause gut microbiota dysbiosis in animal models, although the impacts of gut microbiota dysbiosis on gastrointestinal dysfunction were not examined. Bile acids are key metabolites between gut microbiota and host interactions. Therefore, the aim of this study was to investigate the mechanistic links between them by detecting the alterations of gut microbiota and bile acid profile after TBI. For that, we established TBI in mice using a lateral fluid percussion injury model. Gut microbiota was examined by 16S rRNA sequencing, and bile acids were profiled by ultra-performance liquid chromatography-tandem mass spectrometry. Our results showed that TBI caused intestinal inflammation and gut barrier impairment. Alterations of gut microbiota and bile acid profile were observed. The diversity of gut microbiota experienced a time dependent change from 1 h to 7 days post-injury. Levels of bile acids in feces and plasma were decreased after TBI, and the decrease was more significant in secondary bile acids, which may contribute to intestinal inflammation. Specific bacterial taxa such as Staphylococcus and Lachnospiraceae that may contribute to the bile acid metabolic changes were identifed. In conclusion, our study suggested that TBI-induced gut microbiota dysbiosis may contribute to gastrointestinal dysfunction via altering bile acid profile. Gut microbiota may be a potential treatment target for TBI-induced gastrointestinal dysfunction.

Contribution of Patient Care Technicians to the Prevention of External Ventricular Drain Infection: A Retrospective Study.

ABSTRACT: BACKGROUND: External ventricular drains (EVDs) are commonly used in neurosurgery. Preventing EVD-related infections is important, and nursing plays a significant role in infection control. However, because of the limited number of neurosurgical nurses and heavy workload in developing countries, well-trained patient care technicians (PCTs) might be able to assist nurses under this circumstance. METHODS: This study retrospectively screened patients who underwent EVD procedures in our medical center from January 2012 to June 2018. Clinical characteristics including EVD-related infection rates of patients with or without PCTs were compared. RESULTS: We analyzed 234 patients in total. There were 26 EVD infection cases, and the overall infection rate was 11.1%. There were 122 patients who were given additional care by PCTs. They were elder (58.1 ± 13.1 vs 49.9 ± 17.0 years old, P < .001) and had lower level preoperational Glasgow Coma Scale (7.04 ± 3.66 vs 13.5 ± 2.53, P < .001) and higher intubation rate (28.7% vs 3.6%, P < .001) than those without PCTs. They also had a longer drainage duration (10.3 ± 4.97 vs 8.01 ± 4.35, P < .001) as well as more cerebrospinal fluid sampling times (2.45 ± 2.00 vs 1.75 ± 1.83, P = .006) and were kept at artificial airway status for a longer duration (10.1 ± 18.7 vs 1.93 ± 7.86, P < .001). External ventricular drain-related infection rates were similar between 2 groups (11.5% vs 10.7%, P = .853). CONCLUSION: Patient care technicians with proper training are beneficial to the prevention of EVD-related infection as a measure of improving staffing adequacy.

5-IP7 is a GPCR messenger mediating neural control of synaptotagmin-dependent insulin exocytosis and glucose homeostasis.

5-diphosphoinositol pentakisphosphate (5-IP7) is a signalling metabolite linked to various cellular processes. How extracellular stimuli elicit 5-IP7 signalling remains unclear. Here we show that 5-IP7 in ß cells mediates parasympathetic stimulation of synaptotagmin-7 (Syt7)-dependent insulin release. Mechanistically, vagal stimulation and activation of muscarinic acetylcholine receptors triggers Gαq-PLC-PKC-PKD-dependent signalling and activates IP6K1, the 5-IP7 synthase. Whereas both 5-IP7 and its precursor IP6 compete with PIP2 for binding to Syt7, Ca2+ selectively binds 5-IP7 with high affinity, freeing Syt7 to enable fusion of insulin-containing vesicles with the cell membrane. ß-cell-specific IP6K1 deletion diminishes insulin secretion and glucose clearance elicited by muscarinic stimulation, whereas mice carrying a phosphorylation-mimicking, hyperactive IP6K1 mutant display augmented insulin release, congenital hyperinsulinaemia and obesity. These phenotypes are absent in mice lacking Syt7. Our study proposes a new conceptual framework for inositol pyrophosphate physiology in which 5-IP7 acts as a GPCR second messenger at the interface between peripheral nervous system and metabolic organs, transmitting Gq-coupled GPCR stimulation to unclamp Syt7-dependent, and perhaps other, exocytotic events.

Transcriptomic analysis of long noncoding RNAs and mRNAs expression profiles in the spinal cord of bone cancer pain rats.

Bone cancer pain (BCP) is one of the most common types of chronic cancer pain and its pathogenesis has not been fully understood. Long non-coding RNAs (lncRNAs) are new promising targets in the field of pain research, however, their involvements in BCP have not been reported. In the present study, we established the BCP model by implantation of Walker 256 carcinoma cells into rats' tibial medullary cavity and performed transcriptome sequencing of the ipsilateral lumbar spinal cord to explore changes in expression profiles of lncRNA and mRNA. We identified 1220 differently expressed mRNAs (DEmRNAs) (1171 up-regulated and 49 down-regulated) and 323 differently expressed lncRNAs (DElncRNAs) (246 up-regulated and 77 down-regulated) in BCP model, among which 10 DEmRNAs (5 up-regulated and 5 down-regulated) and 10 DElncRNAs (5 up-regulated and 5 down-regulated) were validated the expression by RT-qPCR. Then, we performed Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis on the expression of DEmRNAs and DElncRNAs, showing that they were mainly enriched in inflammatory and immunologic processes/pathways. Finally, we constructed a co-expression network and a ceRNA network of DEmRNAs and DElncRNAs to exhibit a potential regulatory mechanism of DElncRNAs, directly regulating protein coding gene expression in cis or in trans and indirectly regulating protein coding gene expression by sponging miRNA. In conclusion, our study provided a landscape of dysregulated lncRNA and mRNA in spinal cord of bone cancer pain and detected novel potential targets for treatment in the future.

Genomic data mining for functional annotation of human long noncoding RNAs.

Life may have begun in an RNA world, which is supported by increasing evidence of the vital role that RNAs perform in biological systems. In the human genome, most genes actually do not encode proteins; they are noncoding RNA genes. The largest class of noncoding genes is known as long noncoding RNAs (lncRNAs), which are transcripts greater in length than 200 nucleotides, but with no protein-coding capacity. While some lncRNAs have been demonstrated to be key regulators of gene expression and 3D genome organization, most lncRNAs are still uncharacterized. We thus propose several data mining and machine learning approaches for the functional annotation of human lncRNAs by leveraging the vast amount of data from genetic and genomic studies. Recent results from our studies and those of other groups indicate that genomic data mining can give insights into lncRNA functions and provide valuable information for experimental studies of candidate lncRNAs associated with human disease.