Posterior Pedicle Screw Fixation With Indirect Decompression Versus Direct Decompression in Treating Thoracolumbar Burst Fracture: A Systematic Review and Meta-Analysis.

OBJECTIVE: To compare the safety and efficacy between posterior pedicle screw fixation with direct versus indirect decompression in treating patients with thoracolumbar burst fracture. METHODS: This study was conducted on the basis of PRISMA statement. We systematically searched the PubMed and Embase databases up to July 3, 2023. Relevant studies comparing indirect decompression and direct decompression were recruited. Weighted mean differences (WMDs), odds ratios (ORs) and 95% confidence intervals (CIs) were analyzed for continuous and dichotomous data, respectively. P < 0.05 was considered statistically significant. RESULTS: The operation time (WMD: -37.14, 95% CI: [-42.64, 31.64], P < 0.00001, I2 = 0%) and intraoperative blood loss (WMD: -316.82, 95% CI: [-469.80, -163.85], P < 0.0001, I2 = 99%) of indirect decompression group were significantly lower. Percentage of anterior vertebral body height (WMD: 3.98, 95% CI: [2.36, 5.60], P < 0.00001, I2 = 32%) and encroachment rate of the spinal canal (WMD: 1.48, 95% CI: [0.56, 2.40], P = 0.002, I2 = 35%) of indirect decompression group were significantly higher. No statistical difference was identified in grades of neurologic recovery and Cobb angle. CONCLUSIONS: Posterior pedicle screw fixation with indirect decompression was safe and effective for thoracolumbar burst fracture with or without neurologic deficits when posterior longitudinal ligament was intact.

Anterior, Posterior and Anterior-Posterior Approaches for the Treatment of Thoracolumbar Burst Fractures: A Network Meta-Analysis of Randomized Controlled Trials.

PURPOSE: To compare the clinical and radiological results of the anterior approach versus the posterior approach versus the anterior-posterior approach for the treatment of thoracolumbar burst fractures. METHODS: The network meta-analysis was performed in accordance with the PRISMA Statement. Electronic searches of PubMed and Embase were conducted up to June 22, 2023, for relevant randomized controlled trials. STATA13.0 was used to perform network meta-analysis. p < .05 was considered significant. RESULTS: Nine RCTs with a total of 550 patients receiving surgical treatment in at least two of the three approaches, including anterior, posterior and anterior-posterior approaches, were included. The surgical duration and intraoperative bleeding volume in the posterior approach were significantly lower than those in the anterior (SMD, -1.72; 95% CI, -2.82, -0.62) and anterior-posterior approaches (SMD, 3.33; 95% CI, 1.65, 5.00). The surgical duration in the anterior approach was significantly lower than that in the anterior-posterior approach (SMD, 1.61; 95% CI, 0.12, 3.10). The Cobb angle in the anterior-posterior approach was significantly lower than that in the anterior approach (MD, -4.83; 95% CI, -9.60, -0.05). The VAS score in the posterior approach was significantly higher than that in the anterior approach (MD, 0.85; 95% CI, 0.55, 1.16) and anterior-posterior approach (MD, -0.84; 95% CI, -1.12, -0.55). No significant difference was identified among the three surgical approaches in implant failure rate and infection rate. CONCLUSION: All three approaches were safe approaches with advantages and disadvantages. The selection of surgical approaches for the treatment of thoracolumbar burst fractures may be individualized.

Modic Changes Increase the Cage Subsidence Rate in Spinal Interbody Fusion Surgery: A Systematic Review and Network Meta-Analysis.

OBJECTIVE: To compare the effect of different Modic changes (MC) grades on the cage subsidence rate after spinal interbody fusion surgery. METHODS: We comprehensively searched the PubMed, Embase, and Web of Science databases from inception to August 13, 2023, for relevant randomized controlled trials and prospective and retrospective cohort studies. Review Manager 5.3 and STATA13.0 were used to conduct this meta-analysis. The subsidence rate was assessed using relative risk and 95% confidence intervals. RESULTS: Six studies with a total of 716 segments were allocated to four groups according to the type of MC. The subsidence rate in the non-Modic changes (NMC) was significantly lower than that in the MC. The subsidence rate in the NMC was significantly lower than that in the MC in the subgroup of cages with extra instrumentation. No significant difference was identified between the 2 groups in the oblique lumbar interbody fusion subgroup. The subsidence rate in the NMC was significantly lower than that in the MC in the transforaminal lumbar interbody fusion subgroup. The subsidence rate in the NMC was significantly lower than that in the MC1 and MC2. We found no significant difference between NMC and MC3, MC1 and MC2, MC1 and MC3, or MC2 and MC3. CONCLUSIONS: MC may be associated with a higher cage subsidence rate. With the increase in MC grades, the incidence of subsidence decreased gradually, but it was always higher than that in the NMC. Oblique lumbar interbody fusion may be a better choice for the treatment of lumbar degenerative disease with MC.

Comparison of Lumbar Interbody Fusion with 3D-Printed Porous Titanium Cage Versus Polyetheretherketone Cage in Treating Lumbar Degenerative Disease: A Systematic Review and Meta-Analysis.

OBJECTIVE: To compare the safety and radiological effectiveness of lumbar interbody fusion with a 3D-printed porous titanium (3D-PPT) cage versus a polyetheretherketone (PEEK) cage for the treatment of lumbar degenerative disease. METHODS: This study was registered at PROSPERO (CRD42023461511). We systematically searched the PubMed, Embase, and Web of Science databases for related studies from inception to September 3, 2023. Review Manager 5.3 was used to conduct this meta-analysis. The reoperation rate, complication rate, fusion rate, and subsidence rate were assessed using relative risk and 95% confidence intervals. RESULTS: Ten articles reporting 9 studies comparing lumbar interbody fusion with 3D-PPT cages versus PEEK cages for the treatment of lumbar degenerative disease were included. The subsidence rate at the 1-year follow-up in the 3D-PPT cage was significantly lower than that in the PEEK cage. The fusion rate in the 3D-PPT cage was significantly higher than that in the PEEK cage at the 6-month follow-up. No significant difference was identified between the 2 groups at the 12-month follow-up. No significant difference was identified between the 2 groups in terms of the complication rate and reoperation rate. There was a trend toward a lower complication rate and reoperation rate with the 3D-PPT cage. CONCLUSIONS: Compared with the PEEK cage, the 3D-PPT cage may be a safer implant. The 3D-PPT cage was associated with a higher fusion rate and lower subsidence rate. The 3D-PPT cage may accelerate the intervertebral fusion process, improve the quality of fusion and prevent the occurrence of subsidence.

Splicing factor TRA2A contributes to esophageal cancer progression via a noncanonical role in lncRNA m6 A methylation.

Transformer 2 alpha homolog (TRA2A), a member of the serine/arginine-rich splicing factor family, has been shown to control mRNA splicing in development and cancers. However, it remains unclear whether TRA2A is involved in lncRNA regulation. In the present study, we found that TRA2A was upregulated and correlated with poor prognosis in esophageal cancer. Downregulation of TRA2A suppressed the tumor growth in xenograft nude mice. Epitranscriptomic microarray showed that depletion of TRA2A affected global lncRNA methylation similarly to the key m6 A methyltransferase, METTL3, by silencing. MeRIP-qPCR, RNA pull-down, CLIP analyses, and stability assays indicated that ablation of TRA2A reduced m6 A-modification of the oncogenic lncRNA MALAT1, thus inducing structural alterations and reduced stability. Furthermore, Co-IP experiments showed TRA2A directly interacted with METTL3 and RBMX, which also affected the writer KIAA1429 expression. Knockdown of TRA2A inhibited cell proliferation in a manner restored by RBMX/KIAA1429 overexpression. Clinically, MALAT1, RBMX, and KIAA1429 were prognostic factors of worse survival in ESCA patients. Structural similarity-based virtual screening in FDA-approved drugs repurposed nebivolol, a ß1 -adrenergic receptor antagonist, as a potent compound to suppress the proliferation of esophageal cancer cells. Cellular thermal shift and RIP assay indicated that nebivolol may compete with MALAT1 to bind TRA2A. In conclusion, our study revealed the noncanonical function of TRA2A, which coordinates with multiple methylation proteins to promote oncogenic MALAT1 during ESCA carcinogenesis.

fRNC: Uncovering the dynamic and condition-specific RBP-ncRNA circuits from multi-omics data.

The RNA binding protein (RBP) and non-coding RNA (ncRNA) interacting networks are increasingly recognized as the main mechanism in gene regulation, and are tightly associated with cellular malfunction and disease. Here, we present fRNC, a systems biology tool to uncover the dynamic spectrum of RBP-ncRNA circuits (RNC) by integrating transcriptomics, interactomics and proteomics data. fRNC constructs the RBP-ncRNA network derived from CLIP-seq or PARE experiments. Given scoring on nodes and edges according to differential analysis of expression data, it finds an RNC containing global maximum significant RBPs and ncRNAs. Alternatively, it can also capture the locally maximum scoring RNC according to user-defined starting nodes with the greedy search. When compared with existing tools, fRNC can detect more accurate and robust sub-network with scalability. As shown in the cases of esophageal carcinoma, breast cancer and Alzheimer's disease, fRNC enables users to analyze the collective behaviors between RBP and the interacting ncRNAs, and reveal novel insights into the disease-associated processes. The fRNC R package is available at https://github.com/BioinformaticsSTU/fRNC.

Study on SAW Methane Sensor Based on Cryptophane-A Composite Film.

Surface Acoustic Wave (SAW) methane-sensing technology is a new way to detect methane at room temperature. However, the material and structure of the sensitive film are the important factors affecting the detection performance of the sensor. In this paper-with a SAW methane sensor using graphene-nickel cavitation-a composite film is proposed, which can work at room temperature. A delay linear dual-channel differential oscillator with center frequency of 204.3 MHz and insertion loss of -5.658 dB was designed; Cryptophane-A material was prepared by the "three-step method". The composite sensitive film was synthesized by a drop coating method, electrochemical deposition method and electroplating method. The composite film was characterized by SEM. The sensor performance test system and gas sensitivity test system were constructed to determine the response performance of the sensor at concentrations of 0~5% CH4. The results showed that the sensor had a good response recovery performance in the test concentration range, and the frequency offset was positively correlated with methane concentration. The 90% average response time and recovery times were 41.2 s and 57 s, respectively. The sensor sensitivity was 809.4 ± 6.93 Hz/(1% CH4). This study provides a good theoretical basis for the development of surface acoustic-wave methane sensors.

CRIT: Identifying RNA-binding protein regulator in circRNA life cycle via non-negative matrix factorization.

Circular RNAs (circRNAs) are endogenous non-coding RNAs that regulate gene expression and participate in carcinogenesis. However, the RNA-binding proteins (RBPs) involved in circRNAs biogenesis and modulation remain largely unclear. We developed the circRNA regulator identification tool (CRIT), a non-negative matrix-factorization-based pipeline to identify regulating RBPs in cancers. CRIT uncovered 73 novel regulators across thousands of samples by effectively leveraging genomics data and functional annotations. We demonstrated that known RBPs involved in circRNA control are significantly enriched in these predictions. Analysis of circRNA-RBP interactions using two large cross-linking immunoprecipitation (CLIP) databases, we validated the consistency between CRIT prediction and the CLIP experiments. Furthermore, newly discovered RBPs are functionally connected with authentic circRNA regulators by various biological associations, such as physical interaction, similar binding motifs, common transcription factor modulation, and co-expression. When analyzing RNA sequencing (RNA-seq) datasets after short hairpin RNA (shRNA)/small interfering RNA (siRNA) knockdown, we found several novel RBPs that can affect global circRNA expression, which strengthens their role in the circRNA life cycle. The above evidence provided independent confirmation that CRIT is a useful tool to capture RBPs in circRNA processing. Finally, we show that authentic regulators are more likely the core splicing proteins and peripheral factors and usually harbor more alterations in the vast majority of cancers.

Simulation Study of FEUDT Structure Optimization and Sensitive Film Loading of SAW Devices.

In order to further improve the degree of frequency response of the surface acoustic wave (SAW) sensor for gas detection, the structure of the forked-finger transducer was analyzed, and its optimal structural parameters were simulated and designed. The simulation model of the unidirectional fork-finger transducer is established by using COMSOL finite element software. The thickness of the piezoelectric substrate, the electrode structure and material, and the thickness of the coating film are optimized and simulated. The results show that: the optimal thickness of the piezoelectric substrate is 3λ. The optimal thickness ratio and the lay-up ratio of the forked-finger electrode are 0.02 and 0.5, respectively. The Al electrode is more suitable as the a forked-finger electrode material compared to Cu, Au and Pt materials. Under the same conditions, the metal oxide-sensitive film (ZnO and TiO2) has a higher frequency response than the polymer-sensitive film (polyisobutylene and polystyrene), and the best sensitive film thickness range is 0.5~1 µm.

Computational Drug Repurposing Based on a Recommendation System and Drug-Drug Functional Pathway Similarity.

Drug repurposing identifies new clinical indications for existing drugs. It can be used to overcome common problems associated with cancers, such as heterogeneity and resistance to established therapies, by rapidly adapting known drugs for new treatment. In this study, we utilized a recommendation system learning model to prioritize candidate cancer drugs. We designed a drug-drug pathway functional similarity by integrating multiple genetic and epigenetic alterations such as gene expression, copy number variation (CNV), and DNA methylation. When compared with other similarities, such as SMILES chemical structures and drug targets based on the protein-protein interaction network, our approach provided better interpretable models capturing drug response mechanisms. Furthermore, our approach can achieve comparable accuracy when evaluated with other learning models based on large public datasets (CCLE and GDSC). A case study about the Erlotinib and OSI-906 (Linsitinib) indicated that they have a synergistic effect to reduce the growth rate of tumors, which is an alternative targeted therapy option for patients. Taken together, our computational method characterized drug response from the viewpoint of a multi-omics pathway and systematically predicted candidate cancer drugs with similar therapeutic effects.

Characterizing the tumor RBP-ncRNA circuits by integrating transcriptomics, interactomics and clinical data.

The interactions among non-coding RNA (ncRNA) and RNA binding protein (RBP) are increasingly recognized as one of basic mechanisms in gene regulation, and play a crucial role in cancer progressions. However, the current understanding of this regulation network, especially its dynamic spectrum according to the differentially expressed nodes (i.e. ncRNAs and RBP) is limited. Utilizing transcriptomics and interactomics resources, dysregulated RBP-ncRNA circuits (RNCs) are systematically dissected across 14 tumor types. We found these aberrant RNCs are robust and enriched with cancer-associated ncRNAs, RBPs and drug targets. Notably, the nodes in altered RNCs can jointly predict the clinical outcome while the individual node can't, underscoring RNCs can serve as prognostic biomarkers. We identified 30 pan-cancer RNCs dysregulated at least in six tumor types. Pan-cancer RNC analysis can reveal novel mechanism of action (MOA) and repurpose for existing drugs. Importantly, our experiments elucidated the novel role of hsa-miR-224-5p, a member of the pan-cancer RNC hsa-miR-224-5p_MAGI2-AS3_MBNL2, in EMT program. Our analysis highlights the potential utilities of RNCs in elucidating ncRNA function in cancer, associating with clinical outcomes and discovering novel drug targets or MOA.

Mechanism of Modified Danggui Sini Decoction for Knee Osteoarthritis Based on Network Pharmacology and Molecular Docking.

OBJECTIVE: This study aimed to explore the mechanism of Modified Danggui Sini Decoction in the treatment of knee osteoarthritis via a combination of network pharmacology and molecular docking. METHODS: The main chemical components and corresponding targets of Modified Danggui Sini Decoction were searched and screened in TCMSP database. The disease targets of knee osteoarthritis were summarized in GeneCards, OMIM, PharmGkb, TTD, and DrugBank databases. The visual interactive network of "drugs-active components-disease targets" was drawn by Cytoscape 3.8.1 software. The protein-protein interaction network was constructed by STRING database. Then, GO function and KEGG pathway enrichment were analyzed by Bioconductor/R, and the pathway of the highest degree of correlation with knee osteoarthritis was selected for specific analysis. Finally, molecular docking was used to screen and verify core genes by AutoDockTools software. RESULTS: Seventy-one main components of Modified Danggui Sini Decoction and 116 potential therapeutic targets of knee osteoarthritis were selected. The KEGG pathway and the GO function enrichment analysis showed that the targets of Modified Danggui Sini Decoction in the treatment of knee osteoarthritis were mainly concentrated on PI3K-Akt signaling pathway, TNF signaling pathway, IL-17 signaling pathway, apoptosis signaling pathway, Toll-like receptor signaling pathway, Th17 cell differentiation signaling pathway, HIF-1 signaling pathway, and NF-κB signaling pathway. It mainly involved inflammatory reaction, regulation of apoptotic signaling pathway, cellular response to regulation of inflammatory response, cellular response to oxidative stress, and other biological processes. The molecular docking results showed that ESR1-wogonin, MAPK1-quercetin, RELA-wogonin, RELA-baicalein, TP53-baicalein, TP53-quercetin, and RELA-quercetin have strong docking activities. CONCLUSION: Modified Danggui Sini Decoction has the hierarchical network characteristics of "multicomponent, multitarget, multifunction, and multipathway" in the treatment of knee osteoarthritis. It mainly regulates the proliferation and apoptosis of chondrocytes by regulating the PI3K-Akt signaling pathway and establishes cross-talk with many downstream inflammatory-related pathways to reduce the overall inflammatory response. Meanwhile, HIF-1 expression was used to ensure the normal function and metabolism of knee joint under hypoxia condition, and the above processes play a key role in the treatment of knee osteoarthritis.

Hyperbaric oxygen therapy for spinal cord injury: A protocol for systematic review and meta-analysis.

BACKGROUND: Hyperbaric oxygen (HBO) therapy can prevent further spinal cord injury (SCI) caused by spinal cord ischemia-reperfusion injury to the maximum extent, which has been reported increasingly in recent years. However its security and effectiveness still lack of high-quality medical evidence. In this study, we will perform a systematic review of previously published randomized controlled trials (RCTs) to evaluate the efficacy and safety of HBO therapy for SCI. METHODS: All potential RCTs on HBO therapy for SCI will be searched from the following electronic databases: PubMed, Embase, Cochrane Library, Web of Science, China National Knowledge Infrastructure, Chinese Science and Technology Periodical Database, Wanfang database and Chinese Biomedical Literature Database. We will search all electronic databases from their initiation to the September 30, 2020 in spite of language and publication date. Two contributors will independently select studies from all searched literatures, extract data from included trials, and evaluate study quality for all eligible RCTs using Cochrane risk of bias tool, respectively. Any confusion will be resolved by consulting contributor and a consensus will be reached. We will utilize RevMan 5.3 software to pool the data and to conduct the data analysis. RESULTS: The quality of the assessments will be assessed through Grading of Recommendations Assessment, Development, and Evaluation. Data will be disseminated through publications in peer-reviewed journals. CONCLUSION: This study will provide evidence to evaluate the efficacy and safety of HBO therapy for SCI at evidence-based medicine level. TRIAL REGISTRATION NUMBER: INPLASY 2020100084.

Prognostic Value of Genes and Immune Infiltration in Prostate Tumor Microenvironment.

BACKGROUND: Prostate cancer (PCa) is one of the most common cancers and the fifth leading cause of cancer-related death in men. Immune responses in the tumor microenvironment are hypothesized to be related to the prognosis of PCa patients; however, no studies are available to confirm the same. In this study, we aimed to explore the potential link between these two factors and identify new biomarkers to estimate the survival rate of PCa patients. METHODS: A total of 490 cases were obtained from The Cancer Genome Atlas (TCGA) database. The gene expression data were analyzed by the ESTIMATE algorithm to evaluate the immune and stromal scores. The survival rate was calculated according to the case-specific clinical data. Enrichment analysis was performed to discover the main biological processes and signaling pathways of immune responses. We further identified and analyzed hub genes in the protein-protein interaction (PPI) network and evaluated their prognostic values. RESULTS: Immune score significantly correlated with immune cell infiltration and overall survival of PCa patients. The genes CXCR4 and GPR183, identified as hub genes in the PPI network, correlated with immune cell infiltration and prognosis of PCa patients. CONCLUSION: CXCR4 and GPR183 participate in immune cell infiltration and function in PCa patients. The immune score, as well as the expression of CXCR4 and GPR183 in prostate cancer tissues, could be potential indexes for the prognosis of prostate cancer.

Extracorporeal shockwave therapy combined with multiple drilling and intramedullary drug injection for treating early-stage Femur Head Necrosis: Protocol for a randomized controlled trial.

BACKGROUND: Early diagnosis and treatment of the osteonecrosis of the femoral head (ONFH), a refractory disease, is imperative to prevent femoral head collapse; however, the existing solutions remain controversial. This study assessed the safety and efficacy of extracorporeal shock wave therapy (ESWT) combined with multiple drilling and intramedullary drug injection, a novel cocktail therapy, as a randomized controlled trial (RCT) model to postulate an alternative therapy for patients with early-stage ONFH. METHODS: Femoral head necrosis patients aged 20 to 60 years with stage ARCO I-II were recruited. One hundred twenty eligible participants were randomized into four groups in a 1:1:1:1 ratio: extracorporeal shock wave therapy combined with multiple drilling and intramedullary drug injection (group EMI), extracorporeal shock wave therapy (group E), multiple drilling combined with intramedullary drug injection (group MI), and multiple drilling ("positive" control group; group M). The primary outcomes included effective rate, subchondral collapse rate of the femoral head, lesion size, and grade of bone marrow edema. Secondary outcomes included the Harris Hip Score and the visual analog scale. All outcomes were measured at the screening visit (baseline) and at the planned time intervals during treatment and follow-up, and the efficacy was statistically analyzed according to the intention-to-treat sub-populations and per-protocol sub-populations. OBJECTIVES: To examine the clinical efficacy of ESWT combined with multiple drilling and intramedullary drug injection to provide a safe and more effective method for treating early-stage ONFH. TRIAL REGISTRATION NUMBER: ChiCTR1900020888; Pre-results.

Comparison of the perioperative parameters between computer navigation and fluoroscopy guidance for pedicle screw placement: A protocol for a systematic review and meta-analysis.

BACKGROUND: Computer navigation technology is gradually applied to the placement of pedicle screws, but its security and effectiveness still lack of high-quality evidence-based medical evidence. In this study, we will perform a systematic review of previously published randomized controlled trials to investigate the accuracy and effectiveness of computer navigation vsersus fluoroscopy guidance for pedicle screw placement. METHODS: All study protocols adhered to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines. PubMed (MEDLINE), The excerpta medica database, Web of Science (science and social science citation index), The Cochrane Library (Cochrane Database of Systematic Reviews, Cochrane Central Register of Controlled Trials (CENTRAL), Cochrane Methodology Register), China National Knowledge Infrastructure, Chinese Science and Technology Periodical Database, WanFang, Chinese Biomedical Literature Database will be searched for relevant articles up to 18 April, 2020. We will include randomized controlled trials of computer navigation and fluoroscopy guidance for pedicle screw placement. The Cochrane Handbook (v6) will be used for assessment of study bias and reliability, and a meta-analysis will be performed using STATA 16.0. The main outcome will be the proportion of accurate implanted screws. Additional outcomes including: overall complication rate, radiation dosage, length of surgery, length of stay, estimated blood loss. RESULTS: The quality of the assessments will be assessed through Grading of Recommendations Assessment, Development, and Evaluation. Data will be disseminated through publications in peer-reviewed journals. CONCLUSION: We will evaluate the accuracy and other perioperative parameters between computer navigation and fluoroscopy guidance for pedicle screw placement. TRIAL REGISTRATION NUMBER: PROSPERO 2020 CRD42020172087.

TGStools: A Bioinformatics Suit to Facilitate Transcriptome Analysis of Long Reads from Third Generation Sequencing Platform.

Recent analyses show that transcriptome sequencing can be utilized as a diagnostic tool for rare Mendelian diseases. The third generation sequencing de novo detects long reads of thousands of base pairs, thus greatly expanding the isoform discovery and identification of novel long noncoding RNAs. In this study, we developed TGStools, a bioinformatics suite to facilitate routine tasks such as characterizing full-length transcripts, detecting shifted types of alternative splicing, and long noncoding RNAs (lncRNAs) identification in transcriptome analysis. It also prioritizes the transcripts with a visualization framework that automatically integrates rich annotation with known genomic features. TGStools is a Python package freely available at Github.

Identification of transcription factor-miRNA-lncRNA feed-forward loops in breast cancer subtypes.

Previous studies have demonstrated that transcription factor-miRNA-gene feed-forward loops (FFLs) played important roles in tumorigenesis. However, the lncRNA-involved FFLs have not been explored very well. Understanding the characteristics of lncRNA-involved FFLs in breast cancer subtypes may be a key question with clinical implications. In this study, we firstly constructed an integrated background regulatory network. Then, based on mRNA, miRNA, and lncRNA differential expression, we identified 147, 140, 284, 1031 dysregulated FFLs for luminal A, luminal B, HER2+ and basal-like subtype of breast cancer, respectively. Importantly, the known breast cancer-associated lncRNAs and miRNAs were enriched in the identified dysregulated FFLs. Through merging the dysregulated FFLs, we constructed the regulatory sub-network for each subtype. We found that all sub-networks were enriched in the well-known cancer-related pathways, such as cell cycle, pathways in cancer. Next, we also identified potential prognostic FFLs for subtypes of breast cancer, such as the hsa-miR-182-5p_JUN_XIST in basal-like subtype. Finally, we also discussed the potential application of inferring the candidate drugs for breast cancer treatment through modulating the lncRNA expression in the dysregulated FFLs. Collectively, this study elucidated the roles of lncRNA-involved FFLs in breast cancer subtypes, which could contribute to understanding breast cancer pathogenesis and improving the treatment.

Long non-coding RNA cartilage injury-related promotes malignancy in bladder cancer.

Recent advances have highlighted the important roles of long non-coding RNAs (lncRNAs) in a number of biological processes, including oncogenesis. However, the function of lncRNA cartilage injury-related (lncRNA-CIR) in bladder cancer progression remains elusive. A novel function for lncRNA-CIR in bladder cancer was identified in the present study. Reverse transcription quantitative polymerase chain reaction, viability, invasion assay and in vivo implantation were used to evaluate the role of lncRNA-CIR. It was identified that the expression of lncRNA-CIR was frequently upregulated in 52 cancerous tissues and selected bladder cancer cell lines. Additionally, upregulating lncRNA-CIR was demonstrated to promote viability and invasion in T24 and SW780 cells, whereas siRNA-mediated lncRNA-CIR-knockdown consistently exhibited the opposite effects. High lncRNA-CIR levels also dictated poor overall survival among patients with bladder cancer. Furthermore, in vivo implantation experiments also supported a tumorigenic function for lncRNA-CIR, as decreasing lncRNA-CIR levels markedly attenuated Ki-67 staining and xenograft tumor growth. Overall, the present study identified a novel function of lncRNA-CIR and indicates that lncRNA-CIR may serve as a potential biomarker for bladder cancer treatment.

Systematical analysis of lncRNA-mRNA competing endogenous RNA network in breast cancer subtypes.

BACKGROUND: Breast cancer is one of the most common solid tumors in women involving multiple subtypes. However, the mechanism for subtypes of breast cancer is still complicated and unclear. Recently, several studies indicated that long non-coding RNAs (lncRNAs) could act as sponges to compete miRNAs with mRNAs, participating in various biological processes. METHODS: We concentrated on the competing interactions between lncRNAs and mRNAs in four subtypes of breast cancer (basal-like, HER2+, luminal A and luminal B), and analyzed the impacts of competing endogenous RNAs (ceRNAs) on each subtype systematically. We constructed four breast cancer subtype-related lncRNA-mRNA ceRNA networks by integrating the miRNA target information and the expression data of lncRNAs, miRNAs and mRNAs. RESULTS: We constructed the ceRNA network for each breast cancer subtype. Functional analysis revealed that the subtype-related ceRNA networks were enriched in cancer-related pathways in KEGG, such as pathways in cancer, miRNAs in cancer, and PI3k-Akt signaling pathway. In addition, we found three common lncRNAs across the four subtype-related ceRNA networks, NEAT1, OPI5-AS1 and AC008124.1, which played specific roles in each subtype through competing with diverse mRNAs. Finally, the potential drugs for treatment of basal-like subtype could be predicted through reversing the differentially expressed lncRNA in the ceRNA network. CONCLUSION: This study provided a novel perspective of lncRNA-involved ceRNA network to dissect the molecular mechanism for breast cancer.