Integrated transcriptomic and metabolomic analysis reveals the effects and potential mechanism of hydrogen peroxide on pigment metabolism in postharvest broccoli.

To understand the effects and related potential mechanism of H2O2 on pigment metabolism in postharvest broccoli, an integrated analysis of transcriptome and metabolome was performed. Results suggested that 65 differentially expressed genes and 26 differentially accumulated metabolites involved in chlorophyll, carotenoid, and flavonoid metabolism were identified. H2O2 treatment delayed the decrease of chlorophyll content by upregulating the expressions of chlorophyll synthetic genes, thylakoid synthetic genes, and 15 light-harvesting complex genes compared with the control and diphenylene iodonium treatments. H2O2 treatment decreased the accumulation of 11 flavonoids and 5 flavonols by downregulating the flavonoid synthetic genes. In addition, H2O2 treatment promoted carotenoid biosynthesis to eliminate reactive oxygen species in thylakoids, thereby protecting chlorophyll molecules from degradation. The inhibition of flavonoids and flavonols accumulation and chlorophyll decrease was the crucial reason for the delayed yellowing in H2O2 treatment. This study provides a new method and theoretical support for delaying the yellowing process in postharvest broccoli.

Multifunctional Biomimetic Nanocarriers for Dual-Targeted Immuno-Gene Therapy Against Hepatocellular Carcinoma.

Growing evidences have proved that tumors evade recognition and attack by the immune system through immune escape mechanisms, and PDL1/Pbrm1 genes have a strong correlation with poor response or resistance to immune checkpoint blockade (ICB) therapy. Herein, a multifunctional biomimetic nanocarrier (siRNA-CaP@PD1-NVs) is developed, which can not only enhance the cytotoxic activity of immune cells by blocking PD1/PDL1 axis, but also reduce tumor immune escape via Pbrm1/PDL1 gene silencing, leading to a significant improvement in tumor immunosuppressive microenvironment. Consequently, the nanocarrier promotes DC cell maturation, enhances the infiltration and activity of CD8+ T cells, and forms long-term immune memory, which can effectively inhibit tumor growth or even eliminate tumors, and prevent tumor recurrence and metastasis. Overall, this study presents a powerful strategy for co-delivery of siRNA drugs, immune adjuvant, and immune checkpoint inhibitors, and holds great promise for improving the effectiveness and safety of current immunotherapy regimens.

CRISPR/Cas12b assisted loop-mediated isothermal amplification for easy, rapid and sensitive quantification of chronic HBV DNA in one-pot.

BACKGROUND: Currently, millions of people suffer from undiagnosed chronic hepatitis B (CHB) infection each year, which leads to high mortality rates attributed to cirrhosis and hepatocellular carcinoma. Previously reported assays, such as PCR-based assays, have limitations in terms of convenient for CHB screening in high-burden regions and resource-limited settings. Recently, diagnosis based on CRISPR/Cas, which has been considered as a potential method of point-of-care test (POCT) in resource-limited settings, offers a significant advantage in terms of high sensitivity and specificity. Therefore, there is an urgent need for the hepatitis B virus (HBV) detection utilizing CRISPR/Cas system. RESULTS: We have proposed a one-pot of one-step method for CRISPR/Cas12b assisted loop-mediated isothermal amplification (LAMP) to facilitate the quick, sensitive, and precise quantification of HBV DNA. This method is designed for point-of-care testing following genomic extraction or sample heat treatment. We have optimized several critical factors, such as the reaction buffer, AapCas12b-gRNA concentration, reporter and its concentration, reaction temperature, and chemical additives, to significantly enhance the performance of the one-pot assay for HBV. Importantly, it exhibited no cross-reactivity between HBV and blood-borne pathogens. Moreover, the assay is capable of quantifying HBV DNA within 1 h with a limit of detection (LOD) of 25 copies per milliliter. Additionally, when tested on 236 clinical samples, the assay demonstrated a sensitivity of 99.00 % (198/200) and a specificity of 100.00 % (36/36) at the 99 % confidence level compared to real-time quantitative PCR. SIGNIFICANCE: The utilization of convenient and reliable point-of-care diagnostic methods is crucial for reducing the burden of CHB globally. The assay we developed was helpful to improve the ability of HBV diagnosis for practical clinical translation, especially in high-burden regions and resource-limited settings. It has great advantages for rapid screening of CHB as well as evaluation of therapeutic efficacy as a companion diagnostic method.

Entropy-Based Node Importance Identification Method for Public Transportation Infrastructure Coupled Networks: A Case Study of Chengdu.

Public transportation infrastructure is a typical, complex, coupled network that is usually composed of connected bus lines and subway networks. This study proposes an entropy-based node importance identification method for this type of coupled network that is helpful for the integrated planning of urban public transport and traffic flows, as well as enhancing network information dissemination and maintaining network resilience. The proposed method develops a systematic entropy-based metric based on five centrality metrics, namely the degree centrality (DC), betweenness centrality (BC), closeness centrality (CC), eigenvector centrality (EC), and clustering coefficient (CCO). It then identifies the most important nodes in the coupled networks by considering the information entropy of the nodes and their neighboring ones. To evaluate the performance of the proposed method, a bus-subway coupled network in Chengdu, containing 10,652 nodes and 15,476 edges, is employed as a case study. Four network resilience assessment metrics, namely the maximum connectivity coefficient (MCC), network efficiency (NE), susceptibility (S), and natural connectivity (NC), were used to conduct group experiments. The experimental results demonstrate the following: (1) the multi-functional fitting analysis improves the analytical accuracy by 30% as compared to fitting with power law functions only; (2) for both CC and CCO, the improved metric's performance in important node identification is greatly improved, and it demonstrates good network resilience.

Human serum albumin as the carrier to fabricate STING-activating peptide nanovaccine for antitumor immunotherapy.

Tumor vaccines are emerging as one of the most promising therapeutic strategies for cancer treatment. With the advantages of low toxicity, convenient production and stable quality control, peptide vaccines have been widely used in preclinical and clinical trials involving various malignancies. However, when used alone, they still suffer from significant challenges including poor stability and immunogenicity as well as the low delivery efficiency, leading to limited therapeutic success. Herein, the STING-activating peptide nanovaccine based on human serum albumin (HSA) and biodegradable MnO2 was constructed, which can improve the stability and immunogenicity of antigenic peptides as well as facilitate their uptake by dendritic cells (DCs). Meanwhile, Mn2+ degraded from the nanovaccine can activate the STING pathway and further promote DCs maturation. In this way, the prepared nanovaccine can efficiently mediate T-cell immune responses, thereby exerting the effects of tumor prevention and therapy. Moreover, the prepared nanovaccine possesses the advantages of low cost, convenient preparation and good biocompatibility, showing great potential for practical applications.

Comparisons of ankle arthrodesis with different internal fixation methods in the treatment of post-traumatic osteoarthritis.

BACKGROUND: The aim of this study was to explore the clinical efficacy of ankle arthrodesis with different internal fixation methods in the treatment of post-traumatic osteoarthritis. METHODS: We collected 85 patients with post-traumatic osteoarthritis who underwent different ankle arthrodesis between December 2015 and December 2020. The operation performance, complication rate, hindfoot alignment, talus tilt angle, visual analogue scale (VAS), and American Orthopedic Foot and Ankle Society (AOFAS) score were preoperatively and postoperatively evaluated. RESULTS: In an anterior approach, the locking plate-fixation exhibited a similarity in operation time, incision length, postoperative drainage, bone fusion, hindfoot alignment, and talus tilt angle with fibula support compression screw-fixation, but it was better in increasing postoperative AOFAS. The locking plate-fixation in the anterior approach had lower operation time, incision length, and postoperative drainage than that in the lateral approach. In addition, the lateral locking plate combined with posterolateral compression screw fixation (LLPPCSF) presented shorter bone fusion time, higher AOFAS score, and lower complication rate than either plate- or screw-fixation alone. CONCLUSION: Lateral locking plate fixation was better than fibula support compression screw fixation in relieving postoperative pain. Anterior locking plate fixation was more time-saving and less invasiveness than lateral locking plate fixation, but its application was limited in low degree of ankle deformation. LLPPCSF was the most effective in improving bone fusion and postoperative pain, considering an optimal option for the treatment of post-traumatic osteoarthritis.

Direct visualization of immune status for tumor-infiltrating lymphocytes by rolling circle amplification.

The immune status of tumor-infiltrating lymphocytes (TILs) is essential for the effectiveness of cancer immunotherapies. However, due to the diversity of immune status in TILs, cellular heterogeneity, and the applicability to the clinic, it is still lacking effective strategies to meet clinical needs. We developed a novel immuno-recognition-induced method based on rolling circle amplification (RCA), namely immunoRCA, to in situ visualize the immune status of TILs in actual clinical samples. This developed immunoRCA method, in which, feature mRNAs were used as the biomarkers for the immune status of TILs, has a low fluorescence background, high sensitivity, and specificity. The immunoRCA was able to efficiently evaluate the immune status of CD8+ T cells regulated by activating or inhibiting factors, track the T cell type and immune status during in vitro expansion, and in situ visualize the number, location, and immune status of TILs in clinical specimens.

The impact of manufacturing servitization on consumption-based carbon rebound effect: A global value chain research perspective.

This study investigates the causal effect of manufacturing servitization on the consumption-based carbon rebound effect, employing the empirical approach based on the value-added trade and SBM-DEA model. The results show that improving the servitization level will lead to a significant decrease in the consumption-based carbon rebound effect of the global manufacturing industry. Moreover, the main paths through which the manufacturing servitization inhibits the consumption-based carbon rebound effect are the human capital and government management. We also find that the impact of manufacturing servitization is more substantial in advanced manufacturing and developed economies, which is smaller in manufacturing sectors with higher global value chain positions and lower export penetration levels. These findings suggest that improving the level of manufacturing servitization helps alleviate the consumption-based carbon rebound effect and is conducive to achieving the target of global carbon emission reduction.

Genetically engineered nanovesicles mobilize synergistic antitumor immunity by ADAR1 silence and PDL1 blockade.

Growing evidence has proved that RNA editing enzyme ADAR1, responsible for detecting endogenous RNA species, was significantly associated with poor response or resistance to immune checkpoint blockade (ICB) therapy. Here, a genetically engineered nanovesicle (siAdar1-LNP@mPD1) was developed as an RNA interference nano-tool to overcome tumor resistance to ICB therapies. Small interfering RNA against ADAR1 (siAdar1) was packaged into a lipid nanoparticle (LNP), which was further coated with plasma membrane extracted from the genetically engineered cells overexpressing PD1. siAdar1-LNP@mPD1 could block the PD1/PDL1 immune inhibitory axis by presenting the PD1 protein on the coating membranes. Furthermore, siAdar1 could be effectively delivered into cancer cells by the designed nanovesicle to silence ADAR1 expression, resulting in an increased type I/II interferon (IFN-ß/γ) production and making the cancer cells more sensitive to secreted effector cytokines such as IFN-γ with significant cell growth arrest. These integrated functions confer siAdar1-LNP@mPD1 with robust and comprehensive antitumor immunity, as evidenced by significant tumor growth regression, abscopal tumor prevention, and effective suppression of lung metastasis, through a global remodeling of the tumor immune microenvironment. Overall, we provided a promising translatable strategy to simultaneously silence ADAR1 and block PDL1 immune checkpoint to boost robust antitumor immunity.

Universal two-dimensional labelled probe-mediated melting curve analysis based on multiplex PCR for rapid typing of Plasmodium in a single closed tube.

Currently, malaria is still one of the major public health problems commonly caused by the four Plasmodium species. The similar symptoms of malaria and the COVID-19 epidemic of fever or fatigue lead to frequent misdiagnosis. The disadvantages of existing detection methods, such as time-consuming, costly, complicated operation, need for experienced technicians, and indistinguishable typing, lead to difficulties in meeting the clinical requirements of rapid, easy, and accurate typing of common Plasmodium species. In this study, we developed and optimized a universal two-dimensional labelled probe-mediated melting curve analysis (UP-MCA) assay based on multiplex and asymmetric PCR for rapid and accurate typing of five Plasmodium species, including novel human Plasmodium, Plasmodium knowlesi (Pk), in a single closed tube following genome extraction. The assay showed a limit of detection (LOD) of 10 copies per reaction and could accurately distinguish Plasmodium species from intra-plasmodium and other pathogens. Additionally, we proposed and validated different methods of fluorescence quenching and tag design for probes that are suitable for UP-MCA assays. Moreover, the clinical performance of the Plasmodium UP-MCA assay using a base-quenched universal probe was evaluated using 226 samples and showed a sensitivity of 100% (164/164) and specificity of 100% (62/62) at a 99% confidence interval, with the microscopy method as the gold standard. In summary, the UP-MCA assay showed excellent sensitivity, specificity, and accuracy for genotyping Plasmodium species spp. Additionally, it facilitates convenient and rapid Plasmodium detection in routine clinical practice and has great potential for clinical translation.

Intestinal Flora Derived Metabolites Affect the Occurrence and Development of Cardiovascular Disease.

In recent years, increasing evidence has shown that the gut microbiota and their metabolites play a pivotal role in human health and diseases, especially the cardiovascular diseases (CVDs). Intestinal flora imbalance (changes in the composition and function of intestinal flora) accelerates the progression of CVDs. The intestinal flora breaks down the food ingested by the host into a series of metabolically active products, including trimethylamine N-Oxide (TMAO), short-chain fatty acids (SCFAs), primary and secondary bile acids, tryptophan and indole derivatives, phenylacetylglutamine (PAGln) and branched chain amino acids (BCAA). These metabolites participate in the occurrence and development of CVDs via abnormally activating these signaling pathways more swiftly when the gut barrier integrity is broken down. This review focuses on the production and metabolism of TMAO and SCFAs. At the same time, we summarize the roles of intestinal flora metabolites in the occurrence and development of coronary heart disease and hypertension, pulmonary hypertension and other CVDs. The theories of "gut-lung axis" and "gut-heart axis" are provided, aiming to explore the potential targets for the treatment of CVDs based on the roles of the intestinal flora in the CVDs.

Effects of Moisture on the Ignition and Combustion Characteristics of Lignite Particles: Modeling and Experimental Study.

The influence of the moisture content on the ignition and combustion characteristics of lignite single particles was studied using an ignition model of single coal particles with moisture and experimental investigations in a visual drop tube furnace under the temperature of 1300 K. The moisture content and the lignite particle size were varied within the ranges of 0-20% and 75-250 µm, respectively. The images of the combustion process illustrated that higher moisture content caused a significant ignition delay. The probability of homogeneous ignition was greatest when the particle size was 125-150 µm and the moisture content was 5%. An ignition model was employed to explain the mechanism of the influence of moisture content on the ignition and combustion characteristics, which embedded the chemical percolation devolatilization model to increase the accuracy of predictions. The predicted results show that there was an overlap in the release of moisture and volatile matter from the lignite particle during the combustion at a high heating rate. The devolatilization rate increases with the increase of moisture, which explains the increase in the probability of homogeneous ignition and fragmentation. Both particle size and moisture content have two-sided effects on the ignition mode, which causes the complexity and irregularity of the ignition mode of particles with moisture.

Targeted co-delivery of a photosensitizer and an antisense oligonucleotide based on an activatable hyaluronic acid nanosystem with endogenous oxygen generation for enhanced photodynamic therapy of hypoxic tumors.

Photodynamic therapy (PDT) is a promising cancer treatment modality with advantages of minimal invasiveness, repeatable therapy, and mild systemic toxicity. However, the limited bioavailability of photosensitizer (PS), tumor hypoxia, and the presence of antiapoptotic proteins in cancer cells, has hampered the efficiency of PDT. To address these limitations, herein, we developed a hyaluronic acid (HA) based nanosystem (HA-Ce6-Hemin@DNA-Protamine NPs, HCH@DP) loaded with chlorin e6 (Ce6, as PS), hemin (as mimetic catalase) and antisense oligonucleotide (ASO) of B-cell lymphoma 2 (Bcl-2) anti-apoptosis protein via a simple electrostatic self-assembly method for enhanced PDT of hypoxic solid tumors. The HCH@DP can target deliver the PS and ASO to tumor cells via cancer cell overexpressed HA receptors (i.e., CD44 or RHAMM). The Ce6 was released from HA-ss-Ce6 (HSC conjugates) after the reaction of cleavable disulfide bond with glutathione (GSH), which recovered the fluorescence and phototoxicity of Ce6 upon laser irradiation. Meanwhile, the catalase-mimicking hemin (degradation of HA-eda-hemin by hyaluronidase) decomposed the tumor overdressed endogenous H2O2 to oxygen, which relieved tumor hypoxia and further overcome hypoxia-associated resistance of PDT. Furthermore, the inhibition of Bcl-2 expression by Bcl-2 ASO also greatly improved the cellular sensitivity to PDT. Both in vitro and in vivo results showed the tumor cell targeting ability, hypoxia relief and significantly enhanced antitumor PDT efficacy of HCH@DP for hypoxic tumor cells upon laser irradiation. Thus, by improving the target delivery of PS and ASO, relieving tumor hypoxia, and down-regulation of anti-apoptotic proteins, this HCH@DP nanosystem achieved enhanced PDT efficiency against hypoxic tumors. In general, our work provided a promising strategy to increase the utilization of key components (PS and oxygen) of PDT and the cell sensitivity to PDT by targeting co-delivery PS and oligonucleotides to tumor cells via a biocompatible HA based carrier, thereby achieving efficiently PDT treatment of hypoxic solid tumors with potential translation possibility. STATEMENT OF SIGNIFICANCE: The efficiency of PDT against solid tumor is severely restricted by the limited bioavailability of photosensitizer, tumor hypoxia, and the presence of antiapoptotic proteins in cancer cells. Herein, we have developed an activatable hyaluronic acid (HA) based nanosystem (HA-Ce6-Hemin@DNA-Protamine NPs, HCH@DP) via a simple electrostatic self-assembly method for PDT treatment of hypoxic solid tumors. The HCH@DP enabled to target co-delivery of photosensitizer and antisense oligonucleotide to tumor cells, overcoming tumor hypoxia through in situ oxygen production and improving cellular sensitivity by efficiently reducing anti-apoptosis effect of cancer cells for synergistically enhancing PDT efficiency. This work suggests a promising strategy to develop small molecule drug and oligonucleotides co-delivery nanoplatforms for efficiently PDT treatment of hypoxic solid tumor.

Proteomics study on the changes in amino acid metabolism during broccoli senescence induced by elevated O2 storage.

To better understand the global changes of amino acid catabolism and anabolism in broccoli in response to high O2 stress, iTRAQ-based proteomics combined with amino acid analysis was used to investigate the broccoli proteome at 0 and 4 d after treatment with different O2 concentrations (5% O2 + 5% CO2, 20% O2 + 5% CO2 and 40% O2 + 5% CO2) at 20℃. A total of 106 proteins with changes ≥ 1.2-fold in abundance were observed. Amino acid anabolism was significantly suppressed by high O2 stress, while catabolism was enhanced. High O2 stress-induced amino acid metabolism promoted the conversion of Met to ethylene and the degradation of amino acids to intermediate metabolites of the TCA cycle, thereby suppressing glucosinolate biosynthesis. However, the up-regulation of arginase and urease induced by high O2 stress aggravated ammonium toxicity. These findings enhance our understanding of high O2 stress-induced amino acid metabolism, as well as the effects of amino acid metabolism on broccoli senescence.

A Case of Forearm Soft Tissue Infection Caused by Hypervirulent K. pneumoniae in an Otherwise Healthy 24-Year-Old Woman.

In recent years, hypervirulent Klebsiella pneumoniae (hvKp) has received greater attention. It mainly infects diabetic patients and typically causes a hepatic abscess. Here, we report a case of hvKp that caused forearm muscle and soft tissue infection in addition to bacteremia, hepatic and pulmonary abscess, and hyperglycemia. The patient's condition stabilized after comprehensive treatment. She eventually recovered and was discharged after several debridement and flap operations. At 9 months of follow-up, no signs of infectious recurrence were noted, and the hyperglycemia resolved. Here, we detail important clinical features of a severe hvKp case diagnosed in an otherwise healthy individual. This report underscores the potential of hvKp to cause deep tissue infection and present with clinical symptoms similar to gas gangrene. Symptom onset in the setting of hvKp infection is usually gradual and misdiagnosis is common. The diagnosis of hvKp should be routinely considered in the clinical setting, and be strongly suspected when presenting with characteristic epidemiological, clinical and laboratory features. Although diabetes is a predisposing factor to hvKp infection, hyperglycemia appeared to manifest as a consequence of hvKp infection in this patient.

A comprehensive study of celastrol metabolism in vivo and in vitro using ultra-high-performance liquid chromatography coupled with hybrid triple quadrupole time-of-flight mass spectrometry.

Celastrol has attracted great attention owing to its anti-arthritis, antioxidant, and anticancer activities. Nevertheless, its metabolism in vivo (rats) and in vitro (rat liver microsomes and intestinal flora) has not been comprehensively characterized. In this study, ultra-high-performance liquid chromatography coupled with hybrid triple quadrupole time-of-flight mass spectrometry was used as a rapid and sensitive approach for studying the metabolism of celastrol in vivo and in vitro. A total of 43 metabolites were identified and characterized. These include 26 metabolites in vivo, and 28 metabolites in vitro (nine metabolites in rat liver microsomes and 24 metabolites in rat intestinal flora). Additionally, the celastrol-biotransformation capacity of the intestinal tract was confirmed to exceed that of the liver. Furthermore, the metabolic profile of celastrol is summarised. The information obtained from this study may provide a basis for understanding the pharmacological mechanisms of celastrol and will be beneficial for clinical applications.

Antibacterial mechanism of Cu-bearing 430 ferritic stainless steel.

Copper (Cu)-bearing stainless steel has testified its effectiveness to reduce the risk of bacterial infections. However, its antibacterial mechanism is still controversial. Therefore, three 430 ferritic stainless steels with different Cu contents are selected to conduct deeper research by the way of bacterial inactivation from two aspects of material and biology. Hereinto, electrochemical and antibacterial results show that the increase in Cu content simultaneously improves the corrosion resistance and antibacterial property of 430 stainless steel. In addition, it is found that Escherichia coli (E. coli) on the surface 430 Cu-bearing stainless steel by the dry method of inoculation possesses a rapid inactivation ability. X-ray photoelectron spectroscopy (XPS) aids with ion chelation experiments prove that Cu (I) plays a more crucial role in the contact-killing efficiency than Cu (II), resulting from more production of reactive oxygen species (ROS).

Single-Cell Imaging of m6 A Modified RNA Using m6 A-Specific In Situ Hybridization Mediated Proximity Ligation Assay (m6 AISH-PLA).

N6 -methyladenosine (m6 A) modification-the most prevalent mammalian RNA internal modification-plays key regulatory roles in mRNA metabolism. Current approaches for m6 A modified RNA analysis limit at bulk-population level, resulting in a loss of spatiotemporal and cell-to-cell variability information. Here we proposed a m6 A-specific in situ hybridization mediated proximity ligation assay (m6 AISH-PLA) for cellular imaging of m6 A RNA, allowing to identify m6 A modification at specific location in RNAs and image m6 A RNA with single-cell and single-molecule resolution. Using m6 AISH-PLA, we investigated the m6 A level and subcellular location of HSP70 RNA103-m6 A in response to heat shock stress, and found an increased m6 A modified ratio and an increased distribution ratio in cytoplasm under heat shock. m6 AISH-PLA can serve in the study of m6 A RNA in single cells for deciphering epitranscriptomic mechanisms and assisting clinical diagnosis.

Accurate transcriptome assembly by Nanopore RNA sequencing reveals novel functional transcripts in hepatocellular carcinoma.

The long reads of Nanopore sequencing permit accurate transcript assembly and ease in discovering novel transcripts with potentially important functions in cancers. The wide adoption of Nanopore sequencing for transcript quantification, however, is largely limited by high costs. To address this issue, we developed a bioinformatics software, NovelQuant, that can specifically quantify long-read-assembled novel transcripts with short-read sequencing data. Nanopore Direct RNA Sequencing was carried out on three hepatocellular carcinoma (HCC) patients' tumor, matched portal vein tumor thrombus, and peritumor to reconstruct the HCC transcriptome. Then, based on the reconstructed transcriptome, NovelQuant was applied on Illumina RNA sequencing data of 59 HCC patients' tumor and paired peritumor to quantify novel transcripts. Our further analysis revealed 361 novel transcripts dysregulated in HCC and that 101 of them were significantly associated with prognosis. There were 19 novel prognostic transcripts predicted to be long noncoding RNAs (lncRNAs), and some of them had regulatory targets that were reported to be associated with HCC. Additionally, 42 novel prognostic transcripts were predicted to be protein-coding mRNAs, and many of them could be involved in xenobiotic metabolism. Moreover, the tumor-suppressive roles of two representative novel prognostic transcripts, CDO1-novel (lncRNA) and CYP2A6-novel (protein-coding mRNA), were further functionally validated during HCC progression. Overall, the current study shows a possibility of combining long- and short-read sequencing to explore functionally important novel transcripts in HCC with accuracy and cost-efficiency, which expands the pool of molecular biomarkers that could enhance our understanding of the molecular mechanisms of HCC.

Identification of a potentially novel LncRNA-miRNA-mRNA competing endogenous RNA network in pulmonary arterial hypertension via integrated bioinformatic analysis.

AIMS: Pulmonary arterial hypertension (PAH) is a fatal cardiovascular disease with a cancer-like phenotype. Competing endogenous RNA (ceRNA) networks extensively involve in its pathological processes. But rare ceRNA networks and profound molecular mechanisms have been revealed in PAH. The aim of this study was to illuminate the ceRNA networks in PAH. MATERIALS AND METHODS: In this work, we have chosen the idiopathic PAH as an example. GSE15197 (mRNA) and GSE56914 (miRNA) from the Gene Expression Omnibus (GEO) were selected to explore key genes and novel ceRNA networks in PAH by a series of integrated bioinformatic analysis. To be more scientific, a part of pairs in identified ceRNA network were detected in hypoxia-induced HPASMCs. And the dual-luciferase assay was performed to certify the relationship between miRNAs and mRNAs. KEY FINDINGS: Totally, 311 differentially expressed genes (DEGs) were identified and functional enrichment analysis illuminated that the majority of DEGs were enriched in proliferation, anti-apoptosis, inflammation and cancer-related pathways. And 10 hub genes were determined via Cytohubba after PPI network construction. Sequentially, with stepwise reverse prediction and pan-cancer co-expression analysis from mRNA to LncRNA in TargetScan, miRNet, ENCORI (Starbase V3.0) databases, a crucially ceRNA network was identified including 14 LncRNAs, 2 miRNAs, and 3 mRNAs. Further, in hypoxia-induced HPASMCs, the alterations of mRNAs, miRNAs and LncRNAs and their relationship were in accordance with the results we identified. SIGNIFICANCE: Consequently, the unique hub genes and ceRNA network we proposed may advance our understanding of the molecular mechanisms in PAH.