A bisulfite-assisted and ligation-based qPCR amplification technology for locus-specific pseudouridine detection at base resolution

Over 150 types of chemical modifications have been identified in RNA to date, with pseudouridine (Ψ) being one of the most prevalent modifications in RNA. Ψ plays vital roles in various biological processes, and precise, base-resolution detection methods are fundamental for deep analysis of its distribution and function. In this study, we introduced a novel base-resolution Ψ detection method named pseU-TRACE. pseU-TRACE relied on the fact that RNA containing Ψ underwent a base deletion after treatment of bisulfite (BS) during reverse transcription, which enabled efficient ligation of two probes complementary to the cDNA sequence on either side of the Ψ site and successful amplification in subsequent real-time quantitative PCR (qPCR), thereby achieving selective and accurate Ψ detection. Our method accurately and sensitively detected several known Ψ sites in 28S, 18S, 5.8S, and even mRNA. Moreover, pseU-TRACE could be employed to measure the Ψ fraction in RNA and explore the Ψ metabolism of different pseudouridine synthases (PUSs), providing valuable insights into the function of Ψ. Overall, pseU-TRACE represents a reliable, time-efficient and sensitive Ψ detection method.

HBO1 catalyzes lysine lactylation and mediates histone H3K9la to regulate gene transcription

Lysine lactylation (Kla) links metabolism and gene regulation and plays a key role in multiple biological processes. However, the regulatory mechanism and functional consequence of Kla remain to be explored. Here, we report that HBO1 functions as a lysine lactyltransferase to regulate transcription. We show that HBO1 catalyzes the addition of Kla in vitro and intracellularly, and E508 is a key site for the lactyltransferase activity of HBO1. Quantitative proteomic analysis further reveals 95 endogenous Kla sites targeted by HBO1, with the majority located on histones. Using site-specific antibodies, we find that HBO1 may preferentially catalyze histone H3K9la and scaffold proteins including JADE1 and BRPF2 can promote the enzymatic activity for histone Kla. Notably, CUT&Tag assays demonstrate that HBO1 is required for histone H3K9la on transcription start sites (TSSs). Besides, the regulated Kla can promote key signaling pathways and tumorigenesis, which is further supported by evaluating the malignant behaviors of HBO1- knockout (KO) tumor cells, as well as the level of histone H3K9la in clinical tissues. Our study reveals HBO1 serves as a lactyltransferase to mediate a histone Kla-dependent gene transcription.

Desmoglein 2 and desmocollin 2 depletions promote malignancy through distinct mechanisms in triple-negative and luminal breast cancer

BACKGROUND

Aberrant expressions of desmoglein 2 (Dsg2) and desmocollin 2(Dsc2), the two most widely distributed desmosomal cadherins, have been found to play various roles in cancer in a context-dependent manner. Their specific roles on breast cancer (BC) and the potential mechanisms remain unclear.

METHODS

The expressions of Dsg2 and Dsc2 in human BC tissues and cell lines were assessed by using bioinformatics analysis, immunohistochemistry and western blotting assays. Wound-healing and Transwell assays were performed to evaluate the cells' migration and invasion abilities. Plate colony-forming and MTT assays were used to examine the cells' capacity of proliferation. Mechanically, Dsg2 and Dsc2 knockdown-induced malignant behaviors were elucidated using western blotting assay as well as three inhibitors including MK2206 for AKT, PD98059 for ERK, and XAV-939 for β-catenin.

RESULTS

We found reduced expressions of Dsg2 and Dsc2 in human BC tissues and cell lines compared to normal counterparts. Furthermore, shRNA-mediated downregulation of Dsg2 and Dsc2 could significantly enhance cell proliferation, migration and invasion in triple-negative MDA-MB-231 and luminal MCF-7 BC cells. Mechanistically, EGFR activity was decreased but downstream AKT and ERK pathways were both activated maybe through other activated protein tyrosine kinases in shDsg2 and shDsc2 MDA-MB-231 cells since protein tyrosine kinases are key drivers of triple-negative BC survival. Additionally, AKT inhibitor treatment displayed much stronger capacity to abolish shDsg2 and shDsc2 induced progression compared to ERK inhibition, which was due to feedback activation of AKT pathway induced by ERK inhibition. In contrast, all of EGFR, AKT and ERK activities were attenuated, whereas β-catenin was accumulated in shDsg2 and shDsc2 MCF-7 cells. These results indicate that EGFR-targeted therapy is not a good choice for BC patients with low Dsg2 or Dsc2 expression. Comparatively, AKT inhibitors may be more helpful to triple-negative BC patients with low Dsg2 or Dsc2 expression, while therapies targeting β-catenin can be considered for luminal BC patients with low Dsg2 or Dsc2 expression.

CONCLUSION

Our finding demonstrate that single knockdown of Dsg2 or Dsc2 could promote proliferation, motility and invasion in triple-negative MDA-MB-231 and luminal MCF-7 cells. Nevertheless, the underlying mechanisms were cellular context-specific and distinct.

Locus-specific detection of pseudouridine with CRISPR-Cas13a

We combined the CRISPR-Cas13a system with CMC chemical labeling, developing an approach that enables precise identification of pseudouridine (Ψ) sites at specific loci within ribosomal RNA (rRNA), messenger RNA (mRNA) and small nuclear RNAs (snRNA). This method, with good efficiency and simplicity, detects Ψ sites through fluorescence measurement, providing a straightforward and fast validation for targeted Ψ sites of interest.

The mitochondrial genome of Monoserius pennarius (Linnaeus, 1758) from the East China Sea

The species Monoserius pennarius (Linnaeus, 1758), is particularly abundant in the tropical Indo-West Pacific east of Sri Lanka, yet very limited genetic information exists for this species. Here, we report the assembled-linear mitochondrial genome of M. pennarius collected from the East China Sea. The 15,197 bp mitogenome contains 13 protein-coding genes (PCGs), two tRNA genes, and two rRNA genes. Notably, the gene order in this mitogenome differs from that of other hydrozoans within the same taxonomic order. Phylogenetic analysis, based on 13 concatenated mitochondrial PCGs, recovered M. pennarius as a sister of Nemalecium lighti (Hargitt, 1924), outside the other Leptothecata hydrozoans, suggesting paraphyly of Leptothecata. The mitogenome of M. pennarius, serving as the first publicly available for the family Aglaopheniidae, holds foreseeable value for investigating Leptothecata evolution.

TXNIP/NLRP3 aggravates global cerebral ischemia-reperfusion injury-induced cognitive decline in mice

Global cerebral ischemia/reperfusion (GCI/R) injury poses a risk for cognitive decline, with neuroinflammation considered pivotal in this process. This study aimed to unravel the molecular mechanisms underlying GCI/R injury and propose a potential therapeutic strategy for associated cognitive deficits. Utilizing bioinformatics analysis of a public microarray profile (GSE30655 and GSE80681) in cerebral ischemic mice, it was observed that neuroinflammation emerged as a significant gene ontology item, with an increase in the expression of thioredoxin-interacting protein (TXNIP) and NLRP3 genes. Experimental models involving bilateral occlusion of the common carotid arteries in mice revealed that GCI/R induced cognitive impairment, along with a time-dependent increase in TXNIP and NLRP3 levels. Notably, TXNIP knockdown alleviated cognitive dysfunction in mice. Furthermore, the introduction of adeno-associated virus injection with TXNIP knockdown reduced the number of activated microglia, apoptosis neurons, and levels of oxidative stress and inflammatory cytokines in the hippocampus. Collectively, these findings underscore the significance of TXNIP/NLRP3 in the hippocampus in exacerbating cognitive decline due to GCI/R injury, suggesting that TXNIP knockdown holds promise as a therapeutic strategy.

New onset or recurrence of uveitis following COVID-19 infection

BACKGROUND

While the 2019 novel coronavirus disease (COVID-19) pandemic has resulted in millions of cases worldwide, there is increasing recognition of a wide range of ocular manifestations associated with the virus, including uveitis. Uveitis is an inflammatory condition of the uveal tract of the eye that can lead to permanent vision loss if not treated promptly. Here we report a retrospective observational study of patients who presented with new onset or recurrent uveitis following COVID-19 infection.

METHODS

This is a retrospective observational study conducted at the Beijing Tongren Hospital. We identified patients who presented with symptoms of non-infectious active uveitis with positive real-time reverse transcription polymerase chain reaction (RT-PCR) of COVID-19 within 4 weeks. All patients received ophthalmic examinations, including anterior and posterior segment imaging, to assess the extent of ocular involvement.

RESULTS

The 18 patients with a total of 33 eyes included in this study presented with symptoms of active uveitis within 4 weeks of their positive COVID-19 RT-PCR test. Among them, 9 patients presented with the development of uveitis following COVID-19 infection, and 9 patients had relapsed uveitis after COVID-19 infection. Treatment with corticosteroids resulted in improvement of symptoms and resolution of inflammation in all cases. In this study, all patients did not experience any adverse drug reactions during treatment.

CONCLUSION

Our observational study highlights the potential for new onset or recurrence of uveitis following COVID-19 infection.

TRIAL REGISTRATION

https://www.chictr.org.cn/ ; identifier: ChiCTR2100044365, date: 03/17/2023.

The characteristics of acute macular neuroretinopathy following COVID-19 infection

BACKGROUND

In this study, we report a case series of acute macular neuroretinopathy (AMN) associated with COVID-19 infection.

METHODS

This retrospective observational study was conducted at Beijing Tongren Hospital. We reviewed patients who were diagnosed with AMN within one month of testing positive for COVID-19 using real-time reverse transcription-polymerase chain reaction (RT-PCR).

RESULTS

A total of 11 AMN patients (20 eyes) were included in the study. The mean age was 33.8 ± 12.6 years. The average interval between a positive COVID-19 PCR test and the onset of ocular symptoms was 2.8 ± 2.5 days. The mean follow-up period for the patients was 12.5 ± 3.8 weeks. Imaging characteristics of AMN patients following COVID-19 infection included areas of low reflectivity on near-infrared reflectance (NIR) imaging, hyperreflective lesions at the level of the outer plexiform layer (OPL) and outer nuclear layer (ONL) and disruption of the ellipsoid zone (EZ) on spectral domain optical coherence tomography (SD-OCT) B-scans. Visual field examinations revealed parafoveal scotomas that closely corresponded to the clinical lesions. Optical coherence tomography angiography (OCT-A) demonstrated impaired perfusion in the deep retinal vascular plexus. Fluorescein angiography (FA), indocyanine green angiography (ICGA), and spontaneous fundus autofluorescence showed no significant abnormalities. During follow-up, partial improvement in retinal lesions was observed in NIR imaging and SD-OCT in some patients, but a proportion of patients still exhibited persistent retinal damage and no improvement in visual field scotomas.

CONCLUSION

COVID-19-related AMN share similar clinical and imaging features with AMN due to other causes, as evidenced by the persistent presence of visual field scotomas over a longer duration.

TRAIL REGISTRATION

https://www.chictr.org.cn/ ; identifier: ChiCTR2100044365.

CT-based radiomics for prediction of pulmonary haemorrhage after percutaneous CT-guided transthoracic lung biopsy of pulmonary nodules

AIM

To evaluate the feasibility of intranodular and perinodular computed tomography (CT) radiomics features for predicting the occurrence of pulmonary haemorrhage after percutaneous CT-guided transthoracic lung biopsy (PCTLB) in pulmonary nodules.

MATERIALS AND METHODS

The data for 332 patients with pulmonary nodules who underwent PCTLB were reviewed retrospectively. Pulmonary haemorrhage after PCTLB was evaluated using CT (144 cases occurred). Radiomics features based on gross nodular (GNV) and perinodular volumes (PNV) were extracted from pre-biopsy CT images and features selection using least absolute shrinkage and selection operator (LASSO) regression, and three radiomics scores (rad-scores) were built. Rad-scores, clinical, and clinical-radiomic models were developed and evaluated to predict the occurrence of pulmonary haemorrhage.

RESULTS

Five, five, and six significant features were selected for prediction of pulmonary haemorrhage based on GNV, PNV, and GNV + PNV, respectively. Lesion depth was the only clinical characteristics related to pulmonary haemorrhage. Lesion depth and rad-score based on GNV, PNV, and GNV + PNV for predicting the pulmonary haemorrhage achieved areas under the curves (AUCs) of 0.656, 0.645, 0.651, and 0.635 in the validation group, respectively. Three clinical-radiomic models improved the AUCs to 0.743, 0.723, and 0.748. The performance of rad-score_GNV + PNV combined with lesion depth outperformed the clinical model (p=0.024) and the radiomics signature (p=0.038). In addition, the radiomics signatures were significantly associated with higher-grade pulmonary haemorrhage (p<0.05).

CONCLUSIONS

Radiomics features from intranodular and perinodular regions of pulmonary nodules have good predictive ability for pulmonary haemorrhage after PCTLB, which may provide additional predictive value for clinical practice.

Detection, Clinical Application, and Manipulation of RNA Modifications

ConspectusWith increasing research interest, more than 170 types of chemical modifications of RNA have been characterized. The epigenetic modifications of RNA do not alter the primary sequence of RNA but modulate the gene activity. Increasing numbers of regulatory functions of these RNA modifications, particularly in controlling mRNA fate and gene expression, are being discovered. To gain a deeper understanding of the biological significance and clinical prospects of RNA modifications, the development of innovative labeling and detection methodologies is of great importance. Owing to the dynamic features of RNA modifications and the fact that only a portion of genes are modified, detection methods should accurately reveal the precise distribution and modification level of RNA modifications. In general, detection methodologies identify specific RNA modifications in two ways: (1) enriching modification-containing RNAs; and (2) altering the Watson-Crick base pairing pattern to produce truncation or mutation signatures. Additionally, it is important to develop flexible and accurate manipulation tools that enable the installation or removal of RNA modifications at specific positions to investigate the biological functions of a single site. With the development of detection and manipulation methods, the scientific understanding of the biological functions of RNA modifications has increased, paving the way for applications of RNA modifications in disease diagnosis and treatments.In this Account, we provide a brief summary of recent efforts to develop methodologies for detecting RNA modifications. Through the evolution of these detection techniques, our team has uncovered the potential biological roles of RNA modifications in diseases such as diabetic cardiovascular complications, viral infections, and hematologic malignancies. We mainly summarize the recently developed strategies for manipulating RNA modifications. The advent of these programmable editing tools allows for the precise installation or removal of RNA modifications at specific positions. As a result, the biological functions of RNA modifications at these specific loci could be identified, further advancing our knowledge in this field.With this Account, we anticipate providing chemical and biological researchers with comprehensive strategies to discover the underlying mechanisms of RNA modification-mediated biological processes. Although the field of RNA modifications has undergone rapid progress in recent years, our understanding of most of these RNA modifications remains incomplete. We hope to inspire efforts to expand the toolbox for investigating RNA modifications and promote translational research on epigenetics in clinical diagnosis and treatment.

Comparative Efficacy and Safety of Chinese Patent Medicines for Cervical High-risk Human Papillomavirus Infection: A Bayesian Network Meta-analysis

Background: Many Chinese patent medicines have been reported to show anti-tumor cell effects on cervical cancer. To estimate the comparative effectiveness and safety of Chinese patent medicines for cervical high-risk human papillomavirus (HR-HPV) infection. Methods: Randomized controlled trials (RCTs) of Chinese patent medicines for HR-HPV infection were searched in eight databases until 31 August 2022, and two review authors independently extracted data and assessed the risk of bias. Outcomes concerning efficacy were evaluated as odds ratio (OR) and 95% credible intervals (CrI) utilizing R 4.1.2 and Stata 16.1. The protocol was registered on the International Prospective Register of Systematic Reviews (CRD42022351120). Results: We ultimately identified 60 RCTs that involved 5,951 participants and 8 interventions. Chinese patent medicines combined with recombinant human interferon (rhIFN) have better treatment effects than rhIFN alone. The results showed that Baofukang suppository (BFK) combined with rhIFN is greater for the rate of HR-HPV clearance follow-up at 6 months (SUCRA = 78.16%). Kushen gel (KS) combined with rhIFN ranked first for the rate of HR-HPV clearance after treatment (SUCRA = 90.77%). Furthermore, KS + rhIFN is most likely to be the best intervention for improving the clinical effectiveness rate (SUCRA = 87.39%). Adverse reactions were not statistically significant in BFK + rhIFN versus BFK, BFK + rhIFN versus rhIFN, and BFK versus rhIFN. Conclusion: The combination of Chinese patent medicines with rhIFN may demonstrate a higher efficacy than rhIFN alone in clearing the virus and improving cervical symptoms. Weighing with the clinical comprehensive efficacy, BFK + rhIFN and KS + rhIFN maybe the optimal treatments for cervical HR-HPV infection. However, more high-quality randomized controlled trials are needed in the future to further confirm the efficacy and safety of proprietary Chinese medicines for cervical HR-HPV infection.

Transcriptome-wide identification of single-stranded RNA binding proteins

RNA-protein interactions are precisely regulated by RNA secondary structures in various biological processes. Large-scale identification of proteins that interact with particular RNA structure is important to the RBPome. Herein, a kethoxal assisted single-stranded RNA interactome capture (KASRIC) strategy was developed to globally identify single-stranded RNA binding proteins (ssRBPs). This approach combines RNA secondary structure probing technology with the conventional method of RNA-binding proteins profiling, realizing the transcriptome-wide identification of ssRBPs. Applying KASRIC, we identified 3180 candidate RBPs and 244 candidate ssRBPs in HeLa cells. Importantly, the 244 candidate ssRBPs contained 55 previously reported ssRBPs and 189 novel ssRBPs. Function analysis of the candidate ssRBPs exhibited enrichment in cellular processes related to RNA splicing and RNA degradation. The KASRIC strategy will facilitate the investigation of RNA-protein interactions.

MIF promotes cell invasion by the LRP1-uPAR interaction in pancreatic cancer cells

Introduction

Pancreatic ductal adenocarcinoma (PDAC) is characterized by high aggressiveness and a hypoxic tumour microenvironment. Macrophage migration inhibitory factor (MIF) is a hypoxia-related pleiotropic cytokine that plays important roles in cancer. However, its role in PDAC progression has not been fully elucidated.

Methods

The clinical significance of MIF and hypoxia inducible factor 1 subunit alpha (HIF1A) in PDAC was analysed using immunohistochemical staining on PDAC tissues and data from KM-Plotter database. Spatial distribution of MIF and HIF1A gene expression was visualized by spatial transcriptomics in PDAC cell xenografts. To monitor the role of MIF in PDAC cell malignancy, immunostaining, lentivirus shRNA, migration assays, flow cytometry, transcriptomics and in vivo tumorigenicity were performed.

Results

The spatial distribution of MIF and HIF1A was highly correlated and that high MIF expression was associated with poor prognosis of PDAC patients. MIF knockdown impaired cell invasion, with a decrease in the expression of urokinase-type plasminogen activator receptor (uPAR). Although PLAUR transcript was not reduced, a uPAR endocytic receptor, low-density lipoprotein receptor-related protein 1 (LRP1), was upregulated at both the mRNA and protein levels after MIF knockdown. The LRP1 antagonist RAP restored uPAR expression and invasiveness. MIF attenuated the nuclear translocation of p53, a transcriptional regulator of LRP1. Furthermore, MIF downregulation blunted the growth of PDAC cell xenografts and inhibited cell proliferation under normoxia and hypoxia. Transcriptome analysis also provided evidence for the role of MIF in cancer-associated pathways.

Discussion

We demonstrate a novel link between the two pro-invasive agents MIF and uPAR and explain how MIF increases PDAC cell invasion capability. This finding provides a basis for therapeutic intervention of MIF in PDAC progression.

The relevance between hypoxia-dependent spatial transcriptomics and the prognosis and efficacy of immunotherapy in claudin-low breast cancer

Introduction

Hypoxia is an important characteristic of solid tumors. However, spatial transcriptomics (ST) of hypoxia-associated heterogeneity is not clear.

Methods

This study integrated Spatial Transcriptomics (ST) with immunofluorescence to demonstrate their spatial distribution in human claudin-low breast cancer MDA-MB-231 engraft. ST spots were clustered with differentially expression genes. The data were combined with hypoxia-specific marker and angiogenesis marker-labeled serial sections to indicate the spatial distribution of hypoxia and hypoxia-inducted transcriptional profile. Moreover, marker genes, cluster-specific hypoxia genes, and their co-essential relationship were identified and mapped in every clusters. The clinicopathological association of marker genes of hypoxia-dependent spatial clusters was explored in 1904 breast cancers from METABRIC database.

Results

The tumor from center to periphery were enriched into five hypoxia-dependent subgroups with differentially expressed genes, which were matched to necrosis, necrosis periphery, hypoxic tumor, adaptive survival tumor, and invasive tumor, respectively. Different subgroups demonstrated distinct hypoxia condition and spatial heterogeneity in biological behavior and signaling pathways. Cox regression analysis showed that the invasive tumor (cluster 0) and hypoxic tumor (cluster 6) score could be served as independent prognostic factors in claudin-low patients. KM analysis indicated that high invasive tumor (cluster 0) and hypoxic tumor (cluster 6) score was associated with poor prognoses of claudin-low patients. Further analysis showed that hypoxia-induced immune checkpoints, such as CD276 and NRP1, upregulation in invasive tumor to block infiltration and activation of B cells and CD8+ T cells to change tumor immune microenvironment.

Discussion

This study reveals hypoxia-dependent spatial heterogeneity in claudin-low breast cancer and highlights its potential value as a predictive biomarker of clinical outcomes and immunotherapy response. The molecules found in this study also provided potential molecular mechanisms and therapeutic targets for subsequent studies.

ENO1 expression and Erk phosphorylation in PDAC and their effects on tumor cell apoptosis in a hypoxic microenvironment

OBJECTIVE

Hypoxia is an important feature of pancreatic ductal adenocarcinoma (PDAC). Previously, we found that hypoxia promotes ENO1 expression and PDAC invasion. However, the underlying molecular mechanism was remains unclear.

METHODS

The relationship between ENO1 expression and clinicopathological characteristics was analyzed in 84 patients with PADC. The effects of CoCl₂-induced hypoxia and ENO1 downregulation on the apoptosis, invasion, and proliferation of PDAC cells were evaluated in vitro and in vivo. Hypoxia- and ENO1-induced gene expression was analyzed by transcriptomic sequencing.

RESULTS

The prognosis of PDAC with high ENO1 expression was poor (P < 0.05). High ENO1 expression was closely associated with histological differentiation and tumor invasion in 84 PDAC cases (P < 0.05). Hypoxia increased ENO1 expression in PDAC and promoted its migration and invasion. Apoptotic cells and the apoptosis marker caspase-3 in the CoCl₂-treated ENO1-sh group were significantly elevated (P < 0.05). Transcriptomic sequencing indicated that CoCl₂-induced PDAC cells initiated MAPK signaling. Under hypoxic conditions, PDAC cells upregulated ENO1 expression, thereby accelerating ERK phosphorylation and inhibiting apoptosis (P < 0.05). Consistent results were also observed in a PDAC-bearing mouse hindlimb ischemia model.

CONCLUSIONS

Hypoxia-induced ENO1 expression promotes ERK phosphorylation and inhibits apoptosis, thus leading to PDAC survival and invasion. These results suggest that ENO1 is a potential therapeutic target for PDAC.

Mycn regulates intestinal development through ribosomal biogenesis in a zebrafish model of Feingold syndrome 1

Feingold syndrome type 1, caused by loss-of-function of MYCN, is characterized by varied phenotypes including esophageal and duodenal atresia. However, no adequate model exists for studying the syndrome's pathological or molecular mechanisms, nor is there a treatment strategy. Here, we developed a zebrafish Feingold syndrome type 1 model with nonfunctional mycn, which had severe intestinal atresia. Single-cell RNA-seq identified a subcluster of intestinal cells that were highly sensitive to Mycn, and impaired cell proliferation decreased the overall number of intestinal cells in the mycn mutant fish. Bulk RNA-seq and metabolomic analysis showed that expression of ribosomal genes was down-regulated and that amino acid metabolism was abnormal. Northern blot and ribosomal profiling analysis showed abnormal rRNA processing and decreases in free 40S, 60S, and 80S ribosome particles, which led to impaired translation in the mutant. Besides, both Ribo-seq and western blot analysis showed that mTOR pathway was impaired in mycn mutant, and blocking mTOR pathway by rapamycin treatment can mimic the intestinal defect, and both L-leucine and Rheb, which can elevate translation via activating TOR pathway, could rescue the intestinal phenotype of mycn mutant. In summary, by this zebrafish Feingold syndrome type 1 model, we found that disturbance of ribosomal biogenesis and blockage of protein synthesis during development are primary causes of the intestinal defect in Feingold syndrome type 1. Importantly, our work suggests that leucine supplementation may be a feasible and easy treatment option for this disease.

LncRNA n339260 functions in hepatocellular carcinoma progression via regulation of miRNA30e-5p/TP53INP1 expression

BACKGROUND

Currently, the molecular mechanism of the interaction between lncRNAs and microRNAs (miRNAs) and the target of miRNAs in tumor vasculogenic mimicry (VM) formation have not been clarified. Our aim is to study the interaction between lncRNA n339260 and miRNA30e-5p in the formation of VM.

METHODS

Animal xenografts were established, 104 hepatocellular carcinoma (HCC) patients' frozen tissues were obtained and HCC cells in vitro were used to observe the role of n339260 in HCC progression.

RESULTS

In vivo experiment showed lncRNA n339260 promoted tumor growth and VM formation. LncRNA n339260 and miRNA30e-5p were found to be associated with VM formation, metastasis and survival time in HCC patients. In vitro experiment showed that LncRNA n339260 could inhibit miRNA30e-5p expression and TP53INP1 was found to be the downstream targets of miRNA30e-5p. Snail, MMP2, MMP9, VE-cadherin, vimentin and N-cadherin overexpression and the downregulation of TP53INP1 and E-cadherin were observed in HCCLM3 and HepG2 cells overexpressing lncRNA n339260 or in cells with decreased expression of miRNA30e-5p.

CONCLUSION

LncRNA n339260 promotes the development of VM, and lncRNA n339260 may enhance Snail expression by decreasing the expression of miRNA30e-5p, thereby reducing TP53INP1 expression. Therefore, a potential lncRNA n339260- miRNA30e-5p- TP53INP1 regulatory axis was associated with HCC progression.

Mucosal associated Lymphoid Tissue Lymphoma of the uvea: an analysis of 3 cases

Background

Ocular mucosa-associated lymphoid tissue (MALT) lymphoma involving orbit and conjunctiva usually has an indolent clinical course with “salmon patch” mass as typical presentation. This study is to report a series of rare cases and investigate the clinical and pathological features of ocular MALT lymphoma that involved uveal tissue primarily and presented as posterior scleritis.

Methods

This retrospective, observational study was conducted at Beijing Tongren Hospital. From 2018 to 2020, 3 cases of 3 eyes (2 female patients and 1 male patient) with ocular MALT lymphoma that involved uveal tissue primarily and presented as posterior scleritis were included in the study. All patients had complaints of red eyes with blurred vision. The average age was 56.33 ± 2.08 years old and the average time from initial diagnosis to pathological diagnosis was 3.00 ± 1.73 months. Ophthalmic examinations including best-corrected visual acuity (BCVA), intraocular pressure (IOP), slit lamp microscope examinations, fundus photography, B-scan ultrasonography, ultrasound biomicroscope (UBM), optical coherence tomography (OCT), fundus fluorescein angiography (FFA) and indocyanine green angiography (ICGA) were conducted. Systemic workups including orbital magnetic resonance imaging (MRI), positron emission tomography-computed tomography (PET-CT) and blood autoimmune antibody tests were also conducted. Pathological tissue from patients were obtained through surgeries. Biopsy examinations were performed to accurately determine pathological diagnosis. All the information of clinical, imaging and pathological changes were collected and analyzed.

Results

At the initial diagnosis, the BCVA of involved eyes decreased seriously while the IOP were normal. All involved eyeball showed extensive hyperemia and local thickening in the wall of eyeballs. B-scan ultrasonography showed mass with abundant blood and irregular cysts inside the eyeball wall and in the retrobulbar orbit, surrounding the ocular wall and optic nerve. UBM showed solid lesions with low and medium echo under the conjunctiva and inside the ciliary body of 2 cases. OCT showed posterior polar wavy rise of RPE and local neuroepithelial detachment in all cases. FFA and ICGA showed vascular abnormalities (patch-like strong fluorescence and fluorescence leakage) and local thickening in retina and choroid (Rectangle-like weak fluorescence below the macula). The posterior wall of the eyeball was thickened and enhanced in MRI. PET-CT also showed thickening of posterior wall of eyeballs and increased metabolic activity but there was no sign of autoimmune disease. All patients were diagnosed as MALT lymphoma through pathologic examinations of biopsy tissue.

Conclusions

The onset of primary ocular MALT lymphoma in uvea is hidden. The early clinical manifestations are lack of specificity and misleading. B-scan ultrasonography has characteristic manifestations and is valuable in diagnosis. However, pathological diagnosis through tissue biopsy is irreplaceable.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12886-022-02598-2.

Short term outcomes of extremely low birth weight infants from a multicenter cohort study in Guangdong of China

With the increase in extremely low birth weight (ELBW) infants, their outcome attracted worldwide attention. However, in China, the related studies are rare. The hospitalized records of ELBW infants discharged from twenty-six neonatal intensive care units in Guangdong Province of China during 2008-2017 were analyzed. A total of 2575 ELBW infants were enrolled and the overall survival rate was 55.11%. From 2008 to 2017, the number of ELBW infants increased rapidly from 91 to 466, and the survival rate improved steadily from 41.76% to 62.02%. Increased survival is closely related to birth weight (BW), regional economic development, and specialized hospital. The incidence of complications was neonatal respiratory distress syndrome (85.2%), oxygen dependency at 28 days (63.7%), retinopathy of prematurity (39.3%), intraventricular hemorrhage (29.4%), necrotizing enterocolitis (12.0%), and periventricular leukomalacia (8.0%). Among the 1156 nonsurvivors, 90.0% of infants died during the neonatal period (≤ 28 days). A total of 768 ELBW infants died after treatment withdrawal, for reasons of economic and/or poor outcome. The number of ELBW infants is increasing in Guangdong Province of China, and the overall survival rate is improving steadily.

AB0596 AORTIC MANIFESTATIONS IN GIANT CELL ARTERITIS: SINGLE CENTRE 10-YEAR EXPERIENCE

Background

Disease stratification in GCA is an urgent need, with patients categorised into cranial and large-vessel GCA (LV-GCA) subgroups. LV-GCA may have worse outcomes with regards relapsing disease, poor response to glucocorticoids (GC) and aortic involvement.

Objectives

We report a single centre experience using clinical, imaging and treatment outcomes from a specialist clinic.

Methods

134 patients with LV-GCA were identified over a 10-year period at Southend University Hospital (2012-2022). Medical records were reviewed retrospectively for baseline demographics, clinical presentation, inflammatory markers, imaging (vascular ultrasound, PET-CT, echocardiography), vascular damage and treatment.

Results

There was a female predominance (female n=91). Age at presentation ranged from 46 to 86 years (median 70 years). Co-morbidities implicated in aortic disease included hypertension (n=60), hypercholestrolaemia (n=29), diabetes (n=14), aortic valvular disease (n=5) and atherosclerotic disease including coronary and carotid artery disease (n=19). Constitutional disturbance was most frequently observed presentation (70%, n=94), and the only feature for 11 patients. This was followed by cranial symptoms (62%, n=83), polymyalgia (53%, n=71), ischaemic symptoms i.e., visual disturbance or tongue/jaw claudication (24%, n=32) and cardiovascular presentations (7%, n=9). The latter included limb claudication, stroke, and aortic aneurysm. Although LV-GCA refers to extra-cranial disease, 12 patients (9%) had isolated cranial and/or ischaemic symptoms at initial presentation.

Inflammatory markers were typically elevated at presentation, C-reactive protein ranged from 1-425mg/L and ESR 1-130mm. Vascular ultrasound was used at diagnosis in 93 patients, with positive temporal artery findings in 50% (n=38) and positive axillary findings in 75% (n=57). PET-CT data was available for 125 patients, of which 113 were positive for LV-GCA. Thoracic aorta FDG-uptake was seen in 77%, with 7 ascending and 1 abdominal aortic aneurysm observed. Transthoracic echocardiogram was available for 46% (n=62). Four (6.5%) patients had a dilated aortic root when indexed to height as per British Society of Echocardiography (BSE) guidelines1 (SOV (mm/m) > 21.8mm in males and > 20.7mm in females). Values for our patients were 22.6 and 21.2 mm/m for the female patients and 29.2 and 25.2 mm/m for the male patients. Furthermore, 32 patients showed some extent of diastolic dysfunction as per BSE criteria (52%).

All patients received GC as part of their treatment, 60% (n=82) needing one or more DMARDs and 17% (n=23) Tocilizumab for relapsing disease. DMARDs used included Leflunomide (n=63), Methotrexate (n=18), Mycophenolate mofetil (n=3) and Azathioprine (n=1). One patient received cyclophosphamide.

Conclusion

By combined imaging modalities, 11 patients (8%) had evidence of ascending aortic damage. Grade 1 diastolic dysfunction can be age related, so this may be association rather than causation2,3. Over half of patients had not undergone echocardiogram evaluation, so there may be a hidden burden of disease. Many patients required GC-sparing therapy, showing GC alone are often not enough to halt disease progression, and vascular damage was relatively reduced compared to historical reports. The authors feel GCA services should include standardised protocols for early DMARDs, continuing thorough assessment for LV-GCA and vascular damage, including echocardiography, progressing to cross-sectional imaging if indicated.

References

[1]Harkness A. et al. Normal reference intervals for cardiac dimensions and function for use in echocardiographic practice: a guideline from the British Society of Echocardiography”. Echo Research and Practice 7.1 (2020): G1-G18.

[2]Sanders, D et al. Diastolic dysfunction, cardiovascular aging, and the anesthesiologist. Anesthesiology clinics vol. 27,3 (2009): 497-517.

[3]Jakovljevic and Djordje G. Physical activity and cardiovascular aging: Physiological and molecular insights. Experimental gerontology vol. 109 (2018): 67-74.

Disclosure of Interests

None declared

Comparative Outcomes for Trauma Patients in Prison and the General Population

BACKGROUND

Prisoners are a vulnerable population, and there are few contemporary studies that consider trauma patient outcomes within the prisoner population. Therefore, we sought to provide a descriptive analysis of prisoners involved in trauma and evaluate whether a healthcare disparity exists. We hypothesized that prisoners and non-prisoners have a similar risk of mortality and in-hospital complications after trauma.

METHODS

The Trauma Quality Improvement Program (2015-2016) was queried for trauma patients based upon location inside or outside of prison at the time of injury. A multivariable logistic regression analysis was performed to compare these groups for risk of mortality-the primary outcome.

RESULTS

From 593,818 trauma patients, 1115 were located in prison. Compared to non-prisoners, prisoner trauma patients had no significant difference in mortality (5.1 vs 6.0%, P = .204). However, after adjusting for covariates, prisoners had a shorter length of stay (LOS) (mean days, 6.3 vs 7.8, P < .001), shorter intensive care unit (ICU) LOS (mean days, 5.44 vs 5.89, P = .004), and fewer complications, including lower rates of drug/alcohol withdrawal (.4% vs 1.1%, P = .030), pneumonia (.5 vs 1.6%, P = .004), and urinary tract infections (.0 vs 1.1%, P < .001). Upon performing a multivariable logistic regression model, prisoner trauma patients had a similar associated risk of mortality compared to non-prisoners (OR 1.61, CI .52-4.94, P = .409).

DISCUSSION

Our results suggest that prisoner trauma patients at least receive equivalent treatment in terms of mortality and may have better outcomes when considering some complications. Future prospective studies are needed to confirm these results and explore other factors, which impact prisoner patient outcomes.

Regional variations in discrete collagen fibre mechanics within intact intervertebral disc resolved using synchrotron computed tomography and digital volume correlation

Many soft tissues, such as the intervertebral disc (IVD), have a hierarchical fibrous composite structure which suffers from regional damage. We hypothesise that these tissue regions have distinct, inherent fibre structure and structural response upon loading. Here we used synchrotron computed tomography (sCT) to resolve collagen fibre bundles (∼5μm width) in 3D throughout an intact native rat lumbar IVD under increasing compressive load. Using intact samples meant that tissue boundaries (such as endplate-disc or nucleus-annulus) and residual strain were preserved; this is vital for characterising both the inherent structure and structural changes upon loading in tissue regions functioning in a near-native environment. Nano-scale displacement measurements along >10,000 individual fibres were tracked, and fibre orientation, curvature and strain changes were compared between the posterior-lateral region and the anterior region. These methods can be widely applied to other soft tissues, to identify fibre structures which cause tissue regions to be more susceptible to injury and degeneration. Our results demonstrate for the first time that highly-localised changes in fibre orientation, curvature and strain indicate differences in regional strain transfer and mechanical function (e.g. tissue compliance). This included decreased fibre reorientation at higher loads, specific tissue morphology which reduced capacity for flexibility and high strain at the disc-endplate boundary.

Statement of significance

The analyses presented here are applicable to many collagenous soft tissues which suffer from regional damage. We aimed to investigate regional intervertebral disc (IVD) structural and functional differences by characterising collagen fibre architecture and linking specific fibre- and tissue-level deformation behaviours. Synchrotron CT provided the first demonstration of tracking discrete fibres in 3D within an intact IVD. Detailed analysis of regions was performed using over 200k points, spaced every 8 μm along 10k individual fibres. Such comprehensive structural characterisation is significant in informing future computational models. Morphological indicators of tissue compliance (change in fibre curvature and orientation) and fibre strain measurements revealed localised and regional differences in tissue behaviour.

The Survival Rate of Extremely Low Birth Weight Infants Improved in Guangdong Province, China.. [DOI: 10.21203/rs.3.rs-1019118/v2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0]

Background With the increase in extremely low birth weight (ELBW) infants, their outcomes received special attention. However, in China, studies of the outcomes of ELBW infants are rare. Methods The hospitalized records of ELBW infants discharged from twenty-six neonatal intensive care units were reviewed and analyzed. Results A total of 2575 ELBW infants were enrolled and the overall survival rate was 55.11%. From 2008 to 2017, the number of ELBW infants increased rapidly from 91 to 466, and the survival rate improved steadily from 41.76–62.02%. The survival rate rose with increasing BW, the ascending level of regional economic development and specialist hospitals. The incidence of complications was neonatal respiratory distress syndrome (85.2%), bronchopulmonary dysplasia (63.7%), retinopathy of prematurity (39.3%), intraventricular hemorrhage (29.4%), necrotizing enterocolitis (12.0%), and periventricular leukomalacia (8.0%). Among the 1156 nonsurvivors, 90.0% of infants died during the neonatal period (≤ 28 days), and the other died after the neonatal period. A total of 768 ELBW infants died after medical care withdrawal, with economic factors and expected outcome being important causes. Conclusion The number of ELBW infants is increasing in China, and the overall survival rate is still low but is improving steadily.

Baseline Values of Left Ventricular Systolic Function in Preterm Infants With Septic Shock: A Prospective Observational Study

BACKGROUND AND AIM

Guidelines recommended that cardiac index (CI) of term infants with septic shock should reach the target level of 3.3-6.0L/(min⋅m²). However, there are still no standard values for preterm infants with septic shock. Herein, we investigated the functional echocardiographic baseline values of left ventricular (LV) systolic functional parameters at the onset of septic shock in preterm infants and possible correlations between baseline values and poor outcomes.

MATERIALS AND METHODS

This was a prospective, observational, and longitudinal single-center study. Eligible infants were monitored for LV systolic functional parameters using functional echocardiography at the onset of septic shock. The primary study outcome was the difference in the baseline value of LV systolic functional parameters in preterm infants with septic shock with different gestational age (GA) and birth weight (BW). The secondary outcome was septic shock-associated death or severe brain injury (including grade 3-4 intraventricular hemorrhage or periventricular leukomalacia).

RESULTS

In total, 43 subjects met the criteria, with a median GA of 32^1/7 weeks and BW of 1800 grams. No difference was observed in baseline values of LV systolic functional parameters among infants with different GA and BW. Infants were assigned to good and poor outcomes groups based on septic shock-associated death or severe brain injury. Out of 43 infants, 29 (67.4%) had good outcomes vs. 14 (32.6%) with poor outcomes. Stroke index (SI) [18.2 (11.1, 18.9) mL/m² vs. 23.5 (18.9, 25.8) mL/m², p = 0.017] and cardiac index (CI)[2.7 (1.6, 3.5) L/(min⋅m²) vs. 3.4 (3.0, 4.8) L/(min⋅m²), p = 0.015] in infants with poor outcomes were significantly lower (P < 0.05). Receiver operating characteristic (ROC) curve analysis showed that the cut-off values of SI and CI for predicting poor outcomes in preterm infants with septic shock were 19.5 mL/m² (sensitivity, 73.9%; specificity, 81.8%) and 2.9L/(min⋅m²) (sensitivity, 78.3%; specificity, 72.7%), with area under the ROC curve (AUC) value of 0.755 and 0.759, respectively.

CONCLUSION

There were no differences in baseline LV systolic functional values among preterm infants with septic shock with different GA and BW. However, preterm infants with SI<19.5mL/m² and/or CI<2.9L/(min⋅m²) at the onset of septic shock were at high risk of having poor outcomes.

COVID19db: a comprehensive database platform to discover potential drugs and targets of COVID-19 at whole transcriptomic scale

Many open access transcriptomic data of coronavirus disease 2019 (COVID-19) were generated, they have great heterogeneity and are difficult to analyze. To utilize these invaluable data for better understanding of COVID-19, additional software should be developed. Especially for researchers without bioinformatic skills, a user-friendly platform is mandatory. We developed the COVID19db platform (http://hpcc.siat.ac.cn/covid19db & http://www.biomedical-web.com/covid19db) that provides 39 930 drug–target–pathway interactions and 95 COVID-19 related datasets, which include transcriptomes of 4127 human samples across 13 body sites associated with the exposure of 33 microbes and 33 drugs/agents. To facilitate data application, each dataset was standardized and annotated with rich clinical information. The platform further provides 14 different analytical applications to analyze various mechanisms underlying COVID-19. Moreover, the 14 applications enable researchers to customize grouping and setting for different analyses and allow them to perform analyses using their own data. Furthermore, a Drug Discovery tool is designed to identify potential drugs and targets at whole transcriptomic scale. For proof of concept, we used COVID19db and identified multiple potential drugs and targets for COVID-19. In summary, COVID19db provides user-friendly web interfaces to freely analyze, download data, and submit new data for further integration, it can accelerate the identification of effective strategies against COVID-19.

circMine: a comprehensive database to integrate, analyze and visualize human disease-related circRNA transcriptome

Many circRNA transcriptome data were deposited in public resources, but these data show great heterogeneity. Researchers without bioinformatics skills have difficulty in investigating these invaluable data or their own data. Here, we specifically designed circMine (http://hpcc.siat.ac.cn/circmine and http://www.biomedical-web.com/circmine/) that provides 1 821 448 entries formed by 136 871 circRNAs, 87 diseases and 120 circRNA transcriptome datasets of 1107 samples across 31 human body sites. circMine further provides 13 online analytical functions to comprehensively investigate these datasets to evaluate the clinical and biological significance of circRNA. To improve the data applicability, each dataset was standardized and annotated with relevant clinical information. All of the 13 analytic functions allow users to group samples based on their clinical data and assign different parameters for different analyses, and enable them to perform these analyses using their own circRNA transcriptomes. Moreover, three additional tools were developed in circMine to systematically discover the circRNA-miRNA interaction and circRNA translatability. For example, we systematically discovered five potential translatable circRNAs associated with prostate cancer progression using circMine. In summary, circMine provides user-friendly web interfaces to browse, search, analyze and download data freely, and submit new data for further integration, and it can be an important resource to discover significant circRNA in different diseases.

CanImmunother: a manually curated database for identification of cancer immunotherapies associating with biomarkers, targets, and clinical effects

As immunotherapy is evolving into an essential armamentarium against cancers, numerous translational studies associated with relevant biomarkers, targets, and clinical effects have been reported in recent years. However, a large amount of associated experimental data remains unexplored due to the difficulty in accessibility and utilization. Here, we established a comprehensive high-quality database for cancer immunotherapy called CanImmunother (http://www.biomedical-web.com/cancerit/) through manual curation on 4515 publications. CanImmunother contains 3267 experimentally validated associations between 218 cancer sub-types across 34 body parts and 484 immunotherapies with 642 biomarkers, 108 targets, and 121 control therapies. Each association was manually curated by professional curators, incorporated with valuable annotation and cross references, and assigned with an association score for prioritization. To help clinicians and researchers in identifying and discovering better cancer immunotherapy and their respective biomarkers and targets, CanImmunother offers user-friendly web applications including search, browse, excel table, association prioritization, and network visualization. CanImmunother presents a landscape of experimental cancer immunotherapy association data, serving as a useful resource to improve our insight and to facilitate further discovery of advanced immunotherapy options for cancer patients.

TFPI2 Promotes Perivascular Migration in an Angiotropism Model of Melanoma

Purpose

Angiotropism is the process by which cancer cells attach to and migrate along blood vessels to acquire vasculature, disseminate, and metastasize. However, the molecular basis for such vessel–tumor interactions has not been fully elucidated, partly due to limited experimental models. In this study, we aimed to observe and explore the molecular mechanism underlying angiotropism in melanoma.

Methods

To monitor the interactions of human melanoma cells with the vasculature in vivo, a murine coxenograft model was employed by co-injecting highly and poorly invasive melanoma cells subcutaneously. To identify key pathways and genes involved in the angiotropic phenotype of melanoma, analysis of differentially expressed genes (DEGs) and gene set enrichment analysis (GSEA) were performed. The role of tissue factor pathway inhibitor 2 (TFPI2) in angiotropism was evaluated by immunostaining, adhesion assay, shRNA, and in vivo tumorigenicity. Angiotropism and TFPI2 expression were examined in surgical specimens of melanoma by immunohistochemical staining. Data from The Cancer Genome Atlas (TCGA) were analyzed to explore the expression and prognostic implications of TFPI2 in uveal and cutaneous melanoma.

Results

Highly invasive melanoma cells spread along the branches of intratumor blood vessels to the leading edge of invasion in the coxenograft model, resembling angiotropic migration. Mechanisms underlying angiotropism were primarily associated with molecular function regulators, regulation of cell population proliferation, developmental processes, cell differentiation, responses to cytokines and cell motility/locomotion. TFPI2 downregulation weakened the perivascular migration of highly invasive melanoma cells. High levels of TFPI2 were correlated with worse and better survival in uveal and cutaneous melanoma, respectively.

Conclusion

These results provide a straightforward in vivo model for the observation of angiotropism and suggest that TFPI2 could inhibit the angiotropic phenotype of melanoma.

Intercropping of Peanut-Tea Enhances Soil Enzymatic Activity and Soil Nutrient Status at Different Soil Profiles in Subtropical Southern China

Intercropping is one of the most widely used agroforestry techniques, reducing the harmful impacts of external inputs such as fertilizers. It also controls soil erosion, increases soil nutrients availability, and reduces weed growth. In this study, the intercropping of peanut (Arachishypogaea L.) was done with tea plants (Camellia oleifera), and it was compared with the mono-cropping of tea and peanut. Soil health and fertility were examined by analyzing the variability in soil enzymatic activity and soil nutrients availability at different soil depths (0-10 cm, 10-20 cm, 20-30 cm, and 30-40 cm). Results showed that the peanut-tea intercropping considerably impacted the soil organic carbon (SOC), soil nutrient availability, and soil enzymatic responses at different soil depths. The activity of protease, sucrase, and acid phosphatase was higher in intercropping, while the activity of urease and catalase was higher in peanut monoculture. In intercropping, total phosphorus (TP) was 14.2%, 34.2%, 77.7%, 61.9%; total potassium (TK) was 13.4%, 20%, 27.4%, 20%; available phosphorus (AP) was 52.9%, 26.56%, 61.1%; 146.15% and available potassium (AK) was 11.1%, 43.06%, 46.79% higher than the mono-cropping of tea in respective soil layers. Additionally, available nitrogen (AN) was 51.78%, 5.92%, and 15.32% lower in the 10-20 cm, 20-30 cm, and 30-40 cm layers of the intercropping system than in the mono-cropping system of peanut. Moreover, the soil enzymatic activity was significantly correlated with SOC and total nitrogen (TN) content across all soil depths and cropping systems. The depth and path analysis effect revealed that SOC directly affected sucrase, protease, urease, and catalase enzymes in an intercropping system. It was concluded that an increase in the soil enzymatic activity in the intercropping pattern improved the reaction rate at which organic matter decomposed and released nutrients into the soil environment. Enzyme activity in the decomposition process plays a vital role in forest soil morphology and function. For efficient land use in the cropping system, it is necessary to develop coherent agroforestry practices. The results in this study revealed that intercropping certainly enhance soil nutrients status and positively impacts soil conservation.

[Chaihu Guizhi decoction produces antidepressant-like effects via sirt1-p53 signaling pathway]

OBJECTIVE

To investigate the mechanism of the antidepressant-like effects of Chaihu Guizhi decoction (CGD).

OBJECTIVE

Chaihu Guizhi decoction at the daily dose of 17 g/kg and solvent vehicle were administered by gavage in 12 and 14 male C57BL/6J mice for 7 consecutive days, respectively. Forced swimming test (FST), elevated plus maze (EPM) test, open field test (OFT) and novelty-suppressed feeding test (NSF) were performed to assess the depression- and anxiety-like behaviors and motor ability of the mice. We further used chronic social defeat stress (CSDS) and social interaction test to evaluate the antidepressant-like effects of CGD in comparison with the solvent vehicle. Western blotting and RT-qPCR were performed to detect the expressions of sirt1, p53, acetylated p53, and the neuron plasticity-related genes including synapsin I (Syn1), Rab4B, SNAP25 and tubulin beta4b in the hippocampus of the mice.

OBJECTIVE

In FST, the immobility time of CGDtreated mice was decreased significantly (P < 0.05); no significant differences were found in the performances in EPM, NSF and OFT tests between the two groups. In social interaction test, the mouse models of CSDS treated with CGD showed significantly increased time in the interaction zone (P < 0.05). Compared with those in the vehicle group, the CGD-treated mouse models exhibited significantly increased protein level of SIRT1 and decreased p53 acetylation (P < 0.05) with up-regulated synapsin I mRNA expression in the hippocampus (P < 0.05); no significant difference were found in Rab (P=0.813), SNAP (P=0.820), or Tubb mRNA expressions (P=0.864) between the two groups.

OBJECTIVE

CGD produces antidepressant-like effects in mice possibly through the sirt1-p53 signaling pathway and synaptic plasticity.

N3 -Kethoxal-Based Bioorthogonal Intracellular RNA Labeling

There is growing interest in developing intracellular RNA tools. Herein, we describe a strategy for N₃ -kethoxal (N₃ K)-based bioorthogonal intracellular RNA functionalization. With N₃ K labeling followed by an in vivo click reaction with DBCO derivatives, RNA can be modified with fluorescent or phenol groups. This strategy provides a new way of labeling RNA inside cells.

4-Thiouridine-Enhanced Peroxidase-Generated Biotinylation of RNA

Peroxidase-generated proximity labeling is in widespread use to study subcellular proteomes and the protein interaction networks in living cells, but the development of subcellular RNA labeling is limited. APEX-seq has emerged as a new method to study subcellular RNA in living cells, but the labeling of RNA still has room to improve. In this work, we describe 4-thiouridine (s⁴ U)-enhanced peroxidase-generated biotinylation of RNA with high efficiency. The incorporation of s⁴ U could introduce additional sites for RNA labeling, enhanced biotinylation was observed on monomer, model oligo RNA and total RNA. Through the s⁴ U metabolic approach, the in vivo RNA biotinylation efficiency by peroxidase catalysis was also dramatically increased, which will benefit RNA isolation and study for the spatial transcriptome.

TRADES: Targeted RNA Demethylation by SunTag System

N6-methyladenosine (m6A) is rapidly being studied and uncovered to play a significant role in various biological processes as well as in RNA fate and functions, while the effects of defined m6A sites are rarely characterized for the lack of convenient tools. To provide an applicable method to remove m6A modification at specific loci, an m6A editing system called "targeted RNA demethylation by SunTag system (TRADES)" is engineered. In this system, the targeting element dCas13b is fused to ten copies of GCN4 peptides which can recruit multiple scFv-fusion RNA demethylase to demethylate the target m6A site. Owing to this design, TRADES is more flexible to the indistinct m6A sites for its wide editing window. By site-specific demethylation of messenger RNA (mRNA) SON A2699, the lifetime of SON RNA is successfully prolonged in HeLa cells. Meanwhile, TRADES negligibly influences the lifetime of other non-targeted transcripts. TRADES also can regulate the gene expression of target transcript in an m6A-dependent manner. Moreover, the interference occuring for HBV and HIV replications demonstrates that the TRADES system holds potential in viral life cycle regulation and clinical applications.

The role of fibroblast activation protein in progression and development of osteosarcoma cells

To investigate the expression levels of fibroblast activation protein (FAP) in human osteosarcoma tissues and its possible correlations with clinical pathological characteristics of patients with osteosarcoma, and to explore the potential effects of FAP on progression and development of osteosarcoma. Immunohistochemistry (IHC) assay was initially performed to detect the expression levels of FAP in 66 tumor tissues and adjacent non-tumor tissues. Patients were sequentially divided into two groups based on different expression levels of FAP. The correlations between the expression levels of FAP and the clinical pathological characteristics were investigated, and the role of FAP in proliferation, migration, and invasion of osteosarcoma cells was assessed via colony formation, MTT, wound healing, and transwell assays, respectively. The possible effects of FAP on tumor growth and metastasis were evaluated in vivo. We further attempted to reveal the underlying mechanism of FAP involved in tumor growth through bioinformatics and IHC assays. High expression levels of FAP were noted in human osteosarcoma tissues. It also was unveiled that FAP was significantly associated with the tumor size (P = 0.005*) and clinical stage (P = 0.017*). Our data further confirmed that knockdown of FAP remarkably blocked proliferation, migration, and invasion of osteosarcoma cells in vitro, and suppressed tumor growth and metastasis in mice via AKT signaling pathway. The possible role of FAP in progression and development of osteosarcoma could be figured out. Our data may be helpful to develop a novel therapeutic target for the treatment of osteosarcoma.

Second-order QCD corrections to event shape distributions in deep inelastic scattering

We compute the next-to-next-to-leading order (NNLO) QCD corrections to event shape distributions and their mean values in deep inelastic lepton-nucleon scattering. The magnitude and shape of the corrections varies considerably between different variables. The corrections reduce the renormalization and factorization scale uncertainty of the predictions. Using a dispersive model to describe non-perturbative power corrections, we compare the NNLO QCD predictions with data from the H1 and ZEUS experiments. The newly derived corrections improve the theory description of the distributions and of their mean values.

Short-term outcomes of extremely preterm infants at discharge: a multicenter study from Guangdong province during 2008-2017

BACKGROUND

An increasing number of extremely preterm (EP) infants have survived worldwide. However, few data have been reported from China. This study was designed to investigate the short-term outcomes of EP infants at discharge in Guangdong province.

METHODS

A total of 2051 EP infants discharged from 26 neonatal intensive care units during 2008-2017 were enrolled. The data from 2008 to 2012 were collected retrospectively, and from 2013 to 2017 were collected prospectively. Their hospitalization records were reviewed.

RESULTS

During 2008-2017, the mean gestational age (GA) was 26.68 ± 1.00 weeks and the mean birth weight (BW) was 935 ± 179 g. The overall survival rate at discharge was 52.5%. There were 321 infants (15.7%) died despite active treatment, and 654 infants (31.9%) died after medical care withdrawal. The survival rates increased with advancing GA and BW (p < 0.001). The annual survival rate improved from 36.2% in 2008 to 59.3% in 2017 (p < 0.001). EP infants discharged from hospitals in Guangzhou and Shenzhen cities had a higher survival rate than in others (p < 0.001). The survival rate of EP infants discharged from general hospitals was lower than in specialist hospitals (p < 0.001). The major complications were neonatal respiratory distress syndrome, 88.0% (1804 of 2051), bronchopulmonary dysplasia, 32.3% (374 of 1158), retinopathy of prematurity (any grade), 45.1% (504 of 1117), necrotizing enterocolitis (any stage), 10.1% (160 of 1588), intraventricular hemorrhages (any grade), 37.4% (535 of 1431), and blood culture-positive nosocomial sepsis, 15.7% (250 of 1588). The multivariate logistic regression analysis indicated that improved survival of EP infants was associated with discharged from specialist hospitals, hospitals located in high-level economic development region, increasing gestational age, increasing birth weight, antenatal steroids use and a history of premature rupture of membranes. However, twins or multiple births, Apgar ≤7 at 5 min, cervical incompetence, and decision to withdraw care were associated with decreased survival.

CONCLUSIONS

Our study revealed the short-term outcomes of EP infants at discharge in China. The overall survival rate was lower than the developed countries, and medical care withdrawal was a serious problem. Nonetheless, improvements in care and outcomes have been made annually.

[Molecular Mechanisms of Apoptosis of Leukemia Cell Induced by Reovirus]

OBJECTIVE

To investigate the molecular mechanism of apoptosis of HL60 cells induced by oncolytic virus Reovirus type 3 (Reo3).

METHODS

HL60 cells were infected with Reo3 at different multiplicity of infection (MOI) with the uninfected HL60 cells as control group. After 48 h of infection, the activity of HL60 cells infected with virus at different MOI was detected by CCK8 method to investigate the influence of MOI to cell activity. Simultaneously, the apoptotic rate of HL60 cells was detected by flow cytometry, and the activation level of double-stranded RNA-dependent protein kinase (PKR) and the expression of apoptotic-related protein in HL60 cells were detected by Western blot. Before infection with Reo3 for 48 h, HL60 cells were treated with 2-aminopurine (2-AP), a specific inhibitor of PKR, for 24 h. Afterward, the apoptotic level and expression of apoptotic related proteins were detected.

RESULTS

Activity of HL60 cells was obviously inhibited after infected with Reo3 with a MOI of 1 for 48 h. The cell survival rate was (24.333±3.396)% and the apoptotic rate was (29.96±2.06)%. Both rates were all higher than those in the control group (P < 0.05). Western blot results showed that the expression levels of PKR, p-PKR, Bax, Caspase3 and cleaved Caspase3 in HL60 cells infected with Reo3 were higher than those in the control group (P < 0.05), while the expression level of Bcl-2 was lower (P < 0.05). Compared with the group without inhibitor, the apoptotic rate of HL60 cells pretreated with 2-AP decreased (P < 0.05), the phosphorylation level of PKR and the expression level of apoptotic-related protein also decreased (P < 0.05).

CONCLUSION

Oncolytic virus Reo3 could activate PKR in HL60 cells and thus induce apoptosis of HL60 cells.

IL-33/ST2 Axis Regulates Vasculogenic Mimicry via ERK1/2-MMP-2/9 Pathway in Melanoma

BACKGROUND

Melanoma, an extremely malignant form of cancer, poses a significant health risk. Vasculogenic mimicry (VM), blood vessels formed by tumor cells instead of endothelial cells, is an important factor for the rapid progression of melanoma. Interleukin (IL)-33 is an inflammatory factor commonly found in the tumor microenvironment and plays an important role in the progression of many tumors. IL-33 acts on immune cells and tumor cells through its receptor ST2. This study hypothesized that IL-33 directly affects the progression of melanoma.

OBJECTIVES

This study was designed to investigate the effect of IL-33 on VM of melanoma and its potential mechanism of action.

METHODS

The expression of ST2 was evaluated in 66 cases of melanoma collected from human patients, and the differences were analyzed. In vitro experiments were conducted to study the effects of the IL-33/ST2 axis on cell migration and invasion and to elucidate possible mechanisms.

RESULTS

ST2 expression is associated with that of matrix metalloproteinase (MMP)-2 and VM in melanoma of patients. IL-33 increases the abilities of proliferation, migration and invasion of melanoma cells and VM tube formation through ST2. IL-33 induces the production of MMP-2/9 via ERK1/2 phosphorylation.

CONCLUSION

IL-33 can directly act on melanoma cells and promote its development.

[Wnt/β-catenin signaling pathway involved in the expression and drug resistance of abcb4 gene in transgenic zebrafish induced by chemotherapeutic drugs]

Objective To explore the relationship between the drug resistance gene ATP binding cassette sub-family B member 4 (abcb4) in zebrafish and Wnt/β-catenin signaling pathway. Methods Wild-type zebrafish and transgenic zebrafish were set in the blank control group, doxorubicin treatment group, vinblastine treatment group, gefitinib treatment group, doxorubicin combined with gefitinib treatment group, and vinblastine combined with gefitinib treatment group. The 100 embryos of each group were treated with drugs until the 5th day, and 50 zebrafish juveniles were tested on the 5th day in each group. The drug resistance of wild-type zebrafish was tested by rhodamine 123 experiment. The fluorescence intensity of transgenic zebrafish was tested by microplate reader, and the fluorescence distribution was tested by living cell workstation. The protein levels of transgenic zebrafish β-catenin, GSK-3β, ABCB4 and enhanced green fluorescent protein (EGFP) were tested by Western blot analysis. Results Rhodamine 123 experiments proved that there was drug resistance in zebrafish when treated with doxorubicin and vinblastine. Compared with the blank group, the EGFP fluorescence intensity increased in the transgenic zebrafish when treated with doxorubicin and vinblastine. Western blot assay showed the accumulation of β-catenin accompanied by the increase of EGFP and ABCB4 proteins in the transgenic zebrafish exposed to adriamycin and vincristine. Conclusion The Wnt/β-catenin signaling pathway in zebrafish is involved in the activation and drug resistance of zebrafish abcb4 gene.

Epigenetic modification of nucleic acids: from basic studies to medical applications

The epigenetic modification of nucleic acids represents one of the most significant areas of study in the field of nucleic acids because it makes gene regulation more complex and heredity more complicated, thus indicating its profound impact on aspects of heredity, growth, and diseases. The recent characterization of epigenetic modifications of DNA and RNA using chemical labelling strategies has promoted the discovery of these modifications, and the newly developed single-base or single-cell resolution mapping strategies have enabled large-scale epigenetic studies in eukaryotes. Due to these technological breakthroughs, several new epigenetic marks have been discovered that have greatly extended the scope and impact of epigenetic modifications in nucleic acids over the past few years. Because epigenetics is reversible and susceptible to environmental factors, it could potentially be a promising direction for clinical medicine research. In this review, we have comprehensively discussed how these epigenetic marks are involved in disease, including the pathogenesis, prevention, diagnosis and treatment of disease. These findings have revealed that the epigenetic modification of nucleic acids has considerable significance in various areas from methodology to clinical medicine and even in biomedical applications.

An in-situ thermally regenerated air purifier for indoor formaldehyde removal

Formaldehyde is a common indoor pollutant that is an irritant and has been classified as carcinogen to humans. Adsorption technology is safe and stable and removes formaldehyde efficiently, but its short life span and low adsorption capacity limit its indoor application. To overcome these limitations, we propose an in-situ thermally regenerated air purifier (TRAP) which self-regenerates as needed. This purifier has four working modes: cleaning mode, regeneration mode, exhaust mode, and outdoor air in-take mode, all of which are operated by valve switching. We developed a real-scale TRAP prototype with activated carbon as adsorbent. The experimental testing showed that the regeneration ratios for formaldehyde of TRAP were greater than 90% during 5 cycles of adsorption-regeneration and that through the 5 cycles, there was no damage to the adsorption material as confirmed by scanning electron microscope (SEM) and Brunauer-Emmett-Teller (BET) tests. The total energy consumption by the prototype for purifying 1000 m³ indoor air was 0.26 kWh. This in-situ thermal-regeneration method can recover the purifier's adsorption ability through at least five cycles.

A rapidly photo-activatable light-up fluorescent nucleoside and its application in DNA base variation sensing

A new DNA building block (d(Tet)U) bearing a tetrazole and allyloxy group at N-phenyl ring linked through an aminopropynyl linker to the 5-position of 2'-deoxyuridine was synthesized. The modified DNA can be lit up via a photoinduced intramolecular tetrazole-alkene cycloaddition reaction, but quenched when the fully-matched double strand is formed. This conspicuous difference in fluorescence could open a door for DNA single nucleotide polymorphism (SNP) typing.

Voriconazole and squamous cell carcinoma after lung transplantation: A multicenter study

This study evaluated the independent contribution of voriconazole to the development of squamous cell carcinoma (SCC) in lung transplant recipients, by attempting to account for important confounding factors, particularly immunosuppression. This international, multicenter, retrospective, cohort study included adult patients who underwent lung transplantation during 2005-2008. Cox regression analysis was used to assess the effects of voriconazole and other azoles, analyzed as time-dependent variables, on the risk of developing biopsy-confirmed SCC. Nine hundred lung transplant recipients were included. Median follow-up time from transplantation to end of follow-up was 3.51 years. In a Cox regression model, exposure to voriconazole alone (adjusted hazard ratio 2.39, 95% confidence interval 1.31-4.37) and exposure to voriconazole and other azole(s) (adjusted hazard ratio 3.45, 95% confidence interval 1.07-11.06) were associated with SCC compared with those unexposed after controlling for important confounders including immunosuppressants. Exposure to voriconazole was associated with increased risk of SCC of the skin in lung transplant recipients. Residual confounding could not be ruled out because of the use of proxy variables to control for some confounders. Benefits of voriconazole use when prescribed to lung transplant recipients should be carefully weighed versus the potential risk of SCC. EU PAS registration number: EUPAS5269.