Small RNA sequencing reveals miRNAs important for hypoxic adaptation in the Tibetan chicken

1. The Tibetan chicken, which is an indigenous breed living on the Tibetan Plateau, exhibits hypoxic adaptations to its high-altitude environment. However, the molecular mechanism behind this hypoxic adaptation is still unclear. This study aimed to investigate differentially expressed miRNAs involved in hypoxic adaptation through high-throughput RNA sequencing. 2. Quantitative reverse transcription polymerase chain reaction (qRT-PCR) was used to verify the differentially expressed miRNAs and their target genes in chicken embryonic heart tissues and fibroblasts. Luciferase reporter assays were performed to confirm the relationship between miRNAs and target genes. 3. The study identified 37 differentially expressed miRNAs in Tibetan chicken embryonic heart tissues, including 20 up- and 17 down-regulated miRNAs, compared to those found in lowland chickens. Differentially expressed miRNAs were mainly involved in biological processes, such as cell cycle arrest, toll-like receptor signalling pathways, and I-kappa B kinase/NF-kappa B signalling. The data showed that gga-miR-34 c-5p was significantly upregulated in Tibetan chicken tissues and hypoxic fibroblasts, while EHHADH, a target gene of gga-miR-34 c-5p, was downregulated. Moreover, gga-miR-34 c-5p dramatically decreased the luciferase activity of the wild EHHADH, whereas no effect on the mutational EHHADH was found. 4. This study identified miRNA expression profiles in the Tibetan chicken and suggested that miR-34 c-5p acts as a novel miRNA associated with hypoxic adaptation. This facilitates the understanding of molecular mechanisms that underlie long-term exposure to hypoxia.

Automatic Machine Learning to Differentiate Pediatric Posterior Fossa Tumors on Routine MR Imaging

BACKGROUND AND PURPOSE

Differentiating the types of pediatric posterior fossa tumors on routine imaging may help in preoperative evaluation and guide surgical resection planning. However, qualitative radiologic MR imaging review has limited performance. This study aimed to compare different machine learning approaches to classify pediatric posterior fossa tumors on routine MR imaging.

MATERIALS AND METHODS

This retrospective study included preoperative MR imaging of 288 patients with pediatric posterior fossa tumors, including medulloblastoma (n = 111), ependymoma (n = 70), and pilocytic astrocytoma (n = 107). Radiomics features were extracted from T2-weighted images, contrast-enhanced T1-weighted images, and ADC maps. Models generated by standard manual optimization by a machine learning expert were compared with automatic machine learning via the Tree-Based Pipeline Optimization Tool for performance evaluation.

RESULTS

For 3-way classification, the radiomics model by automatic machine learning with the Tree-Based Pipeline Optimization Tool achieved a test micro-averaged area under the curve of 0.91 with an accuracy of 0.83, while the most optimized model based on the feature-selection method χ2 score and the Generalized Linear Model classifier achieved a test micro-averaged area under the curve of 0.92 with an accuracy of 0.74. Tree-Based Pipeline Optimization Tool models achieved significantly higher accuracy than average qualitative expert MR imaging review (0.83 versus 0.54, P < .001). For binary classification, Tree-Based Pipeline Optimization Tool models achieved an area under the curve of 0.94 with an accuracy of 0.85 for medulloblastoma versus nonmedulloblastoma, an area under the curve of 0.84 with an accuracy of 0.80 for ependymoma versus nonependymoma, and an area under the curve of 0.94 with an accuracy of 0.88 for pilocytic astrocytoma versus non-pilocytic astrocytoma.

CONCLUSIONS

Automatic machine learning based on routine MR imaging classified pediatric posterior fossa tumors with high accuracy compared with manual expert pipeline optimization and qualitative expert MR imaging review.

Wnt/beta-Catenin Signaling Contributes to Vincristine-Induced Neuropathic Pain

Chemotherapy-induced neuropathic pain (CNP) is the major dose-limiting factor in cancer chemotherapy. However, the mechanisms underlying CNP remain elusive. In the present study, CNP was induced by repeated intraperitoneal injection of vincristine (VCR) into male C57BL/6J mice. VCR administration caused significant activation of Wnt/beta-catenin signaling, which led to the activation of astrocytes, microglia, the release of inflammatory cytokines tumour necrosis factor (TNF)-alpha, monocyte chemoattractant protein-1 (MCP-1) and the activation of subsequent mitogen-activated protein kinase (MAPK)/extracellular signal-regulated protein kinase (ERK) signaling pathway in CNP mice. Blocking Wnt/beta-catenin signaling by intrathecal administration of the inhibitors of Wnt response (IWR) effectively attenuated VCR-induced neuropathic pain. Furthermore, IWR inhibited the activation of astrocytes, microglia, TNF-alpha, MCP-1 and MAPK/ERK signaling in the spinal cord, which was triggered by VCR-induced Wnt/beta-catenin signaling upregulation. These results suggest that Wnt/beta-catenin signaling plays a critical role in VCR-induced neuropathic pain and provides evidence for potential interfering with Wnt/beta-catenin signaling to ameliorate VCR-induced neuropathic pain.

Spatial genetic structure and historical demography of East Asian wild boar

Pleistocene climatic fluctuations may have had a profound impact on the evolutionary history of many species. The geographical pattern of European wild boar (Sus scrofa) is clearly studied, and it was greatly influenced by ancient climatic events, especially the Last Glacial Maximum. Previous research on genetic variation has mainly focused on the origin and distribution histories of domestic pigs. However, some questions have not been answered, including those concerning the genetic diversity, geographical pattern and possible historic influence of climate on East Asian wild boar (EAWB). Employing the control region of mtDNA (511 bp), we investigated the contributions of historic climate, which possibly shaped the genetic pattern of wild boar. Given that the level of genetic diversity of wild boars is higher in East Asia than in Europe, 172 haplotypes were detected from 680 individuals. Phylogenetic analysis demonstrated the complex phylogeographic structure of EAWB. Mismatch analysis, neutrality tests and the Bayesian Skyline Plot results all retrieved signals of a rapid population expansion, which might have played an important role in driving the formation of complex spatial genetic structure. Genetic data and species distribution modelling showed that the Last Glacial Maximum had weak effect on the distribution of the EAWB. We suggest that, in shaping spatial genetic structure in East Asian, long-term gene flow and population history played more important roles than Pleistocene climate fluctuations.

FRI0367 ADALIMUMAB IS MORE EFFECTIVE THAN ETANERCEPT AT PREVENTING TNF-ENHANCED OSTEOCLAST DEVELOPMENT THROUGH DOWNREGULATION OF PRO-OSTEOCLASTOGENIC FACTORS ICAM-1 AND IGFBP2 AND UPREGULATION OF ANTI-OSTEOCLASTOGENIC FACTOR FABP4

Background:

TNF has been shown to contribute to osteoclastogenesis independently and in conjunction with M-CSF and RANKL. We have previously demonstrated that TNF enhances the kinetics of RANKL-induced human osteoclastogenesis and that its effects are mitigated more effectively by the anti-TNF biologic adalimumab (ADA) as compared to etanercept (ETN).

Objectives:

To determine the mechanism responsible for the difference in effectiveness between the two biologics, a label-free quantitative proteomics study was conducted on TNF-activated human osteoclasts (OC) upon biologic treatment.

Methods:

Human bone marrow-derived OC precursors (OCP, 3 donors) were exposed for 5 days to M-CSF, M-CSF+RANKL (RANKL) alone or in combination with 100 ng/mL TNF +/- 5 ug/mL ADA, ETN or human IgG1 (IGG) as pre-formed complexes. OC differentiation was confirmed by measuring TRAP5b activity. Shotgun proteomics was performed on peptides generated from detergent based cell extracts subjected to methanol/chloroform precipitation and trypsin/Lys-C digestion. Data acquisition was performed with Orbitrap Q Exactive™ HF-X mass spectrometer. MaxQuant was utilized to quantify proteins based on MS1 peak intensities. Data matrix was normalized, imputed and subjected to differential expression analysis by limma. DAVID pathway analysis (DPA) was used to identify pathways impacted by various treatment conditions based on proteins exhibiting significant (p<0.05) 1.2-fold change in expression as compared to RANKL. Protein levels within culture supernatant or cell lysate were verified by ELISA or MSD.

Results:

Principle component analysis (PCA) of the proteomic profiling data for the 3 donors indicated that exposure of OCP to TNF induced a distinct profile from that of M-CSF and RANKL. The addition of ADA:TNF complexes restored the profile to that of RANKL, whereas those exposed to ETN:TNF complexes exhibited an intermediate profile matching differences observed in TRAP 5b activity levels. DPA identified 3 pathways most associated with osteoclastogenesis: receptor-mediated endocytosis (e.g. CD163, IGFBP2), oxidation-reduction process (e.g. FABP4), and cell adhesion (e.g. ICAM-1, TGFBI) that were significantly impacted by TNF with ADA:TNF being more effective than ETN:TNF in restoring most pathway-associated proteins to RANKL levels. Based on ELISA, two pro-osteoclastogenic factors IGFBP2 and ICAM-1 were increased 2-fold in OCP culture supernatants in response to TNF with only ADA:TNF complexes reducing these levels of both to RANKL. TNF-induced reduction of intracellular levels of CD163, an M2 macrophage polarization marker, and TGFBI were not only restored to RANKL levels by ADA:TNF but brought to a level closer to M-CSF alone, unlike ETN:TNF. One anti-osteoclastogenic factor FABP4 was found to be increased intracellularly above that of RANKL only following exposure to ADA:TNF complexes.

Conclusion:

Shotgun proteomic profiling of human OCP differentiatedin vitrowith TNF revealed at least 3 novel pathways by which TNF exerts its pro-osteoclastogenic effects. Only with the addition of ADA:TNF, not with ETN:TNF, were most pathway-associated proteins significantly restored to RANKL levels including pro-osteoclastogenic factors ICAM-1 and IGFBP2. Moreover, ADA:TNF complexes enhanced the intracellular levels of CD163 and the anti-osteoclastogenic factor FABP4, suggesting these complexes are exerting an effect on OCP beyond simple TNF neutralization. Additionalin vitroandin vivostudies need to be performed to verify our findings.

Acknowledgments:

The authors thank Drs. Jochen Salfeld, Yonghao Cao and Dhaval Nanavati for their critical review of our data, and Yucheng Zhang for her technical support.

Disclosure of Interests:

Bohdan Harvey Shareholder of: AbbVie, Inc., Employee of: AbbVie, Inc., Liang Jin Shareholder of: AbbVie, Inc., Employee of: AbbVie, Inc., John Maull Shareholder of: AbbVie, Inc., Employee of: AbbVie, Inc., Chenqi Hu Shareholder of: AbbVie, Inc., Employee of: AbbVie, Inc., Yu Tian Shareholder of: AbbVie, Inc., Employee of: AbbVie, Inc., Zehra Kaymakcalan Shareholder of: AbbVie, Inc., Employee of: AbbVie, Inc.

Upregulation of SNHG12 accelerates cell proliferation, migration, invasion and restrain cell apoptosis in breast cancer by enhancing regulating SALL4 expression via sponging miR-15a-5p

Breast cancer (BC) is malignant cancer that threatens the health of millions of females worldwide. Long non-coding RNA (lncRNA) small nucleolar RNA host gene 12 (SNHG12) has been identified as an oncogene in multiple cancers. However, the regulatory role of SNHG12 in BC cell progression is still obscured. The levels of SNHG12, miR-15a-5p, and Sal-like 4 (SALL4) in BC tumor tissues and cells were measured by qRT-PCR. Cell viability, apoptosis, migration, and invasion were examined by CCK8, flow cytometry, and transwell assay, respectively. The interaction between miR-15a-5p and SNHG12 or SALL4 was evaluated by dual-luciferase reporter assay. Protein expression of SALL4 was analyzed by western blot. Xenograft mice were established by subcutaneously injecting BC cells stably transfected with sh-SNHG12 and sh-NC. SNHG12 and SALL4 expressions were upregulated whereas miR-15a-5p was downregulated in BC tumors compared with normal tissues. Besides, miR-15a-5p was correlated with SNHG12 and SALL4 inversely as calculated by Pearson's correlation coefficient. More importantly, SNHG12 knockdown attenuated BC tumor growth in vitro and in vivo. Subsequently, dual-luciferase reporter assay confirmed the interaction between miR-15a-5p and SNHG12 or SALL4. The rescue experiments revealed that miR-15a-5p inhibitor restored SNHG12 silencing induced inhibition on BC cell proliferation, migration, invasion, and promotion of apoptosis. Additionally, SNHG12 was found to accelerate BC cell progression by absorbing miR-15a-5p to enhance SALL4 expression. SNHG12 promotes cell proliferation, migration, and invasion but suppresses apoptosis in BC by upregulating SALL4 expression via sponging miR-15a-5p, representing potential targets for the development of novel diagnosis and treatment methods.

[Preliminary efficacy analysis of Cheng's Giraffe reconstruction after proximal gastrectomy in adenocarcinoma of esophagogastric junction]

Objective: To investigate the safety and feasibility of proximal partial gastrectomy with Cheng's Giraffe esophagogastric reconstruction for the treatment of early Siewert II adenocarcinoma of esophagogastric junction (AEG). Methods: Indication of Cheng's Giraffe esophagogastric reconstruction: (1) Siewert II AEG or Siewert III AEG with diameter < 4 cm; (2) preoperative staging as cT1-2N0M0. A descriptive case series study was carried out. Clinical data of 34 patients with Siewert II AEG undergoing proximal partial gastrectomy and Cheng's Giraffe esophagogastric reconstruction at Department of Abdominal Surgery of Zhejiang Cancer Hospital and Department of Gastrointestinal Surgery, The First Affiliated Hospital of Zhejiang University of Traditional Chinese Medicine from February to July 2018 were retrospectively collected and analyzed, including 14 cases in IA stage, 11 cases in IIA stage and 8 cases in IIB stage. Brief procedure of Cheng's Giraffe esophagogastric reconstruction was as follows: Firstly, 12 cm long tubular stomach was formed by longitudinal incision 4 cm away from the great curvature of the stomach. Secondly, the gastric fundus and His angle were formed. Finally, the distance from His angle to esophagal-tubular gastric anastomosis should be more than 5 cm. The reflux disease questionare (RDQ) scores, radionuclide gastric emptying scintigraphy, and 24-hour multichannel intraluminal (MII)-pH monitoring technology were used to evaluate postoperative gastric emptying and gastroesophageal reflux. Result: All 34 patients successfully completed proximal partial gastrectomy with Cheng's Giraffe esophagogastric reconstruction, including 13 cases by open surgery and 21 cases by laparoscopic surgery. The operation time was (144.6±39.8) minutes, the blood loss during operation was (35.4±17.2) ml. No laparoscopic case was converted to open surgery and no postoperative complication was observed. The postoperative hospital stay was (8.4±2.5) days. The postoperative RDQ score was 4.4±3.1 one month after operation, and 3.3±2.5 six months after operation. Gastric-half emptying time was (67.0±21.5) minutes, and the residual ratio was (52.2±7.7)% in 1 hour, (36.4±3.1)% in 2 hours and (28.8±3.6)% in 3 hours at postoperative 1-month. The 24-hour MII-pH monitoring at postoperative 2-month revealed the frequency of acid reflux was (12.6±7.9) times, frequency of non-acid reflux was (19.6±9.7) times, DeMeester score was 5.8±2.9. Conclusion: Cheng's Giraffe esophagogastric reconstruction is safe and feasible in the treatment of Siewert type II AEG, and has good dynamic and anti-reflux effects.

Overexpression of the human cytomegalovirus UL111A is correlated with favorable survival of patients with gastric cancer and changes T-cell infiltration and suppresses carcinogenesis

Purpose

We previously found that human cytomegalovirus (HCMV) infection is associated with gastric cancer (GC) development. UL111A plays a role during HCMV productive or latent infection. However, UL111A expression profiles in GC tissues and their relationship with this disease are unknown.

Methods

PCR and nested RT-PCR were performed to verify UL111A expression in 71 GC tissues and its transcripts in 16 UL111A-positive GC samples. UL111A expression levels in GC patients were evaluated by immunohistochemistry on a tissue microarray for 620 GC patients. The correlations among UL111A expression levels, clinicopathological characteristics, and prognosis were analyzed. Further, the effects of overexpression of latency-associated viral interleukin-10 (LAcmvIL-10) and cmvIL-10 on GC cell proliferation, colony formation, migration, and invasion were assessed.

Results

The UL111A detection rate in GC tissues was 32.4% (23/71) and that of its mRNA expression was 68.75% (11/16). High expression of UL111A was also related to better overall and disease-free survival in GC patients. GC patients with TNM II/III stage expressing higher UL111A levels might benefit from adjuvant chemotherapy (ACT) after surgery. Moreover, high UL111A expression was also associated with increased CD4+ , CD8+ T-lymphocyte and Foxp3+ T-cell infiltration. In vitro assays further demonstrated that LAcmvIL-10 and cmvIL-10 overexpression inhibits GC cell line proliferation, colony formation, migration, and invasion.

Conclusions

High UL111A expression changes the number of infiltrating T cells and is associated with favorable survival. Therefore, UL111A could be used as an independent prognostic biomarker and might be a potential therapeutic target for GC.

Electronic supplementary material

The online version of this article (10.1007/s00432-019-03092-x) contains supplementary material, which is available to authorized users.

Associations of eczema phenotypes with emotional and behavioural problems from birth until school age. The Generation R Study

Background

Eczema phenotypes and emotional and behavioural problems are highly prevalent in childhood, but their mutual relationship is not fully clear.

Objectives

To examine the associations of eczema phenotypes with school‐age emotional and behavioural problems, and the bidirectional associations of eczema and emotional and behavioural problems from birth until 10 years.

Methods

This study among 5265 individuals was embedded in a prospective population‐based cohort study. Never, early transient, mid‐transient, late transient and persistent eczema phenotypes were identified based on parent‐reported, physician‐diagnosed eczema from age 6 months until 10 years. Emotional (internalizing) and behavioural (externalizing) problems were measured repeatedly using the Child Behavior Checklist from age 1·5 to 10 years. Cross‐lagged models were applied for bidirectional analyses.

Results

All eczema phenotypes were associated with more internalizing problems and attention problems at age 10 years, compared with never having eczema: range of Z‐score differences 0·14 [95% confidence interval (CI) 0·01–0·27] to 0·39 (95% CI 0·18–0·60). Children with early transient eczema had more aggressive behaviour symptoms at age 10 years (Z = 0·16, 95% CI 0·05–0·27). Bidirectional analysis showed that eczema at 0–2 years was associated with more internalizing and externalizing problems at ages 3–6 and 10 years, while, inversely, only internalizing problems at 0–2 years were associated with an increased risk of eczema at age 10 years.

Conclusions

Eczema phenotypes are very modestly associated with more somatic symptoms and attention problems at school age. Early transient eczema is associated with more aggressive behaviour symptoms. Directional effects seem to occur from early‐life eczema to later‐life internalizing and externalizing problems, rather than the reverse.

What's already known about this topic?

Previous cohort studies using non‐data‐driven methods to define eczema phenotypes observed that children with early‐onset and persistent eczema had a higher risk of emotional and behavioural problems in preadolescence.

Alternatively, previous cohort studies showed that children with emotional and behavioural problems had more severe eczema and eczema exacerbations in childhood.

The direction of effects between eczema and emotional and behavioural problems is not fully clear.

What does this study add?

Taking the variability of eczema onset and persistence within and between children over time into account, all identified eczema phenotypes were very modestly associated with more somatic symptoms and attention problems at school age.

Directional effects seem to occur from eczema leading to emotional and behavioural problems, rather than the reverse.

Future research should focus on the effect of early optimal eczema management on mental health disorders in children later in life.

Plain language summary available online

MiR-200a improves respiratory distress syndrome in newborn rabbits via the Wnt/β-catenin signaling pathway

OBJECTIVE

The aim of this study was to investigate the effect of micro-ribonucleic acid (miR)-200a on respiratory distress syndrome (RDS) in newborn rabbits by regulating the Wnt/β-catenin signaling pathway.

MATERIALS AND METHODS

In this work, newborn rabbits aged three days were selected from our laboratory as research objects. The messenger RNA (mRNA) and protein expression levels of miR-200a, β-catenin and interleukin-10 (IL-10) in blood samples of healthy newborn rabbits and newborn rabbits with RDS were determined by fluorescence quantitative Polymerase Chain Reaction (PCR) and Western blotting, respectively. Lentivirus-packaged plasmids containing miR-200a were then injected into newborn rabbits suffering from RDS. After 2 d, the mRNA and protein expression levels of miR-200a, β-catenin and IL-10 in blood samples of newborn rabbits in different treatment groups were measured. Meanwhile, lung sections were collected from newborn rabbits in different treatment groups. After that, the sections were observed via hematoxylin and eosin (H&E) staining. At the same time, lung coefficient of newborn rabbits in different treatment groups was also measured.

RESULTS

Compared with healthy newborn rabbits, the mRNA and protein expression levels of miR-200a and IL-10 in the blood of newborn rabbits with RDS decreased significantly (p<0.05), while β-catenin increased markedly (p<0.05). The mRNA and protein expression levels of β-catenin and IL-10 in newborn RDS rabbits with miR-200a over-expression and knockout were detected as well. The results revealed that lowly expressed miR-200a could remarkably promote the expression level of β-catenin, whereas inhibiting the expression of IL-10. However, highly expressed miR-200a could significantly inhibit the expression level of β-catenin and promote the expression level of IL-10. H&E staining results manifested that miR-200a knockout markedly promoted the increase of pulmonary alveoli with increased lung coefficients. However, the up-regulation of miR-200a could reduce lung coefficients and remarkably improve RDS.

CONCLUSIONS

MiR-200a regulates RDS in newborn rabbits by regulating the Wnt/β-catenin signaling pathway.

[Effect of hypocaloric versus standard enteral feeding on clinical outcomes in critically ill adults - A meta-analysis of randomized controlled trials with trial sequential analysis]

OBJECTIVES

To compare the effect of hypocaloric versus standard enteral feeding on clinical outcomes in critically ill adults, and to investigate the influence of protein intake upon the outcome effects of hypocaloric feeding.

DESIGN

A meta-analysis of randomized controlled trials (RCTs) and trial sequential analysis (TSA) were carried out.

SETTING

Intensive Care Unit (ICU).

PATIENTS

Or participants Critically ill adults.

INTERVENTIONS

Hypocaloric enteral feeding versus standard enteral feeding.

MAIN VARIABLES OF INTEREST

The primary outcomes were all-cause short-term mortality and the incidence of nosocomial infection.

RESULTS

Eleven RCTs met the inclusion criteria; of these trials, two were judged as having low risk of bias. Compared with standard enteral feeding, hypocaloric enteral feeding had no benefits in terms of reducing short-term mortality, the incidence of nosocomial infection, or long-term mortality, though it had a positive impact upon the incidence of gastrointestinal intolerance. The TSA further confirmed these results. In turn, hypocaloric enteral feeding had no effects upon the incidence of bloodstream infection, pneumonia, hypoglycemia or the duration of mechanical ventilation, ICU stay, or in-hospital stay. The above results remained unchanged in the sub-analysis of trials with a low risk of bias, trials administering a similar dose of protein, or trials administering different doses of protein.

CONCLUSIONS

Compared with standard enteral feeding, hypocaloric enteral feeding was not associated with better clinical outcomes in critically ill adults, except for a lower risk of gastrointestinal intolerance. The difference in protein intake between groups might have no influence on the outcome effects of hypocaloric enteral feeding. High quality randomized controlled trials are needed to confirm this, however.