AMBRA1-mediated autophagy and apoptosis associated with an epithelial-mesenchymal transition in the development of cleft palate induced by all-trans retinoic acid

BACKGROUND

Autophagy and apoptosis are involved in embryogenesis. However, little is known about the regulatory mechanism of AMBRA1-mediated autophagy and apoptosis associated with epithelial-mesenchymal transition (EMT) in the development of cleft palate (CP). This study is aimed to elucidate a novel regulatory mechanism by which AMBRA1 regulates autophagy and apoptosis associated with EMT during palatal fusion.

METHODS

We performed lncRNA and mRNA co-expression profile analysis on embryonic gestation day 14.5 (E14.5) mouse embryos from control (n=3) and all-trans retinoic acid-treated (to induce cleft palate, n=3) C57BL/6J mice. Functional prediction for transcription factor (TF)-target gene relationship, which was obtained using Gene Ontology/Kyoto Encyclopedia of Genes and Genomes analyses (GO/KEGG) pathway analysis, identified the regulatory "lncRNA-TF-target gene" using the trans model.

RESULTS

The trans analysis revealed that some TFs (e.g., LEF1, SMAD4, and FOXD3) regulate lncRNA and gene expression. Finally, we identified a NONMMUT034790.2-LEF1-AMBRA1 trans-regulatory network associated with CP. Our results indicate that AMBRA1 might be a novel epigenetic biomarker in palatogenesis.

CONCLUSIONS

AMBRA1-mediated autophagy and apoptosis associated with EMT by a NONMMUT034790.2-LEF1-AMBRA1 trans-regulatory network might be an important mechanism underlying dysfunctional palatal fusion.

Genome-Wide mRNA-Seq Profiling Reveals that LEF1 and SMAD3 Regulate Epithelial-Mesenchymal Transition Through the Hippo Signaling Pathway During Palatal Fusion

BACKGROUND

Epithelial-mesenchymal transition (EMT) of the medial edge epithelium (MEE) occurs through fusion of the palatal shelves and is a crucial step in palatogenesis. The key genes, however, and the related signaling pathway of EMT are not yet fully understood. Therefore, the aim of this study was to reveal the key genes and the related signaling pathway of EMT during palatal fusion.

MATERIALS AND METHODS

C57BL/6J mice at embryonic gestation day 14.5 (E14.5; n = 6) were used to establish the cleft palate model for mRNA-Seq (HiSeq X Ten). The Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed for functional annotations of the differentially expressed genes. Quantitative polymerase chain reaction (qPCR) assays were used to validate the RNAseq data.

RESULTS

A total of 936 differentially expressed genes, including 558 upregulated and 378 downregulated genes were identified in cases versus controls, respectively. Among these genes, the GO analysis showed that Lymphoid Enhancer-Binding Factor 1 (LEF1) and SMAD Family Member 3 (SMAD3) significantly enriched biological processes, which were EMT related. The KEGG analysis showed that these genes regulated EMT through the Hippo signaling pathway. LEF1 and SMAD3 were downregulated, and the qPCR results corroborated the RNA-seq data.

CONCLUSIONS

These results demonstrate that LEF1 and SMAD3 inhibits EMT at the MEE through the Hippo signaling pathway; and that this could contribute to cleft palate formation in embryonic palatal fusion at E 14.5.

Vitamin B6 catabolism and lung cancer risk: results from the Lung Cancer Cohort Consortium (LC3)

BACKGROUND

Increased vitamin B6 catabolism related to inflammation, as measured by the PAr index (the ratio of 4-pyridoxic acid over the sum of pyridoxal and pyridoxal-5'-phosphate), has been positively associated with lung cancer risk in two prospective European studies. However, the extent to which this association translates to more diverse populations is not known.

MATERIALS AND METHODS

For this study, we included 5323 incident lung cancer cases and 5323 controls individually matched by age, sex, and smoking status within each of 20 prospective cohorts from the Lung Cancer Cohort Consortium. Cohort-specific odds ratios (ORs) and 95% confidence intervals (CIs) for the association between PAr and lung cancer risk were calculated using conditional logistic regression and pooled using random-effects models.

RESULTS

PAr was positively associated with lung cancer risk in a dose-response fashion. Comparing the fourth versus first quartiles of PAr resulted in an OR of 1.38 (95% CI: 1.19-1.59) for overall lung cancer risk. The association between PAr and lung cancer risk was most prominent in former smokers (OR: 1.69, 95% CI: 1.36-2.10), men (OR: 1.60, 95% CI: 1.28-2.00), and for cancers diagnosed within 3 years of blood draw (OR: 1.73, 95% CI: 1.34-2.23).

CONCLUSION

Based on pre-diagnostic data from 20 cohorts across 4 continents, this study confirms that increased vitamin B6 catabolism related to inflammation and immune activation is associated with a higher risk of developing lung cancer. Moreover, PAr may be a pre-diagnostic marker of lung cancer rather than a causal factor.

A novel lncRNA-mediated trans-regulatory mechanism in the development of cleft palate in mouse

BACKGROUND

Increasing evidence indicates that long non-coding RNAs (lncRNAs) play crucial regulatory roles in epithelial-mesenchymal transition (EMT). However, the regulatory mechanisms during EMT of the medial edge epithelium (MEE) remain elusive. The aim of this work is to reveal a novel lncRNA-regulated dysfunction of EMT involved in the development of cleft palate (CP).

METHODS

C57BL/6 J mice at embryonic gestation day 14.5 (n = 6, 3 case samples vs. 3 control samples) were used to establish the CP model for lncRNA-mRNA co-expression profile analysis after high-throughput sequencing. Functional predictions for the differentially expressed lncRNA-mRNA co-expression with transcription factor (TF)-target gene relationship Gene Ontology/Kyoto Encyclopedia of Genes and Genomes pathway (GO/KEGG) analyses identified the regulatory "lncRNA-TF-target gene" trans model.

RESULTS

A total of 583 differentially expressed lncRNAs and 703 differentially expressed mRNAs were identified. The results of trans analysis revealed that some TFs (LEF1, SMAD4, and FOXD3) regulate lncRNAs and gene expression. Finally, we identified the NONMMUT034790.2-LEF1-SMAD7 co-expression trans-regulatory network that might be associated with CP.

CONCLUSIONS

Our results revealed that NONMMUT034790.2 might be a novel epigenetic biomarker in CP. The integration of lncRNA modulators into trans-regulatory networks will further enhance our understanding of lncRNA functions and regulatory mechanisms during palatal fusion in ATRA-induced mouse CP.

DNA hypermethylation of Fgf16 and Tbx22 associated with cleft palate during palatal fusion

OBJECTIVE

Cleft palate (CP) is a congenital birth defect caused by the failure of palatal fusion. Little is known about the potential role of DNA methylation in the pathogenesis of CP. This study aimed to explore the potential role of DNA methylation in the mechanism of CP.

METHODOLOGY

We established an all-trans retinoic acid (ATRA)-induced CP model in C57BL/6J mice and used methylation-dependent restriction enzymes (MethylRAD, FspEI) combined with high-throughput sequencing (HiSeq X Ten) to compare genome-wide DNA methylation profiles of embryonic mouse palatal tissues, between embryos from ATRA-treated vs. untreated mice, at embryonic gestation day 14.5 (E14.5) (n=3 per group). To confirm differentially methylated levels of susceptible genes, real-time quantitative PCR (qPCR) was used to correlate expression of differentially methylated genes related to CP.

RESULTS

We identified 196 differentially methylated genes, including 17,298 differentially methylated CCGG sites between ATRA-treated vs. untreated embryonic mouse palatal tissues (P<0.05, log2FC>1). The CP-related genes Fgf16 (P=0.008, log2FC=1.13) and Tbx22 (P=0.011, log2FC=1.64,) were hypermethylated. Analysis of Fgf16 and Tbx22, using Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG), identified 3 GO terms and 1 KEGG pathway functionally related to palatal fusion. The qPCR showed that changes in expression level negatively correlated with methylation levels.

CONCLUSIONS

Taken together, these results suggest that hypermethylation of Fgf16 and Tbx22 is associated with decreased gene expression, which might be responsible for developmental failure of palatal fusion, eventually resulting in the formation of CP.

Correlation between HDAC4 enhancer DNA methylation and mRNA expression during palatal fusion induced by all-trans retinoic acid

Epithelial-mesenchymal transformation of the medial edge epithelium is the most crucial process in embryonic palatal fusion. This study aimed to explore the relationship and potential mechanism between enhancer DNA methylation and mRNA expression of histone deacetylase 4 (HDAC4) during palatal fusion induced by maternal exposure to all-trans retinoic acid (ATRA). Pregnant mice were administered ATRA (70 mg/kg) by gavage at embryonic gestation day 10.5 (E10.5) to establish a cleft palate (CP) model in C57BL/6J mice. Control groups were given an equivalent volume of corn oil. Pregnant mice were dissected at E14.5 (n = 6) to obtain embryonic palates. HDAC4 enhancer DNA methylation data were obtained from a previous MethylRAD-seq. Methylation-specific polymerase chain reaction (MSP) and real-time quantitative PCR were used to quantify enhancer methylation and the mRNA expression level of HDAC4. Enhancer DNA methylation at a non-CpG site within the HDAC4 gene was hyper-methylated at E14.5 (P: 0.011, log₂ FC:1.67). The MSP results indicated a similar trend, in agreement with the MethylRAD-seq results. The change in the HDAC4 expression level was negatively correlated with its enhancer DNA methylation level, at the non-CpG site, during palatal fusion induced by ATRA. Enhancer DNA methylation of HDAC4 might play an important regulatory role during palatogenesis, especially in embryonic palatal fusion at E 14.5, and may facilitate the development of novel epigenetic biomarkers in the treatment of CP.

Genome-Wide DNA Methylation Profile of Gene cis-Acting Element Methylations in All-trans Retinoic Acid-Induced Mouse Cleft Palate

DNA methylation epigenetically regulates gene expression. This study is aimed to investigate genome-wide DNA methylations involved in the regulation of palatal fusion in the all-trans retinoic acid-induced mouse cleft palate model. There were 4,718,556 differentially CCGG methylated sites and 367,504 CCWGG methylated sites for 1497 genes between case and control embryonic mouse palatal tissues. The enhancers (HDAC4 and SMAD3) and promoter (MID1) of these three genes had cis-acting element methylation. HDAC4 is localized within the CCWGG, while MID1 and SMAD3 are localized within the CCGG of the gene intron. The methylation-specific polymerase chain reaction data confirmed the MethylRAD-seq results, while the quantitative reverse transcriptase-polymerase chain reaction result showed that changes in gene expression inversely were associated with the cis-acting element methylation of the gene during retinoic acid-induced palatal fusion. The GO and KEGG data showed that these three genes could regulate cell proliferation, skeletal muscle fiber development, and development-related gene signaling or activity. The cis-acting element methylation of HDAC4, SMAD3, and MID1 may play a regulatory role during palatal fusion. Further research is needed to verify these novel epigenetic biomarkers for cleft palate.

Genome-Wide DNA Methylation Analysis During Palatal Fusion Reveals the Potential Mechanism of Enhancer Methylation Regulating Epithelial Mesenchyme Transformation

Epithelial mesenchyme transformation (EMT) of the medial edge epithelium (MEE) is the crucial process during palatal fusion. This work is aimed to elucidate the enhancer regulatory mechanism by genome-wide DNA methylation analysis of EMT during palatal fusion. Over 800 million clean reads, 325 million enzyme reads, and 234 million mapping reads were generated. The mapping rate was 68.85-74.32%, which included differentially methylated 17299 CCGG sites and 2363 CCWGG sites (p < 0.05, log₂FC >1). Methylated sites in intron and intergenic regions were more compared to other regions of all DNA elements. GO and KEGG analysis indicated that differential methylation sites related to embryonic palatal fusion genes (HDAC4, TCF7L2, and PDGFRB) at the enhancer were located on CCWGG region of non-CpG islands. In addition, the results showed that the enhancer for HDAC4 was hypermethylated, whereas the enhancers for TCF7L2 and PDGFRB were hypomethylated. The methylation status of enhancer regions of HDAC4, PDGFRB, and TCF7L2, involved in the regulation of the EMT during palatal fusion, may enlighten the development of novel epigenetic biomarkers in the treatment of cleft palate.

Efficiency of stem cell based therapy in the treatment of diabetic foot ulcer: a meta-analysis

Diabetic foot ulcer is a chronic, refractory, frequent complication in diabetic patient. Its treatment often requires multidisciplinary joint efforts, diverse strategies have been adopted to address this annoying issue, including stem cell-based therapy/acellular dermal matrix/negative pressure wound therapy etc. However, consensus has not been reached. To assess the current evidence regarding the efficiency and potential advantages of stem cell-based therapy compared with conventional standard treatment and/or placebo in the treatment of diabetic foot ulcer. A comprehensive search in PubMed, EmBase, Cochrane Central and Web of Science databases was conducted during December 2016 and a systematic review and meta-analysis of all relevant studies were performed. A total of 7 studies that involved 224 diabetic foot patients, classified as Wagner grades 1-5, were analyzed. The pooled results confirmed the benefits of using the stem cell treatment. Partial and/or complete healing were significantly higher in the stem cell group compared with the control group (77.4% vs. 31.9%; RR: 2.22; 95% CI, 1.65-2.98). Subgroup analysis on ABI and TCP02 also confirmed the results. The present meta-analysis indicates that stem cell-based therapy can enhance the healing of diabetic foot ulcers and is associated with lesser pain, lower amputation rate and improved prognosis compared with normal treatment. Well-designed randomized controlled trials are required in the future in order to confirm and update these findings.

Comparison of two kinds of skin imaging analysis software: VISIA® from Canfield and IPP® from Media Cybernetics

BACKGROUND

Skin imaging analysis, acting as a supplement to noninvasive bioengineering devices, has been widely used in medical cosmetology and cosmetic product evaluation. The main aim of this study is to assess the differences and correlations in measuring skin spots, wrinkles, vascular features, porphyrin, and pore between two commercially available image analysis software.

MATERIALS AND METHODS

Seventy healthy women were included in the study. Before taking pictures, the dermatologist evaluated subjects' skin conditions. Test sites included the forehead, cheek, and periorbital skin. A 2 × 2 cm cardboard was used to make a mark on the skin surface. Pictures were taken using VISIA^® under three kinds light conditions and analyzed using VISIA^® and IPP^® respectively.

RESULTS

(1) Skin pore, red area, ultraviolet spot, brown spot, porphyrin, and wrinkle measured with VISIA^® were correlated with those measured with IPP^® (P < .01). (2) Spot, wrinkle, fine line, brown spot, and red area analyzed with VISIA^® were correlated with age on the forehead and periorbital skin (P < .05). L-value, Crow's feet, ultraviolet spot, brown spot, and red area analyzed with IPP^® were correlated with age on the periorbital skin (P < .05). (3) L-value, spot, wrinkle, fine line, porphyrin, red area, and pore analyzed with VISIA^® and IPP^® showed correlations with the subjective evaluation scores (P < .05).

CONCLUSIONS

VISIA^® and IPP^® showed acceptable correlation in measuring various skin conditions. VISIA^® showed a high sensibility when measured on the forehead skin. IPP^® is available as an alternative software program to evaluate skin features.

Primary antibiotic resistance of Helicobacter pylori in Chinese patients: a multiregion prospective 7-year study

OBJECTIVES

To explore the characteristics of Helicobacter pylori resistance in China and the association between antibiotic resistance and several clinical factors.

METHODS

H. pylori strains were collected from patients in 13 provinces or cities in China between 2010 and 2016. Demographic data including type of disease, geographic area, age, gender and isolation year were collected to analyse their association with antibiotic resistance. Antibiotic resistance was detected using the Etest test and the Kirby-Bauer disc diffusion method.

RESULTS

H. pylori were successfully cultured from 1117 patients. The prevalence of metronidazole, clarithromycin (CLA), azithromycin, levofloxacin (LEV), moxifloxacin, amoxicillin (AMO), tetracycline and rifampicin resistance was 78.2, 22.1, 23.3, 19.2, 17.2, 3.4, 1.9 and 1.5%, respectively. No resistance to furazolidone was observed. The resistance rates to LEV and moxifloxacin were higher in strains isolated from patients with gastritis compared to those with duodenal ulcer and among women. Compared to patients ≥40 years old, younger patients exhibited lower resistance rates to CLA, azithromycin, LEV and moxifloxacin. The resistance rates to CLA and AMO were higher in strains isolated more recently, and we also found that the prevalence of resistance to metronidazole, CLA, azithromycin and AMO were significantly different among different regions of China.

CONCLUSIONS

The resistance rates to metronidazole, CLA and LEV were high in China. Patient age, gender, disease and location were associated with the resistance of H. pylori to some antibiotics. Furazolidone, AMO and tetracycline are better choices for H. pylori treatment in China.

Severe obesity prior to diagnosis limits survival in colorectal cancer patients evaluated at a large cancer centre

Background:

In contrast to the consistent evidence for obesity and colorectal cancer (CRC) risk, the impact of obesity in CRC patients is less clear. In a well-characterised cohort of CRC patients, we prospectively evaluated class I and class II obesity with survival outcomes.

Methods:

The CRC patients (N=634) were followed from the date of diagnosis until disease progression/first recurrence (progression-free survival (PFS)) or death (overall survival (OS)). Body mass index (BMI) was calculated from reported usual weight prior to diagnosis. Hazard ratios (HRs) and 95% confidence intervals (CIs) were estimated in models adjusted for clinicopathologic, treatment, and lifestyle factors.

Results:

Over a median follow-up of 4 years, 208 (33%) patients died and 235 (37%) recurred or progressed. Class II obesity, as compared with either overweight or normal weight, was associated with an increased risk of death (HR and 95% CI: 1.55 (0.97–2.48) and 1.65 (1.02–2.68), respectively), but no clear association was observed with PFS. In analyses restricted to patients who presented as stages I–III, who reported stable weight, or who were aged <50 years, obesity was associated with a significant two- to five-fold increased risk of death.

Conclusions:

In CRC patients evaluated at a large cancer centre, severely obese patients experienced worse survival outcomes independent of many other factors.

Adult patients with respiratory syncytial virus infection: impact of solid organ and hematopoietic stem cell transplantation on outcomes

BACKGROUND

Respiratory syncytial virus (RSV) is a common community-acquired pathogen responsible for a substantial disease burden in adults. We investigated the outcomes after RSV infection in hospitalized adults over a 3-year period.

METHODS

This single-center, retrospective study identified 174 patients hospitalized with RSV upper or lower respiratory tract infection (LRTI) between January 1, 2009 and June 30, 2012. Clinical data were extracted from medical records. The primary outcome analyzed was all-cause mortality, defined as death during the index hospital admission. Subjects were divided into 3 groups for comparison: hematopoietic stem cell transplant (HSCT) patients, solid organ transplant (SOT) patients, and non-transplant patients.

RESULTS

In our study, 41/174 (23.6%) were HSCT recipients and 28/174 (16.1%) were SOT recipients. Twelve of 174 (6.9%) died. Death occurred in 2/41 (4.9%) HSCT and 3/28 (10.7%) SOT recipients, compared to 7/106 (6.6%) non-transplant patients. When compared to the non-transplant cohort, HSCT and SOT were not found to be significant risk factors for mortality (P = 0.685 and 0.645, respectively). In multivariate logistic regression, age >60 was associated with mortality (P = 0.019), while lymphopenia on admission trended toward an association with death (P = 0.054). HSCT patients were less likely to be admitted to an intensive care unit (odds ratio [OR] 0.26, P = 0.04), but were significantly more likely to receive ribavirin therapy (OR 11.62, P < 0.0001).

CONCLUSION

Adults hospitalized with RSV LRTI are at significant risk of mortality, and this risk may be increased in patients age >60 or with lymphopenia on admission. This study did not identify any significant increased mortality or morbidity associated with RSV infection in immune suppressed transplant recipients vs. patients who had not received a transplant.