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.

Pathological changes from the originating to the peripheral sites of Sinonasal Inverted Papilloma are the underlying mechanisms of preoperative MRI-tumor origin prediction

BACKGROUND

Our previous study showed that convoluted cerebriform pattern (CCP)-based reverse tracing method in preoperative magnetic resonance imaging (MRI) is a reliable tool in predicting originating site of sinonasal inverted papilloma (SNIP). This study aimed to determine the underlying pathological mechanism of the preoperative MRI-CCP reverse tracing method by assessing the histopathological changes from the origin to the peripheral sites of SNIP.

METHODOLOGY

The originating site of SNIP was predicted by preoperative MRI in 30 consecutive patients suspected to have primary SNIP. Samples of SNIP originating and peripheral sites were processed by pathological staining for evaluation of stroma score, micro-vessel density (MVD), and tight junction proteins (claudin-5, zonula occludens (ZO)-1 and occludin) expression.

RESULTS

The originating site of SNIP was accurately predicted by preoperative MRI in all patients. Stroma scores, and MVD were significantly greater in the periphery of SNIP than in the originating site. In contrast, Claudin-5 expression in micro-vessels was greater at the originating site than the periphery.

CONCLUSIONS

More edematous stroma and intensive micro-vessels with defective tight junction in periphery of SNIP result in more contrast agent diffusing and CCP that can only be observed at the periphery of SNIP on T2 and contrast-enhanced T1 weighted MR images, which may be the mechanisms underlying the CCP reverse tracing method.

Calibration and validation of the DNDC model to estimate nitrous oxide emissions and crop productivity for a summer maize-winter wheat double cropping system in Hebei, China

The main aim of this paper was to calibrate and evaluate the DeNitrification-DeComposition (DNDC) model for estimating N₂O emissions and crop productivity for a summer maize-winter wheat double cropping system with different N fertilizer rates in Hebei, China. The model's performance was assessed before and after calibration and model sensitivity was investigated. The calibrated and validated DNDC performed effectively in estimating cumulative N₂O emissions (coefficient of determination (1:1 relationship; r²) = 0.91; relative deviation (RD) = -13 to 16%) and grain yields for both crops (r² = 0.91; RD = -21 to 7%) from all fertilized treatments, but poorly estimated daily N₂O patterns. Observed and simulated results showed that optimal N fertilizer treatment decreased cumulative N₂O flux, compared to conventional N fertilizer, without a significant impact on grain yields of the summer maize-winter wheat double cropping system. The high sensitivity of the DNDC model to rainfall, soil organic carbon and temperature resulted in significant overestimation of N₂O peaks during the warm wet season. The model also satisfactorily estimated daily patterns/average soil temperature (^o C; 0-5 cm depth) (r² = 0.88 to 0.89; root mean square error (RMSE) = 4 °C; normalized RMSE (nRMSE) = 25% and index of agreement (d) = 0.89-0.97) but under-predicted water filled pore space (WFPS; %; 0-20 cm depth) (r² = 0.3 to 0.4) and soil ammonium and nitrate (exchangeable NH₄⁺ & NO₃^-; kg N ha^-1; r² = 0.97). With reference to the control treatment (no N fertilizer), DNDC was weak in simulating both N₂O emissions and crop productivity. To be further improved for use under pedo-climatic conditions of the summer maize-winter wheat double cropping system we suggest future studies to identify and resolve the existing problems with the DNDC, especially with the control treatment.

HIF-1α Mediates Osteoclast-Induced Mandibular Condyle Growth via AMPK Signaling

During the mandibular condylar growth, the absorption of calcified cartilage matrix induced by osteoclasts is crucial for the continuous endochondral osteogenesis. Meanwhile, recent studies showed that subchondral bone resided within the low-oxygen microenvironment, and our previous study revealed that hypoxia-inducible transcription factor 1α (HIF-1α) promoted osteoclastogenesis under hypoxia. However, whether HIF-1α regulates the function of osteoclasts in the mandibular condyle cartilage remains elusive. Our study indicated that severe deformity of the mandibular condyle was displayed in 10-wk-old osteoclast-specific HIF-1α conditional knockout (CKO) mice, accompanied by shortened length of condylar process and disorganized fibrocartilage. In 1-, 2-, and 4-wk-old CKO mice, the size of the hypertrophic layer and chondrocytic layer was significantly thickened. In the chondrocytic layer, chondrocytes were atrophied, showing a form of apoptosis in 4-wk-old CKO mice. Furthermore, an increase in the thickness of the fibrous and proliferating layer was observed in 10-wk-old CKO mice, as well as a significant decrease in that of the chondrocytic and hypertrophic chondrocyte layers. Interestingly, the articular surface of the condylar process abnormally presented a horizontal concave shape, and a disk-like acellular connective tissue appeared. In addition, genetic ablation of HIF-1α blunted cartilage matrix loss by subchondral osteoclast deficiency, resulting in a high subchondral bone mass phenotype, accompanied with a decreased number of blood vessels, alkaline phosphatase staining, and vascular endothelial growth factor (VEGF) expression. Mechanistically, the number of osteoclasts in the center of the condyle in CKO mice was significantly reduced by attenuated expression of adenosine 5′-monophosphate-activated protein kinase (AMPK) signaling. These findings reveal a novel influence of HIF-1α function in osteoclasts on maintenance of osteoclast-induced resorption of calcified cartilage matrix via AMPK signaling, as well as subchondral bone formation through VEGF-dependent angiogenesis in bone marrow.

Genomic Signature of Mismatch Repair Deficiency in Areca Nut-Related Oral Cancer

Areca nut (AN) chewing contributes to an increase of oral squamous cell carcinoma (OSCC) cases in South and Southeast Asia; however, genomic events underlying the carcinogenesis process of AN-related OSCC remain unclear. Here, we comprehensively describe the genomic and transcriptome alterations of 113 Chinese OSCC patients (89 AN related and 24 AN negative) by whole-exome sequencing and RNA sequencing, and we compared the genomic differences between AN-related and AN-negative samples by integrating sequencing data of 325 OSCC patients from The Cancer Genome Atlas database and 50 from a published Taiwanese study. We identified 11 significantly mutated genes for OSCC, including 4 novel ones (ATG2A, WEE1, DST, and TSC2), of which WEE1 and ATG2A mutated with significantly higher rates in AN-related samples (P = 0.04 and P = 0.003, respectively). Mutational signature analysis revealed that AN-related OSCCs were specially characterized by the genomic signature of mismatch repair deficiency (dMMR), which could also predict the prognosis status of AN-related OSCC. In addition, an elevated PD-L1 expression was also observed in both AN-related patients (P = 3.71 × 10^-11) and those with a high dMMR level (P = 1.99 × 10^-4). Further differential expression analysis and in vitro experiments confirmed the role of dMMR in the development of OSCC induced by AN exposure. Taken together, this study first revealed the molecular profiles and highlighted the role of dMMR in AN-related OSCC among the Chinese population and identified that AN-related OSCC may represent a potential cohort for effective anti-PD-1/L1 immunotherapy.

Functional diversification of three delta-class glutathione S-transferases involved in development and detoxification in Tribolium castaneum

Glutathione S-transferases (GSTs) are members of a multifunctional enzyme superfamily. Forty-one GSTs have been identified in Tribolium castaneum; however, none of the 41 GSTs has been functionally characterized. Here, three delta-class GSTs, TcGSTd1, TcGSTd2 and TcGSTd3, of T. castaneum were successfully cloned and expressed in Escherichia coli. All of the studied GSTs catalysed the conjugation of reduced glutathione with 1-chloro-2,4-dinitrobenzene. Insecticide treatment showed that the expression levels of TcGSTd3 and TcGSTd2 were significantly increased after exposure to phoxim and lambda-cyhalothrin, whereas TcGSTd1 was slightly upregulated only in response to phoxim. A disc diffusion assay showed that overexpression of TcGSTD3, but not TcGSTD1 or TcGSTD2, in E. coli increased resistance to paraquat-induced oxidative stress. RNA interference knockdown of TcGSTd1 caused metamorphosis deficiencies and reduced fecundity by regulating insulin/target-of-rapamycin signalling pathway-mediated ecdysteroid biosynthesis, and knockdown of TcGSTd3 led to reduced fertility and a decreased hatch rate of the offspring, probably caused by the reduced antioxidative activity in the reproductive organs. These results indicate that TcGSTd3 and TcGSTd2 may play vital roles in cellular detoxification, whereas TcGSTd1 may play essential roles in normal development of T. castaneum. These delta-class GSTs in T. castaneum have obtained different functions during the evolution.

Locoregional management of in-transit metastasis in melanoma: an Ontario Health (Cancer Care Ontario) clinical practice guideline

Objective

The purpose of this guideline is to provide guidance on appropriate management of satellite and in-transit metastasis (itm) from melanoma.

Methods

The guideline was developed by the Program in Evidence-Based Care (pebc) of Ontario Health (Cancer Care Ontario) and the Melanoma Disease Site Group. Recommendations were drafted by a Working Group based on a systematic review of publications in the medline and embase databases. The document underwent patient- and caregiver-specific consultation and was circulated to the Melanoma Disease Site Group and the pebc Report Approval Panel for internal review; the revised document underwent external review.

Recommendations

"Minimal itm" is defined as lesions in a location with limited spread (generally 1-4 lesions); the lesions are generally superficial, often clustered together, and surgically resectable. "Moderate itm" is defined as more than 5 lesions covering a wider area, or the rapid development (within weeks) of new in-transit lesions. "Maximal itm" is defined as large-volume disease with multiple (>15-20) 2-3 cm nodules or subcutaneous or deeper lesions over a wide area.■ In patients presenting with minimal itm, complete surgical excision with negative pathologic margins is recommended. In addition to complete surgical resection, adjuvant treatment may be considered.■ In patients presenting with moderate unresectable itm, consider using this approach for localized treatment: intralesional interleukin 2 or talimogene laherparepvec as 1st choice, topical diphenylcyclopropenone as 2nd choice, or radiation therapy as 3rd choice. Evidence is insufficient to recommend intralesional bacille Calmette- Guérin or CO2 laser ablation outside of a research setting.■ In patients presenting with maximal itm confined to an extremity, isolated limb perfusion, isolated limb infusion, or systemic therapy may be considered. In extremely select cases, amputation could be considered as a final option in patients without systemic disease after discussion at a multidisciplinary case conference.■ In cases in which local, regional, or surgical treatments for itm might be ineffective or unable to be performed, or if a patient has systemic metastases at the same time, systemic therapy may be considered.

Thumb lengthening using a three-dimensional half-ring distraction frame

The purpose of this study was to evaluate the use of a three-dimensional half-ring distraction frame for thumb phalangeal lengthening. From February 2009 to March 2015, 23 patients (23 thumbs) with thumb loss were treated with a half-ring distraction frame. Active movements of the metacarpophalangeal (MCP) joint were measured with a goniometer. These measurements were compared with the opposite hand. Differences were considered statistically significant at p<0.05. Clinical outcome was assessed based on the modified Mayo score. Bone union and good alignment were achieved in all patients. The mean distraction time was 44 days (range, 35-62 days). The mean time to union was 20 days (range, 49-86 days). The mean palmar and radial abduction of the thumb was 60° (range, 53°-65°) and 63° (range, 58°-70°), respectively; on the uninjured side, these measurements were 62° (range, 56°-65°) and 64° (range, 60°-73°), respectively (p>0.05). The mean extension-flexion arc of the MCP joint was 46° (range, 40°-50°); the measurement on the uninjured side was 48° (40°-54°) (p>0.05). The mean follow-up period was 51 months (4.25 years) (range, 48-65 months). The mean modified Mayo Score was 138 (range, 113-145). There were 19 excellent, 3 good, and 1 fair results. The half-ring distraction frame is a viable alternative for thumb lengthening as it provides stable, three-dimensional fixation, resulting in good hand function.

Is Laguncularia racemosa more invasive than Sonneratia apetala in northern Fujian, China in terms of leaf energetic cost?

Laguncularia racemosa and Sonneratia apetala are fast-growing exotic mangrove species in Southern China and widely used for afforestation. However, the invasiveness of the two exotic species is still unclear. We compared structural and physiological traits and energy-use related traits between L. racemosa and S. apetala, and with two natives (Kandelia obovata and Aegiceras corniculatum) in northern Fujian. Results showed that leaf construction cost based on mass (CCM) and caloric values of L. racemosa were significantly lower than S. apetala, and the two natives had highest CCM. Because lower CCM, L. racemosa grew faster with a taller height (4.83 m) and wider ground diameter circumference (40.03 cm) than S. apetala (4.43 m tall and 35.63 cm wide) and the two natives (2.42 m tall and 26.78 cm wide). These findings indicated that L. racemosa could be more invasive than S. apetala in mangrove forests in northern Fujian, China where it still grew well, which deserves more attention.

A Canadian cancer trials group phase IB study of durvalumab (anti-PD-L1) plus tremelimumab (anti-CTLA-4) given concurrently or sequentially in patients with advanced, incurable solid malignancies

Background The IND.226 study was a phase Ib study to determine the recommended phase II dose of durvalumab + tremelimumab in combination with standard platinum-doublet chemotherapy. Sequential administration of multiple agents increases total chair time adding costs overall and inconvenience for patients. This cohort of the IND.226 study evaluated the safety and tolerability of durvalumab + tremelimumab given either sequentially (SEQ) or concurrently (CON). Methods Patients with advanced solid tumours were enrolled and randomised to either SEQ tremelimumab 75 mg IV over 1 h followed by durvalumab 1500 mg IV over 1 h q4wks on the same day, or CON administration over 1 h. The serum pharmacokinetic profile of SEQ versus CON of durvalumab and tremelimumab administration was also evaluated. Results 14 patients either received SEQ (n = 7pts) or CON (n = 7 pts). There were no infusion related reactions. Drug related adverse events (AEs) were mainly low grade and manageable, and comparable in frequency between SEQ/CON- fatigue (43%/57%), rash (43%/43%), pruritus (43%/29%) and nausea (14%/29%). One patient in each cohort discontinued treatment due to toxicity. The PK profiles of durvalumab and tremelimumab were similar between CON and SEQ, and to historical reference data. Conclusions Concurrent administration of durvalumab and tremelimumab over 1 h is safe with a comparable PK profile to sequential administration.

[The cutoff value of FEV(1)/FVC as the criteria of airway obstruction in children]

Objective: To explore the cutoff value of FEV(1)/FVC for evaluating obstructive ventilation dysfunction in children. Methods: Three hundred and eighty-three healthy children (190 boys and 193 girls) aged 6-14 years in primary and middle school in Beijing, who were enrolled from May 2010 to June 2011, had their spirometry done with the Jaeger lung function instrument, and the lower limit of normal (LLN) of FEV(1)/FVC was calculated. Two hundred and thirteen asthmatic children (151 boys and 62 girls) aged 6-14 years from the outpatient Department of Allergy, Capital Institute of Pediatrics were enrolled consecutively from June to July 2018, whose clinical history and pulmonary function parameters were collected. The expected value of spirometric parameters of asthmatic children was calculated according to Zapletal prediction equations. And the LLN of FEV(1)/FVC in healthy children was used as the gold standard to calculate the sensitivity, specificity, Youden index and Kappa value of FEV(1)/FVC<80% and FEV(1)/FVC< 92% predicted. Results: In healthy children, the FEV(1)/FVC and the LLN were 91%±5% and 82% respectively, while 90%±6% and 81% in boys, and 92%±5% and 84% in girls. There were 27 (12.7%) asthmatic children whose FEV(1)/FVC<80% but FEV(1)/FVC≥92% predicted (χ(2)=123.7, P<0.01). The sensitivity, specificity, Youden index and Kappa value of FEV(1)/FVC<80% were 80.3%, 100%, 0.803 and 0.787 respectively when FEV(1)/FVC<80% was used as the criteria to assess lung function, while they were 57.3%, 100%, 0.573 and 0.547, respectively, when FEV(1)/FVC<92% predicted was used as criteria. Conclusions: The 80% of FEV(1)/FVC has a better consistency with the LLN of FEV(1)/FVC than 92% of FEV(1)/FVC% predicted. It is more accarate to use FEV(1)/FVC<80% as the diagnostic criteria for airway obstruction.

Systemic adjuvant therapy for adult patients at high risk for recurrent cutaneous or mucosal melanoma: an Ontario Health (Cancer Care Ontario) clinical practice guideline

Background

Previous versions of the guideline from the Program in Evidence-Based Care (pebc) at Ontario Health (Cancer Care Ontario) recommended that the use of high-dose interferon alfa 2b therapy be discussed and offered to patients with resected cutaneous melanoma with a high risk of recurrence. Subsequently, several clinical trials in patients with resected or metastatic melanoma found that immune checkpoint inhibitors and targeted therapies have a benefit greater than that with interferon. It was therefore considered timely for an update to the guideline about adjuvant systemic therapy in melanoma.

Methods

The present guideline was developed by the pebc and the Melanoma Disease Site Group (dsg). Based on a systematic review from a literature search conducted using medline, embase, and the Evidence Based Medicine Reviews databases for the period 1996 to 28 May 2019, the Working Group drafted recommendations. The systematic review and recommendations were then circulated to the Melanoma dsg and the pebc Report Approval Panel for internal review; the revised document underwent external review.

Recommendations

For patients with completely resected cutaneous or mucosal melanoma with a high risk of recurrence, the recommended adjuvant therapies are nivolumab, pembrolizumab, or dabrafenib-trametinib for patients with BRAF V600E or V600K mutations; nivolumab or pembrolizumab are recommend for patients with BRAF wild-type disease. Use of ipilimumab is not recommended. Molecular testing should be conducted to help guide treatment decisions. Interferon alfa, chemotherapy regimens, vaccines, levamisole, bevacizumab, bacillus Calmette-Guérin, and isolated limb perfusion are not recommended for adjuvant treatment of cutaneous melanoma except as part of a clinical trial.

MicroRNA-370-3p inhibits cell proliferation and induces chronic myelogenous leukaemia cell apoptosis by suppressing PDLIM1/Wnt/β-catenin signaling

Growing evidence has suggested that microRNA-370-3p (miR-370-3p) is downregulated and acts as a suppressor in several cancers. However, the role of miR-370-3p in chronic myeloid leukemia (CML) remains unknown. Here, the expression level and molecular mechanism of miR-370-3p in CML were investigated. Firstly, the expression of miR-370-3p has markedly decreased in the peripheral blood mononuclear cells (PBMCs) of patients with CML and in cell lines. Moreover, miR-370-3p in CML cells upregulated and downregulated proliferation and apoptosis, respectively. Notably, miR-370-3p directly targeted the 3'-untranslated region of PDZ and LIM domain protein 1 (PDLIM1). A negative correlation was observed between the levels of miR-370-3p and PDLIM1 in the PBMCs of patients with CML and healthy volunteers. PDLIM1 was shown to have an oncogenic role in CML cells by promoting proliferation and suppressing apoptosis. Finally, the miR-370-3p-PDLIM1-Wnt/β-catenin signaling axis was indicated to play an important role in CML progression.

A Linear Regression Predictor for Identifying N6-Methyladenosine Sites Using Frequent Gapped K-mer Pattern

N6-methyladenosine (m⁶A) is one of the most common and abundant modifications in RNA, which is related to many biological processes in humans. Abnormal RNA modifications are often associated with a series of diseases, including tumors, neurogenic diseases, and embryonic retardation. Therefore, identifying m⁶A sites is of paramount importance in the post-genomic age. Although many lab-based methods have been proposed to annotate m⁶A sites, they are time consuming and cost ineffective. In view of the drawbacks of the intrinsic methods in RNA sequence recognition, computational methods are suggested as a supplement to identify m⁶A sites. In this study, we develop a novel feature extraction algorithm based on the frequent gapped k-mer pattern (FGKP) and apply the linear regression to construct the prediction model. The new predictor is used to identify m⁶A sites in the Saccharomyces cerevisiae database. It has been shown by the 10-fold cross-validation that the performance is better than that of recent methods. Comparative results indicate that our model has great potential to become a useful and effective tool for genome analysis and gain more insights for locating m⁶A sites.

A C-type lectin with a single carbohydrate-recognition domain involved in the innate immune response of Tribolium castaneum

C-type lectins are one of the pattern-recognition proteins involved in innate immunity in invertebrates. Although there are 16 C-type lectin genes that have been identified in the genome of Tribolium castaneum, their functions and mechanisms in innate immunity remain unknown. Here, we identified one C-type lectin orthologue, TcCTL6 (TC003708), by sequencing random clones from the cDNA library of the coleopteran beetle, T. castaneum. TcCTL6 contains a 654 bp open reading frame encoding a protein of 217 amino acids that includes a single carbohydrate-recognition domain. The expression of TcCTL6 was significantly induced by Escherichia coli, Staphylococcus aureus and stimulation with carbohydrates, including lipopolysaccharide and peptidoglycan. A binding assay suggested that the recombinant TcCTL6 not only bound to lipopolysaccharide and peptidoglycan but also bound to Gram-positive (S. aureus, Bacillus subtilis and Bacillus thuringiensis) and Gram-negative bacteria (E. coli and Pseudomonas aeruginosa) in the presence of calcium ions. Furthermore, when TcCTL6 was knocked down by RNA interference, four antimicrobial peptides (attacin1, attacin2, coleoptericin1 and coleoptericin2) were significantly decreased. These results demonstrate that TcCTL6 plays a vital role in the immune response towards pathogen infection by influencing the expression of antimicrobial peptides and the agglutination of bacteria in the presence of calcium ions in T. castaneum.

FoxP3 in Treg cell biology: a molecular and structural perspective

Regulatory T cells (T_regs) are specialized in immune suppression and play a dominant role in peripheral immune tolerance. T_reg cell lineage development and function maintenance is determined by the forkhead box protein 3 (FoxP3) transcriptional factor, whose activity is fine‐tuned by its post‐translational modifications (PTMs) and interaction partners. In this review, we summarize current studies in the crystal structures, the PTMs and interaction partners of FoxP3 protein, and discuss how these insights may provide a roadmap for new approaches to modulate T_reg suppression, and new therapies to enhance immune tolerance in autoimmune diseases.