MYOD1 c.365G>T, p.L122R Variant Detection by Droplet Digital PCR (ddPCR)

Introduction/Objective

Rhabomyosarcomas (RMS) are a group of skeletal muscle tumors that include embryonal, alveolar, pleomorphic, spindle cell/sclerosing subtypes (SC/SRMS). Spindle cell RMS occurs in both adult and pediatric populations, and is associated with either more aggressive or better clinical outcomes respectively. A recurrent hotspot variant in MYOD1, p.L122R (NM_002478.4 c.365G>T), has been described in SC/SRMS. The classification of this diagnosis is evolving, with VGLL2 and NCOA2 fusions defining the diagnosis in young children, and MYOD1 p.L122R defining the diagnosis in older children. The MYOD1 p.L122R variant seems to be associated with more aggressive disease, and may be increasingly used in risk stratification with intensification of treatment.

Methods/Case Report

A digital droplet PCR (ddPCR) assay was used to detect the MYOD1 p.L122R in DNA samples with RMS. Patients and controls were coded as positive or negative, and tested for association with clinical features and outcome.

Results (if a Case Study enter NA)

Known-positive cohort of samples was limited by the extreme rarity of this tumor. “Known-positive” status was established by confirmation of the variant with an external clinically-validated assay. The six known positive samples were assessed by ddPCR for the presence of MYOD1 L122R. The L122R variant was detected in all six variants for a sensitivity of 100%. DNA and/or TNA obtained from known wild-type FFPE and frozen material was assessed, for a total of nine unique samples (1 synthetic, 8 patient-derived). All 9 samples were wild- type, with no positive droplets detected, for a specificity of 100%.

Conclusion

Our MYOD1 c.365G>T, p.L122R variant detection by droplet digital PCR (ddPCR) assay is a robust, reproducible, specific and sensitive method to detect the MYOD1 hotspot mutation.

Carbapenem-resistant Enterobacterales colonization and subsequent infection in a neonatal intensive care unit in Shanghai, China

Background

Colonization has been reported to play an important role in carbapenem-resistant Enterobacterales (CRE) infection; however, the extent to which carriers develop clinical CRE infection and related risk factors in neonatal intensive care unit (NICU) patients is unclear.

Aim

To investigate the frequency of CRE colonization and its contribution to infections in NICU patients.

Methods

CRE colonization screening and CRE infection surveillance were performed in the NICU in 2017 and 2018.

Findings

Among 1230 unique NICU patients who were screened for CRE colonization, 144 patients tested positive (11.7%, 144/1230), with 9.2% (110/1197) in the intestinal tract, which was higher than that in the upper respiratory tract (6.6%, 62/945) (P=0.026). Gestational age, low birth weight and prolonged hospitalization were risk factors for CRE colonization (all P<0.001). Diversilab homology monitoring found an overall 17.4% (25/144) risk of infection among patients colonized with CRE. For carbapenem-resistant Klebsiella pneumoniae (CR-KP) and carbapenem-resistant Escherichia coli (CR-ECO), the risks were 19.1% (21/110) and 13.8% (4/29), respectively. The independent risk factors for CR-KP clinical infection among CR-KP carriers were receiving mechanical ventilation (odds ratio (OR), 10.177; 95% confidence interval (CI), 2.667–38.830; P=0.013), a high level of neonatal nutritional risk assessment (OR, 0.251; 95% CI, 0.072–0.881; P=0.031) and a high neonatal acute physiology II (SNAP-II) score (OR, 0.256; 95% CI, 0.882–1.034; P=0.025).

Conclusions

The colonization of CRE may increase the incidence of corresponding CRE infection in NICU patients. Receiving mechanical ventilation, malnutrition and critical conditions with high SNAP-II scores were independent risk factors for subsequent CR-KP clinical infection.

Comparison of Levitt's CO breath test and the 15 N-glycine labeling technique for measuring the lifespan of human red blood cells

The red blood cell (RBC) lifespan is an important physiological indicator of clear significance in clinical research, used for the differential diagnosis of various diseases such as anemia, compensatory phase hemolysis, and polycythemia. The ¹⁵ N-glycine labeling technique is the gold standard method for determining RBC lifespans. However, the usefulness of this technique in clinical settings is seriously hindered by the several weeks required to complete the analyses. Levitt's CO breath test is another reliable technique for determining RBC lifespans, with a simpler protocol giving much faster results, making it more useful in clinical applications. We compared the CO breath test and ¹⁵ N-glycine labeling technique for measuring the human RBC lifespan. We investigated human RBC lifespans where each subject undertook both the ¹⁵ N-glycine labeling technique and the CO breath test. The correlation between the results from these two methods was analyzed. Eight of the ten subjects successfully completed the study. The RBC lifespan values obtained by Levitt's CO breath test were lower than those obtained by the ¹⁵ N-glycine labeling technique. The RBC lifespan values determined from the ¹⁵ N-glycine labeling technique and the CO breath test were significantly correlated, with a Pearson correlation coefficient of R = 0.98 (p < 0.05), while the R² of the linear regression equation was 0.96. The CO breath test exhibits as good performance as the ¹⁵ N-glycine labelling technique in distinguishing healthy subjects from subjects with hemolysis. The result suggests that the CO breath test is a reliable method for quickly determining human RBC lifespans in clinical applications.

PIGN spatiotemporally regulates the spindle assembly checkpoint proteins in leukemia transformation and progression

Phosphatidylinositol glycan anchor biosynthesis class N (PIGN) has been linked to the suppression of chromosomal instability. The spindle assembly checkpoint complex is responsible for proper chromosome segregation during mitosis to prevent chromosomal instability. In this study, the novel role of PIGN as a regulator of the spindle assembly checkpoint was unveiled in leukemic patient cells and cell lines. Transient downregulation or ablation of PIGN resulted in impaired mitotic checkpoint activation due to the dysregulated expression of spindle assembly checkpoint-related proteins including MAD1, MAD2, BUBR1, and MPS1. Moreover, ectopic overexpression of PIGN restored the expression of MAD2. PIGN regulated the spindle assembly checkpoint by forming a complex with the spindle assembly checkpoint proteins MAD1, MAD2, and the mitotic kinase MPS1. Thus, PIGN could play a vital role in the spindle assembly checkpoint to suppress chromosomal instability associated with leukemic transformation and progression.

Efficient passivation of n-type and p-type silicon surface defects by hydrogen sulfide gas reaction

An efficient surface defect passivation is observed by reacting clean Si in a dilute hydrogen sulfide-argon gas mixture (<5% H₂S in Ar) for both n-type and p-type Si wafers with planar and textured surfaces. Surface recombination velocities of 1.5 and 8 cm s^-1are achieved on n-type and p-type Si wafers, respectively, at an optimum reaction temperature of 550 °C that are comparable to the best surface passivation quality used in high efficiency Si solar cells. Surface chemical analysis using x-ray photoelectron spectroscopy shows that sulfur is primarily bonded in a sulfide environment, and synchrotron-based soft x-ray emission spectroscopy of the adsorbed sulfur atoms suggests the formation of S-Si bonds. The sulfur surface passivation layer is unstable in air, attributed to surface oxide formation and a simultaneous decrease of sulfide bonds. However, the passivation can be stabilized by a low-temperature (300 °C) deposited amorphous silicon nitride (a-Si:N_X:H) capping layer.

Micromagnetic simulation of microstructure effect for binary-main-phase Nd-Ce-Fe-B magnets

We investigate the magnetic properties of a chemically heterogeneous binary-main-phase (BMP) Nd-Ce-Fe-B magnet with a core-shell structure via micromagnetic simulation. It is found that the coercivity strongly depends on the shell thickness. The BMP magnet's coercivity initially increases and then decreases with increasing Nd-rich shell thickness, and so there is the optimal shell thickness which shows the maximum coercivity for any given Ce concentration. The simulation shows the significant difference in coercivity and maximum energy product between the BMP and single-main-phase magnets. Notably, the magnetization reversal mechanism of the BMP magnet is revealed in the simulation. Local reversals in the BMP magnet first occur in the Ce-rich shells, followed by the Nd-rich cores. Then, the magnetization in Ce-rich core/Nd-rich shell typed grains is switched after reversed magnetization of all the Nd-rich core/Ce-rich shell typed grains. The BMP magnet represents a further increased coercivity for a larger GB thickness, which can be well explained by a maximum stray field.

A genome-wide association study reveals additive and dominance effects on growth and fatness traits in large white pigs

The dominance effect is a kind of non-additive effect due to the interaction between alleles at the same locus. Quantitative traits such as growth traits in farm animals have been found to be influenced by dominance effects. However, dominance effects are usually ignored in the genome-wide association study (GWAS) of complex traits for farm animals. In this study, we performed GWAS and genetic parameters estimation for the two traits age at 100 kg (AGE) and backfat thickness at 100 kg (BF) of 3572 Large White pigs. The pigs were from three breeding farms of China and were genotyped by an in-house designed 50k SNP chip. Our results showed significant non-zero variance for the dominance effect of AGE, while the dominance effect of BF was not significant. Using a GWAS model accounting for both additive and dominance effects, we identified three additive and two dominance significant SNPs for the trait AGE. For the trait BF, three genome-wide significant additive SNPs were detected, but no significant SNP was found for the dominance effect. In total, six important functional genes (NPAS3, USP16, PARN, ARL15, GPC3, ABHD4) near significant SNPs were identified as candidate genes associated with AGE or BF. Notably, ARL15 and PARN were associated with AGE near the dominance association signals. Overall, the newly detected SNPs and newly identified candidate genes in our study added new information about the genetic architectures of growth and fatness traits in pigs, and have the potential to be applied to the pig breeding program in the future.

Development and usage of the digital SAMG system

In order to reduce the work burden during the training and drilling of the severe accident and severe accident management guidelines, and improve the implementation efficiency of the guidelines, a method of digitizing the SAMG program files is proposed. A set of digital SAMG system supported by information technology and combined with software and hardware is developed to transform the manual processes of paper file browsing, data searching, logical judgment and auxiliary calculation into automatic and digital processes, which can be used for SAMG training and drilling, and also for verifying the SAMG execution process and the effectiveness of mitigation measures.

Hsa-miR-4730 as a new and potential diagnostic and prognostic indicators for pancreatic cancer

OBJECTIVE

Pancreatic cancer is a gastrointestinal tumor with the highest malignancy and few diagnostic and prognostic markers. Patients with disease have a 5-year survival rate that is not more than 10%. As a research hotspot in recent years, miRs (microRNAs) are differentially expressed in various tumors, so they can be used as the potential diagnostic and prognostic markers. In this study, differentially expressed miRs in patients with pancreatic cancer were screened out through the GEO chip, to provide potential markers for clinical practice. This study aimed to explore the expression and potential value of miR-4730 in pancreatic cancer.

PATIENTS AND METHODS

Differentially expressed miRs in pancreatic cancer were analyzed through logging in GEO DataSets to download GSE112264. Fifty patients with pancreatic cancer who were treated in our hospital from May 2012 to January 2014 (Group A), 50 patients with benign pancreatic lesions during the same period (Group B), and 50 healthy individuals undergoing physical examinations (Group C) were enrolled in this study. The expression of miR-4730 in the serum and the cancer tissue was detected by qRT-PCR. The correlation of miR-4730 with pathological data, and the diagnostic values of differential indicators in the data were analyzed. The patients were followed up for 5 years to observe the relationship between miR-4730 and their survival.

RESULTS

The analysis of the GEO chip showed 305 differentially expressed miRs, among which 225 were highly expressed and 80 were lowly expressed, with miR-4730 differentially expressed most. The expression of serum miR-4730 in Group A was significantly lower than that in Groups B and C (p<0.05), so miR-4730 had a diagnostic value. The expression of miR-4730 in the cancer tissue was significantly lower than that in the adjacent tissue. The correlation analysis showed that the expression of miR-4730 in the cancer tissue was positively correlated with that in the serum. Patients with low miR-4730 expression had poorly differentiated pancreatic cancer, and patients with stages III+IV of pancreatic cancer had higher incidences of lymphatic invasion and distal metastasis (p<0.05), so miR-4730 had a diagnostic value. The 3- and 5-year survival rates in the high miR-4730 expression group were higher than those in the low expression group (both p<0.05). TNM staging, lymphatic invasion, distal metastasis, and miR-4730 were independent prognostic factors for the 3- and 5-year survival of patients with pancreatic cancer.

CONCLUSIONS

For patients with pancreatic cancer, those with low miR-4730 expression have poor survival and prognoses, so miR-4730 can be used as a potential observational index for the prognosis and diagnosis of the disease.

Optimal NH4 + /NO3 - ratios enhance the shade tolerance of soybean seedlings under low light conditions

In the maize-soybean intercropping system, shade is the major chronic restraint that affects normal growth of soybean. Different spatial patterns of this system affect the microclimate of soybean through shading from maize plants. However, the negative impacts of shading stress can be mitigated by providing optimal ratios of different fertilizers. Therefore, to test this hypothesis, soybean plants were grown under different light conditions (normal light or shade) to evaluate the response to varying NH4 + /NO3 - ratios. Seeds of soybean (Glycine max L. cv. Nan-99-6) were grown in nutrient solution with a total concentration of 5 mM N using different NH4 + /NO3 - ratios (T0  = 0:0, T1  = 0:100, T2  = 25:75, T3  = 50:50 and T4  = 75:25) for 40 days in a greenhouse at PPFD 320.95 μmol m-2  s-1 (low light) or 967.53 μmol m-2  s-1 (normal light). Under low light, growth and photosynthesis of soybean seedlings significantly decreased as compared to normal light conditions. However, the optimal ratios of NH4 + / NO3 - improved growth and photosynthesis of soybean seedlings under both light conditions. Our results indicated that soybean seedlings supplied with optimal NH4 + /NO3 - ratios (25:75 and 50:50) have maximum biomass yield, chlorophyll pigments, leaf gas exchange, photochemical activity and root growth as compared to low and high NH4 + /NO3 - ratios (T1 and T4 ). High ratios of NH4 + /NO3 - (T4 ) resulted in reduced plant growth due to nutrient accumulation in plant tissues; therefore, we suggest that optimal ratios of NH4 + /NO3 - (T2 and T3 ) can enhance the shade tolerance of soybean seedlings.

Adverse childhood experiences and co-occurring psychological distress and substance abuse among juvenile offenders: the role of protective factors

OBJECTIVE

The purpose of this study was to estimate associations between cumulative exposure to adverse childhood experiences (ACEs), protective factors, and co-occurrence among male and female juvenile offenders.

STUDY DESIGN

Cross-sectional study.

METHODS

Validated measures of ACEs, internal resilience, external youth assets, psychological distress, and substance abuse were collected from 429 youths involved in the juvenile justice system in Nevada. A three-level outcome variable was created using the psychological distress and substance use measures: no problems, one problem, or co-occurring problems. Hierarchical multinomial logistic regression models were used to determine the independent, direct, and moderating impact of the protective factors on ACEs and the outcome.

RESULTS

Internal resilience, family communication, school connectedness, peer role models, and non-parental adult role models were associated with lower odds of co-occurrence compared to having no problems (adjusted odds ratios [AORs] ranged from 0.11 to 0.33). When ACEs were added to the model, internal resilience and all assets except for one (non-parental adult role models) continued to offer protection against co-occurrence. Internal resilience was the only protective factor that significantly moderated the association between ACEs and co-occurrence (AOR, 0.24; 95% CI, 0.06, 0.99).

CONCLUSION

Most protective factors decreased co-occurring mental health and substance abuse problems in the presence of ACE exposure and internal resilience moderated the relationship between ACEs and co-occurrence. Juvenile justice systems should use positive youth development approaches to help prevent co-occurrence among youths.

LncRNA APPAT regulated miR-328a/Pkp1 signal pathway to participate in breast cancer

OBJECTIVE

Recent studies indicated long non-coding RNA (lncRNA) is involved in the development of breast cancer, which is the pathological basis of breast cancer. Here, we reported the molecular mechanisms by which lncRNA APPAT regulated in the progression of breast cancer.

MATERIALS AND METHODS

QPCR was used to inspect the expression of lncRNA APPAT and miR-328a in breast cancer cell lines. Luciferase reporter assay confirmed the direct target effect of APPAT and miR-328a. Western blot was used to check Pkp1 protein expression in breast cancer cell lines.

RESULTS

The expressions of lncRNA APPAT, Pkp1 protein levels and miR-328a were commonly expressed in breast cancer cells. The inhibition of lncRNA APPAT expression repressed cell proliferation, migration and invasion in breast cancer and reverse results were found after lncRNA APPAT overexpressing. Mechanistically, the binding targets of lncRNA APPAT vs. miR-328a and Pkp1 vs. miR-328a were checked in breast cancer. Meanwhile, miR-328a silencing enhanced the proliferation, migration and invasion of breast cancer cells. Moreover, the effect caused by Pkp1 silencing on cell proliferation, migration and invasion was reversed by miR-328a inhibitor in MCF-7 and BT594 cells. Additionally, Pkp1 knockout reversed the effect of cell proliferation, migration and invasion triggered by APPAT elevated. Taken together, these results showed miR-328a as a downstream target of lncRNA APPAT linking lncRNA APPAT to Pkp1.

CONCLUSIONS

LncRNA APPAT regulated the proliferation, migration, invasion of breast cancer by regulating miR-328a/Pkp1 signaling pathway, providing a novel possible strategy for the treatment of breast cancer.

Circular RNA-ABCB10 suppresses hepatocellular carcinoma progression through upregulating NRP1/ABL2 via sponging miR-340-5p/miR-452-5p

OBJECTIVE

Hepatocellular carcinoma (HCC) is one of the most common liver malignancies worldwide with a high rate of recurrence and mortality. Circular RNA-ABCB10 (circ-ABCB10), 724 nucleotides in length, plays a pro-oncogenic role in tumor progression. However, the role of circ-ABCB10 in HCC is still unknown. Therefore, the objective of this study was to determine the role of circ-ABCB10 in HCC progression in vitro and in vivo and to elucidate the underlying mechanism.

PATIENTS AND METHODS

Tumor tissues from patients with HCC and multiple HCC cell lines were used for in vitro experiments and a mouse xenograft model was used for in vivo experiments. Quantitative Real Time-PCR, Western blots, lentivirus transfection, cell proliferation assays, cloning formation, migration, and invasion assays, flow cytometry, Luciferase reporter assays, and biotin-coupled probe pull-down assays were performed to investigate the mechanism underlying the effect of circ-ABCB10 on HCC.

RESULTS

The results revealed that the expression of circ-ABCB10 was downregulated in both HCC tissues and cell lines and was positively correlated with histological grade and tumor size. The overexpression of circ-ABCB10 exerted inhibitory effects on HCC cell proliferation, invasion, and migration. Mechanistic and functional evidence together showed that circ-ABCB10 elevated expressions of neuropilin-1 (NRP1) and ABL related gene (ABL2) by sponging miR-340-5p and miR-452-5p, which inhibited the progression of HCC. Furthermore, the in vivo study suggests that circ-ABCB10 inhibited tumor growth in nude mice.

CONCLUSIONS

In brief, the results demonstrate that circ-ABCB10 exerts anti-tumor roles via miR-340-5p/miR-452-5p-NRP1/ABL2 signaling axis, providing a promising biomarker and therapeutic target for HCC.

Genomic scan revealed KIT gene underlying white/gray plumage color in Chinese domestic geese

Goose is an important type of domesticated poultry. The wild geese that are regarded as the ancestors of modern domestic geese present gray plumage. Domesticated, geese have both white and gray feathers. To elucidate the genetic mechanisms underlying the formation of white and gray plumage in geese, we resequenced the whole genome of 18 geese from six populations including white and gray goose breeds. The average sequencing depth per individual was 9.81× and the average genome coverage was 96.8%. A total of 346 genes were detected in the top 1% of F_ST scores of gray- and white-feathered geese, and a significant F_ST site was located in the intron region within the KIT gene, the 18 bp deletion in KIT having the strongest potential association with white feathers. It has been reported that a number of genes are associated with plumage colors in birds. However, no studies have identified the relationship between KIT and plumage color in birds at present, although the white coat can be attributed to mutations in KIT in some mammals. Our study showed that that KIT is a plausible candidate gene for white/gray plumage color in Chinese domestic geese.

Design of Geiger Muller detector system for searching lost γ-ray source

If a radiation source is lost, it will do harm to human being, especially for the searching person. In order to find the lost radiation source easily, a detector system, including 3 detectors, was designed to search the lost c-ray radiation source autonomously in any environment. First, based on GEANT4 simulation, the radiation dose rates in 3 Geiger Muller (GM) counters were simulated at the different source-detector distances, distances between detectors and angles. Various analyses were performed by experimentally and verified the simulated detector designed system. A Mono-energetic 137Cs c-ray source with energy 662 keV and activity of 1.11 GBq was used for the observation. The simulated results were compared with the experimental dose rate values and obtained good agreements for various cases. Only based on the dose rates in three detectors, the radiation source was searched in a different location at a specific source activity and angle. The corresponding angles of deviation and detection limit were calculated for sensitivity and ability of detector designed system. The proposed detector designed system can be used to navigate radiation sources in the low level and high radiation environments.

Eltrombopag, oral immunosuppressant and androgen combination therapy in twelve patients with refractory severe aplastic anemia

Objective: Eltrombopag monotherapy or eltrombopag combined with immunosuppressant has achieved robust hematologic responses in severe aplastic anemia (SAA). In patients with refractory SAA, for whom hematopoietic stem cell transplantation is unavailable, we attempted to combine eltrombopag with oral immunosuppressant and androgen, to further improve hematologic response. Methods: We collected and analyzed data retrospectively from twelve refractory SAA cases who had received combination therapy of eltrombopag, oral immunosuppressant and androgen. All these patients had received intensive immunosuppressive treatment (IST) for more than 6 months and were evaluated as nonresponders. Results: A total of 12 SAA patients were treated with a combination of eltrombopag, an oral immunosuppressant (cyclosporine, N = 9; tacrolimus, N = 3) and androgen. The median maximum dose of eltrombopag was 75 mg/day (range, 75-150). After a median follow-up of 8.5 months (7-23), the overall response rate (ORR) was 42% (5/12, including trilineage, N = 4; hemoglobin + platelet, N = 1). Two of 5 responders reached normal blood counts. Optimal hematological response rates were reached at 6 months. The median increase in neutrophil, hemoglobin and platelet count were 1.64 × 10⁹ /L (0.71-2.66), 53 g/L (25-66.5) and 25 × 10⁹ /L (14-230), respectively. In general, the combination therapy was well tolerated; however, two patients suffered from non-lethal upper extremity venous thrombosis when they were platelet transfusion-dependent. Conclusion: Eltrombopag, oral immunosuppressant and androgen combination therapy in patients with IST-refractory SAA is feasible and could restore multi-lineage hematopoiesis. Thrombosis risk of eltrombopag still needs to be monitored.

Effect of Polyphenols on Cognitive Function: Evidence from Population-Based Studies and Clinical Trials

Due to progressive population aging, a new dementia case occurs at every 3 seconds, placing a heavy burden of disease. Identifying potential risk or preventive factors is emphasized owing to a lack of effective treatment for dementia. There has been emerging evidence on the link of certain dietary components, particularly polyphenols, to brain wellness and cognitive outcomes. Findings from animal and in vitro studies appear more consistent and conclusive. However, such an association has not been investigated in depth in human beings. In this review, we examined studies on the effect of dietary polyphenols (including flavonoids, curcumin, and resveratrol) on cognitive function. Intervention in early stages of dementia/Alzheimer's disease might be a target to slow down age-related cognitive decline before disease onset. We summarized 28 epidemiological studies (8 cross-sectional and 20 cohort studies) and 55 trials in this review. Preliminary evidence from epidemiological data provides the necessity for intervention trials, even though the measures of polyphenol intake tend to be less precise. Clinical trials are in favor of the role of some polyphenols in benefiting specific domains of cognition. This review also describes the divergence of results and current limitations of research in this field.