Genetic variants in the folate metabolic pathway genes predict cutaneous melanoma-specific survival

BACKGROUND

Folate metabolism plays an important role in DNA methylation and nucleic acid synthesis and thus may function as a regulatory factor in cancer development. Genome-wide association studies (GWASs) have identified some single-nucleotide polymorphisms (SNPs) associated with cutaneous melanoma-specific survival (CMSS), but no SNPs were found in genes involved in the folate metabolic pathway.

OBJECTIVES

To examine associations between SNPs in folate metabolic pathway genes and CMSS.

METHODS

We comprehensively evaluated 2645 (422 genotyped and 2223 imputed) common SNPs in folate metabolic pathway genes from a published GWAS of 858 patients from The University of Texas MD Anderson Cancer Center and performed the validation in another GWAS of 409 patients from the Nurses' Health Study and Health Professionals Follow-up Study, in which 95/858 (11·1%) and 48/409 (11·7%) patients died of cutaneous melanoma, respectively.

RESULTS

We identified two independent SNPs (MTHFD1 rs1950902 G>A and ALPL rs10917006 C>T) to be associated with CMSS in both datasets, and their meta-analysis yielded an allelic hazards ratio of 1·75 (95% confidence interval 1·32-2·32, P = 9·96 × 10^-5 ) and 2·05 (1·39-3·01, P = 2·84 × 10^-4 ), respectively. The genotype-phenotype correlation analyses provided additional support for the biological plausibility of these two variants' roles in tumour progression, suggesting that variation in SNP-related mRNA expression levels is likely to be the mechanism underlying the observed associations with CMSS.

CONCLUSIONS

Two possibly functional genetic variants, MTHFD1 rs1950902 and ALPL rs10917006, were likely to be independently or jointly associated with CMSS, which may add to personalized treatment in the future, once further validated. What is already known about this topic? Existing data show that survival rates vary among patients with melanoma with similar clinical characteristics; therefore, it is necessary to identify additional complementary biomarkers for melanoma-specific prognosis. A hypothesis-driven approach, by pooling the effects of single-nucleotide polymorphisms (SNPs) in a specific biological pathway as genetic risk scores, may provide a prognostic utility, and genetic variants of genes in folate metabolism have been reported to be associated with cancer risk. What does this study add? Two genetic variants in the folate metabolic pathway genes, MTHFD1 rs1950902 and ALPL rs10917006, are significantly associated with cutaneous melanoma-specific survival (CMSS). What is the translational message? The identification of genetic variants will make a risk-prediction model possible for CMSS. The SNPs in the folate metabolic pathway genes, once validated in larger studies, may be useful in the personalized management and treatment of patients with cutaneous melanoma.

Diversity and abundance of comammox bacteria in the sediments of an urban lake

AIMS

Although comammox have been discovered in a variety of ecosystems, there are few studies in urban lakes. This paper attempted to confirm whether this ammonia-oxidizing microbe exists in urban lakes and to determine the factors influencing its existence.

METHODS AND RESULTS

This study investigated the diversity and abundance of comammox bacteria in sediments of a typical urban lake in China, and their ecological relationship with other ammonia-oxidizing micro-organisms. The phylogenetic analysis indicated that comammox clade A existed in the sediment of Lake Donghu, and the comammox bacteria co-existed with ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB) and anaerobic ammonia-oxidizing (anammox) bacteria in the sediment of this lake. The abundances of the ammonia monooxygenase subunit A (amoA) genes for comammox, AOA, AOB and anammox 16S rRNA were 2·43 × 10⁸ , 1·07 × 10⁸ , 3·24 × 10⁷ and 3·21 × 10¹¹ copies per gram dry sediment respectively. Moreover, the amoA gene abundance of comammox was positively correlated with that of AOA and AOB. The redundancy analysis showed that the abundance of the comammox amoA gene was negatively correlated with the concentration of main indicators for nitrogen status in both the sediment and the water column, indicating that eutrophication may inhibit the growth of comammox bacteria.

CONCLUSIONS

Comammox bacteria play an important ecological role in the nitrogen cycle of urban lake sediments.

SIGNIFICANCE AND IMPACT OF THE STUDY

Our results indicated comammox bacteria were widespread in urban lakes and eutrophication may inhibit their growth.

Chloride inputs to the North Saskatchewan River watershed: the role of road salts as a potential driver of salinization downstream of North America's northern most major city (Edmonton, Canada)

Multiple anthropogenic activities are driving the salinization of freshwater environments threatening water resources worldwide. Accordingly, this research will first examine the spatial and temporal variability of major ions (i.e. Ca²⁺, Mg²⁺, Na⁺, K⁺, SO₄^2-, CO₃^2-, and HCO₃^-) upstream and downstream of the northernmost major city in North America (Edmonton, Canada). Second, this research will estimate the relative contributions of the major sources of chloride (Cl), the main constituent of road deicers, to the sub-basin around Edmonton. Monthly water quality data was for three sites on the North Saskatchewan River (NSR): Rocky Mountain House (RMH - downstream of the Rocky Mountain headwaters), Devon Bridge (upstream of Edmonton) and Pakan Bridge (downstream of Edmonton). Change ratios investigate the downstream alterations of major ions at Pakan and Devon, relative to RMH. Seasonal Kendall tests examine temporal trends (1987-2017). A mass-balance approach then quantifies the major sources of Cl in the sub-basin of the NSR between Devon and Pakan. Progressing from the Rocky Mountain headwaters (at RMH) to downstream of Edmonton (at Pakan), Cl^- increased by >5.5 times, Na⁺ by 4.8 times and K by 2.7 times. No significant temporal trends for Cl^-, Na⁺ and K⁺ were evident at Devon (upstream of Edmonton), whereas all three significantly increased at Pakan (downstream of Edmonton). Deicers (54%), agriculture (20%), along with waste water treatment plant and industrial effluent (15%) were the largest Cl sources in the NSR Devon-Pakan sub-basin. In total, 77 Gg yr^-1 of Cl (or 6 t km² yr^-1) is added to the Devon-Pakan sub-basin, of which, 43 Gg yr^-1 is retained. Understanding and managing the major drivers of freshwater salinization will be of increasing importance in the 21^st century owing to the potential salinization of freshwater resources in the context of a changing climate.

Training of quantum circuits on a hybrid quantum computer

Generative modeling is a flavor of machine learning with applications ranging from computer vision to chemical design. It is expected to be one of the techniques most suited to take advantage of the additional resources provided by near-term quantum computers. Here, we implement a data-driven quantum circuit training algorithm on the canonical Bars-and-Stripes dataset using a quantum-classical hybrid machine. The training proceeds by running parameterized circuits on a trapped ion quantum computer and feeding the results to a classical optimizer. We apply two separate strategies, Particle Swarm and Bayesian optimization to this task. We show that the convergence of the quantum circuit to the target distribution depends critically on both the quantum hardware and classical optimization strategy. Our study represents the first successful training of a high-dimensional universal quantum circuit and highlights the promise and challenges associated with hybrid learning schemes.

[Clinical and genotypic characteristics of infantile inflammatory bowel disease]

Objective: To analyze the clinical and genotypic characteristics of infantile inflammatory bowel disease (IBD). Methods: The age of onset, family history, clinical manifestations, and treatment effect were retrospectively analyzed in 39 infants (male 23 cases, female 16 cases) with IBD who were admitted to the Department of Gastroenterology in Children's Hospital, Capital Institute of Pediatrics from January 2007 to December 2017. Next generation sequencing (NGS) based on target gene panel was used for gene analysis in 17 patients. Results: The median age of onset was 0.5 (0.5, 1.0) month. The most common clinical symptoms included diarrhea (39, 100%), malnutrition (38, 97%), hematochezia (34, 87%), fever (25, 64%), and perianal diseases (24, 61%). Four children had associated family history. Among the 17 patients whose gene was analyzed, 10 were found to have the pathogenic gene variation, within whom 7 had interleukin-10 receptor α subunit (IL-10RA) mutation, 2 had CYBB heterozygous mutation, 1 had interleukin-10 receptor β subunit (IL-10RB) mutation. The therapeutic medicine included mesalazine, steroids, and thalidomide. Eighteen children (46%) reached clinical remission (10 cases) or partial remission (8 cases). Conclusions: The incidence of single gene mutation in infants with IBD is high, with IL-10RA mutation as the most common. Refractory diarrhea and malnutrition may indicate infantile IBD.

Tumor suppressor miR-145-5p sensitizes prolactinoma to bromocriptine by downregulating TPT1

PURPOSE

Prolactinoma is the most commonly seen secretory tumor of pituitary glands, which accounts for approximately up to 40% of total pituitary adenomas. Due to its high drug resistance, dopamine agonist, such as bromocriptine, has limited effect on the treatment of patients with prolactinoma. Recent discoveries have revealed that multiple miRNAs were involved in regulating drug resistance. In this research, we explored the relationship between miR-145-5p expression as well as bromocriptine sensitivity both in vitro and in vivo.

METHODS

To study the role of miR-145-5p in drug resistance of prolactinoma, the expression levels of miR-145-5p in bromocriptine-resistant prolactinoma cell line MMQ/BRC and its parental cell line MMQ cells, 24 bromocriptine-resistant as well as eight sensitive clinical samples were measured by qRT-PCR. Moreover, CCK8, flow cytometry and immunofluorescence were performed to identify the biological characteristics of MMQ/BRC and MMQ. TPT1 was predicted as a direct target gene of miR-145-5p by bioinformatic methods. In addition, qRT-PCR, western blot and immunohistochemistry were used to detect the expression level of TPT1 in clinical specimens and cell lines. Xenograft mouse model was constructed to analyze whether miR-145-5p could reverse bromocriptine resistance in prolactinoma in vivo.

RESULTS

In our study, bromocriptine-resistant prolactinoma clinical samples and cell line had decreased miR-145-5p levels and expressed high levels of TPT1 compared with their sensitive counterparts. Bioinformatic methods and our preliminary dual luciferase reporter assay were utilized to elucidate that TPT1 was a direct target gene of miR-145-5p. Furthermore, introducing miR-145-5p mimic into MMQ cells led to a decrease of IC50 along with upregulation of TPT1; nevertheless, transfecting the corresponding inhibitor into MMQ cells resulted in an upregulation of IC50 as well as reduction of TPT1.

CONCLUSIONS

Collectively, our findings elucidated the role of miR-145-5p as an important regulator of drug resistance in prolactinoma by controlling TPT1, and implicated the potential application of miR-145-5p in cancer therapy as well.

Pharmacological inhibition of β-catenin/BCL9 interaction overcomes resistance to immune checkpoint blockades by modulating Treg cells

The Wnt/β-catenin (β-cat) pathway plays a critical role in cancer. Using hydrocarbon-stapled peptide technologies, we aim to develop potent, selective inhibitors targeting this pathway by disrupting the interaction of β-cat with its coactivators B-cell lymphoma 9 (BCL9) and B-cell lymphoma 9-like (B9L). We identified a set of peptides, including hsBCL9CT-24, that robustly inhibits the activity of β-cat and suppresses cancer cell growth. In animal models, these peptides exhibit potent anti-tumor effects, favorable pharmacokinetic profiles, and minimal toxicities. Markedly, these peptides promote intratumoral infiltration of cytotoxic T cells by reducing regulatory T cells (Treg) and increasing dendritic cells (DCs), therefore sensitizing cancer cells to PD-1 inhibitors. Given the strong correlation between Treg infiltration and APC mutation in colorectal cancers, it indicates our peptides can reactivate anti-cancer immune response suppressed by the oncogenic Wnt pathway. In summary, we report a promising strategy for cancer therapy by pharmacological inhibition of the Wnt/β-cat signaling.

Ultrastructure of duck Tembusu virus observed by electron microscopy with negative staining

Duck Tembusu virus (DTMUV) is a newly emerging enveloped flavivirus. This study shows the ultrastructure of DTMUV using viral purification, negative staining and electron microscopy. Electron microscopic examinations revealed mature DTMUV particles with 50 to 75 nm in diameter and typical enveloped flavivirus structure that consists of the internal nucleocapsid, an inner layer of lipid bilayer and an external layer of E glycoprotein ectodomain. Particles appear to be mostly spherical. In particular, RNA core is deep colored and dense, both capsid and lipid bilayer are clearly visible, the capsid forms regular hexagon, and E glycoprotein ectodomain forms a fringe instead of visible spikes. Thus, this report about the clear ultrastructure of the DTMUV particles will be the major driving forces behind structural biology of DTMUV.

Effects of T cell subsets with different proportions on renal function and blood lipids in patients with preeclampsia

This study aimed to investigate the effect of T cell subsets with different proportions on renal function and blood lipids in patients with preeclampsia (PE). Ninety pregnant women were included in this experiment and classified into 3 groups: group A (30 with severe PE), group B (30 with mild PE) and group C (30 healthy pregnant women). Clinical characteristics were examined. The ratio of T cell subsets in the three groups was detected by flow cytometry. The relationship between PE and T cell subsets was determined. The results showed that no significant difference was found in age or gestational age (P>0.05). The number of CD4+ T cells (CD4 is mainly expressed in helper T cells, referred to as TH) in group A increased significantly compared with group B and group C (P less than 0.05), while the number of CD8+ T cells (CD8+ T cell, also known as cytotoxic T cell (CTL) in group A decreased noticeably in comparison to group C (P less than 0.05). The ratio of CD4+ cell number to CD8+ cell number (TH/CTL) in group A was elevated significantly compared with group B and group C (P less than 0.05). The uric acid (UA) concentration of group A was noticeably elevated compared to group C (P less than 0.05), which differed insignificantly between group B and C (P>0.05). Glomerular filtration rate (GFR) of group A was obviously impaired in comparison to group B and group C (P less than 0.05), which differed insignificantly between group B and C (P>0.05). Total cholesterol (TC) concentrations in group A, C and B were examined. TC concentrations in the former two groups were slightly higher compared to the latter (P less than 0.05), and those in the former two groups were also higher than the normal range (P less than 0.05). Mean triglyceride (TG) concentrations in all 3 groups were above the normal range, and those in group A and B were significantly higher compared to group C (P less than 0.05). TG concentrations differed insignificantly between group B and C (P>0.05). Serum TG, UA and TC in PE patients were positively related to TH/CTL (P less than 0.05). In conclusion, PE is related to T cell subsets, and T cell subsets are closely related to kidney injury and dyslipidemia.

Genomics and biochemistry investigation on the metabolic pathway of milled wood and alkali lignin-derived aromatic metabolites of Comamonas serinivorans SP-35

BACKGROUND

The efficient depolymerization and utilization of lignin are one of the most important goals for the renewable use of lignocelluloses. The degradation and complete mineralization of lignin by bacteria represent a key step for carbon recycling in land ecosystems as well. However, many aspects of this process remain unclear, for example, the complex network of metabolic pathways involved in the degradation of lignin and the catabolic pathway of intermediate aromatic metabolites. To address these subjects, we characterized the deconstruction and mineralization of lignin with milled wood lignin (MWL, the most representative molecule of lignin in its native state) and alkali lignin (AL), and elucidated metabolic pathways of their intermediate metabolites by a bacterium named Comamonas serinivorans SP-35.

RESULTS

The degradation rate of MWL reached 30.9%, and its particle size range was decreased from 6 to 30 µm to 2-4 µm-when cultured with C. serinivorans SP35 over 7 days. FTIR analysis showed that the C-C and C-O-C bonds between the phenyl propane structures of lignin were oxidized and cleaved and the side chain structure was modified. More than twenty intermediate aromatic metabolites were identified in the MWL and AL cultures based on GC-MS analysis. Through genome sequencing and annotation, and from GC-MS analysis, 93 genes encoding 33 enzymes and 5 regulatory factors that may be involved in lignin degradation were identified and more than nine metabolic pathways of lignin and its intermediates were predicted. Of particular note is that the metabolic pathway to form the powerful antioxidant 3,4-dihydroxyphenylglycol is described for the first time in bacteria.

CONCLUSION

Elucidation of the β-aryl ether cleavage pathway in the strain SP-35 indicates that the β-aryl ether catabolic system is not only present in the family of Sphingomonadaceae, but also other species of bacteria kingdom. These newly elucidated catabolic pathways of lignin in strain SP-35 and the enzymes responsible for them provide exciting biotechnological opportunities for lignin valorization in future.

[Effect of functional exercises on patients with rheumatoid arthritis: a meta-analysis]

OBJECTIVE

To evaluate the effect of functional exercises on disease activity, joint function and quality of life of patients with rheumatoid arthritis (RA).

METHODS

Randomized controlled trials were searched in Cochrane Library, PubMed, China National Knowledge Infrastructure (CNKI), VIP database and Wanfang database with keywords being "rheumatoid arthritis/RA", "function exercise (training)/joint exercise (training)/physical exercise (training)/resistance movement (exercise)/isotonic and isometric/stretching exercise/muscle exercise", and "trials/clinical trials". Then literature selection, extraction and literature quality evaluation were carried out by two of the authors independently following the including and excluding standards. Then the outcome indicators were analyzed with Review Manager 5.3 software.

RESULTS

In the study, 2 173 articles were achieved by searching in databases, including 1 522 English papers and 651 Chinese papers. Then 913 duplicated papers were identified and removed using EndNote software. After reading the titles and abstracts, 1 194 papers were excluded that did not satisfy the including standards. Finally, the full texts of these papers were read and papers with insufficient data were excluded, resulting in 13 included papers for systematic review, including 8 English and 5 Chinese papers. A total of 812 cases were studied in these papers, including 426 in the experimental groups and 386 in the conventional groups. For the outcome index in these articles, disease activity score 28 (DAS28) was used in 5 of them, health assessment questionnaire (HAQ) was used in 8 articles, visual analogue scale (VAS) for pain was used in 6 articles, and morning stiffness duration was used in 3 articles. The meta-analysis showed that functional exercises could delay the development of the disease activity of RA patients (mean difference=-0.76; 95%CI: -1.13, -0.38; P<0.001), improve the joint function (mean difference=-0.36; 95%CI: -0.47, -0.24; P<0.001), alleviate the pain of joints (mean difference=-1.75; 95%CI: -1.98, -1.53; P<0.001), and reduce the duration of morning stiffness (mean difference=-17.65; 95%CI: -22.09, -13.21; P<0.001).

CONCLUSION

This study showed the positive effects of functional exercises on alleviating the pain of joints, reducing the morning stiffness duration, and delaying the disease exacerbation of RA patients. It has a positive effect on improving the joint function and improving the quality of life in patients with RA.

Construction of expression vectors of capsid proteins from goose parvovirus and investigation of the immunogenicity

Goose parvovirus (GPV) is a highly contagious and lethal disease in goslings and Muscovy ducklings, and is of concern to the waterfowl industry. With the aim of comparing the cellular immunogenicity of three capsid proteins of GPV, plasmids of pcDNA3.1(+)-VP1, pcDNA3.1(+)-VP2, and pcDNA3.1(+)-VP3 were constructed, and the recombinant protein VPs were expressed using an eukaryotic expression system. We detected the levels of immune-related genes (CD4, CD8α, IL-1β, IL-6, IFNα, IFNγ, and IFNλ) in both goose embryo fibroblasts (GEF) and goose peripheral blood mononuclear cells (PBMCs) cellular models. The immune response conferred by a VP2 DNA vaccine in vivo was observed in a time course. Our data suggested that the cellular immune response to VP2 and VP3 was stronger than that to VP1, while VP2 and VP3 shared similar cellular immune reactivity. In addition, vaccination with VP2 plasmid can induce high level of IgY antibody that continued to increase through 28 days post vaccination. Therefore, our findings shed light on the host cellular immune response against GPV capsid proteins. Keywords: GPV; capsid proteins; cellular immune response; humoral immunity.

Oncologic outcomes of nephron-sparing surgery in patients with T1 multifocal renal cell carcinoma

OBJECTIVE

This study is performed to explore the pathological characteristics and oncologic outcomes of T1 multifocal renal cell carcinoma (RCC).

METHODS

The clinical data of 600 patients (442 males and 158 females) between the age of 29 and 73 years, diagnosed with T1 RCC were collected from three hospitals in China, out of which 421 cases had undergone nephron-sparing surgery (NSS) and 179 cases had undergone radical nephrectomy (RN) between December 2010 and January 2015.

RESULTS

Tumor was identified with multifocality in 32 patients (5.33%), out of which 21 were set to receive NSS, and 11 to receive RN, respectively; 21 cases of clear cell tumor, 8 cases of papillary tumor, 1 case of chromophobe tumor and 2 cases of Xp.11.2 translocation RCC. Among 568 cases of monofocal tumors, 400 patients underwent NSS, and the remaining 168 patients underwent RN, respectively. After a median follow-up of 5 years, 13 patients were found with recurrent tumors out of those who had undergone NSS, 11 with monofocal tumors and 2 with multifocal tumors containing satellite tumor nodules (p = 0.13). Out of the 32 individuals with multifocal RCC, 4 cases were reported to have died of cancer, 2 of NSS and 2 of RN. From these findings, the cancer-specific survival for NSS and RN was estimated to be 90.48% and 81.82%, respectively (p = 0.48).

CONCLUSION

The findings from the study suggested that there were pathological differences in multifocal renal tumors, and that papillary carcinoma may be more common than clear cell carcinoma. The recurrence rate and survival rate of multifocal RCC were similar to monofocal tumors. Tumor recurrence may be related to satellite tumor nodules, which can only be detected once surgery is performed.

[Effects of Blood-brain Barrier and Simulated metabolic system on Apoptosis of SH-SY5Y Induced by Acrylamide in Vitro]

Objective: To evaluate the effect of acrylamide on the apoptosis of nerve cells by integral cell modelling in vitro which simulates the barrier effect and metabolic micro-environment. Methods: A non-contact and co-cultured in vitro blood brain barrier (BBB) model was established by using human umbilical vein endothelial cells (HUVEC) and rat glioma cells (C6) . The trans-endotheilal electrical resistance (TEER) and horseradish peroxidase (HRP) tracer effects were measured to verify the tight connectivity and permeability of the established BBB model. An integrate discrete multiple organ cell co-culture (idMOC) model was established by inoculating the human renal cortical proximal tubular epithelial cells (HK-2) , human normal hepatocytes (L-02) and human neuroblastoma cells (SH-SY5Y) into the self-made multi-organ plate for co-culturing. Then the model was verified by observing the growth curve of various tissue cells under co-culturing or culturing individually. SH-SY5Y cells were exposed to different concentrations of acrylamide directly and indirectly (through BBB model and idMOC model) . The changes of cell apoptosis rate were analyzed by flow cytometry to explore the impact of model on Acrylamide (ACR) injury of typical neurotoxic agents. Results: HUVEC cells can form a wide range of close-connected complex and then inhibit the external electric field under the cross-endothelial movement, and the mean was lower than that of endothelial cell culture group at 4, 5 and 6 days (P<0.05) ; After 20 min, the penetration rate of HRP in the co-culture group was less than that in the individual culture group, and the difference was statistically significant (P<0.05) , indicating that the barrier function of the co-culture group was higher than that of the individual culture group. All cells can exchange substances through the exchange hole of the culture plate, the cells grow well and there was no obvious death. The growth curve in individual culture group and co-culture group were basically the same, the difference was not statistically significant (P>0.05) . Under the condition of different concentrations of ACR (140, 270 g/ml) , compared with the direct exposure group, the apoptosis rate of the BBB model and the idMOC model were significantly decreased, and the difference was statistically significant (P<0.05) . Conclusion: Based on HUVEC cells and C6 cells co-culture system, a blood-brain barrier model in vitro was established and based on co-culture of HK-2, L-02 and SH-SY5Y, the idMOC model was established. The toxicity and toxic action characteristics of ACR on SH-SY5Y cells were evaluated by validation tests.