New whole-genome alignment tools are needed for tapping into plant diversity

Genome alignment is one of the most foundational methods for genome sequence studies. With rapid advances in sequencing and assembly technologies, these newly assembled genomes present challenges for alignment tools to meet the increased complexity and scale. Plant genome alignment is technologically challenging because of frequent whole-genome duplications (WGDs) as well as chromosome rearrangements and fractionation, high nucleotide diversity, widespread structural variation, and high transposable element (TE) activity causing large proportions of repeat elements. We summarize classical pairwise and multiple genome alignment (MGA) methods, and highlight techniques that are widely used or are being developed by the plant research community. We also outline the remaining challenges for precise genome alignment and the interpretation of alignment results in plants.

Combined GWAS and eGWAS reveals the genetic basis underlying drought tolerance in emmer wheat (Triticum turgidum L.)

Drought is one of the major environmental constraints for wheat production world-wide. As the progenitor and genetic reservoir of common wheat, emmer wheat is considered as an invaluable gene pool for breeding drought-tolerant wheat. Combining GWAS and eGWAS analysis of 107 accessions, we identified 86 QTLs, 105 462 eQTLs as well as 68 eQTL hotspots associating with drought tolerance (DT) in emmer wheat. A complex regulatory network composed of 185 upstream regulator and 2432 downstream drought-responsive candidates was developed, of which TtOTS1 was found to play a negative effect in determining DT through affecting root development. This study sheds light on revealing the genetic basis underlying DT, which will provide the indispensable genes and germplasm resources for elite drought tolerance wheat improvement and breeding.

The value of MRI in predicting hepatocellular carcinoma with cytokeratin 19 expression: a systematic review and meta-analysis

AIM

To evaluate the overall diagnostic performance of magnetic resonance imaging (MRI), different image features, and different image analysis methods in predicting hepatocellular carcinoma (HCC) with cytokeratin 19 (CK19) expression.

MATERIALS AND METHODS

A systematic literature search was performed to identify studies using MRI to predict HCC with CK19 expression between 2012 and 2023. Data were extracted to calculate the pooled sensitivity and specificity. Overall diagnostic performance was assessed using areas under the summary receiver operating characteristic curve (AUC). Subgroup analyses were conducted for specific image features and according to image analysis methods (traditional image feature, radiomics, and combined methods). Z-test statistics was used to analyse the differences in diagnostic performance between combined and individual methods.

RESULTS

Eleven studies with 14 datasets (1,278 lesions from 1,264 patients) were included. The overall pooled sensitivity, specificity, and AUC with corresponding 95% confidence intervals were estimated to be 0.72 (0.55, 0.85), 0.88 (0.80, 0.93), and 0.89 (0.86, 0.91) for MRI in predicting HCC with CK19 expression. Combined methods had higher sensitivity than image feature methods (0.86 versus 0.54, p=0.001), with no difference in specificity (0.85 versus 0.87, p=0.641). There were no significant differences between radiomics and combined methods regarding sensitivity (p=0.796) and specificity (p=0.535), respectively.

CONCLUSION

MRI shows moderate sensitivity and high specificity in identifying HCC with CK19 expression. The application of radiomics can improve the sensitivity of MRI in identifying HCC with CK19 expression.

Combined analysis of transposable elements and structural variation in maize genomes reveals genome contraction outpaces expansion

Structural differences between genomes are a major source of genetic variation that contributes to phenotypic differences. Transposable elements, mobile genetic sequences capable of increasing their copy number and propagating themselves within genomes, can generate structural variation. However, their repetitive nature makes it difficult to characterize fine-scale differences in their presence at specific positions, limiting our understanding of their impact on genome variation. Domesticated maize is a particularly good system for exploring the impact of transposable element proliferation as over 70% of the genome is annotated as transposable elements. High-quality transposable element annotations were recently generated for de novo genome assemblies of 26 diverse inbred maize lines. We generated base-pair resolved pairwise alignments between the B73 maize reference genome and the remaining 25 inbred maize line assemblies. From this data, we classified transposable elements as either shared or polymorphic in a given pairwise comparison. Our analysis uncovered substantial structural variation between lines, representing both simple and complex connections between TEs and structural variants. Putative insertions in SNP depleted regions, which represent recently diverged identity by state blocks, suggest some TE families may still be active. However, our analysis reveals that within these recently diverged genomic regions, deletions of transposable elements likely account for more structural variation events and base pairs than insertions. These deletions are often large structural variants containing multiple transposable elements. Combined, our results highlight how transposable elements contribute to structural variation and demonstrate that deletion events are a major contributor to genomic differences.

Correlation between Lymph Node Regression Grading and Tumor Regression Grading after Neoadjuvant Chemoradiotherapy for Locally Advanced Rectal Cancer

PURPOSE/OBJECTIVE(S)

This study aimed to determine the relationship between tumor regression grading (TRG) and lymph node regression grading (LRG) after neoadjuvant chemoradiotherapy (nCRT) for locally advanced rectal cancer (LARC).

MATERIALS/METHODS

The study was a retrospective analysis of the clinical data of LARC patients who underwent preoperative nCRT at one institution. A total of 101 rectal cancer patients who received nCRT and underwent total rectal mesenteric excision (TME) were included. Pathologists independently assessed the pathological response of the primary tumor and lymph nodes (LN) to nCRT using TRG and LRG, respectively. The highest LRG score for each patient was defined as LRGmax, and LRGsum was the overall tumor burden of all LNs in the specimen.

RESULTS

The study included 101 LARC patients who underwent nCRT and TME. The patient population consisted of 65 males and 36 females with an average age of 54.86 years (range 20-81 years), of which 68 were aged 60 years or younger and 33 were older than 60. The radiotherapy treatment plan consisted of 1.8-2Gy per dose, administered 5 times per week for a total dose of 45-50.4Gy, along with oral capecitabine chemotherapy (825 mg/m2, bid) on the day of radiation therapy. The chemotherapy treatment plan included XELOX, mFOLFOX6, and FOLFOX4. The cTNM stage of the tumor before surgery was cT2 in 2 cases, cT3 in 63 cases, and cT4 in 36 cases. Eight cases were cN0 and 93 were cN+. After surgery, the ypTNM stage was T0 in 19 cases, T1 in 4 cases, T2 in 27 cases, T3 in 45 cases, and T4 in 6 cases. The N stage was N0 in 76 cases, N1 in 20 cases, and N2 in 5 cases. TRG was 0 in 17 cases (16.8%), 1 in 15 cases (14.9%), 2 in 61 cases (60.4%), and 3 in 8 cases (7.9%). LRGmax scores were 0 in 66 cases (65.3%), 1 in 17 cases (16.8%), 2 in 5 cases (5.0%), 3 in 3 cases (3.0%), 4 in 5 cases (5.0%), and 5 in 5 cases (5.0%). LRGsum scores were ≤3 in 85 cases (84.2%), 4-9 in 11 cases (10.9%), and ≥10 in 5 cases (5.0%). Correlation analysis showed that LRGmax was significantly correlated with TRG, ypT, and ypN (P = 0.038, P = 0.015, P < 0.01), with correlation coefficients of 0.184, 0.212, and 0.626, respectively. There was no significant correlation between LRGmax and cT and cN+. Similarly, LRGsum was significantly correlated with TRG, ypT, and ypN (P = 0.022, P = 0.002, P < 0.01) with correlation coefficients of 0.212, 0.276, and 0.707, respectively. There was no significant correlation between LRGsum and cT and cN. The results of our study indicate a significant correlation between LRG and TRG (P = 0.022). Additionally, LRG was found to be positively correlated with the ypT and ypN stages of the primary tumor and lymph nodes post-surgery, with correlation coefficients of 0.276 and 0.707, respectively (P = 0.002 and P<0.01). No significant correlations were observed between LRG and cT and cN+ stages.

CONCLUSION

Our findings demonstrate a significant association between LRG and TRG, as well as a positive correlation between LRG and the ypT and ypN stages of the primary tumor and lymph nodes following surgery.

Evaluating the Effects of Bone Marrow Sparing Radiotherapy on Acute Hematologic Toxicity for Patients with Locoregionally Advanced Cervical Cancer: A Prospective Phase II Randomized Controlled Trial

PURPOSE/OBJECTIVE(S)

Bone marrow sparing intensity modulated radiotherapy (BMS-IMRT) can reduce the incidence of acute hematologic toxicity (HT) for locoregionally advanced cervical cancer (LACC) patients receiving concurrent chemoradiotherapy (CCRT), but the norm has been controversial. The purpose of the study was to evaluate the effects of bone marrow (BM) V40 <25% on decreasing the incidence of acute HT in a prospective clinical trial.

MATERIALS/METHODS

A total of 242 LACC patients were recruited from May 2021 to May 2022, who were evenly randomized into BMS-IMRT group and standard IMRT group according to a computer-generated random number list. All patients received pelvic irradiation with concurrent cisplatin (40 mg/m2 weekly), followed by brachytherapy. For patients in BMS-IMRT group, the outer contour of pelvic bone, lumbar spine and left and right femur heads were additionally delineated as a surrogate for BM, and V40 <25% was prescribed. Blood counts were tested weekly, of which nadirs during external beam radiotherapy (EBRT) were graded to assess acute HT as primary observation index. Second observation index were dosimetric parameters of EBRT plan from the dose volume histograms (DVHs). Binary logistic regression model and receiver operating characteristic (ROC) curve were used for predictive value analysis.

RESULTS

Baseline demographic, disease and treatment characteristics were all balanced between BMS-IMRT group and standard IMRT group. BMS-IMRT was associated with a lower incidence of grade ≥2 and grade ≥3 acute HT, leukopenia and neutropenia (72.70% vs 90.90%, P <0.001*; 16.50% vs 65.30%, P <0.001*; 66.10% vs 85.10%, P = 0.001*; 13.20% vs 54.50%, P <0.001*; 37.20% vs 66.10%, P <0.001*; 10.70% vs 43.80%, P <0.001*). Plan target volume (PTV) for all patients satisfied the clinical requirement of V(100%) ≥95%, and conformity and homogeneity were both comparable between 2 groups. BMS also decreased dose delivered to the organs at risk (OARs) including rectum, bladder and left and right femur head. Univariate and multivariate analyses showed that BM V40 was an independent risk factor for grade ≥3 acute HT (odds ratio [OR] = 2.734, 95% confidence interval [CI] = 1.959-3.815, P <0.001*). Cutoff value was 25.036% and area under the curve (AUC) was 0.786. The nomogram was constructed, which was rigorously evaluated and internally cross-validated, showing good predictive performance.

CONCLUSION

BM V40 <25% can reduce the risks of acute HT for LACC patients receiving CCRT while the dose delivery of target volume and other normal tissues were not compromised. With great practicality and applicability, BM V40 <25% is a promising strategy, making BMS-IMRT widespread especially in the area where application of image guided radiotherapy (IGRT) such as 18F-fluorodeoxyglucose positron emission tomography (18FDG-PET)/CT is not popularized. Chinese clinical trial registry (ChiCTR2200066485).

Cloning of the wheat leaf rust resistance gene Lr47 introgressed from Aegilops speltoides

Leaf rust, caused by Puccinia triticina Eriksson (Pt), is one of the most severe foliar diseases of wheat. Breeding for leaf rust resistance is a practical and sustainable method to control this devastating disease. Here, we report the identification of Lr47, a broadly effective leaf rust resistance gene introgressed into wheat from Aegilops speltoides. Lr47 encodes a coiled-coil nucleotide-binding leucine-rich repeat protein that is both necessary and sufficient to confer Pt resistance, as demonstrated by loss-of-function mutations and transgenic complementation. Lr47 introgression lines with no or reduced linkage drag are generated using the Pairing homoeologous1 mutation, and a diagnostic molecular marker for Lr47 is developed. The coiled-coil domain of the Lr47 protein is unable to induce cell death, nor does it have self-protein interaction. The cloning of Lr47 expands the number of leaf rust resistance genes that can be incorporated into multigene transgenic cassettes to control this devastating disease.

Pan-European study of genotypes and phenotypes in the Arabidopsis relative Cardamine hirsuta reveals how adaptation, demography, and development shape diversity patterns

We study natural DNA polymorphisms and associated phenotypes in the Arabidopsis relative Cardamine hirsuta. We observed strong genetic differentiation among several ancestry groups and broader distribution of Iberian relict strains in European C. hirsuta compared to Arabidopsis. We found synchronization between vegetative and reproductive development and a pervasive role for heterochronic pathways in shaping C. hirsuta natural variation. A single, fast-cycling ChFRIGIDA allele evolved adaptively allowing range expansion from glacial refugia, unlike Arabidopsis where multiple FRIGIDA haplotypes were involved. The Azores islands, where Arabidopsis is scarce, are a hotspot for C. hirsuta diversity. We identified a quantitative trait locus (QTL) in the heterochronic SPL9 transcription factor as a determinant of an Azorean morphotype. This QTL shows evidence for positive selection, and its distribution mirrors a climate gradient that broadly shaped the Azorean flora. Overall, we establish a framework to explore how the interplay of adaptation, demography, and development shaped diversity patterns of 2 related plant species.

[Prevalence and trends of anemia among pregnant women in eight provinces of China from 2016 to 2020]

This study analyzed the anemia status and change trend of 219 835 pregnant women in eight provinces from 2016 to 2020 in the Maternal and Newborn Health Monitoring Program(MNHMP). The results showed that from 2016 to 2020, the anemia rate of pregnant women in eight provinces was 41.27%, and the rates of mild, moderate and severe anemia were 28.56%, 12.59% and 0.12% respectively; the anemia rates in eastern, central and western regions were 41.87%, 36.09% and 44.63% respectively, and the anemia rates in urban and rural areas were 39.87% and 42.23%. From 2016 to 2020, the anemia rate of pregnant women decreased from 44.93% to 38.22%, with an average annual decline of 3.86% (95%CI:-5.84%, -1.85%). The anemia rate among pregnant women of the eastern region (AAPC=-6.16%, 95%CI:-9.79%, -2.38%) fell faster than that among pregnant women of the central region (AAPC=0.71%, 95%CI:-6.59%, 8.57%) and western region (AAPC=-1.53%, 95%CI:-5.19%, 2.28%). From 2016 to 2020, the moderate anemia rate in pregnant women decreased from 14.98% to 10.74%, with an average annual decline of 8.72% (95%CI:-12.90%, -4.34%), with a statistically significant difference (P<0.05); AAPC for mild and severe anemia in pregnant women was 1.56% (95%CI: 3.44%, 0.36%) and 18.86% (95%CI: 39.88%, 9.52%), respectively, without statistically significant difference (P>0.05).

Phylogenomic discovery of deleterious mutations facilitates hybrid potato breeding

Hybrid potato breeding will transform the crop from a clonally propagated tetraploid to a seed-reproducing diploid. Historical accumulation of deleterious mutations in potato genomes has hindered the development of elite inbred lines and hybrids. Utilizing a whole-genome phylogeny of 92 Solanaceae and its sister clade species, we employ an evolutionary strategy to identify deleterious mutations. The deep phylogeny reveals the genome-wide landscape of highly constrained sites, comprising ∼2.4% of the genome. Based on a diploid potato diversity panel, we infer 367,499 deleterious variants, of which 50% occur at non-coding and 15% at synonymous sites. Counterintuitively, diploid lines with relatively high homozygous deleterious burden can be better starting material for inbred-line development, despite showing less vigorous growth. Inclusion of inferred deleterious mutations increases genomic-prediction accuracy for yield by 24.7%. Our study generates insights into the genome-wide incidence and properties of deleterious mutations and their far-reaching consequences for breeding.

[Expert consensus on late stage of critical care management]

We wished to establish an expert consensus on late stage of critical care (CC) management. The panel comprised 13 experts in CC medicine. Each statement was assessed based on the Grading of Recommendations Assessment, Development, and Evaluation (GRADE) principle. Then, the Delphi method was adopted by 17 experts to reassess the following 28 statements. (1) ESCAPE has evolved from a strategy of delirium management to a strategy of late stage of CC management. (2) The new version of ESCAPE is a strategy for optimizing treatment and comprehensive care of critically ill patients (CIPs) after the rescue period, including early mobilization, early rehabilitation, nutritional support, sleep management, mental assessment, cognitive-function training, emotional support, and optimizing sedation and analgesia. (3) Disease assessment to determine the starting point of early mobilization, early rehabilitation, and early enteral nutrition. (4) Early mobilization has synergistic effects upon the recovery of organ function. (5) Early functional exercise and rehabilitation are important means to promote CIP recovery, and gives them a sense of future prospects. (6) Timely start of enteral nutrition is conducive to early mobilization and early rehabilitation. (7) The spontaneous breathing test should be started as soon as possible, and a weaning plan should be selected step-by-step. (8) The waking process of CIPs should be realized in a planned and purposeful way. (9) Establishment of a sleep-wake rhythm is the key to sleep management in post-CC management. (10) The spontaneous awakening trial, spontaneous breathing trial, and sleep management should be carried out together. (11) The depth of sedation should be adjusted dynamically in the late stage of CC period. (12) Standardized sedation assessment is the premise of rational sedation. (13) Appropriate sedative drugs should be selected according to the objectives of sedation and drug characteristics. (14) A goal-directed minimization strategy for sedation should be implemented. (15) The principle of analgesia must be mastered first. (16) Subjective assessment is preferred for analgesia assessment. (17) Opioid-based analgesic strategies should be selected step-by-step according to the characteristics of different drugs. (18) There must be rational use of non-opioid analgesics and non-drug-based analgesic measures. (19) Pay attention to evaluation of the psychological status of CIPs. (20) Cognitive function in CIPs cannot be ignored. (21) Delirium management should be based on non-drug-based measures and rational use of drugs. (22) Reset treatment can be considered for severe delirium. (23) Psychological assessment should be conducted as early as possible to screen-out high-risk groups with post-traumatic stress disorder. (24) Emotional support, flexible visiting, and environment management are important components of humanistic management in the intensive care unit (ICU). (25) Emotional support from medical teams and families should be promoted through"ICU diaries"and other forms. (26) Environmental management should be carried out by enriching environmental content, limiting environmental interference, and optimizing the environmental atmosphere. (27) Reasonable promotion of flexible visitation should be done on the basis of prevention of nosocomial infection. (28) ESCAPE is an excellent project for late stage of CC management.

A role for heritable transcriptomic variation in maize adaptation to temperate environments

Background

Transcription bridges genetic information and phenotypes. Here, we evaluated how changes in transcriptional regulation enable maize (Zea mays), a crop originally domesticated in the tropics, to adapt to temperate environments.

Result

We generated 572 unique RNA-seq datasets from the roots of 340 maize genotypes. Genes involved in core processes such as cell division, chromosome organization and cytoskeleton organization showed lower heritability of gene expression, while genes involved in anti-oxidation activity exhibited higher expression heritability. An expression genome-wide association study (eGWAS) identified 19,602 expression quantitative trait loci (eQTLs) associated with the expression of 11,444 genes. A GWAS for alternative splicing identified 49,897 splicing QTLs (sQTLs) for 7614 genes. Genes harboring both cis-eQTLs and cis-sQTLs in linkage disequilibrium were disproportionately likely to encode transcription factors or were annotated as responding to one or more stresses. Independent component analysis of gene expression data identified loci regulating co-expression modules involved in oxidation reduction, response to water deprivation, plastid biogenesis, protein biogenesis, and plant-pathogen interaction. Several genes involved in cell proliferation, flower development, DNA replication, and gene silencing showed lower gene expression variation explained by genetic factors between temperate and tropical maize lines. A GWAS of 27 previously published phenotypes identified several candidate genes overlapping with genomic intervals showing signatures of selection during adaptation to temperate environments.

Conclusion

Our results illustrate how maize transcriptional regulatory networks enable changes in transcriptional regulation to adapt to temperate regions.

Supplementary information

The online version contains supplementary material available at 10.1186/s13059-023-02891-3.

[Evaluation of clinical safety and diagnostic efficacy of domestic liver-specific magnetic resonance contrast agent (gadoxetate disodium)]

Objective: To evaluate the clinical safety and diagnostic efficacy of domestic gadoxetate disodium (GdEOBDTPA). Methods: The imaging data from patients with space-occupying liver lesions who underwent GdEOBDTPA enhanced magnetic resonance examination at West China Hospital of Sichuan University between January 2020 and September 2020 were analyzed retrospectively. Clinical indicators were evaluated by the incidental condition of transient severe respiratory motion artifacts (TSM) in the arterial phase to assess the safety profile.The differences in quantitative and qualitative indicators for the risk factors of TSM in the arterial phase between the TSM group and the non-TSM group were compared by t-test and χ2 test. Observational indicators of the accuracy of diagnostic procedures: The 2018 version of the Liver Imaging Reporting and Data System (LI-RADS) was used to evaluate the main signs, auxiliary signs, and LR grades of lesions. Postoperative pathological findings were used as the gold standard for evaluating and diagnosing hepatocellular carcinoma (HCC). Simultaneously, the relative enhancement degree of the liver, the contrast between the lesion and the liver, and the cholangiography in the hepatobiliary phase were evaluated. The McNemar test was used to compare the differences in the diagnostic efficiency of physician 1 and physician 2 in the diagnosis of hepatocellular carcinoma according to the 2018 version of LI-RADS. Results: A total of 114 cases were included in this study. The incidence rate of TSM was 9.6% (11/114). Age [(53.8 ± 11.3) years vs. (55.4 ± 15.4) years, t = 0.465, P = 0.497], body weight [(65.8 ± 11.1) kg vs. (60.8 ± 7.6) kg, t = 1.468, P = 0.228], body mass index [(23.9 ± 3.1) kg/m(2) vs. (23.4 ± 3.0) kg/m(2), t = 0.171, P = 0.680], liver cirrhosis ratio (39 cases vs. 4 cases, χ (2) =1.776, P = 0.183), proportion of mild to moderate pleural effusion (32 cases vs. 4 cases, χ (2) = 0.000, P = 0.986), and proportion of mild to moderate ascites (47 cases vs. 5 cases χ (2) = 0.000, P = 0.991) had no statistically significant difference between the groups of non-TSM and TSM patients. According to the 2018 version of LI-RADS for the LR5 category, there was no statistically significant difference between the two physicians' HCC diagnoses in terms of sensitivity (91.4% vs.86.4%, χ (2) = 1.500, P = 0.219), specificity (72.7 % vs. 69.7%, χ (2) = 0.000, P = 1.000), positive predictive value (89.2% vs. 87.5%, χ (2) = 2.250, P = 0.125), negative predictive value (77.4% vs. 67.6%, χ (2) = 2.250, P = 0.125), and accuracy (86.0% vs. 81.6%, χ (2) = 0.131, P = 0.125). According to physicians 1 and 2 film review results, 91.2% (104/114) and 89.5% (102/114) of the contrast agent were discharged into the common bile duct or duodenum, respectively. In addition, 86.0% (98/114) of the patients had good liver enhancement, and 91.2% (104/114) of the lesions showed low signals relative to the liver background. Conclusion: Domestic gadoxetate disodium has a good clinical safety profile and diagnostic efficacy.

Circular RNA 0000157 depletion protects human bronchial epithelioid cells from cigarette smoke extract-induced human bronchial epithelioid cell injury through the microRNA-149-5p/bromodomain containing 4 pathway

BACKGROUND

Circular RNA (circRNA) has been reported to regulate respiratory diseases. In the study, we aimed to elucidate the role of circ_0000157 in smoke-related chronic obstructive pulmonary disease (COPD) and the inner mechanism.

METHODS

COPD-like cell injury was induced by treating human bronchial epithelioid cells (16HBE) with cigarette smoke extract (CSE). The expression of circ_0000157, miR-149-5p, bromodomain containing 4 (BRD4), BCL2-associated x protein (Bax) and B-cell lymphoma-2 (Bcl-2) was analyzed by quantitative real-time polymerase chain reaction (qRT-PCR) or Western blotting. Enzyme-linked immunosorbent assay was performed to detect interleukin-6 (IL-6) and tumor necrosis factor-α (TNF-α) levels. Malondialdehyde (MDA) production was detected by a lipid peroxidation MDA assay kit. Superoxide dismutase (SOD) activity was analyzed by a SOD activity assay kit.

RESULTS

Circ_0000157 and BRD4 expression were upregulated, while miR-149-5p expression was downregulated in the blood of smokers with COPD and CSE-induced 16HBE cells compared with control groups. CSE treatment inhibited 16HBE cell proliferation and induced cell apoptosis, inflammation, and oxidative stress; however, these effects were remitted when circ_0000157 expression was decreased. In addition, circ_0000157 acted as a miR-149-5p sponge and regulated CSE-caused 16HBE cell damage by targeting miR-149-5p. The overexpression of BRD4, a target gene of miR-149-5p, attenuated the inhibitory effects of miR-149-5p introduction on CSE-induced cell damage. Further, circ_0000157 modulated BRD4 expression by associating with miR-149-5p in CSE-treated 16HBE cells.

CONCLUSION

Circ_0000157 knockdown ameliorated CSE-caused 16HBE cell damage by targeting the miR-149-5p/BRD4 pathway, providing a potential therapeutic strategy for clinic intervention in COPD.

[The prevalence of atrial cardiomyopathy in patients with different types of acute ischemic stroke and its relationship with cryptogenic stroke]

Objective: To investigate the prevalence of atrial cardiomyopathy in patients with different types of acute ischemic stroke and its relationship with cryptogenic stroke. Methods: Patients with acute ischemic stroke within 7 days of onset who were admitted to the Department of Neurology of the First Affiliated Hospital of Zhengzhou University from January to September 2019 were prospectively and consecutively enrolled. All included patients were classified according to TOAST classification of ischemic stroke. Chi-square test was used to compare the prevalence of atrial cardiomyopathy among patients with different TOAST classifications. Multivariate logistic regression model was used to analyze the related factors of cryptogenic stroke. Results: A total of 1 098 patients with acute ischemic stroke were enrolled in the study, including 661 males and 437 females, with a median age [M(Q₁,Q₃)] of 61 (53, 68) years. The prevalence of atrial cardiomyopathy in patients with cryptogenic stroke[53.5% (46/86)] was higher than that in patients with large artery atherosclerosis [38.0%(63/166), P=0.018] and small vessel occlusion [19.4%(37/191), P<0.001], but was lower than that of patients in the cardioembolic group [97.3% (72/74), P<0.001]. Multivariate logistic regression analysis showed that atrial cardiomyopathy was an associated factor for cryptogenic stroke (OR=2.945, 95%CI: 1.766-4.911, P<0.001). Conclusions: Atrial cardiomyopathy is associated with cryptogenic stroke. The prevalence of atrial cardiomyopathy in patients with cryptogenic stroke is higher than that in patients with large artery atherosclerosis and small vessel occlusion, but lower than that in patients with cardiac embolism.

Chromosome-scale genome assembly of Camellia sinensis combined with multi-omics provides insights into its responses to infestation with green leafhoppers

The tea plant (Camellia sinensis) is an important economic crop, which is becoming increasingly popular worldwide, and is now planted in more than 50 countries. Tea green leafhopper is one of the major pests in tea plantations, which can significantly reduce the yield and quality of tea during the growth of plant. In this study, we report a genome assembly for DuyunMaojian tea plants using a combination of Oxford Nanopore Technology PromethION^™ with high-throughput chromosome conformation capture technology and used multi-omics to study how the tea plant responds to infestation with tea green leafhoppers. The final genome was 3.08 Gb. A total of 2.97 Gb of the genome was mapped to 15 pseudo-chromosomes, and 2.79 Gb of them could confirm the order and direction. The contig N50, scaffold N50 and GC content were 723.7 kb, 207.72 Mb and 38.54%, respectively. There were 2.67 Gb (86.77%) repetitive sequences, 34,896 protein-coding genes, 104 miRNAs, 261 rRNA, 669 tRNA, and 6,502 pseudogenes. A comparative genomics analysis showed that DuyunMaojian was the most closely related to Shuchazao and Yunkang 10, followed by DASZ and tea-oil tree. The multi-omics results indicated that phenylpropanoid biosynthesis, α-linolenic acid metabolism, flavonoid biosynthesis and 50 differentially expressed genes, particularly peroxidase, played important roles in response to infestation with tea green leafhoppers (Empoasca vitis Göthe). This study on the tea tree is highly significant for its role in illustrating the evolution of its genome and discovering how the tea plant responds to infestation with tea green leafhoppers will contribute to a theoretical foundation to breed tea plants resistant to insects that will ultimately result in an increase in the yield and quality of tea.

How sulfur species can accelerate the biological immobilization of the toxic selenium oxyanions and promote stable hexagonal Se0 formation

Toxic selenium oxyanions and sulfur species are often jointly present in contaminated waters and soils. This study investigated the effect on kinetics and resulting products for bio-reduction of selenium oxyanions in the presence of biologically produced sulfur resulting from bio-oxidation of sulfide in (bio)gas-desulfurization (bio-S⁰) and of sulfate. Selenite and selenate (~2 mmol L^-1) bio-reduction was studied in batch up to 28 days at 30 ^oC and pH 7 using lactic acid and a sulfate-reducing sludge, 'Emmtec'. Bio-S⁰ addition increased the selenite removal rate, but initially slightly decreased selenate reduction rates. Selenite reacted with biologically generated sulfide resulting in selenium-sulfur, which upon further bio-reduction creates a sulfur bio-reduction cycle. Sulfate addition increased the bio-reduction rate for both selenite and sulfate. Bio-S⁰ or sulfate promoted hexagonal selenium formation, whereas without these, mostly amorphous Se⁰ resulted. With another inoculum, 'Eerbeek', bio-S⁰ accelerated the selenite reduction rate less than for 'Emmtec' because of lower sulfur and higher selenite bio-reduction rates. Bio-S⁰ addition increased the selenate reduction rate slightly and accelerated hexagonal selenium formation. Hexagonal selenium formation is advantageous because it facilitates separation and recovery and is less mobile and toxic than amorphous Se⁰. Insights into the interaction between selenium and sulfur bio-reduction are valuable for understanding environmental pathways and considerations regarding remediation and recovery.

The Practical Haplotype Graph, a platform for storing and using pangenomes for imputation

MOTIVATION

Pangenomes provide novel insights for population and quantitative genetics, genomics, and breeding not available from studying a single reference genome. Instead, a species is better represented by a pangenome or collection of genomes. Unfortunately, managing and using pangenomes for genomically diverse species is computationally and practically challenging. We developed a trellis graph representation anchored to the reference genome that represents most pangenomes well and can be used to impute complete genomes from low density sequence or variant data.

RESULTS

The Practical Haplotype Graph (PHG) is a pangenome pipeline, database (PostGRES & SQLite), data model (Java, Kotlin, or R), and Breeding API (BrAPI) web service. The PHG has already been able to accurately represent diversity in four major crops including maize, one of the most genomically diverse species, with up to 1000-fold data compression. Using simulated data, we show that, at even 0.1X coverage, with appropriate reads and sequence alignment, imputation results in extremely accurate haplotype reconstruction. The PHG is a platform and environment for the understanding and application of genomic diversity.

AVAILABILITY

All resources listed here are freely available. The PHG Docker used to generate the simulation results is https://hub.docker.com/ as maizegenetics/phg:0.0.27. PHG source code is at https://bitbucket.org/bucklerlab/practicalhaplotypegraph/src/master/. The code used for the analysis of simulated data is at https://bitbucket.org/bucklerlab/phg-manuscript/src/master/. The PHG database of NAM parent haplotypes is in the CyVerse data store (https://de.cyverse.org/de/) and named /iplant/home/shared/panzea/panGenome/PHG_db_maize/phg_v5Assemblies_20200608.db.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

A multiple alignment workflow shows the effect of repeat masking and parameter tuning on alignment in plants

Alignments of multiple genomes are a cornerstone of comparative genomics, but generating these alignments remains technically challenging and often impractical. We developed the msa_pipeline workflow (https://bitbucket.org/bucklerlab/msa_pipeline) to allow practical and sensitive multiple alignment of diverged plant genomes and calculation of conservation scores with minimal user inputs. As high repeat content and genomic divergence are substantial challenges in plant genome alignment, we also explored the effect of different masking approaches and parameters of the LAST aligner using genome assemblies of 33 grass species. Compared with conventional masking with RepeatMasker, a masking approach based on k-mers (nucleotide sequences of k length) increased the alignment rate of coding sequence and noncoding functional regions by 25 and 14%, respectively. We further found that default alignment parameters generally perform well, but parameter tuning can increase the alignment rate for noncoding functional regions by over 52% compared with default LAST settings. Finally, by increasing alignment sensitivity from the default baseline, parameter tuning can increase the number of noncoding sites that can be scored for conservation by over 76%. Overall, tuning of masking and alignment parameters can generate optimized multiple alignments to drive biological discovery in plants.

Autophagy-Sirtuin1(SIRT1) Alleviated the Coronary Atherosclerosis (AS)in Mice through Regulating the Proliferation and Migration of Endothelial Progenitor Cells (EPCs) via wnt/β-catenin/GSK3β Signaling Pathway

BACKGROUND AND PURPOSE

SIRT1 was associated with AS risk and EPCs were reported to participate in the endothelial repair in Coronary Atherosclerosis (CAS). In this study, we explored the role of SIRT1 in AS mice and also its modulation in EPCs.

METHODS AND MATERIALS

ApoE-/-mice were fed on high-fat and high-glucose diet to establish the AS animal model with the normally-raised C57BL/6 mice as a control group. SIRT1 activator, SRT 2104 was injected intravenously into 5 ApoE-/-mice and its inhibitor Nicotinamide was injected in tail in another 5 ApoE-/-mice. Weight changes were recorded. Blood samples were taken from posterior orbital venous plexus and were detected by automatic biochemical analyzer. HE staining displayed the pathological conditions while Immunohistochemistry (IHC) evaluated the CD34+/VEGFR2+ relative density in the aorta tissues. EPCs were isolated from bone marrow and verified using immunofluorescence staining (IFS). The modulatory mechanism of SIRT1 in EPCs were studied by using RT-PCR, MTT, Western Blot and colony formation, scratch methods.

RESULTS

SIRT1 activator negatively regulated the weight and TC, TG and LDL levels, alleviated the lesion conditions and decreased the CD34+/VEGFR2+ density compared to the AS control. In vitro, SIRT1 activator promoted the proliferation and migration of EPCs and activated wnt/β-catenin/GSK3β signaling pathway. SIRT1 activator also inhibited the autophagy biomarkers ATG1 and LC3II. Furthermore, inhibitor of autophagy promoted SIRT1 expression and induced EPC proliferation, migration and activated wnt/β-catenin/GSK3β pathway. The suppression of the wnt/β-catenin/GSK3β pathway inhibited SIRT1 expression in EPCs, attenuated the proliferation and migration and promoted autophagy of EPCs.

CONCLUSION

SIRT1 activation might be protective in AS mice through autophagy inhibition in EPCs via wnt/β-catenin/GSK3β signaling pathway.

QTL mapping and genomic analyses of earliness and fruit ripening traits in a melon Recombinant Inbred Lines population supported by de novo assembly of their parental genomes

Earliness and ripening behavior are important attributes of fruits on and off the vine, and affect quality and preference of both growers and consumers. Fruit ripening is a complex physiological process that involves metabolic shifts affecting fruit color, firmness, and aroma production. Melon is a promising model crop for the study of fruit ripening, as the full spectrum of climacteric behavior is represented across the natural variation. Using Recombinant Inbred Lines (RILs) population derived from the parental lines "Dulce" (reticulatus, climacteric) and "Tam Dew" (inodorus, non-climacteric) that vary in earliness and ripening traits, we mapped QTLs for ethylene emission, fruit firmness and days to flowering and maturity. To further annotate the main QTL intervals and identify candidate genes, we used Oxford Nanopore long-read sequencing in combination with Illumina short-read resequencing, to assemble the parental genomes de-novo. In addition to 2.5 million genome-wide SNPs and short InDels detected between the parents, we also highlight here the structural variation between these lines and the reference melon genome. Through systematic multi-layered prioritization process, we identified 18 potential polymorphisms in candidate genes within multi-trait QTLs. The associations of selected SNPs with earliness and ripening traits were further validated across a panel of 177 diverse melon accessions and across a diallel population of 190 F1 hybrids derived from a core subset of 20 diverse parents. The combination of advanced genomic tools with diverse germplasm and targeted mapping populations is demonstrated as a way to leverage forward genetics strategies to dissect complex horticulturally important traits.

AnchorWave: Sensitive alignment of genomes with high sequence diversity, extensive structural polymorphism, and whole-genome duplication

Millions of species are currently being sequenced, and their genomes are being compared. Many of them have more complex genomes than model systems and raise novel challenges for genome alignment. Widely used local alignment strategies often produce limited or incongruous results when applied to genomes with dispersed repeats, long indels, and highly diverse sequences. Moreover, alignment using many-to-many or reciprocal best hit approaches conflicts with well-studied patterns between species with different rounds of whole-genome duplication. Here, we introduce Anchored Wavefront alignment (AnchorWave), which performs whole-genome duplication-informed collinear anchor identification between genomes and performs base pair-resolved global alignment for collinear blocks using a two-piece affine gap cost strategy. This strategy enables AnchorWave to precisely identify multikilobase indels generated by transposable element (TE) presence/absence variants (PAVs). When aligning two maize genomes, AnchorWave successfully recalled 87% of previously reported TE PAVs. By contrast, other genome alignment tools showed low power for TE PAV recall. AnchorWave precisely aligns up to three times more of the genome as position matches or indels than the closest competitive approach when comparing diverse genomes. Moreover, AnchorWave recalls transcription factor-binding sites at a rate of 1.05- to 74.85-fold higher than other tools with significantly lower false-positive alignments. AnchorWave complements available genome alignment tools by showing obvious improvement when applied to genomes with dispersed repeats, active TEs, high sequence diversity, and whole-genome duplication variation.

LncRNA DCST1-AS1 regulated cell proliferation, migration, invasion and apoptosis in gastric cancer by targeting miR-605-3p

The article "LncRNA DCST1-AS1 regulated cell proliferation, migration, invasion and apoptosis in gastric cancer by targeting miR-605-3p", by Y.-Z. Su, M.-F. Cui, J. Du, B. Song, published in Eur Rev Med Pharmacol Sci 2020; 24 (3): 1158-1167-DOI: 10.26355/eurrev_202002_20167-PMID: 32096164, has been retracted by the authors since some experiment reagent in this article might be questionable (that may influence the accuracy of the final results). The Publisher apologizes for any inconvenience this may cause. https://www.europeanreview.org/article/20167.

[Cognition and related factors on the use of HIV non-occupational post-exposure prevention among men who have sex with men]

Objective: To understand the cognition and related factors on the use of HIV non-occupational post-exposure prophylaxis (nPEP) among men who have sex with men (MSM). Methods: The snowballing method was applied to recruit research subjects who were ≥18 years old, had sex with men in the past three months, and were aware of nPEP in MSM groups in Beijing, Shenzhen, and Kunming from March 15 to April 14, 2019. Data on social demographics, behavioral characteristics, basic knowledge of nPEP, consultation, and using nPEP were collected through "i guardian Platform". The logistic regression model was used to analyze the related factors affecting the use of nPEP. Results: Among 1 809 investigated, 39.8% (720 persons) were aware of the basic knowledge of nPEP, 33.4% (605 persons) had consulted nPEP, and 15.0% (271 persons) had used nPEP. In addition, multivariate logistic regression analysis showed that factors as whether to have sex with men infected with HIV in the last three months (OR=2.58, 95%CI: 1.64-4.07), the frequency of HIV testing in the past year (OR=2.47, 95%CI: 1.28-5.11), nPEP knowledge awareness (OR=0.70, 95%CI: 0.49-0.99), whether to consult nPEP (OR=70.98, 95%CI: 40.51-136.83) were related to the use of nPEP. Conclusions: MSM still have poor cognition of nPEP. It is necessary to strengthen the publicity and education of nPEP in MSM and promote the use of nPEP after HIV exposure as soon as possible.

Gene expression evolution in pattern-triggered immunity within Arabidopsis thaliana and across Brassicaceae species

Plants recognize surrounding microbes by sensing microbe-associated molecular patterns (MAMPs) to activate pattern-triggered immunity (PTI). Despite their significance for microbial control, the evolution of PTI responses remains largely uncharacterized. Here, by employing comparative transcriptomics of six Arabidopsis thaliana accessions and three additional Brassicaceae species to investigate PTI responses, we identified a set of genes that commonly respond to the MAMP flg22 and genes that exhibit species-specific expression signatures. Variation in flg22-triggered transcriptome responses across Brassicaceae species was incongruent with their phylogeny, while expression changes were strongly conserved within A. thaliana. We found the enrichment of WRKY transcription factor binding sites in the 5'-regulatory regions of conserved and species-specific responsive genes, linking the emergence of WRKY-binding sites with the evolution of gene expression patterns during PTI. Our findings advance our understanding of the evolution of the transcriptome during biotic stress.

Conserved noncoding sequences provide insights into regulatory sequence and loss of gene expression in maize

Thousands of species will be sequenced in the next few years; however, understanding how their genomes work, without an unlimited budget, requires both molecular and novel evolutionary approaches. We developed a sensitive sequence alignment pipeline to identify conserved noncoding sequences (CNSs) in the Andropogoneae tribe (multiple crop species descended from a common ancestor ∼18 million years ago). The Andropogoneae share similar physiology while being tremendously genomically diverse, harboring a broad range of ploidy levels, structural variation, and transposons. These contribute to the potential of Andropogoneae as a powerful system for studying CNSs and are factors we leverage to understand the function of maize CNSs. We found that 86% of CNSs were comprised of annotated features, including introns, UTRs, putative cis-regulatory elements, chromatin loop anchors, noncoding RNA (ncRNA) genes, and several transposable element superfamilies. CNSs were enriched in active regions of DNA replication in the early S phase of the mitotic cell cycle and showed different DNA methylation ratios compared to the genome-wide background. More than half of putative cis-regulatory sequences (identified via other methods) overlapped with CNSs detected in this study. Variants in CNSs were associated with gene expression levels, and CNS absence contributed to loss of gene expression. Furthermore, the evolution of CNSs was associated with the functional diversification of duplicated genes in the context of maize subgenomes. Our results provide a quantitative understanding of the molecular processes governing the evolution of CNSs in maize.

[Analysis of the reported data of National Cervical Cancer Screening Program in Rural Areas in China from 2009 to 2018]

Objective: To analyze the effectiveness of the National Cervical Cancer Screening Program in Rural Areas (NCCSPRA) in China. Methods: Data were collected in the form of quarterly statistical tables reported by NCCSPRA counties in 30 provinces (Hong Kong, Macao and Taiwan province of China were not included into the NCCSPRA, and Tibet Autonomous Region carried out the program but did not reported the data) from 2009 to 2018. The women aged 35-64 years with sexual behavior and the identity (Hukou) of rural area in these project counties were included into the NCCSPRA, and women receiving hysterectomy for non-cervical cancer or non-cervical lesions were excluded. The following indicators were analyzed: the positive rates of different screening methods, the abnormality rates of colposcopy and histopathology, the detection rate of precancerous lesions, the detection rate of cervical cancer and the rate of early diagnosis. Results: A total of 85 041 490 women aged 35-64 in rural areas received free cervical cancer screening and diagnosis if necessary. On the whole, the abnormality rate of cytology, HPV testing, VIA/VILI, colposcopy and histopathology was 3.71%(2 567 610), 9.91%(331 158), 10.10%(1 167 930), 28.85%(1 420 847), and 21.20%(303 068) respectively. The detection rate of cervical precancerous lesions was 153.88/100 000, and increased from 106.85/100 000 in 2012 to 223.89/100 000 in 2018 (P<0.001). Regionally, the east (207.37/100 000) reached higher rate than the middle (177.65/100 000), and the middle higher than the west (108.65/100 000) (P<0.001). The detection rate of invasive cervical cancer was 21.58/100 000, and increased from 18.02/100 000 in 2012 to 26.54/100 000 in 2018 (P<0.001). Regionally, the middle of China (25.46/100 000) reached the higher rate than the east (19.62/100 000) and the west (19.30/100 000) (P<0.001). The rate of early detection was 91.24%(136 140), which increased from 89.60% (11 883)in 2012 to 92.80%(26 962) in 2018 (P<0.001). Regionally, the east of China (94.02%, 37 600) reached the higher rate than the middle(91.06%, 56 488), and the middle higher than the west (89.12%, 42 052) (P<0.001). Conclusions: There are obvious difference in terms of the detection rate of cervical precancerous lesions and the rate of early diagnosis reflecting cervical cancer screening capacity among the eastern, middle and western regions,which showed service inequity among different areas indirectly. The middle and western regions, especially the western regions, are still the focus of future works.

Using high-throughput multiple optical phenotyping to decipher the genetic architecture of maize drought tolerance

BACKGROUND

Drought threatens the food supply of the world population. Dissecting the dynamic responses of plants to drought will be beneficial for breeding drought-tolerant crops, as the genetic controls of these responses remain largely unknown.

RESULTS

Here we develop a high-throughput multiple optical phenotyping system to noninvasively phenotype 368 maize genotypes with or without drought stress over a course of 98 days, and collected multiple optical images, including color camera scanning, hyperspectral imaging, and X-ray computed tomography images. We develop high-throughput analysis pipelines to extract image-based traits (i-traits). Of these i-traits, 10,080 were effective and heritable indicators of maize external and internal drought responses. An i-trait-based genome-wide association study reveals 4322 significant locus-trait associations, representing 1529 quantitative trait loci (QTLs) and 2318 candidate genes, many that co-localize with previously reported maize drought responsive QTLs. Expression QTL (eQTL) analysis uncovers many local and distant regulatory variants that control the expression of the candidate genes. We use genetic mutation analysis to validate two new genes, ZmcPGM2 and ZmFAB1A, which regulate i-traits and drought tolerance. Moreover, the value of the candidate genes as drought-tolerant genetic markers is revealed by genome selection analysis, and 15 i-traits are identified as potential markers for maize drought tolerance breeding.

CONCLUSION

Our study demonstrates that combining high-throughput multiple optical phenotyping and GWAS is a novel and effective approach to dissect the genetic architecture of complex traits and clone drought-tolerance associated genes.

[Relationship between insulin resistance, serum VCAM-1, FGF19, IGF-1 and colorectal polyps]

Objective: To explore the relationship between insulin resistance, glucose and lipid metabolism related molecules and colorectal polyps. Methods: A total of 262 healthy people who underwent colonoscopy in Shandong cancer hospital from June 2019 to September 2020 were selected. The levels of serum vascular cell adhesion molecule-1 (VCAM-1), fibroblast growth factor 19 (FGF19), insulin like growth factor (IGF-1), fasting blood glucose and fasting blood insulin were detected by enzyme-linked immunosorbent assay (ELISA). Insulin resistance index (HOMA-IR) was calculated, and the influencing factors of occurrence, pathological type, size and number of polyps were analyzed. Results: Among 262 cases, 116 cases were polyp free, 113 cases were adenomatous polyp and 33 cases were inflammatory polyp. HOMA-IR, VCAM-1 and FGF19 in polyp group were 2.904±1.754, (334.415±139.573) ng/ml and (135.865±98.470) pg/ml, respectively, which were higher than 2.369±1.306, (302.480±99.946) ng/ml and(110.694±76.044) ng/ml in non-polyp group, respectively (P<0.05). Multivariate Logistic regression analysis showed that the gender (OR=4.269, 95%CI: 1.963-9.405) and FGF19 (77.0-131.4 pg/ml: OR=2.385, 95%CI: 1.155-4.926) were independent factors of colorectal polyps. The gender (OR=3.799, 95%CI: 1.650-8.748) and FGF19 (77.0-131.4 pg/ml: OR=2.290, 95%CI: 1.072-4.891) were independent factors of colorectal adenomatous polyps. The gender(OR=6.725, 95%CI: 1.853-24.410) and fasting plasma glucose (≥6.5 mmol/L: OR=0.047, 95%CI: 0.009-0.245) were independent factors of colorectal inflammatory polyps. The gender (OR=3.539, 95% CI: 1.293-9.689) was an independent factor for the occurrence of single polyp. The gender (OR=5.063, 95% CI: 2.048-12.515), FGF19 (77.0-131.4 pg/ml: OR=2.502, 95%CI: 1.102-5.681), fasting plasma glucose (≥6.5 mmol/L: OR=0.282, 95%CI: 0.095-0.839) were independent factors of multiple polyps. The gender (OR=3.416, 95% CI: 1.134-10.289) and fasting insulin (≥9.4 μU/ml: OR=9.480, 95% CI: 1.485-60.521) were independent risk factors for colorectal polyps<0.5 cm. The gender (OR=3.151, 95%CI: 1.244-7.984) and fasting plasma glucose (≥6.5 mmol/L: OR=0.310, 95%CI: 0.102-0.941) were independent risk factors for colorectal polyps with the size of 0.5-0.9 cm. The gender (OR=22.649, 95%CI: 4.154-123.485), age (55 to 64 years old: OR=4.473, 95%CI: 1.070-18.704; ≥65 years old: OR=5.815, 95%CI: 1.300-26.009), BMI (≥28 kg/m(2): OR=5.310, 95%CI: 1.224-23.032) and FGF19 (77.0-131.4 pg/ml: OR=7.474, 95%CI: 1.903-29.351) were independent factors for colorectal polyps with size ≥ 1.0 cm. Gender stratification analysis showed that FGF19 was an independent factor for the occurrence of male polyps (77.0-131.4 pg/ml: OR=6.109, 95%CI: 1.688-22.104) and adenomas (77.0-131.4 pg/ml: OR=6.401, 95%CI: 1.717-23.864). The age (55 to 64 years old: OR=3.783, 95%CI: 1.052-13.611) and VCAM-1 (≥352.8 ng/ml: OR=4.341, 95%CI: 1.142-16.493) were independent risk factors of female polyps. The age (55 to 64 years old: OR=5.743, 95%CI: 1.205-27.362, ≥65 years old: OR=6.885, 95%CI: 1.143-41.467), VCAM-1 (≥352.8 ng/ml: OR=6.313, 95%CI: 1.415-28.159) and IGF-1 (≥7.6 ng/ml: OR=5.621, 95%CI: 1.069-29.543) were independent factors of female adenoma. Conclusions: The occurrences of colorectal polyps and adenomatous polyps are related to insulin resistance and glucose and lipid metabolism. Serum FGF19 is an independent influencing factor for the occurrence of colorectal polyps and adenomatous polyps, and is a potential serological diagnostic marker and therapeutic target for colorectal polyps and adenomatous polyps.

[Breast ultrasound optimization process analysis based on breast cancer screening for 1 501 753 rural women in China]

Objective: To evaluate the effectiveness and quality of ultrasound-based (BUS) process optimization in breast cancer screening. Methods: The program collected the first to fourth quarterly breast cancer screening statistic data and case report data from 30 provinces, autonomous regions and municipalities in 2015 by the online report system of national key service program of women and children's public health. The call rate, mammography (MG) subsequent screen rate, biopsy rate, detection rate, early diagnosis rate, carcinoma in situ rate, missing detection rate, false positive rate and positive predictive value (PPV) of breast cancer were calculated. Results: A total of 1 501 753 rural women attended the BUS process optimization screening. The nationwide recall rate was 3.01%(45 156/1 501 753), and in the eastern and central area were 3.41%(17 173/503 130) and 3.56%(14 499/407 739), respectively, higher than 2.28% (13 484/590 884) of western area (P<0.05). The nationwide MG subsequent screen rate was 2.78%(41 694/1 501 753), and in the eastern and central area were 3.19%(16 036/503 130) and 3.29% (13 421/407 739), respectively, higher than 2.07%(12 237/590 884) of western area (P<0.05). The nationwide biopsy rate was 0.23%(3 462/1 501 753), and in the central area were 0.26%(1 078/407 739), respectively, higher than 0.21%(1 247/590 884) of western area and 0.23% (1 137/503 130) of eastern area (P<0.05). The nationwide biopsy PPV was 37.00%(1 281/3 462). The biopsy PPV of eastern area was (34.30%, 390/1 137), lower than 39.33% (424/1 078) of central area (P<0.05). A total of 1 281 cases of breast cancer were detected, the detection rate was 0.85‰(1 281/1 501 753), and the detection rates of central area was 1.04‰ (424/407 739), higher than 0.79‰(467/590 884) of western area and 0.78‰(390/503 130) of eastern area (P<0.05). The BUS initiate screening positive rate from detected breast cancer cases was 96.96%(1 242/1 281), the MG subsequent screening positive rate was 2.42%(31/1 281). The nationwide early diagnosis rate was 85.25%(1 092/1 281), and in the eastern and central areas were 87.95%(343/390) and 88.21%(374/424), higher than 80.30%(375/467) of western area (P<0.05). The screening rate of on or above stage Ⅱ breast cancer in eastern area was 55.64%(217/390), lower than 64.62%(374/424) of central area and 62.31%(291/467) of western area. The missing detection rate was 0.62%(8/1 281) and false positive rate was 1.20%(17 528/1 464 149). Conclusions: The BUS process optimization of breast cancer screening scheme is reasonable and applicable to China rural women. The effectiveness and quality of eastern area are superior to those of central and western area.

High-rate biological selenate reduction in a sequencing batch reactor for recovery of hexagonal selenium

Recovery of selenium (Se) from wastewater provides a solution for both securing Se supply and preventing Se pollution. Here, we developed a high-rate process for biological selenate reduction to elemental selenium. Distinctive from other studies, we aimed for a process with selenate as the main biological electron sink, with minimal formation of methane or sulfide. A sequencing batch reactor, fed with an influent containing 120 mgSe L^-1 selenate and ethanol as electron donor and carbon source, was operated for 495 days. The high rates (419 ± 17 mgSe L^-1 day^-1) were recorded between day 446 and day 495 for a hydraulic retention time of 6 h. The maximum conversion efficiency of selenate amounted to 96% with a volumetric conversion rate of 444 mgSe L^-1 day^-1, which is 6 times higher than the rates reported in the literature thus far. At the end of the experiment, a highly enriched selenate reducing biomass had developed, with a specific activity of 856 ± 26 mgSe^-1day^-1g_biomass^-1, which was nearly 1000-fold higher than that of the inoculum. No evidence was found for the formation of methane, sulfide, or volatile reduced selenium compounds like dimethyl-selenide or H₂Se, revealing a high selectivity. Ethanol was incompletely oxidized to acetate. The produced elemental selenium partially accumulated in the reactor as pure (≥80% Se of the total mixture of biomass sludge flocs and flaky aggregates, and ~100% of the specific flaky aggregates) selenium black hexagonal needles, with cluster sizes between 20 and 200 µm. The new process may serve as the basis for a high-rate technology to remove and recover pure selenium from wastewater or process streams with high selectivity.

LncRNA DCST1-AS1 regulated cell proliferation, migration, invasion and apoptosis in gastric cancer by targeting miR-605-3p

OBJECTIVE

Gastric cancer (GC) is one of the most common cancers in the world, with a high incidence and a poor prognosis. A large number of lncRNAs have been demonstrated to play multiple important roles in cancer development and progression. LncRNA is usually used as ceRNA and forms a regulatory network with miRNA in gastric cancer. However, the function and regulatory network of lncRNA in gastric cancer have not been fully elucidated.

MATERIALS AND METHODS

The qRT-PCR assay was used to detect DCST1-AS1 and miR-605-3p expression. Western blot was applied to measure the protein expression of CDK4, cyclin D1, MMP-2, MMP-9, cleaved caspase 3, Bcl-2, Bax and β-actin. MTT assay and flow cytometry were performed to assess cell proliferation and apoptosis, respectively. Transwell migration and invasion assay were used to determine cell migration capacity and invasion ability. Luciferase reporter assay was applied to determine the relationship of DCST-AS1 and miR-605-3p in GC.

RESULTS

In this study, we found that DCST1-AS1 was highly expressed while miR-605-3p was low expressed in GC tissues and cells. Moreover, DCST1-AS1 expression negatively regulated miR-605-3p expression in GC. Functionally test demonstrated that knockdown of DCST1 inhibited cell proliferation, migration and invasion as well as promoted cell apoptosis in GC cells. Interestingly, miR-605-3p has been verified to be a target miRNA of DCST1-AS1 with luciferase reporter assay. More than that, the reverse experiment determined that the inhibition of miR-605-3p could alleviate the suppressive effects of low DCST1-AS1 expression on cell growth in GC.

CONCLUSIONS

We proved the regulatory network of lncRNA DCST1-AS1 for the first time, and also explored and found that lncRNA DCST1-AS1 regulated cell proliferation, migration, invasion and apoptosis by regulation of miR-605-3p, providing a new therapeutic target for gastric cancer treatment.

Effect of seasonal changes on the innate immunity of wild pseudois nayaur: potential reason for its endangerment

It has been widely concerned that seasonal climate change may impose stress on mammal's immune system, but this has never been connected to wildlife endangerment reasons. This study focuses on pseudois nayaur, a rare Chinese sheep facing a severe situation of disappearing. Wild pseudois nayaurs in Sichuan, China were observed in this research by an integrated method including habitat environment, foraging rules, and breeding activities investigation in ecology filed, accompanied with immunity research by PB (peripheral blood), including erythrocyte, neutrophils, NK(natural kill) cells, and macrophages immunity by means of erythrocyte rosette, phagocytosis, LDH (lactatedehydrogenase) release and ANAE (acid α-naphthyl acetate esterase) method, respectively. The results show that pseudois nayaurs's innate and red blood cell immune functions were in degradation in autumn and winter, which were speculated to be the results of energy reallocation between reproduction and the immune system. In addition, the environment pressure found in Zhu Balong, Sichuan, China including food reduction, human disturbance, low temperature, and severe drought still existed, which may prevent the pseudois nayaur from normally immunity enhancement before winter. In conclusion, the innate immunosuppression found in this study especially at their breeding season in autumn and winter may be the ignored cause of wild pseudois nayaur endangerment and should be considered in their protection strategy.

[Effects of acute paraquat poisoning on cognitive ability in humans]

Objective: To explore the effects of acute paraquat poisoning on cognitive function of patients through neuropsychologic test. Methods: In June 2019, 36 patients with acute paraquat poisoning in the emergency department of a provincial hospital in Hebei Province were selected as the case group. 36 healthy individuals were selected as control group. The cognitive function and depressive state were assessed by mini mental state scale, auditory word learning test, digit span test, connection test, Boston Naming Test and geriatric depression scale. Results: The results of Mini-Mental State examination showed that the total score of the case group was lower than that of the control group, the difference was statistically significant (P<0.05) . The results of the Auditory Vocabulary Learning test showed that the scores of delayed recall, clue recall, corrective ability and semantic learning strategies of the case group were significantly lower than those in the control group (P<0.05) . There was no significant difference in the scores of immediate memory between the two groups (P>0.05) . The scores of Digit Span test and Boston Naming test in the control group were higher than those in the case group, the Trail Making test time in the control group was shorter than that in the case group, and the differences were statistically significant (P<0.05) . Conclusion: Acute paraquat poisoning can impair human cognitive ability to a certain extent.

Transcriptome profiling analysis of tea plant (Camellia sinensis) using Oxford Nanopore long-read RNA-Seq technology

Transcriptome profiles have been widely captured using short-read sequencing technology, but there are still limitations partially due to the read length. Here, we generated long reads using Oxford Nanopore PromethION™ technology and short reads using the Illumina sequencing platform to study the transcriptome of root, stem, and leaf of Camellia sinensis cv. Fudingdabai. We mapped the Nanopore reads to the Shuchazao of C. sinensis genome sequence, and the mapping rates ranged from 82.63% to 90.59% (average 86.44%); this is lower than that of the Illumina reads which was 87.83% to 91.14% (average 90.12%). Gene expression level was quantified using the Nanopore and Illumina data and we observed a good agreement. The same tea leaf flavor synthesis pathways were highlighted using both sequencing technologies when analyzing the differentially expressed genes between leaf and root. Alternative splicing was then analyzed, and the intron-retention was observed as the most common alternative splicing. Moreover Nanopore long reads could correct transcript isoform annotation for differential expression investigation purposes. Nanopore sequencing techniques can provide a novel reference basis for molecular analysis of tea plants.

MicroRNA-223 negatively regulates LPS-induced inflammatory responses by targeting NLRP3 in human dental pulp fibroblasts

AIM

To investigate the effect of miR-223 on NLRP3, subsequently regulating the production of the NLRP3/CASP1 inflammasome pathway-mediated proinflammatory cytokines IL-1β and IL-18 in human dental pulp fibroblasts (HDPFs).

METHODOLOGY

Human dental pulp tissue (HDPT) and HDPFs were obtained from impacted third molars. The miR-223 mimics and inhibitor or NLRP3 plasmid were used to upregulate or downregulate miR-223 or NLRP3 in HDPFs, respectively. Computational prediction via TargetScan 5.1 and a luciferase reporter assay was conducted to confirm target association. The mRNA and protein expression of NLRP3, caspase-1, IL-1β and IL-18 was determined by qRT-PCR and Western blotting, respectively. The release of IL-1β and IL-18 was analysed by ELISA. The significance of the differences between the experimental and the control groups was determined using one-way analysis of variance; P < 0.05 indicated statistical significance.

RESULTS

A decrease in miR-223 and an increase in NLRP3 in HDPT occurred during the transformation of reversible pulpitis into irreversible pulpitis compared to that in healthy pulp tissue (P < 0.05). The computational prediction and luciferase reporter assay confirmed that NLRP3 was a direct target of miR-223 in HDPFs. The miR-223 inhibitor further promoted ATP plus LPS-induced NLRP3/CASP1 inflammasome pathway activation compared to the ATP plus LPS-induced group (P < 0.05). In contrast, the miR-223 mimic significantly inhibited the NLRP3/CASP1 inflammasome pathway activation induced by ATP plus LPS compared to the ATP plus LPS-induced group (P < 0.05).

CONCLUSION

MiR-223 served as a negative regulator involved in the control of the production and secretion of proinflammatory cytokines mediated by the NLRP3/CASP1 inflammasome pathway by targeting NLRP3. These data provide insight into the potential regulatory effects of miRNAs on the NLRP3 inflammasome, thus opening up novel potential therapeutic avenues for future endodontic treatment.

MiR-143 regulates proliferation and apoptosis of myelocytic leukemia cell HL-60 via modulating ERK1

Since this article has been suspected of research misconduct and the corresponding authors did not respond to our request to prove originality of data and figures, "MiR-143 regulates proliferation and apoptosis of myelocytic leukemia cell HL-60 via modulating ERK1, by B. Song, Y.-J. Tang, W.-G. Zhang, C.-C. Wan, Y. Chen, L.-J. Zhang, published in Eur Rev Med Pharmacol Sci 2018; 22 (11): 3333-3341-DOI: 10.26355/eurrev_201806_15153-PMID: 29917183" has been withdrawn. The Publisher apologizes for any inconvenience this may cause. https://www.europeanreview.org/article/15153.

[Oncologic outcomes of early stage cervical cancer performed operation by different laparoscopic surgical procedures: analysis of clinical data from mutiple centers]

Objective: To evaluate the oncologic outcomes of different laparoscopic radical hysterectomy. Methods: From January 2011 to December 2014, the laparoscopic operation cases of cervical cancer at stage Ⅰb1, Ⅰb2, Ⅱa1 and Ⅱa2, including the histologic subtypes of squamous-cell carcinoma, adenocarcinoma and adenosquamous carcinoma, were collected in five clinical centers. The data were divided into two groups according to the surgical procedures, that is, modified laparoscopic-vaginal radical hysterectomy (mLVRH) and total laparoscopic radical hysterectomy (TLRH). The overall survival rate (OS), disease-free survival rate (DFS) at 5 years were retrospectively analyzed in this study. Results: There were 674 cases in total, including 377 cases of mLVRH, 297 cases of TLRH. (1) The OS at 5 years: the mLVRH was 96.1% and the TLRH was 92.0%, and the mLVRH was higher than that of TLRH （P=0.010）. Stratify analysis， including stage of disease （Ⅰb1 and Ⅱa1）， histologic subtypes （squamous-cell carcinoma, adenocarcinoma）， lymph node metastasis， revealed that, ① Stage of disease: in stage Ⅰb1, the OS at five years of mLVRH was higher than that in TLRH group （98.6% vs 93.6%, P=0.012）. In stage Ⅱa1, there was significant difference between the two groups, the OS at five years of mLVRH and TLRH were 93.6% and 77.6% （P=0.007）. ② Histologic subtypes: for the OS at five years of squamous-cell carcinoma, mLVRH and TLRH were 96.1% and 92.3%, and there was significant difference （P=0.046）； for adenocarcinoma, the OS at five years were 91.0% and 88.6%， and there was no difference between two groups （P=0.230）. ③ Lymph node metastasis： the mLVRH and TLRH with lymph node metastasis, the OS at five years were 98.6% and 96.4%; the mLVRH and TLRH without lymph node metastasis, the OS at five years were 89.3% and 80.8%. There were no significant differences between the two groups,respectively (P=0.156， P=0.093）. (2) The DFS at 5 years: there was no significant difference between mLVRH and TLRH (94.1% vs 90.9%, P=0.220). Stratify analysis for stage of disease, the mLVRH group was higher than that in the TLRH group in stage Ⅰb1 (97.0% vs 92.8%, P=0.039). However, for stage Ⅱa1, there was no significant difference between mLVRH and TLRH group （88.2% vs 75.8%, P=0.074）. Conclusions: The results of this retrospective study indicated that different laparoscopy surgical procedures had diverse oncologic outcomes. The OS at 5 years of the mLVRH is superior to the TLRH. The DFS at 5 years in Ⅰb1 stage, the mLVRH is higher than the TLRH. Therefore, the modified laparoscopy is still an alternative surgery for early cervical cancer patients when following the principle of no-tumor-exposure.

Blockage of PAK1 alleviates the proliferation and invasion of NSCLC cells via inhibiting ERK and AKT signaling activity

PURPOSE

P21-activated kinase 1 (PAK1), a serine/threonine protein kinase which functions downstream of RAC and CDC42 GTPase, is activated by a variety of stimuli, including RAS and other growth signaling factors. The extracellular signal kinase (ERK) and protein kinase B (AKT) signal pathways have been implicated in the pathogenesis of cancers. Whether PAK1 is sensitive to KRAS mutation signals and plays a role through ERK and AKT signaling pathways in NSCLC needs to be studied.

METHODS

The expression of PAK1, ERK and AKT was detected in both lung cancer cell lines and clinical samples. PAK1 RNA interference and specific inhibitor of PAK1(IPA-3) were applied to lung cancer cell lines and mouse xenograft tumors. Cell growth was measured by MTT and colony formation assays. Cell migration and invasion were detected by wound healing and transwell assays. RAS mutation was detected by Taqman probe method. Correlation between KRAS, PAK1, ERK and AKT activities was analyzed in lung cancer patients.

RESULTS

PAK1 was highly expressed not only in RAS mutant but also in RAS wild-type lung cancer cells. Using specific inhibitor of PAK1, IPA-3 and PAK1 RNA interference, cell proliferation, migration and invasion of lung cancer cells were reduced significantly, accompanied by decreased activities of ERK and AKT. Dual inhibition of ERK and AKT suppressed these cellular processes to levels comparable to those achieved by reduction in PAK1 expression. In NSCLC patients, PAK1 was not correlated with KRAS mutation but was significantly positively correlated with pERK and pAKT.

CONCLUSION

PAK1 played roles in NSCLC proliferation and invasion via ERK and AKT signaling and suggested a therapeutic target for NSCLC.

Resveratrol promotes mammary cell proliferation and antioxidation capacity during pregnancy and lactation in mice

AIMS

Reproduction can induce maternal oxidative stress, and resveratrol is able to alleviate oxidative stress. This study aimed to investigate the protective effects of resveratrol supplementation in mice during pregnancy and lactation.

METHODS AND RESULTS

Pregnant mice were randomly divided into three groups: (i) Pure water (Con); (ii) Cellulose sodium dissolves with 20 mg kg^-1 resveratrol (R1) and (iii) Cellulose sodium dissolves with 40 mg kg^-1 resveratrol (R2). The experiment starts at pregnancy and ends at weaning. The results showed that resveratrol increased mammary cell proliferation and the mRNA expressions of UDP glucuronosyltransferase family 1 member A1 (UGT1A1) and cytochrome P450 proteins (CYP1A1), while decreased superoxide dismutase, extracellular (SOD3) in the mammary gland. Further study showed that resveratrol promoted the mRNA expressions of genes involved in mitophagy, such as transcription factor Eβ (Tfeβ), Bcl1lc3β, homosapiens microtubule-associated protein 1 light-chain 3 beta (Map1lc3β), Parkin, sequestosome1 (p62), autophagy-related protein (Atg5) and Beclin-1 (Becn1) in the mammary gland. Moreover, resveratrol increased the abundances of some intestinal microbial species. 40 mg kg^-1 resveratrol significantly increased the contents of Acidobacteri, unidentified acidbacteria, Bacilales, Staphylococcaceae and Staphylococcus at phylum, class, order, family and genus level respectively.

CONCLUSION

Our results indicate that resveratrol supplementation may promote mammary cell proliferation and antioxidant ability through mitophagy and regulating gut microbiota in pregnant mice.

SIGNIFICANCE AND IMPACT OF THE STUDY

Current study proved that resveratrol could affect mammary cell proliferation and antioxidation capacity during pregnancy and lactation in mice for the first time. The underlying mechanisms may be related to mitophagy and gut microbiota.

Serum soluble ST2 is a potential long-term prognostic biomarker for transient ischaemic attack and ischaemic stroke

BACKGROUND AND PURPOSE

Soluble ST2 (sST2) is a promising biomarker in inflammation, atherosclerosis and cardiovascular diseases. We investigated the association between serum sST2 and poor outcome in patients with transient ischaemic attack (TIA)/ischaemic stroke.

METHODS

Patients within 24 h after onset and with measured serum sST2 were prospectively enrolled in this study. Poor outcome was a combination of a new stroke event (ischaemic or haemorrhagic) and all-cause death within 90 days and 1 year. The associations of serum sST2 with poor outcome were analysed by Cox proportional hazards.

RESULTS

Among the 430 patients included, the median (interquartile range) sST2 was 17.72 (9.31-28.84) ng/mL. A total of 19 (4.4%) and 38 (8.8%) patients experienced poor outcome within 90 days and 1 year, respectively. Compared with the lowest sST2 tertile, hazard ratios (HRs) [95% confidence intervals (CI)] for the highest tertile were 5.14 (1.43-18.51) for poor outcome within 90 days and 3.00 (1.29-6.97) at 1 year after multivariate adjustments. Adding sST2 to a prediction model significantly improved risk stratification of poor outcome in TIA/ischaemic stroke, as observed by the continuous net reclassification improvement of 60.98% (95% CI, 15.37-106.6%, P = 0.009) and integrated discrimination improvement of 2.63% (95% CI, 0.08-5.18%, P = 0.043) at 90 days and the continuous net reclassification improvement of 41.68% (95% CI, 8.74-74.61%, P = 0.013) at 1 year.

CONCLUSIONS

Increased serum sST2 levels in TIA/ischaemic stroke were associated with increased risks of poor outcome within 90 days and 1 year, suggesting that serum sST2 may be a potential long-term prognostic biomarker for TIA/ischaemic stroke.

Mutagenesis of a Quintuple Mutant Impaired in Environmental Responses Reveals Roles for CHROMATIN REMODELING4 in the Arabidopsis Floral Transition

Several pathways conferring environmental flowering responses in Arabidopsis (Arabidopsis thaliana) converge on developmental processes that mediate the floral transition in the shoot apical meristem. Many characterized mutations disrupt these environmental responses, but downstream developmental processes have been more refractory to mutagenesis. Here, we constructed a quintuple mutant impaired in several environmental pathways and showed that it possesses severely reduced flowering responses to changes in photoperiod and ambient temperature. RNA-sequencing (RNA-seq) analysis of the quintuple mutant showed that the expression of genes encoding gibberellin biosynthesis enzymes and transcription factors involved in the age pathway correlates with flowering. Mutagenesis of the quintuple mutant generated two late-flowering mutants, quintuple ems1 (qem1) and qem2 The mutated genes were identified by isogenic mapping and transgenic complementation. The qem1 mutant is an allele of the gibberellin 20-oxidase gene ga20ox2, confirming the importance of gibberellin for flowering in the absence of environmental responses. By contrast, qem2 is impaired in CHROMATIN REMODELING4 (CHR4), which has not been genetically implicated in floral induction. Using co-immunoprecipitation, RNA-seq, and chromatin immunoprecipitation sequencing, we show that CHR4 interacts with transcription factors involved in floral meristem identity and affects the expression of key floral regulators. Therefore, CHR4 mediates the response to endogenous flowering pathways in the inflorescence meristem to promote floral identity.

[Comparison on efficacy and safety of different bridging anticoagulation therapies in patients undergoing mechanical heart valve replacement surgery]

Objective: To evaluate the efficacy and safety of different bridging anticoagulant therapies in patients undergoing mechanical heart valve replacement (MHVR) surgery. Methods: Consecutive patients undergoing MHVR surgery from January 2018 to December 2018 in First Hospital of Lanzhou University were prospectively enrolled in this study. Patients were divided into unfractionated heparin (UFH) group and low molecular weight heparin (LMWH) group according to the postoperative bridging anticoagulation methods. Preoperative clinical data and postoperative related time and cost parameters, including drainage time, duration of stay in intensive care unit (ICU), postoperative time (interval from end of operation to discharge) and INR stabilization time (interval from start of bridge anticoagulation to INR value reaching the standard for 2 consecutive days) of all enrolled patients were collected, and all patients were followed up for 4 weeks and thromboembolic or bleeding events were analyzed. Multivariate logistic regression was used to determine the independent prognostic factors of thromboembolic or bleeding events after MHVR receiving various bridging anticoagulant therapies. Results: A total of 217 patients were included in the study, including 120 patients in the UFH group and 97 patients in the LMWH group. Stroke occurred in two patients in the UFH group, while no stroke event occurred in the LMWH group. The incidence of bleeding events was significantly higher (9.28%(9/97) vs. 1.67%(2/120), P=0.02), while the drainage time, duration of stay in ICU, postoperative time, INR stabilization time were all significantly shorter in LMWH group than in UFH group (all P<0.05). Multivariate logistic regression analysis showed that bridging anticoagulation therapies (OR=0.18, 95%CI 0.04-0.86, P=0.03), fibrinogen level (OR=1.99, 95%CI 1.16-3.41, P=0.01) and creatinine level (OR=1.05, 95%CI 1.01-1.08, P=0.04) were independent prognostic factors for bleeding events. Conclusion: LMWH use is associated with increased risk of bleeding events, but can significantly reduce the drainage time, duration of stay in ICU, postoperative time, INR stabilization time in patients post MHVR surgery.

MiR-143 regulates proliferation and apoptosis of myelocytic leukemia cell HL-60 via modulating ERK1

OBJECTIVE

Extracellular signal-regulated kinase (ERK)/mitogen activated protein kinase (MAPK) signaling pathway is widely involved in cell proliferation and invasion regulation. Enhanced expression or function of ERK1 is important for leukemia. Abnormal down-regulation of microRNA (miR)-143 is correlated with leukemia pathogenesis, indicating possible tumor-suppressing role. Bioinformatics analysis showed the existence of complementary binding sites between miR-143 and ERK1. This study aims to investigate whether the miR-143 plays a role in mediating ERK1 expression and proliferation and apoptosis of leukemia cells.

PATIENTS AND METHODS

Dual luciferase reporter gene assay confirmed targeted regulation between miR-143 and ERK1. Quantitative RT-PCR (qRT-PCR) was used to measure and compare the peripheral miR-143 and ERK1 expression between healthy and acute promyelocytic leukemia (APL) patients to analyze the effect of miR-143 and MEK1 on survival and prognosis. Cultured HL-60 cells were treated with miR-143 mimic or small interfering RNA (siRNA)-ERK1, followed by qRT-PCR to measure miR-143 expression. Western blot quantified expression of ERK1 and p-ERK1, flow cytometry measured apoptosis, and EdU staining measured proliferation.

RESULTS

MiR-143 targeted and modulated ERK1. APL patients presented lower miR-143 and higher ERK1 in peripheral blood. Those with miR-143 down-regulation displayed worse prognosis than those with high miR-143 expression (χ2 = 5.198, p = 0.039). Patients with ERK1 mRNA low-expression presented better prognosis than those a having higher expression (Log-rank test, χ2 = 5.873, p = 0.028). Transfection of miR-143 mimic or siRNA-ERK1 remarkably suppressed ERK1 and p-ERK1 expression in HL-60 cells, inhibited cell proliferation and induced cell apoptosis.

CONCLUSIONS

MiR-143 down-regulation and ERK1 up-regulation are correlated with APL pathogenesis. Their expression level affected patient's prognosis. MiR-143 targeted and inhibited ERK1 expression, weakened proliferation potency of HL-60 cells, and induced apoptosis.